This Telomere Length in Preterm Infantsreadme.txt file was generated on 2023-01-04 by NAME
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GENERAL INFORMATION

1. Title of Dataset: Telomere Length in Preterm Infants

2. Author Information
	A. Principal Investigator Contact Information
		Name: Daniel A. Notterman
		Institution: Princeton University
		Address: Department of Molecular Biology, Princeton University, Princeton, NJ USA
		Email: dan1@princeton.edu

	B. Associate or Co-investigator Contact Information
		Name: Chinthika Piyasena
		Institution: Evelina London Children's Hospital
		Address: Guys’ and St Thomas’ NHS Foundation Trust, London, UK
		Email: chinthika.piyasena@gstt.nhs.uk

	C. Alternate Contact Information
		Name:  Lisa M Schneper
		Institution: Princeton University
		Address: Department of Molecular Biology, Princeton University, Princeton, NJ USA
		Email: lweis@princeton.edu

3. Date of data collection (single date, range, approximate date) <suggested format YYYY-MM-DD>: 2014-2018

4. Geographic location of data collection <latitude, longiute, or city/region, State, Country, as appropriate>: Edinburgh, UK; Princeton, NJ, USA

5. Information about funding sources that supported the collection of the data: Funding for the study was provided by a Scottish Senior Clinical Fellowship (SCD/09 to Amanda Drake) and the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the National Institutes of Health (5R01HD076592 to Daniel Notterman)).


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: None

2. Links to publications that cite or use the data: N/A

3. Links to other publicly accessible locations of the data: None

4. Links/relationships to ancillary data sets: None

5. Was data derived from another source? yes/no
	A. If yes, list source(s): no

6. Recommended citation for this dataset: TBD


DATA & FILE OVERVIEW

1. File List: 
<list all files (or folders, as appropriate for dataset organization) contained in the dataset, with a brief description>
Schneper_et_al_telomere_length_preterm_infants.xlsx - Excel file containing telomere length data as well as variables used in the cited publication

2. Relationship between files, if important: N/A

3. Additional related data collected that was not included in the current data package: N/A

4. Are there multiple versions of the dataset? no
	A. If yes, name of file(s) that was updated: 
		i. Why was the file updated? 
		ii. When was the file updated? 


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 
<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>

Study participants
A cohort of 50 preterm infants (< 32 weeks gestation) and 40 term control infants (37 – 42 weeks gestation) were recruited during the first week of age  from the Simpson Centre for Reproductive Health, Edinburgh, UK  Royal Infirmary of Edinburgh as previously described (1). Most of the parents of the term babies were approached prior to delivery.  None of the term babies had suspected or proven fetal anomaly or proven infection.  The term infants were apparently healthy with the exception of one who had jaundice.  The term babies stayed in the hospital for an average of 4.5 days (range 2-9) with their mothers.  Ethical approval was obtained from the South East Scotland Research Ethics Committee (Reference 11/AL/0329). NHS management approval was obtained (Lothian R&D Project number 2011/R/ NE/03). Infant samples were collected under the framework of the Edinburgh Reproductive Tissue BioBank (West of Scotland Research Ethics Service Reference 09/S0704/3) following an amendment to ethical approval (Reference AM07/1). All parents gave written informed consent, and all studies were performed in accordance with the Declaration of Helsinki.  Term controls were born at least 37 completed weeks post last menstrual period (LMP) with no identified maternal or fetal complications. In the control group, only women with singleton pregnancies, without pre-existing hypertension or diabetes and who were non-smokers in the current pregnancy were included. Demographic and clinical data were collected from hospital and research visits and hospital records. From the main cohort, there were 32 preterm and 39 term infants with available DNA for the TL assay.  Socioeconomic status is approximated using deprivation category (DEPCAT) scores derived from the Carstairs score of the subject’s postal code (2). The DEPCAT scores are categorical variables ranging from 1 – 7 with 1 and 2 being the most affluent.

Sample collection
Saliva for DNA was collected from the preterm infants at birth; at term-adjusted age); and at one year corrected; and from term infants at birth and one year of age. Samples were collected from preterm infants within a median of 3 days (interquartile range (IQR) of 1.75-4 days from birth) and term infants within a median of 2 days (IQR of 1 - 2.3 days) from birth.  Saliva was collected using the Oragene DNA (OG-250) kits and saliva sponges CS-1 and extracted using prepIT-2LP (DNA Genotek, Ottawa, ON, Canada). DNA was quantified using the Qubit 2.0 Fluorometer (Life Technologies, Paisley, UK) and stored at -20°C until received by the Notterman laboratory, where it was stored at -80°C. 

Telomere length
TL was measured by absolute quantitative real-time PCR (qPCR) (3–6). Two double stranded oligonucleotides (Integrated DNA Technologies), an 84-mer consisting of (TTAGG)16 and a 79-mer containing sequence from the 36B4 gene were used to construct standard curves to determine absolute telomere length and number of diploid genomes copies, respectively. TL and single copy gene qPCR assays were performed on separate plates. Each sample was assayed in triplicate and the results averaged. Individual TL was determined by dividing the telomere length per genome by 92, the number of telomeres per diploid genome.  Each plate contained DNA from a cell line with a relatively short telomere length (3C167b) (7) and a fibroblast cell line containing a stable integration of TERT, which encodes the protein component of telomerase (NHFpreT) (8). These were used to control for inter-plate variation as described (4,5). Human genomic DNA was also included to determine the coefficient of variation (0.09) (4,5).  The intraclass correlation coefficients (calculated using the Ct values) were 0.975 (CI 0.968-0.981) and 0.949 (CI 0.934-0.961), respectively for the telomere and 36B4 technical replicates.

References
1.	Piyasena C, Cartier J, Provençal N, Wiechmann T, Khulan B, Sunderesan R, et al. Dynamic changes in DNA methylation occur during the first year of life in preterm infants. Front Endocrinol (Lausanne). 2016;7:158.
 
2.	McCloone P. Carstairs scores for Scottish postcode sectors from the 1991 census. University of Glasgow; 1994. 

3.	Cawthon RM. Telomere measurement by quantitative PCR. Nucleic Acids Res. 2002 May;30(10):e47. 

4.	Mitchell C, Hobcraft J, McLanahan SS, Siegel SR, Berg A, Brooks-Gunn J, et al. Social disadvantage, genetic sensitivity, and children’s telomere length. Proc Natl Acad Sci U S A. 2014/04/07 ed. 2014 Apr;111(16):5944–9. 

5.	Mitchell C, McLanahan S, Schneper L, Garfinkel I, Brooks-Gunn J, Notterman D. Father loss and child telomere length. Pediatrics [Internet]. 2017/07/19 ed. 2017 Aug;140(2). Available from: https://www.ncbi.nlm.nih.gov/pubmed/28716823

6.	O’Callaghan NJ, Fenech M. A quantitative PCR method for measuring absolute telomere length. Biol Proced Online. 2011/01/31 ed. 2011 Jan;13:3. 

7.	Wang S, Zhu J. Evidence for a relief of repression mechanism for activation of the human telomerase reverse transcriptase promoter. J Biol Chem. 2003/03/04 ed. 2003 May 23;278(21):18842–50. 

8.	Cheng, Zhao Y, Wang S, Zhang F, Russo M, McMahon SB, et al. Repression of telomerase gene promoter requires human-specific genomic context and is mediated by multiple HDAC1-containing corepressor complexes. FASEB J. 2016/12/13 ed. 2017 Mar;31(3):1165–78.

2. Methods for processing the data: 
<describe how the submitted data were generated from the raw or collected data>

3. Instrument- or software-specific information needed to interpret the data: 
<include full name and version of software, and any necessary packages or libraries needed to run scripts>

4. Standards and calibration information, if appropriate: 

5. Environmental/experimental conditions: 

6. Describe any quality-assurance procedures performed on the data: 

7. People involved with sample collection, processing, analysis and/or submission: 


DATA-SPECIFIC INFORMATION FOR: Schneper_et_al_telomere_length_preterm_infants.xlsx
<repeat this section for each dataset, folder or file, as appropriate>

1. Number of variables: 15

2. Number of cases/rows: 74

3. Variable List: 
<list variable name(s), description(s), unit(s)and value labels as appropriate for each>
ID, randomized subject identifier, numerical from 1 to 74
Group, categorical value corresponding to gestational age, preterm = if the subject was born before 37 weeks of gestation; term =  if the subject was born after 37 weeks of gestation
Sex, birth sex, M = male; F = female
Gestational_Age, Z-score of the subject's gestational age, -1.684 to 1.268
Birthweight, Z-score of the subject's birthweight, -3.148 to 2.917
Fetal_Smoke_Exposure, categorical value indicating mother's smoking status, 0 = mother never-smoker or former, pre-pregnancy smoker; 1 = former, during pregnancy or current smoker
Father_Age_at_Birth, Age (years) of father at subject's birth, 24 to 47
DEPCAT_greater_than_3, categorical variable indicating deprivation category based on postal code. Deprivation category (DEPCAT) scores range from 1 (most affluent) to 7 (most deprived), 0 = DEPCAT score of 1, 2, or 3; 1 = DEPCAT score of 4, 5, 6, or 7
Mother_Age_at_Birth, Age (years) of mother at subject's birth, 20 to 44
Mother_Illness, categorical variable indicating if mother suffered from a chronic illness, 0 = mother did not suffer from chronic illness condition; 1 = mother had chronic illness
Mother_Booking_BMI, categorical variable indicating mother's Body Mass Index at first antenatal contact, Underweight = BMI < 18.5; Normal = BMI 18.5 - 24.9; Overweight = BMI 25.0 - 29.9; Obese = BMI >= 30 
Mother_Tertiary_Education, categorical variable indicating whether mother attended tertiary school, 0 = did not attend tertiary school; 1 = attended tertiary school
TL_at_birth, Subject's telomere length (kilobase (kb)/telomere) in samples collected within the first week after birth, 7.96 to 24.87
TL_at_termadjusted_age, Subject's telomere length (kb/telomere) in samples collected at corrected full-term age; only for preterm infants, 9.44 to 23.23
TL_at_one_year, Subject's telomere length (kb/telomere) at one year of age, 7.12 to 23.45

4. Missing data codes: 
<list code/symbol and definition>n
NA indicates missing data

5. Specialized formats or other abbreviations used: N/A