title: Participant 302 at Baseline- Oral Contracept group

city: Norfolk

first: Irina

middle: A

last: Zalenskaya

state: Virginia

address: 601 Colley ave

department: Ob/Gyn

institute: Eastern Virginia Medical School

hyb_protocol: Labeled cRNA was fragmented in a 0.5ug/mL reaction and hybridized to Affymetrix U133 Plus 2 arrays at 45C for 16 h. Arrays were washed on an Affymetrix FS450 Fluidics station.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip scanner 3000 7G

data_processing: The data were processed and analyzed using Biometric Research Branch Array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). RMA was used for background correction and normalization

source_name: Ectocerviccal Tissue Biopsy

label_protocol: RNA samples were processed by Asuragen, Inc. according to the company's standard operating procedures. RNA (1ug) was biotin-labeled using modified MessageAmp-based protocols (Ambion inc., Austin, TX)

growth_protocol: Clinical study; 63 healthy women enrolled.

extract_protocol: RNA was extracted using Trizol according to manufacturer's instructions.

treatment_protocol: Women were given hormonal contraception (HC): injectable DMPA ( n=31) one injection or combined oral contraception (COC, n=32) daily. Ectocervical biopsies were taked at baseline and after six weeksof HC use.

tag: individual

value: Participant 302

value: Ectocervial tissue biopsy

tag: intervention

value: baseline (no intervention)


title: Participant 317 after DMPA use

status: Public on Apr 10 2018

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

value: Participant 317

tag: tissue

value: injectable DMPA


title: Namalwa_shTRRAP_d6

city: Heidelberg

first: Alexander

last: Jethwa

address: Im Neuenheimer Feld 460

department: Translational Oncology

country: Germany

institute: German Cancer Research Center (DKFZ) / National Center for Tumor Diseases (NCT)

description:
Sample 3
Nam_TRRAP_6

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). 750 ng of cRNA were hybridized for 17 h at 58°C on an HumanHT-12 v4 Expression BeadChip.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing: Data were normalized using quantile normalization with the Bioconductor package preprocessCore for R.

label: Biotin

source_name: Namalwa, shTRRAP, d6

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) was used to generate single-stranded cRNA from input amounts of 200 ng total RNA.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin at 37°C in a humidified, 5% CO2 atmosphere.

extract_protocol: Total DNase-digested RNA was extracted using the QIAGEN RNeasy Mini Kit according to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were transduced with a shRNA against TRRAP or a non-targeting control (NT), selected with 1 µg/mL puromycin for 48 h, and harvested at the indicated time points.

tag: cell line

value: Namalwa

tag: entity

value: Burkitt's lymphoma

tag: genotype/variation

value: mutant p53 (R248Q)

tag: shRNA

value: shTRRAP

tag: time point

value: 6 d post-transduction


title: Participant 320 after DMPA use

value: Participant 320


title: Participant 319 after DMPA use

value: Participant 319


title: Namalwa_shNT_d8

description:
Sample 2
Nam_NT_8

source_name: Namalwa, shNT, d8

value: shNT

value: 8 d post-transduction


title: Participant 318 after DMPA use

value: Participant 318


title: Namalwa_shNT_d6

description:
Sample 1
Nam_NT_6

source_name: Namalwa, shNT, d6


title: Participant 311 after DMPA use

value: Participant 311


title: Participant 219 after Oral Contracept use

value: Participant 219

value: combined oral contraceptive


title: Treated tumour 2, replicate 1

city: Nottingham

first: Cinzia

last: Allegrucci

state: Notts

address: Science Road

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

description: Each biological sample hybridised in triplicate.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio Module v1.0.

source_name: Mouse xenograft

label_protocol: Biotin (according to the Illumina Whole-Genome gene Expression Direct Hybridisation Assay Guide-using the Ambion Kit: Illumina TotalPrep-96 RNA amplification kit).

growth_protocol: MCF-7 cells were grown in RPMI medium containing 10% FCS, 1% glutamine, 1% NEAA, 1% sodium pyruvate, 1% penicillin/streptomycin.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini kit with DNase I treatment. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: Cells were permeabilised with digitonin and incubated either in medium or in axolotl oocyte extracts for 6 hours, recovered in overnight culture and then injected into nude mice.

tag: human cell line

tag: treatment

value: axolotl oocyte extract

tag: mouse strain

value: MF1 nude

value: tumor xenograft


title: Participant 308 after DMPA use

value: Participant 308

value: Ectocervial tissue biopsy

value: injectable DMPA


title: Treated tumour 2, replicate 2


title: Untreated tumour 1, replicate 3


title: Untreated tumour 1, replicate 1


title: BCSC4 patient tumor

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

description:
BCSC4_patient_tumor
Array ID: 2627770012

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

source_name: patient tumor

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: All primary tumors were from individuals who had received chemotherapy before tissue collection and were classified as triple-negative. Primary breast cancer stem cell (BCSC) lines were isolated by mechanical dissociation of the tumor material with a subsequent enzymatical digest in 5 ml DPBS (Gibco) supplemented with 6 units DNAse I (Machery-Nagel) and 1 mg liberase (Roche) for 1 h at 37 °C. Afterwards, the digest medium was diluted with 10 ml DPBS and filtered through a cell strainer (40 µm, BD) and remaining tissue clumps smashed through with a piston from a 2 ml syringe. Following centrifugation at 200 g for 5 min, the supernatant was discarded and the cell pellet was washed once with MEBM (Gibco). Subsequently, if red blood cells were visible in the pellet, 1 ml ACK Lysis-buffer (Gibco) was added to the cell pellet. After 1 min incubation at room temperature, it was filled up to 6 ml with MEBM and centrifuged at 200 g for 5 min. After the supernatant was discarded, the pellet was resuspended in 1 ml MEBM and filtered through a 40 µm strainer. Following centrifugation at 200 g for 5 min, the supernatant was discarded and remaining cell pellet taken up in MSC medium. Isolated cells were counted in a Neubauer chamber and 2 x 104 cells per well plated in a 24-well low attachment plate (Corning) in a 1:1 mix of MSC medium and Matrigel (ice cold, Corning, 354230). After solidification of Matrigel at 37 °C for 30 min, each well was topped with 500 µl of MSC medium. The cells were cultured at 37 °C and under low oxygen conditions (3 % O2, 5 % CO2, 92 % N2). When cells proliferated stably in 3D, they were cultured in 2D culture for cell expansion.  The basis of the mammary stem cell (MSC) medium is the mammary epithelial basal medium (Gibco, 31331-028), supplemented with 1 x B27 (Gibco, 17504-044), 1 x amphotericin B (Sigma-Aldrich, A2942), and 1 x penicillin-streptomycin (Gibco, 15140122). Furthermore, epidermal growth factor (f.c. 20 ng/ml, PeproTech, AF-100-15), heparin (f.c. 4 µg/ml, Sigma-Aldrich, H3149), fibroblast growth factor (f.c. 20 ng/ml, PeproTech, AF-100-18B), gentamicin (f.c. 35 µg/ml, Gibco, 15750-045), and rho kinase inhibitor (f.c. 500 nM, Calbiochem, 555552) were added.

extract_protocol: Total RNA was isolated from sub-confluent cultures grown in 6-well plates using the RNeasy Plus Kit from Qiagen, A43:M50 the Qiagen Supplementary Protocol: Purification of miRNA from animal cells using the RNeasy® Plus Mini kit and RNeasy MinElute® Cleanup Kit (Protocol 1). RNA concentration was quantified using the NanoDrop 2000 (Thermo Scientific). Reverse transcription was performed using the RevertAid First Strand cDNA Synthesis Kit (Thermo Scientific) according to the manufacturer’s manual.

treatment_protocol: To culture the BCSCs A68:O75 spheres in a 3D environment, 2 x 104 cells per well of a 24-well low-attachment plate were seeded in 100 µl of a 1:1 mixture of Matrigel (Corning, 354230) and MSC medium. After solidification of the Matrigel at 37 °C for 30 min, the dish was topped up with 500 µl of MSC medium. Cells were grown under low oxygen conditions as described above. 1 ml Medium was added after 2 days. Cells were split once a week using Dispase (Corning) to solve residual Matrigel and Accutase for sphere dissociation. The cell number was determined by counting with a Neubauer chamber. To expand the BCSCs in a 2D environment, 4 x 105 cells per 10 cm culture dish were seeded in 2 ml MSC medium containing 2 % Matrigel (ice-cold). After solidification of the Matrigel at 37 °C for 30 min, the dish was topped up with 8 ml of MSC medium. Cells were grown under low oxygen conditions as described above. Medium was changed after 3 days. Cells were split once a week using Accutase for detachment and the cell number was determined by counting.

tag: cell type

value: primary tumor cells

value: Patient 4

tag: gender

value: female

value: breast

tag: stimulus


title: Participant 218 after Oral Contracept use

value: Participant 218


title: Untreated tumour 2, replicate 2


title: Treated tumour 2, replicate 3


title: Treated tumour 1, replicate 1


title: Untreated tumour 2, replicate 3


title: Participant 217 after Oral Contracept use

value: Participant 217


title: Untreated tumour 1, replicate 2


title: BCSC4 xenograft

description:
BCSC4_xenograft
Array ID: 2627770012

source_name: patient derived xenograft

value: mouse xenograft


title: Participant 216 after Oral Contracept use

value: Participant 216


title: BCSC3 cells

description:
BCSC3_cells
Array ID: 3998720052

source_name: patient derived breast cancer stem cells

value: tumor-derived cancer stem cells

value: Patient 3


title: BCSC3 xenograft

description:
BCSC3_xenograft
Array ID: 3998720052


title: Participant 214 after Oral Contracept use

value: Participant 214

value: combined oral contraceptive


title: BCSC4 cells

description:
BCSC4_cells
Array ID: 2627770012


title: Participant 207 after Oral Contracept use

value: Participant 207


title: Participant 215 after Oral Contracept use

value: Participant 215


title: Participant 213 after Oral Contracept use

value: Participant 213


title: Untreated tumour 2, replicate 1

value: MF1 nude

value: tumor xenograft


title: BCSC2 patient tumor

description:
BCSC2_patient_tumor
Array ID: 2627770012

value: primary tumor cells

value: Patient 2


title: Participant 124 after Oral Contracept use

value: Participant 124

value: Ectocervial tissue biopsy


title: BCSC2 xenograft

description:
BCSC2_xenograft
Array ID: 2627770012

value: female

value: breast


title: BCSC3 patient tumor

description:
BCSC3_patient_tumor
Array ID: 3998720052


title: BCSC2 cells

description:
BCSC2_cells
Array ID: 2627770012


title: BCSC1 patient tumor

description:
BCSC1_patient_tumor
Array ID: 3998720052

value: Patient 1


title: SKOV3_KO1#_rep1

city: Guangzhou

first: Xiaolin

last: Luo

state: Guangdong

address: 651 Dongfeng East Road

department: Gynecology Oncology

country: China

institute: Sun Yat'sen University Cancer Center

description: Gene expression data from WT and MED12 KO ovarian cancer cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: SKOV3 KO1# cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: The cells were maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (Invitrogen, Carlsbad, CA) at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Cells were rinsed with PBS and placed on ice in the Trizol solution.

value: Ovarian cancer cells

tag: genotype

value: MED12 KO


title: BCSC1 cells

description:
BCSC1_cells
Array ID: 3998720052

value: tumor-derived cancer stem cells


title: BCSC1 xenograft

description:
BCSC1_xenograft
Array ID: 3998720052

value: mouse xenograft


title: Tgd.IFNg.2hr.Sp#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

organism: Mus musculus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: genetic background

tag: Sex

value: Male

tag: age

value: 6 Weeks Old

tag: issue

value: Spleen

tag: exclusion markers

value: TCRB-

tag: phenotype markers

value: TCRgd+

tag: separation method

value: FACSAria


title: Participant 119 after Oral Contracept use

tag: individual

value: Participant 119

tag: tissue

tag: intervention

value: combined oral contraceptive


title: Tgd.IFNg.2hr.Sp#2


title: Participant 120 after Oral Contracept use

value: Participant 120


title: Treg.IFNg.2hr.Sp#2

value: CD4+ TCRB+ CD25+


title: Participant 117 after Oral Contracept use

value: Participant 117

value: Ectocervial tissue biopsy


title: Participant 123 after Oral Contracept use

value: Participant 123


title: T8.IFNg.2hr.Sp#2

value: CD8+ TCRB+


title: T4.IFNg.2hr.Sp#2

value: CD4+ TCRB+


title: Treg.IFNg.2hr.Sp#3


title: NKT.IFNg.2hr.Sp#2

value: NK1.1+ TCRB+


title: Participant 116 after Oral Contracept use

value: Participant 116


title: Participant 115 after Oral Contracept use

value: Participant 115


title: T8.IFNg.2hr.Sp#3

value: Male

value: 6 Weeks Old


title: T4.IFNg.2hr.Sp#3

value: Spleen


title: NKT.IFNg.2hr.Sp#1


title: NK.IFNg.2hr.Sp#2

value: TCRB-


title: MF.IFNg.2hr.PC#3

value: Peritoneal Cavity

value: FACSAria


title: NK.IFNg.2hr.Sp#3


title: MF.IFNg.2hr.PC#2


title: B1a.IFNg.2hr.PC#3


title: DC.IFNg.2hr.Sp#1

value: CD11c+ MHCII+ Flt3+


title: GN.IFNg.2hr.Sp#1


title: Participant 111 after Oral Contracept use

value: Participant 111

value: combined oral contraceptive


title: Participant 113 after Oral Contracept use

value: Participant 113


title: B1a.IFNg.2hr.PC#2


title: GN.IFNg.2hr.Sp#2


title: B.IFNg.2hr.Sp#2

value: CD19+ IgM+


title: Participant 110 after Oral Contracept use

value: Participant 110

value: Ectocervial tissue biopsy


title: Treated tumour 1, replicate 3

tag: human cell line

value: axolotl oocyte extract

value: MF1 nude

value: tumor xenograft


title: B.IFNg.2hr.Sp#3


title: Participant 107 after Oral Contracept use

value: Participant 107


title: Participant 106 after Oral Contracept use

value: Participant 106


title: Participant 109 after Oral Contracept use

value: Participant 109


title: Participant 108 after Oral Contracept use

value: Participant 108


title: DC.IFNg.2hr.Sp#2

value: Male

value: 6 Weeks Old

value: Spleen


title: Treated tumour 1, replicate 2

tag: treatment


title: Participant 315 after Oral Contracept use

value: Participant 315


title: Participant 104 after Oral Contracept use

value: Participant 104


title: Sleep deprived subject 6341 blood collection 15 [D9]

city: Oklahoma City

first: Hilary

last: Uyhelji

state: OK

address: 6500 S. MacArthur Blvd.

department: Civil Aerospace Medical Institute

institute: Federal Aviation Administration

description:
SD_6341_t15
Reanalysis of sample SD_6341_t15 in GSE98564

hyb_protocol: Hybridization cocktail was prepared according to the NuGEN Encore® Biotin module manual. Affymetrix GeneChip Human Gene 1.0 ST arrays were prewet with hybridization solution, and then incubated with hybridization cocktail.

scan_protocol: Affymetrix Wash and Stain kit reagents and fluidics protocol were used with the GeneChip Fluidics Station 450 for post-hybridization chip processing. Scanning was done on an Affymetrix Scanner with G7 upgrade.

data_processing: Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6. This Series contains values for all cel files in GSE98564 except those for the 3 fatigue resistant subjects.

source_name: blood

label_protocol: Reverse transcription was performed with Ovation Pico WTA System V2 kit (NuGEN), and fragmentation and biotin labeling was performed using the Encore® Biotin module (NuGEN).

growth_protocol: Blood was collected in PAXgene tubes from healthy adult human volunteers.

extract_protocol: RNA was extracted from blood collected in PAXgene™ tubes using a QIAcube robotic workstation (Qiagen).

treatment_protocol: Blood was drawn every 4 hours during time awake on day 2 (Baseline), day 4 (Experimental), and day 6 (Recovery) of the 7 days in the sleep lab, amounting to 4 draws per day for 12 total timepoints per subject. On all 7 days, Control (C) subjects had 10 h TIB. The Sleep Deprived (SD) subjects experienced 10 h TIB during Baseline and Recovery days, but underwent 62 h continued wakefulness in the Experimental phase. Blood draws on day 4 (Experimental) for the Sleep Deprived subjects correspond to hours 24-36 of continued wakefulness.

tag: subject id

value: susceptible

tag: subject group

value: Sleep Deprived

tag: study phase

value: recovery

tag: timepoint


title: Participant 114 after Oral Contracept use

value: Participant 114

value: combined oral contraceptive


title: Sleep deprived subject 6341 blood collection 11 [D9]

description:
SD_6341_t11
Reanalysis of sample SD_6341_t11 in GSE98564

value: experimental


title: Sleep deprived subject 6341 blood collection 12 [D9]

description:
SD_6341_t12
Reanalysis of sample SD_6341_t12 in GSE98564


title: Sleep deprived subject 6341 blood collection 09 [D9]

description:
SD_6341_t09
Reanalysis of sample SD_6341_t09 in GSE98564

data_processing: Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6. This Series contains values for all cel files in the lo hasmith except those for the 3 fatigue resistant subjects.


title: Sleep deprived subject 6341 blood collection 14 [D9]

description:
SD_6341_t14
Reanalysis of sample SD_6341_t14 in GSE98564


title: Sleep deprived subject 6341 blood collection 13 [D9]

description:
SD_6341_t13
Reanalysis of sample SD_6341_t13 in GSE98564


title: Sleep deprived subject 6341 blood collection 10 [D9]

description:
SD_6341_t10
Reanalysis of sample SD_6341_t10 in GSE98564


title: Sleep deprived subject 6341 blood collection 08 [D9]

description:
SD_6341_t08
Reanalysis of sample SD_6341_t08 in GSE98564


title: Sleep deprived subject 6341 blood collection 02 [D9]

description:
SD_6341_t02
Reanalysis of sample SD_6341_t02 in GSE98564

value: baseline


title: Sleep deprived subject 6336 blood collection 15 [D9]

description:
SD_6336_t15
Reanalysis of sample SD_6336_t15 in GSE98564


title: Participant 314 after Oral Contracept use

value: Participant 314

value: Ectocervial tissue biopsy


title: Sleep deprived subject 6336 blood collection 14 [D9]

description:
SD_6336_t14
Reanalysis of sample SD_6336_t14 in GSE98564


title: Sleep deprived subject 6336 blood collection 13 [D9]

description:
SD_6336_t13
Reanalysis of sample SD_6336_t13 in GSE98564


title: Sleep deprived subject 6341 blood collection 01 [D9]

description:
SD_6341_t01
Reanalysis of sample SD_6341_t01 in GSE98564


title: Sleep deprived subject 6336 blood collection 12 [D9]

description:
SD_6336_t12
Reanalysis of sample SD_6336_t12 in GSE98564


title: Participant 312 after Oral Contracept use

value: Participant 312


title: Sleep deprived subject 6336 blood collection 09 [D9]

description:
SD_6336_t09
Reanalysis of sample SD_6336_t09 in GSE98564


title: Sleep deprived subject 6336 blood collection 08 [D9]

description:
SD_6336_t08
Reanalysis of sample SD_6336_t08 in GSE98564


title: Participant 309 after Oral Contracept use

value: Participant 309


title: Sleep deprived subject 6336 blood collection 11 [D9]

description:
SD_6336_t11
Reanalysis of sample SD_6336_t11 in GSE98564


title: Sleep deprived subject 6336 blood collection 10 [D9]

description:
SD_6336_t10
Reanalysis of sample SD_6336_t10 in GSE98564


title: Participant 313 after Oral Contracept use

value: Participant 313


title: Sleep deprived subject 6336 blood collection 02 [D9]

description:
SD_6336_t02
Reanalysis of sample SD_6336_t02 in GSE98564


title: Sleep deprived subject 6336 blood collection 04 [D9]

description:
SD_6336_t04
Reanalysis of sample SD_6336_t04 in GSE98564


title: Sleep deprived subject 6336 blood collection 03 [D9]

description:
SD_6336_t03
Reanalysis of sample SD_6336_t03 in GSE98564


title: Participant 303 after Oral Contracept use

value: Participant 303


title: Participant 302 after Oral Contracept use

value: Participant 302


title: Sleep deprived subject 6307 blood collection 12 [D9]

description:
SD_6307_t12
Reanalysis of sample SD_6307_t12 in GSE98564


title: Sleep deprived subject 6307 blood collection 11 [D9]

description:
SD_6307_t11
Reanalysis of sample SD_6307_t11 in GSE98564


title: Sleep deprived subject 6307 blood collection 14 [D9]

description:
SD_6307_t14
Reanalysis of sample SD_6307_t14 in GSE98564


title: Sleep deprived subject 6307 blood collection 15 [D9]

description:
SD_6307_t15
Reanalysis of sample SD_6307_t15 in GSE98564


title: Sleep deprived subject 6307 blood collection 04 [D9]

description:
SD_6307_t04
Reanalysis of sample SD_6307_t04 in GSE98564


title: Sleep deprived subject 6307 blood collection 13 [D9]

description:
SD_6307_t13
Reanalysis of sample SD_6307_t13 in GSE98564


title: Sleep deprived subject 6307 blood collection 08 [D9]

description:
SD_6307_t08
Reanalysis of sample SD_6307_t08 in GSE98564


title: Participant 219 at Baseline- Oral Contracept group

value: Participant 219

value: baseline (no intervention)


title: Sleep deprived subject 6307 blood collection 10 [D9]

description:
SD_6307_t10
Reanalysis of sample SD_6307_t10 in GSE98564


title: Sleep deprived subject 6307 blood collection 09 [D9]

description:
SD_6307_t09
Reanalysis of sample SD_6307_t09 in GSE98564


title: Participant 307 after Oral Contracept use

value: Participant 307


title: Participant 216 at Baseline- Oral Contracept group

value: Participant 216


title: Participant 218 at Baseline- Oral Contracept group

value: Participant 218


title: Participant 217 at Baseline- Oral Contracept group

value: Participant 217


title: Participant 215 at Baseline- Oral Contracept group

value: Participant 215


title: Participant 214 at Baseline- Oral Contracept group

value: Participant 214


title: Sleep deprived subject 6307 blood collection 03 [D9]

description:
SD_6307_t03
Reanalysis of sample SD_6307_t03 in GSE98564

value: susceptible

value: Sleep Deprived


title: Sleep deprived subject 6307 blood collection 02 [D9]

description:
SD_6307_t02
Reanalysis of sample SD_6307_t02 in GSE98564

value: baseline


title: Sleep deprived subject 6307 blood collection 01 [D9]

description:
SD_6307_t01
Reanalysis of sample SD_6307_t01 in GSE98564


title: Sleep deprived subject 6291 blood collection 12 [D9]

description:
SD_6291_t12
Reanalysis of sample SD_6291_t12 in GSE98564

value: recovery


title: Sleep deprived subject 6291 blood collection 15 [D9]

description:
SD_6291_t15
Reanalysis of sample SD_6291_t15 in GSE98564


title: Participant 124 at Baseline- Oral Contracept group

value: Participant 124

value: Ectocervial tissue biopsy


title: Participant 213 at Baseline- Oral Contracept group

value: Participant 213


title: Participant 207 at Baseline- Oral Contracept group

value: Participant 207


title: Sleep deprived subject 6291 blood collection 14 [D9]

description:
SD_6291_t14
Reanalysis of sample SD_6291_t14 in GSE98564


title: Sleep deprived subject 6291 blood collection 11 [D9]

description:
SD_6291_t11
Reanalysis of sample SD_6291_t11 in GSE98564

value: experimental


title: Sleep deprived subject 6291 blood collection 13 [D9]

description:
SD_6291_t13
Reanalysis of sample SD_6291_t13 in GSE98564


title: Sleep deprived subject 6234 blood collection 13 [D9]

description:
SD_6234_t13
Reanalysis of sample SD_6234_t13 in GSE98564


title: Sleep deprived subject 6291 blood collection 09 [D9]

description:
SD_6291_t09
Reanalysis of sample SD_6291_t09 in GSE98564


title: Sleep deprived subject 6291 blood collection 10 [D9]

description:
SD_6291_t10
Reanalysis of sample SD_6291_t10 in GSE98564


title: Sleep deprived subject 6291 blood collection 08 [D9]

description:
SD_6291_t08
Reanalysis of sample SD_6291_t08 in GSE98564


title: Sleep deprived subject 6234 blood collection 12 [D9]

description:
SD_6234_t12
Reanalysis of sample SD_6234_t12 in GSE98564


title: Sleep deprived subject 6291 blood collection 04 [D9]

description:
SD_6291_t04
Reanalysis of sample SD_6291_t04 in GSE98564


title: Participant 120 at Baseline- Oral Contracept group

value: Participant 120


title: Sleep deprived subject 6291 blood collection 03 [D9]

description:
SD_6291_t03
Reanalysis of sample SD_6291_t03 in GSE98564


title: Sleep deprived subject 6234 blood collection 15 [D9]

description:
SD_6234_t15
Reanalysis of sample SD_6234_t15 in GSE98564


title: Sleep deprived subject 6291 blood collection 02 [D9]

description:
SD_6291_t02
Reanalysis of sample SD_6291_t02 in GSE98564


title: Sleep deprived subject 6234 blood collection 14 [D9]

description:
SD_6234_t14
Reanalysis of sample SD_6234_t14 in GSE98564


title: Participant 123 at Baseline- Oral Contracept group

value: Participant 123

value: baseline (no intervention)


title: Sleep deprived subject 6234 blood collection 11 [D9]

description:
SD_6234_t11
Reanalysis of sample SD_6234_t11 in GSE98564


title: Participant 119 at Baseline- Oral Contracept group

value: Participant 119


title: Participant 116 at Baseline- Oral Contracept group

value: Participant 116


title: Sleep deprived subject 6291 blood collection 01 [D9]

description:
SD_6291_t01
Reanalysis of sample SD_6291_t01 in GSE98564


title: Sleep deprived subject 6234 blood collection 10 [D9]

description:
SD_6234_t10
Reanalysis of sample SD_6234_t10 in GSE98564


title: Participant 115 at Baseline- Oral Contracept group

value: Participant 115


title: Participant 117 at Baseline- Oral Contracept group

value: Participant 117


title: Sleep deprived subject 6234 blood collection 04 [D9]

description:
SD_6234_t04
Reanalysis of sample SD_6234_t04 in GSE98564


title: Sleep deprived subject 6234 blood collection 09 [D9]

description:
SD_6234_t09
Reanalysis of sample SD_6234_t09 in GSE98564


title: Participant 114 at Baseline- Oral Contracept group

value: Participant 114


title: Sleep deprived subject 6234 blood collection 02 [D9]

description:
SD_6234_t02
Reanalysis of sample SD_6234_t02 in GSE98564

value: susceptible


title: Participant 113 at Baseline- Oral Contracept group

value: Participant 113


title: Participant 111 at Baseline- Oral Contracept group

value: Participant 111


title: Sleep deprived subject 6212 blood collection 15 [D9]

description:
SD_6212_t15
Reanalysis of sample SD_6212_t15 in GSE98564

value: Sleep Deprived

value: recovery


title: Sleep deprived subject 6234 blood collection 03 [D9]

description:
SD_6234_t03
Reanalysis of sample SD_6234_t03 in GSE98564

value: baseline


title: Sleep deprived subject 6234 blood collection 08 [D9]

description:
SD_6234_t08
Reanalysis of sample SD_6234_t08 in GSE98564


title: Sleep deprived subject 6212 blood collection 11 [D9]

description:
SD_6212_t11
Reanalysis of sample SD_6212_t11 in GSE98564


title: Sleep deprived subject 6212 blood collection 12 [D9]

description:
SD_6212_t12
Reanalysis of sample SD_6212_t12 in GSE98564


title: Sleep deprived subject 6212 blood collection 09 [D9]

description:
SD_6212_t09
Reanalysis of sample SD_6212_t09 in GSE98564


title: Sleep deprived subject 6212 blood collection 03 [D9]

description:
SD_6212_t03
Reanalysis of sample SD_6212_t03 in GSE98564


title: Participant 110 at Baseline- Oral Contracept group

value: Participant 110

value: Ectocervial tissue biopsy


title: Sleep deprived subject 6212 blood collection 02 [D9]

description:
SD_6212_t02
Reanalysis of sample SD_6212_t02 in GSE98564


title: Sleep deprived subject 6212 blood collection 08 [D9]

description:
SD_6212_t08
Reanalysis of sample SD_6212_t08 in GSE98564

value: experimental


title: Sleep deprived subject 6212 blood collection 04 [D9]

description:
SD_6212_t04
Reanalysis of sample SD_6212_t04 in GSE98564


title: Sleep deprived subject 6212 blood collection 13 [D9]

description:
SD_6212_t13
Reanalysis of sample SD_6212_t13 in GSE98564


title: Sleep deprived subject 6212 blood collection 01 [D9]

description:
SD_6212_t01
Reanalysis of sample SD_6212_t01 in GSE98564


title: Sleep deprived subject 6207 blood collection 15 [D9]

description:
SD_6207_t15
Reanalysis of sample SD_6207_t15 in GSE98564


title: Participant 108 at Baseline- Oral Contracept group

value: Participant 108


title: Participant 109 at Baseline- Oral Contracept group

value: Participant 109


title: Participant 104 at Baseline- Oral Contracept group

value: Participant 104

value: baseline (no intervention)


title: Participant 107 at Baseline- Oral Contracept group

value: Participant 107


title: Sleep deprived subject 6207 blood collection 11 [D9]

description:
SD_6207_t11
Reanalysis of sample SD_6207_t11 in GSE98564


title: Sleep deprived subject 6207 blood collection 13 [D9]

description:
SD_6207_t13
Reanalysis of sample SD_6207_t13 in GSE98564


title: Sleep deprived subject 6207 blood collection 12 [D9]

description:
SD_6207_t12
Reanalysis of sample SD_6207_t12 in GSE98564


title: Sleep deprived subject 6341 blood collection 03 [D9]

description:
SD_6341_t03
Reanalysis of sample SD_6341_t03 in GSE98564


title: Participant 106 at Baseline- Oral Contracept group

value: Participant 106


title: Sleep deprived subject 6212 blood collection 10 [D9]

description:
SD_6212_t10
Reanalysis of sample SD_6212_t10 in GSE98564


title: Sleep deprived subject 6207 blood collection 10 [D9]

description:
SD_6207_t10
Reanalysis of sample SD_6207_t10 in GSE98564


title: Sleep deprived subject 6207 blood collection 08 [D9]

description:
SD_6207_t08
Reanalysis of sample SD_6207_t08 in GSE98564


title: Sleep deprived subject 6207 blood collection 09 [D9]

description:
SD_6207_t09
Reanalysis of sample SD_6207_t09 in GSE98564


title: Participant 314 at Baseline- Oral Contracept group

value: Participant 314


title: Participant 315 at Baseline- Oral Contracept group

value: Participant 315


title: Sleep deprived subject 6207 blood collection 14 [D9]

description:
SD_6207_t14
Reanalysis of sample SD_6207_t14 in GSE98564

value: susceptible


title: Sleep deprived subject 6207 blood collection 01 [D9]

description:
SD_6207_t01
Reanalysis of sample SD_6207_t01 in GSE98564


title: Sleep deprived subject 6207 blood collection 03 [D9]

description:
SD_6207_t03
Reanalysis of sample SD_6207_t03 in GSE98564


title: Sleep deprived subject 6207 blood collection 04 [D9]

description:
SD_6207_t04
Reanalysis of sample SD_6207_t04 in GSE98564


title: Participant 313 at Baseline- Oral Contracept group

value: Participant 313


title: Participant 312 at Baseline- Oral Contracept group

value: Participant 312


title: Sleep deprived subject 6207 blood collection 02 [D9]

description:
SD_6207_t02
Reanalysis of sample SD_6207_t02 in GSE98564

value: Sleep Deprived


title: Sleep deprived subject 6166 blood collection 15 [D9]

description:
SD_6166_t15
Reanalysis of sample SD_6166_t15 in GSE98564

value: recovery


title: Sleep deprived subject 6166 blood collection 12 [D9]

description:
SD_6166_t12
Reanalysis of sample SD_6166_t12 in GSE98564


title: Sleep deprived subject 6166 blood collection 09 [D9]

description:
SD_6166_t09
Reanalysis of sample SD_6166_t09 in GSE98564


title: Sleep deprived subject 6166 blood collection 11 [D9]

description:
SD_6166_t11
Reanalysis of sample SD_6166_t11 in GSE98564


title: Sleep deprived subject 6166 blood collection 13 [D9]

description:
SD_6166_t13
Reanalysis of sample SD_6166_t13 in GSE98564


title: Sleep deprived subject 6166 blood collection 14 [D9]

description:
SD_6166_t14
Reanalysis of sample SD_6166_t14 in GSE98564


title: Sleep deprived subject 6166 blood collection 10 [D9]

description:
SD_6166_t10
Reanalysis of sample SD_6166_t10 in GSE98564


title: Participant 309 at Baseline- Oral Contracept group

value: Participant 309


title: Participant 307 at Baseline- Oral Contracept group

value: Participant 307


title: Sleep deprived subject 6166 blood collection 04 [D9]

description:
SD_6166_t04
Reanalysis of sample SD_6166_t04 in GSE98564

value: baseline


title: Participant 303 at Baseline- Oral Contracept group

value: Participant 303

value: Ectocervial tissue biopsy


title: Sleep deprived subject 6166 blood collection 08 [D9]

description:
SD_6166_t08
Reanalysis of sample SD_6166_t08 in GSE98564

value: experimental


title: Sleep deprived subject 6166 blood collection 01 [D9]

description:
SD_6166_t01
Reanalysis of sample SD_6166_t01 in GSE98564


title: Sleep deprived subject 6166 blood collection 03 [D9]

description:
SD_6166_t03
Reanalysis of sample SD_6166_t03 in GSE98564


title: Sleep deprived subject 6166 blood collection 02 [D9]

description:
SD_6166_t02
Reanalysis of sample SD_6166_t02 in GSE98564


title: Control subject 6297 blood collection 14 [D9]

description:
C_6297_t14
Reanalysis of sample C_6297_t14 in GSE98564

value: unknown

value: Control


title: Control subject 6297 blood collection 11 [D9]

description:
C_6297_t11
Reanalysis of sample C_6297_t11 in GSE98564


title: Participant 212 after DMPA use

value: Participant 212

value: injectable DMPA


title: Control subject 6297 blood collection 12 [D9]

description:
C_6297_t12
Reanalysis of sample C_6297_t12 in GSE98564


title: Control subject 6297 blood collection 13 [D9]

description:
C_6297_t13
Reanalysis of sample C_6297_t13 in GSE98564


title: Participant 209 after DMPA use

value: Participant 209


title: Participant 210 after DMPA use

value: Participant 210


title: Participant 305 after DMPA use

value: Participant 305


title: Participant 211 after DMPA use

value: Participant 211


title: Control subject 6297 blood collection 03 [D9]

description:
C_6297_t03
Reanalysis of sample C_6297_t03 in GSE98564


title: Control subject 6297 blood collection 15 [D9]

description:
C_6297_t15
Reanalysis of sample C_6297_t15 in GSE98564


title: Control subject 6297 blood collection 01 [D9]

description:
C_6297_t01
Reanalysis of sample C_6297_t01 in GSE98564


title: Participant 304 after DMPA use

value: Participant 304


title: Participant 208 after DMPA use

value: Participant 208


title: Control subject 6297 blood collection 04 [D9]

description:
C_6297_t04
Reanalysis of sample C_6297_t04 in GSE98564


title: Control subject 6296 blood collection 14 [D9]

description:
C_6296_t14
Reanalysis of sample C_6296_t14 in GSE98564

value: recovery


title: Control subject 6297 blood collection 08 [D9]

description:
C_6297_t08
Reanalysis of sample C_6297_t08 in GSE98564


title: Control subject 6296 blood collection 15 [D9]

description:
C_6296_t15
Reanalysis of sample C_6296_t15 in GSE98564


title: Control subject 6297 blood collection 10 [D9]

description:
C_6297_t10
Reanalysis of sample C_6297_t10 in GSE98564


title: Control subject 6297 blood collection 02 [D9]

description:
C_6297_t02
Reanalysis of sample C_6297_t02 in GSE98564


title: Participant 220 after DMPA use

value: Participant 220


title: Control subject 6297 blood collection 09 [D9]

description:
C_6297_t09
Reanalysis of sample C_6297_t09 in GSE98564


title: Participant 206 after DMPA use

value: Participant 206


title: Control subject 6296 blood collection 12 [D9]

description:
C_6296_t12
Reanalysis of sample C_6296_t12 in GSE98564


title: Participant 204 after DMPA use

value: Participant 204


title: Participant 135 after DMPA use

value: Participant 135


title: Participant 131 after DMPA use

value: Participant 131

value: Ectocervial tissue biopsy


title: Control subject 6296 blood collection 03 [D9]

description:
C_6296_t03
Reanalysis of sample C_6296_t03 in GSE98564

value: unknown

value: baseline


title: Participant 134 after DMPA use

value: Participant 134


title: Control subject 6296 blood collection 13 [D9]

description:
C_6296_t13
Reanalysis of sample C_6296_t13 in GSE98564

value: Control


title: Control subject 6296 blood collection 08 [D9]

description:
C_6296_t08
Reanalysis of sample C_6296_t08 in GSE98564

value: experimental


title: Control subject 6296 blood collection 02 [D9]

description:
C_6296_t02
Reanalysis of sample C_6296_t02 in GSE98564


title: Participant 130 after DMPA use

value: Participant 130

value: injectable DMPA


title: Control subject 6296 blood collection 11 [D9]

description:
C_6296_t11
Reanalysis of sample C_6296_t11 in GSE98564


title: Control subject 6296 blood collection 09 [D9]

description:
C_6296_t09
Reanalysis of sample C_6296_t09 in GSE98564


title: Control subject 6296 blood collection 10 [D9]

description:
C_6296_t10
Reanalysis of sample C_6296_t10 in GSE98564


title: Control subject 6296 blood collection 04 [D9]

description:
C_6296_t04
Reanalysis of sample C_6296_t04 in GSE98564


title: Control subject 6231 blood collection 15 [D9]

description:
C_6231_t15
Reanalysis of sample C_6231_t15 in GSE98564


title: Participant 132 after DMPA use

value: Participant 132


title: Control subject 6296 blood collection 01 [D9]

description:
C_6296_t01
Reanalysis of sample C_6296_t01 in GSE98564


title: Participant 129 after DMPA use

value: Participant 129


title: Control subject 6231 blood collection 14 [D9]

description:
C_6231_t14
Reanalysis of sample C_6231_t14 in GSE98564


title: Control subject 6231 blood collection 12 [D9]

description:
C_6231_t12
Reanalysis of sample C_6231_t12 in GSE98564


title: Control subject 6231 blood collection 13 [D9]

description:
C_6231_t13
Reanalysis of sample C_6231_t13 in GSE98564


title: Participant 127 after DMPA use

value: Participant 127


title: Control subject 6231 blood collection 09 [D9]

description:
C_6231_t09
Reanalysis of sample C_6231_t09 in GSE98564


title: Control subject 6231 blood collection 10 [D9]

description:
C_6231_t10
Reanalysis of sample C_6231_t10 in GSE98564


title: Control subject 6231 blood collection 04 [D9]

description:
C_6231_t04
Reanalysis of sample C_6231_t04 in GSE98564


title: Participant 126 after DMPA use

value: Participant 126


title: Control subject 6231 blood collection 08 [D9]

description:
C_6231_t08
Reanalysis of sample C_6231_t08 in GSE98564


title: Participant 128 after DMPA use

value: Participant 128


title: Participant 125 after DMPA use

value: Participant 125


title: Control subject 6231 blood collection 11 [D9]

description:
C_6231_t11
Reanalysis of sample C_6231_t11 in GSE98564


title: Control subject 6231 blood collection 02 [D9]

description:
C_6231_t02
Reanalysis of sample C_6231_t02 in GSE98564


title: Control subject 6089 blood collection 11 [D9]

description:
C_6089_t11
Reanalysis of sample C_6089_t11 in GSE98564


title: Control subject 6089 blood collection 10 [D9]

description:
C_6089_t10
Reanalysis of sample C_6089_t10 in GSE98564


title: Control subject 6089 blood collection 14 [D9]

description:
C_6089_t14
Reanalysis of sample C_6089_t14 in GSE98564

value: recovery


title: Participant 122 after DMPA use

value: Participant 122


title: Control subject 6231 blood collection 03 [D9]

description:
C_6231_t03
Reanalysis of sample C_6231_t03 in GSE98564


title: Control subject 6089 blood collection 15 [D9]

description:
C_6089_t15
Reanalysis of sample C_6089_t15 in GSE98564


title: Control subject 6231 blood collection 01 [D9]

description:
C_6231_t01
Reanalysis of sample C_6231_t01 in GSE98564


title: Participant 320 at Baseline- DMPA group

value: Participant 320

value: baseline (no intervention)


title: Participant 105 after DMPA use

value: Participant 105

value: Ectocervial tissue biopsy


title: Participant 101 after DMPA use

value: Participant 101


title: Participant 118 after DMPA use

value: Participant 118


title: Control subject 6089 blood collection 08 [D9]

description:
C_6089_t08
Reanalysis of sample C_6089_t08 in GSE98564

value: unknown

value: Control

value: experimental


title: Control subject 6089 blood collection 12 [D9]

description:
C_6089_t12
Reanalysis of sample C_6089_t12 in GSE98564


title: Control subject 6089 blood collection 09 [D9]

description:
C_6089_t09
Reanalysis of sample C_6089_t09 in GSE98564


title: Control subject 6089 blood collection 13 [D9]

description:
C_6089_t13
Reanalysis of sample C_6089_t13 in GSE98564


title: Participant 319 at Baseline- DMPA group

value: Participant 319


title: Participant 103 after DMPA use

value: Participant 103

value: injectable DMPA


title: Control subject 6089 blood collection 01 [D9]

description:
C_6089_t01
Reanalysis of sample C_6089_t01 in GSE98564

value: baseline


title: Control subject 6068 blood collection 14 [D9]

description:
C_6068_t14
Reanalysis of sample C_6068_t14 in GSE98564


title: Control subject 6068 blood collection 12 [D9]

description:
C_6068_t12
Reanalysis of sample C_6068_t12 in GSE98564


title: Control subject 6089 blood collection 03 [D9]

description:
C_6089_t03
Reanalysis of sample C_6089_t03 in GSE98564


title: Control subject 6089 blood collection 02 [D9]

description:
C_6089_t02
Reanalysis of sample C_6089_t02 in GSE98564


title: Control subject 6068 blood collection 15 [D9]

description:
C_6068_t15
Reanalysis of sample C_6068_t15 in GSE98564


title: Control subject 6089 blood collection 04 [D9]

description:
C_6089_t04
Reanalysis of sample C_6089_t04 in GSE98564


title: Control subject 6068 blood collection 11 [D9]

description:
C_6068_t11
Reanalysis of sample C_6068_t11 in GSE98564


title: Control subject 6068 blood collection 13 [D9]

description:
C_6068_t13
Reanalysis of sample C_6068_t13 in GSE98564


title: Participant 308 at Baseline- DMPA group

value: Participant 308


title: Participant 317 at Baseline- DMPA group

value: Participant 317


title: Participant 311 at Baseline- DMPA group

value: Participant 311


title: Control subject 6068 blood collection 09 [D9]

description:
C_6068_t09
Reanalysis of sample C_6068_t09 in GSE98564


title: Control subject 6068 blood collection 10 [D9]

description:
C_6068_t10
Reanalysis of sample C_6068_t10 in GSE98564


title: Control subject 6068 blood collection 08 [D9]

description:
C_6068_t08
Reanalysis of sample C_6068_t08 in GSE98564


title: Control subject 6045 blood collection 13 [D9]

description:
C_6045_t13
Reanalysis of sample C_6045_t13 in GSE98564

value: recovery


title: Control subject 6045 blood collection 14 [D9]

description:
C_6045_t14
Reanalysis of sample C_6045_t14 in GSE98564


title: Control subject 6045 blood collection 12 [D9]

description:
C_6045_t12
Reanalysis of sample C_6045_t12 in GSE98564


title: Control subject 6045 blood collection 15 [D9]

description:
C_6045_t15
Reanalysis of sample C_6045_t15 in GSE98564


title: Participant 212 at Baseline- DMPA group

value: Participant 212


title: Control subject 6068 blood collection 03 [D9]

description:
C_6068_t03
Reanalysis of sample C_6068_t03 in GSE98564


title: Control subject 6068 blood collection 02 [D9]

description:
C_6068_t02
Reanalysis of sample C_6068_t02 in GSE98564


title: Participant 305 at Baseline- DMPA group

value: Participant 305

value: baseline (no intervention)


title: Control subject 6068 blood collection 04 [D9]

description:
C_6068_t04
Reanalysis of sample C_6068_t04 in GSE98564


title: Participant 211 at Baseline- DMPA group

value: Participant 211

value: Ectocervial tissue biopsy


title: Control subject 6045 blood collection 08 [D9]

description:
C_6045_t08
Reanalysis of sample C_6045_t08 in GSE98564


title: Control subject 6045 blood collection 03 [D9]

description:
C_6045_t03
Reanalysis of sample C_6045_t03 in GSE98564


title: Participant 220 at Baseline- DMPA group

value: Participant 220


title: Control subject 6045 blood collection 04 [D9]

description:
C_6045_t04
Reanalysis of sample C_6045_t04 in GSE98564

value: unknown


title: Control subject 6045 blood collection 09 [D9]

description:
C_6045_t09
Reanalysis of sample C_6045_t09 in GSE98564

value: Control


title: Participant 318 at Baseline- DMPA group

value: Participant 318


title: Participant 304 at Baseline- DMPA group

value: Participant 304


title: Control subject 6068 blood collection 01 [D9]

description:
C_6068_t01
Reanalysis of sample C_6068_t01 in GSE98564


title: Control subject 6045 blood collection 11 [D9]

description:
C_6045_t11
Reanalysis of sample C_6045_t11 in GSE98564

value: experimental


title: Participant 206 at Baseline- DMPA group

value: Participant 206


title: Sleep deprived subject 6341 blood collection 15 [D8]

description:
SD_6341_t15
Reanalysis of sample SD_6341_t15 in GSE98564

data_processing: Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6. This Series contains values for all cel files in GSE98564 excepting 6 cel files identified as outliers.

value: susceptible

value: Sleep Deprived


title: Participant 208 at Baseline- DMPA group

value: Participant 208


title: Participant 210 at Baseline- DMPA group

value: Participant 210


title: Control subject 6045 blood collection 01 [D9]

description:
C_6045_t01
Reanalysis of sample C_6045_t01 in GSE98564

value: baseline


title: Participant 209 at Baseline- DMPA group

value: Participant 209


title: Sleep deprived subject 6341 blood collection 12 [D8]

description:
SD_6341_t12
Reanalysis of sample SD_6341_t12 in GSE98564

value: recovery


title: Control subject 6045 blood collection 02 [D9]

description:
C_6045_t02
Reanalysis of sample C_6045_t02 in GSE98564


title: Sleep deprived subject 6341 blood collection 14 [D8]

description:
SD_6341_t14
Reanalysis of sample SD_6341_t14 in GSE98564


title: Sleep deprived subject 6341 blood collection 02 [D8]

description:
SD_6341_t02
Reanalysis of sample SD_6341_t02 in GSE98564


title: Sleep deprived subject 6341 blood collection 11 [D8]

description:
SD_6341_t11
Reanalysis of sample SD_6341_t11 in GSE98564


title: Sleep deprived subject 6341 blood collection 10 [D8]

description:
SD_6341_t10
Reanalysis of sample SD_6341_t10 in GSE98564


title: Sleep deprived subject 6341 blood collection 03 [D8]

description:
SD_6341_t03
Reanalysis of sample SD_6341_t03 in GSE98564


title: Sleep deprived subject 6341 blood collection 09 [D8]

description:
SD_6341_t09
Reanalysis of sample SD_6341_t09 in GSE98564


title: Participant 134 at Baseline- DMPA group

value: Participant 134

value: baseline (no intervention)


title: Sleep deprived subject 6336 blood collection 13 [D8]

description:
SD_6336_t13
Reanalysis of sample SD_6336_t13 in GSE98564


title: Participant 135 at Baseline- DMPA group

value: Participant 135

value: Ectocervial tissue biopsy


title: Participant 132 at Baseline- DMPA group

value: Participant 132


title: Participant 204 at Baseline- DMPA group

value: Participant 204


title: Sleep deprived subject 6336 blood collection 12 [D8]

description:
SD_6336_t12
Reanalysis of sample SD_6336_t12 in GSE98564


title: Sleep deprived subject 6341 blood collection 08 [D8]

description:
SD_6341_t08
Reanalysis of sample SD_6341_t08 in GSE98564


title: Participant 131 at Baseline- DMPA group

value: Participant 131


title: Sleep deprived subject 6336 blood collection 15 [D8]

description:
SD_6336_t15
Reanalysis of sample SD_6336_t15 in GSE98564


title: Sleep deprived subject 6341 blood collection 01 [D8]

description:
SD_6341_t01
Reanalysis of sample SD_6341_t01 in GSE98564


title: Sleep deprived subject 6336 blood collection 11 [D8]

description:
SD_6336_t11
Reanalysis of sample SD_6336_t11 in GSE98564


title: Sleep deprived subject 6336 blood collection 14 [D8]

description:
SD_6336_t14
Reanalysis of sample SD_6336_t14 in GSE98564


title: Sleep deprived subject 6336 blood collection 10 [D8]

description:
SD_6336_t10
Reanalysis of sample SD_6336_t10 in GSE98564


title: Sleep deprived subject 6336 blood collection 09 [D8]

description:
SD_6336_t09
Reanalysis of sample SD_6336_t09 in GSE98564


title: Sleep deprived subject 6336 blood collection 03 [D8]

description:
SD_6336_t03
Reanalysis of sample SD_6336_t03 in GSE98564


title: Sleep deprived subject 6336 blood collection 04 [D8]

description:
SD_6336_t04
Reanalysis of sample SD_6336_t04 in GSE98564


title: Sleep deprived subject 6311 blood collection 15 [D8]

description:
SD_6311_t15
Reanalysis of sample SD_6311_t15 in GSE98564

value: resistant


title: Participant 130 at Baseline- DMPA group

value: Participant 130


title: Participant 125 at Baseline- DMPA group

value: Participant 125


title: Participant 129 at Baseline- DMPA group

value: Participant 129


title: Participant 128 at Baseline- DMPA group

value: Participant 128


title: Participant 127 at Baseline- DMPA group

value: Participant 127


title: Participant 126 at Baseline- DMPA group

value: Participant 126


title: Sleep deprived subject 6336 blood collection 02 [D8]

description:
SD_6336_t02
Reanalysis of sample SD_6336_t02 in GSE98564

value: susceptible

value: Sleep Deprived

value: baseline


title: Sleep deprived subject 6311 blood collection 08 [D8]

description:
SD_6311_t08
Reanalysis of sample SD_6311_t08 in GSE98564

value: experimental


title: Sleep deprived subject 6311 blood collection 03 [D8]

description:
SD_6311_t03
Reanalysis of sample SD_6311_t03 in GSE98564


title: Sleep deprived subject 6311 blood collection 14 [D8]

description:
SD_6311_t14
Reanalysis of sample SD_6311_t14 in GSE98564

value: recovery


title: Sleep deprived subject 6311 blood collection 09 [D8]

description:
SD_6311_t09
Reanalysis of sample SD_6311_t09 in GSE98564


title: Sleep deprived subject 6311 blood collection 10 [D8]

description:
SD_6311_t10
Reanalysis of sample SD_6311_t10 in GSE98564


title: Sleep deprived subject 6336 blood collection 08 [D8]

description:
SD_6336_t08
Reanalysis of sample SD_6336_t08 in GSE98564


title: Sleep deprived subject 6311 blood collection 02 [D8]

description:
SD_6311_t02
Reanalysis of sample SD_6311_t02 in GSE98564


title: Sleep deprived subject 6311 blood collection 11 [D8]

description:
SD_6311_t11
Reanalysis of sample SD_6311_t11 in GSE98564


title: Sleep deprived subject 6311 blood collection 13 [D8]

description:
SD_6311_t13
Reanalysis of sample SD_6311_t13 in GSE98564


title: Sleep deprived subject 6311 blood collection 12 [D8]

description:
SD_6311_t12
Reanalysis of sample SD_6311_t12 in GSE98564


title: Sleep deprived subject 6311 blood collection 04 [D8]

description:
SD_6311_t04
Reanalysis of sample SD_6311_t04 in GSE98564


title: Sleep deprived subject 6311 blood collection 01 [D8]

description:
SD_6311_t01
Reanalysis of sample SD_6311_t01 in GSE98564


title: Participant 122 at Baseline- DMPA group

value: Participant 122

value: baseline (no intervention)


title: Sleep deprived subject 6307 blood collection 13 [D8]

description:
SD_6307_t13
Reanalysis of sample SD_6307_t13 in GSE98564


title: Participant 118 at Baseline- DMPA group

value: Participant 118

value: Ectocervial tissue biopsy


title: Participant 103 at Baseline- DMPA group

value: Participant 103


city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
Gene expression data from human OCPs treated with CSF-1 and RANKL for 96h
SS-HsaCR96h

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: Gene expression levels were estimated from Expression console software from affymetrix.

source_name: Human osteoclast precursors (Lonzza) treated with CSF-1 alone according to Lonza Blue Kit OCP protocol (33 ng/ml CSF1 and 66 ng/ml RANKL for 96h)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For all mouse experiments bone marrow cells were flushed, grown on plastic plates with 100 ng/ml CSF-1 in DMEM supplemented with 10% FBS,

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Enriched myeloid precursors from mouse as well as Lonza Poietics human osteoclast precurosrs were seeded at 100,000 cells/ml in OCP-BlueKit (PT-8001, Lonza) according to manufacturer's protocol for indicated time.

tag: strain

tag: cell type

value: Murine enriched myeloid precurosrs

tag: treated with


title: Sleep deprived subject 6307 blood collection 14 [D8]

description:
SD_6307_t14
Reanalysis of sample SD_6307_t14 in GSE98564


title: Participant 105 at Baseline- DMPA group

value: Participant 105


title: Sleep deprived subject 6307 blood collection 15 [D8]

description:
SD_6307_t15
Reanalysis of sample SD_6307_t15 in GSE98564


title: oocytes matured in vivo (IVO) rep3

type: SRA

city: Beijing

first: Yang

last: Yu

address: 49 North Garden Rd.,Haidian District

department: Ministry of Education Key Laboratory of Assisted Reproduction, and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Center of Reproductive Medicine

institute: Peking University Third Hospital

description:
C42
processed data file: Supplemental_materials_3_B2-C42.xlsx

library_source: transcriptomic

data_processing:
All reads were mapped to the human genome (version hg19) using TopHat (version 2.0.6) with default settings.
Cufflinks (version 2.0.2) was used to estimate fragments per kilobase of exon per million fragments mapped (FPKM) values, and genes with an FPKM value of ≥3 were considered to be expressed.
For differential expression analysis, we aligned reads against the refSeq human transcriptome using Bowtie software (v. 2.0.2). Expression levels were then estimated using eXpress (version 1.3.0), with gene-level effective counts and RPKM values derived from the sum of the corresponding values for all isoforms of a gene.
The effective count values were then used as input for DESeq to assess differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include DEGs.

molecule: polyA RNA

source_name: oocytes matured in vivo (IVO)

extract_protocol:
Oocytes were rinsed in Ca2+/Mg2+-free PBS solution and individually placed in 0.2-ml PCR tubes containing a 5-μl mixture of lysis buffer and RNase inhibitor. RNA from a single oocyte was amplified using the SMARTer Ultra Low RNA kit for Illumina sequencing.
The cDNA library was generated as follows. The quantified cDNA (20 ng) was fragmented into 200-bp lengths by ultrasonic waves using a Bioruptor® Sonication System. The cDNA fragments then underwent end repair, adaptor addition and purification using AMPure XP Beads. The products with adaptors were amplified by PCR. The different samples were marked with different index tags. PCR amplification products were electrophoresed on 2% agarose gels, and 200–300-bp DNA fragments were recovered using the CWBIO Gel Extraction Kit (CW2302A, Cwbiotech, Inc., China) and dissolved in EB buffer. cDNA library quality was tested using an Agilent 2100 Bioanalyzer, and the effective concentration was quantified by quantitative real-time PCR.

value: oocyte

tag: growing environment

value: In vivo


title: oocytes matured in vivo (IVO) rep2

description:
C41
processed data file: Supplemental_materials_2_B1-C41.xlsx


title: Sleep deprived subject 6307 blood collection 04 [D8]

description:
SD_6307_t04
Reanalysis of sample SD_6307_t04 in GSE98564


title: Sleep deprived subject 6307 blood collection 11 [D8]

description:
SD_6307_t11
Reanalysis of sample SD_6307_t11 in GSE98564


title: Sleep deprived subject 6307 blood collection 10 [D8]

description:
SD_6307_t10
Reanalysis of sample SD_6307_t10 in GSE98564


title: Sleep deprived subject 6307 blood collection 12 [D8]

description:
SD_6307_t12
Reanalysis of sample SD_6307_t12 in GSE98564


title: oocytes matured in vivo (IVO) rep1

description:
C0
processed data file: Supplemental_materials_1_B0-C0.xlsx


description:
Gene expression data from human OCPs treated with CSF-1 and RANKL for 36h
SS-HsaCR36h

source_name: Human osteoclast precursors (Lonzza) treated with CSF-1 alone according to Lonza Blue Kit OCP protocol (33 ng/ml CSF1 and 66 ng/ml RANKL for 36h)


description:
Gene expression data from human OCPs treated with CSF-1 and RANKL for 72h
SS-HsaCR72h

source_name: Human osteoclast precursors (Lonzza) treated with CSF-1 alone according to Lonza Blue Kit OCP protocol (33 ng/ml CSF1 and 66 ng/ml RANKL for 72h)


title: human OCPs treated with CSF-1 alone

description:
Gene expression data from human OCPs treated with CSF-1 alone.
SS-HsaCSF-1

source_name: Human osteoclast precursors (Lonzza) treated with CSF-1 alone according to Lonza Blue Kit OCP protocol (33 ng/ml CSF1)


title: Participant 101 at Baseline- DMPA group

value: Participant 101


title: Sleep deprived subject 6307 blood collection 08 [D8]

description:
SD_6307_t08
Reanalysis of sample SD_6307_t08 in GSE98564


title: Sleep deprived subject 6307 blood collection 02 [D8]

description:
SD_6307_t02
Reanalysis of sample SD_6307_t02 in GSE98564


title: oocytes matured in vitro (IVM) rep3

description:
B21
processed data file: Supplemental_materials_3_B2-C42.xlsx

source_name: oocytes matured in vitro (IVM)

value: In vitro


title: Sleep deprived subject 6307 blood collection 03 [D8]

description:
SD_6307_t03
Reanalysis of sample SD_6307_t03 in GSE98564


title: oocytes matured in vitro (IVM) rep1

description:
B0
processed data file: Supplemental_materials_1_B0-C0.xlsx


title: Sleep deprived subject 6307 blood collection 01 [D8]

description:
SD_6307_t01
Reanalysis of sample SD_6307_t01 in GSE98564


title: oocytes matured in vitro (IVM) rep2

description:
B1
processed data file: Supplemental_materials_2_B1-C41.xlsx


title: Sleep deprived subject 6291 blood collection 11 [D8]

description:
SD_6291_t11
Reanalysis of sample SD_6291_t11 in GSE98564


title: Sleep deprived subject 6291 blood collection 12 [D8]

description:
SD_6291_t12
Reanalysis of sample SD_6291_t12 in GSE98564


title: Sleep deprived subject 6291 blood collection 15 [D8]

description:
SD_6291_t15
Reanalysis of sample SD_6291_t15 in GSE98564


title: Sleep deprived subject 6291 blood collection 13 [D8]

description:
SD_6291_t13
Reanalysis of sample SD_6291_t13 in GSE98564


title: Sleep deprived subject 6291 blood collection 14 [D8]

description:
SD_6291_t14
Reanalysis of sample SD_6291_t14 in GSE98564


title: Sleep deprived subject 6291 blood collection 03 [D8]

description:
SD_6291_t03
Reanalysis of sample SD_6291_t03 in GSE98564


title: Sleep deprived subject 6291 blood collection 10 [D8]

description:
SD_6291_t10
Reanalysis of sample SD_6291_t10 in GSE98564


title: Sleep deprived subject 6291 blood collection 08 [D8]

description:
SD_6291_t08
Reanalysis of sample SD_6291_t08 in GSE98564


title: Sleep deprived subject 6291 blood collection 04 [D8]

description:
SD_6291_t04
Reanalysis of sample SD_6291_t04 in GSE98564


title: Sleep deprived subject 6291 blood collection 02 [D8]

description:
SD_6291_t02
Reanalysis of sample SD_6291_t02 in GSE98564


title: Input DNA from DNA2-null cells

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Input DNA from DNA2-null cells
16643_D2_4OH_input_S3S14_L999

library_source: genomic

data_processing:
bases were called using Illumina's RTA software
Sequences were aligned to hg38 genome using Novoalign, only unique aligned reads were kept
Reads were extended to 200bp and coverage of each base in the genome were calculated using R scripts
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files containing base wise coverage

molecule: genomic DNA

source_name: HCT-116 cells

growth_protocol: HCT-116 cells were rountinly cultured in 10% FBS and 1% penicillin and streptomycin

extract_protocol:
For CHIP-DNA2, lysates were clarified from sonicated nuclei and DNA2-DNA complexes were isolated with antibody. For collection of BrdU negative DNA, separation of BrdU-labeled DNA from unlabeled DNA was done as previously described (Roux-Michollet et al, 2010; Viggiani et al, 2010). Briefly, 20 µL of DNA at ~20 ng/µL in PBS was heat denatured at 100 ºC for 1 min, and transferred to an ice-ethanol bath for 30-50 s to flash freeze. Tubes of DNA were then thawed completely at RT (less than 3 min), mixed with 2 μL of a BrdU antibody (BD Biosciences, cat# 347580), and incubated at RT for 30-40 min in the dark with occasional mixing. The BrdU-labeled DNA, bound with antibody, was then isolated with 20 µL of prepared Dynabeads Sheep anti-Mouse IgG (Thermo Scientific cat# 11031). The BrdU-negative DNA was collected by sequencing.
Libraries were constructed using Kapa's HyperPlus Kits

tag: cell line

value: Colorectal cancer cell line

tag: genotype/variation

value: DNA2 KO


title: CHIP-phosphor-ATR from DNA2-null cells

description:
CHIP-phosphor-ATR from DNA2-null cells
16767_Re_D2_4OH_ChIP_pART_S4_L999

tag: chip antibody

value: Rabbit phosphor-ATR antibody (Genetex, GTX128145)


title: IgG control for CHIP-phosphor-ATR

description:
IgG control
12505_HCT-D2-4OH-IgG-for-ATR_GCCAAT_L999


title: Sleep deprived subject 6291 blood collection 09 [D8]

description:
SD_6291_t09
Reanalysis of sample SD_6291_t09 in GSE98564

value: susceptible

value: Sleep Deprived


title: CHIP-phosphor-ATR from WT cells

description:
CHIP-phosphor-ATR from WT cells
16642_WT_ChIP_pATR_S2_L999

value: WT


title: Input DNA from WT cells

description:
Input DNA from WT cells
16641_WT_input_S1S10_L999


title: Sleep deprived subject 6291 blood collection 01 [D8]

description:
SD_6291_t01
Reanalysis of sample SD_6291_t01 in GSE98564

value: baseline


title: Sleep deprived subject 6234 blood collection 13 [D8]

description:
SD_6234_t13
Reanalysis of sample SD_6234_t13 in GSE98564

value: recovery


title: Sleep deprived subject 6234 blood collection 09 [D8]

description:
SD_6234_t09
Reanalysis of sample SD_6234_t09 in GSE98564

value: experimental


title: Sleep deprived subject 6234 blood collection 10 [D8]

description:
SD_6234_t10
Reanalysis of sample SD_6234_t10 in GSE98564


title: Sleep deprived subject 6234 blood collection 14 [D8]

description:
SD_6234_t14
Reanalysis of sample SD_6234_t14 in GSE98564


title: Sleep deprived subject 6234 blood collection 08 [D8]

description:
SD_6234_t08
Reanalysis of sample SD_6234_t08 in GSE98564


title: IgG control for CHIP-DNA2

description:
IgG control
12504_HCT-WT-Beads-for-DNA2_AGTCAA_L999


title: Sleep deprived subject 6234 blood collection 04 [D8]

description:
SD_6234_t04
Reanalysis of sample SD_6234_t04 in GSE98564


title: Sleep deprived subject 6234 blood collection 11 [D8]

description:
SD_6234_t11
Reanalysis of sample SD_6234_t11 in GSE98564


title: CHIP-DNA2

description:
CHIP-DNA2
11799_HCT-WT-AbGent_TCTCGA_L999

value: Rabbit anti-DNA2 (Abgent, cat# AP10182c)


title: Sleep deprived subject 6234 blood collection 02 [D8]

description:
SD_6234_t02
Reanalysis of sample SD_6234_t02 in GSE98564


title: BrdU negative

description:
BrdU negative
10802_Isolated_TCTCGA_L999

value: Mouse anti-BrdU (BD Biosciences, clone B44)


title: Input DNA

description:
Input DNA
11008_input-genomic_TGACTG_L999


title: Sleep deprived subject 6212 blood collection 12 [D8]

description:
SD_6212_t12
Reanalysis of sample SD_6212_t12 in GSE98564


title: Sleep deprived subject 6212 blood collection 11 [D8]

description:
SD_6212_t11
Reanalysis of sample SD_6212_t11 in GSE98564


title: Sleep deprived subject 6234 blood collection 03 [D8]

description:
SD_6234_t03
Reanalysis of sample SD_6234_t03 in GSE98564


title: Sleep deprived subject 6212 blood collection 08 [D8]

description:
SD_6212_t08
Reanalysis of sample SD_6212_t08 in GSE98564


title: Sleep deprived subject 6212 blood collection 13 [D8]

description:
SD_6212_t13
Reanalysis of sample SD_6212_t13 in GSE98564


title: Sleep deprived subject 6207 blood collection 15 [D8]

description:
SD_6207_t15
Reanalysis of sample SD_6207_t15 in GSE98564


title: Sleep deprived subject 6212 blood collection 01 [D8]

description:
SD_6212_t01
Reanalysis of sample SD_6212_t01 in GSE98564


title: Sleep deprived subject 6212 blood collection 04 [D8]

description:
SD_6212_t04
Reanalysis of sample SD_6212_t04 in GSE98564


title: Sleep deprived subject 6212 blood collection 15 [D8]

description:
SD_6212_t15
Reanalysis of sample SD_6212_t15 in GSE98564


title: Sleep deprived subject 6212 blood collection 09 [D8]

description:
SD_6212_t09
Reanalysis of sample SD_6212_t09 in GSE98564


title: Sleep deprived subject 6234 blood collection 12 [D8]

description:
SD_6234_t12
Reanalysis of sample SD_6234_t12 in GSE98564


title: Sleep deprived subject 6212 blood collection 10 [D8]

description:
SD_6212_t10
Reanalysis of sample SD_6212_t10 in GSE98564


title: Sleep deprived subject 6212 blood collection 02 [D8]

description:
SD_6212_t02
Reanalysis of sample SD_6212_t02 in GSE98564


title: Sleep deprived subject 6207 blood collection 10 [D8]

description:
SD_6207_t10
Reanalysis of sample SD_6207_t10 in GSE98564


title: Sleep deprived subject 6207 blood collection 14 [D8]

description:
SD_6207_t14
Reanalysis of sample SD_6207_t14 in GSE98564


title: Sleep deprived subject 6212 blood collection 03 [D8]

description:
SD_6212_t03
Reanalysis of sample SD_6212_t03 in GSE98564


title: Sleep deprived subject 6207 blood collection 02 [D8]

description:
SD_6207_t02
Reanalysis of sample SD_6207_t02 in GSE98564


title: Sleep deprived subject 6207 blood collection 04 [D8]

description:
SD_6207_t04
Reanalysis of sample SD_6207_t04 in GSE98564


title: Sleep deprived subject 6207 blood collection 13 [D8]

description:
SD_6207_t13
Reanalysis of sample SD_6207_t13 in GSE98564


title: Sleep deprived subject 6207 blood collection 03 [D8]

description:
SD_6207_t03
Reanalysis of sample SD_6207_t03 in GSE98564


title: Sleep deprived subject 6207 blood collection 08 [D8]

description:
SD_6207_t08
Reanalysis of sample SD_6207_t08 in GSE98564


title: Sleep deprived subject 6207 blood collection 12 [D8]

description:
SD_6207_t12
Reanalysis of sample SD_6207_t12 in GSE98564


title: Sleep deprived subject 6207 blood collection 09 [D8]

description:
SD_6207_t09
Reanalysis of sample SD_6207_t09 in GSE98564


title: Sleep deprived subject 6166 blood collection 13 [D8]

description:
SD_6166_t13
Reanalysis of sample SD_6166_t13 in GSE98564


title: Sleep deprived subject 6166 blood collection 12 [D8]

description:
SD_6166_t12
Reanalysis of sample SD_6166_t12 in GSE98564


title: Sleep deprived subject 6166 blood collection 11 [D8]

description:
SD_6166_t11
Reanalysis of sample SD_6166_t11 in GSE98564


title: Sleep deprived subject 6166 blood collection 15 [D8]

description:
SD_6166_t15
Reanalysis of sample SD_6166_t15 in GSE98564


title: Sleep deprived subject 6166 blood collection 03 [D8]

description:
SD_6166_t03
Reanalysis of sample SD_6166_t03 in GSE98564


title: Sleep deprived subject 6166 blood collection 09 [D8]

description:
SD_6166_t09
Reanalysis of sample SD_6166_t09 in GSE98564


title: Sleep deprived subject 6166 blood collection 04 [D8]

description:
SD_6166_t04
Reanalysis of sample SD_6166_t04 in GSE98564


title: Sleep deprived subject 6207 blood collection 01 [D8]

description:
SD_6207_t01
Reanalysis of sample SD_6207_t01 in GSE98564


title: Sleep deprived subject 6166 blood collection 08 [D8]

description:
SD_6166_t08
Reanalysis of sample SD_6166_t08 in GSE98564


title: Sleep deprived subject 6166 blood collection 10 [D8]

description:
SD_6166_t10
Reanalysis of sample SD_6166_t10 in GSE98564


title: Sleep deprived subject 6125 blood collection 09 [D8]

description:
SD_6125_t09
Reanalysis of sample SD_6125_t09 in GSE98564

value: resistant


title: Sleep deprived subject 6125 blood collection 11 [D8]

description:
SD_6125_t11
Reanalysis of sample SD_6125_t11 in GSE98564


title: Sleep deprived subject 6125 blood collection 13 [D8]

description:
SD_6125_t13
Reanalysis of sample SD_6125_t13 in GSE98564


title: Sleep deprived subject 6125 blood collection 04 [D8]

description:
SD_6125_t04
Reanalysis of sample SD_6125_t04 in GSE98564


title: Sleep deprived subject 6125 blood collection 02 [D8]

description:
SD_6125_t02
Reanalysis of sample SD_6125_t02 in GSE98564


title: Sleep deprived subject 6166 blood collection 02 [D8]

description:
SD_6166_t02
Reanalysis of sample SD_6166_t02 in GSE98564


title: Sleep deprived subject 6166 blood collection 01 [D8]

description:
SD_6166_t01
Reanalysis of sample SD_6166_t01 in GSE98564


title: Sleep deprived subject 6125 blood collection 10 [D8]

description:
SD_6125_t10
Reanalysis of sample SD_6125_t10 in GSE98564


title: Sleep deprived subject 6125 blood collection 08 [D8]

description:
SD_6125_t08
Reanalysis of sample SD_6125_t08 in GSE98564


title: Sleep deprived subject 6093 blood collection 15 [D8]

description:
SD_6093_t15
Reanalysis of sample SD_6093_t15 in GSE98564


title: Sleep deprived subject 6125 blood collection 03 [D8]

description:
SD_6125_t03
Reanalysis of sample SD_6125_t03 in GSE98564


title: Sleep deprived subject 6093 blood collection 08 [D8]

description:
SD_6093_t08
Reanalysis of sample SD_6093_t08 in GSE98564


title: Sleep deprived subject 6093 blood collection 11 [D8]

description:
SD_6093_t11
Reanalysis of sample SD_6093_t11 in GSE98564


title: Sleep deprived subject 6093 blood collection 13 [D8]

description:
SD_6093_t13
Reanalysis of sample SD_6093_t13 in GSE98564


title: Sleep deprived subject 6093 blood collection 03 [D8]

description:
SD_6093_t03
Reanalysis of sample SD_6093_t03 in GSE98564


title: Sleep deprived subject 6093 blood collection 09 [D8]

description:
SD_6093_t09
Reanalysis of sample SD_6093_t09 in GSE98564


title: Sleep deprived subject 6125 blood collection 12 [D8]

description:
SD_6125_t12
Reanalysis of sample SD_6125_t12 in GSE98564


title: Sleep deprived subject 6093 blood collection 14 [D8]

description:
SD_6093_t14
Reanalysis of sample SD_6093_t14 in GSE98564


title: Sleep deprived subject 6125 blood collection 01 [D8]

description:
SD_6125_t01
Reanalysis of sample SD_6125_t01 in GSE98564


title: Sleep deprived subject 6125 blood collection 15 [D8]

description:
SD_6125_t15
Reanalysis of sample SD_6125_t15 in GSE98564


title: Sleep deprived subject 6093 blood collection 02 [D8]

description:
SD_6093_t02
Reanalysis of sample SD_6093_t02 in GSE98564


title: Control subject 6297 blood collection 13 [D8]

description:
C_6297_t13
Reanalysis of sample C_6297_t13 in GSE98564

value: unknown

value: Control


title: Sleep deprived subject 6093 blood collection 04 [D8]

description:
SD_6093_t04
Reanalysis of sample SD_6093_t04 in GSE98564


title: Sleep deprived subject 6093 blood collection 10 [D8]

description:
SD_6093_t10
Reanalysis of sample SD_6093_t10 in GSE98564


title: Sleep deprived subject 6093 blood collection 01 [D8]

description:
SD_6093_t01
Reanalysis of sample SD_6093_t01 in GSE98564


title: Control subject 6297 blood collection 14 [D8]

description:
C_6297_t14
Reanalysis of sample C_6297_t14 in GSE98564


title: Control subject 6297 blood collection 02 [D8]

description:
C_6297_t02
Reanalysis of sample C_6297_t02 in GSE98564


title: Control subject 6297 blood collection 10 [D8]

description:
C_6297_t10
Reanalysis of sample C_6297_t10 in GSE98564


title: Sleep deprived subject 6093 blood collection 12 [D8]

description:
SD_6093_t12
Reanalysis of sample SD_6093_t12 in GSE98564


title: Control subject 6297 blood collection 09 [D8]

description:
C_6297_t09
Reanalysis of sample C_6297_t09 in GSE98564


title: Control subject 6297 blood collection 15 [D8]

description:
C_6297_t15
Reanalysis of sample C_6297_t15 in GSE98564


title: Control subject 6297 blood collection 01 [D8]

description:
C_6297_t01
Reanalysis of sample C_6297_t01 in GSE98564


title: Control subject 6297 blood collection 12 [D8]

description:
C_6297_t12
Reanalysis of sample C_6297_t12 in GSE98564


title: Control subject 6297 blood collection 08 [D8]

description:
C_6297_t08
Reanalysis of sample C_6297_t08 in GSE98564


title: Control subject 6297 blood collection 03 [D8]

description:
C_6297_t03
Reanalysis of sample C_6297_t03 in GSE98564


title: Control subject 6297 blood collection 04 [D8]

description:
C_6297_t04
Reanalysis of sample C_6297_t04 in GSE98564


title: Control subject 6296 blood collection 08 [D8]

description:
C_6296_t08
Reanalysis of sample C_6296_t08 in GSE98564


title: Control subject 6296 blood collection 01 [D8]

description:
C_6296_t01
Reanalysis of sample C_6296_t01 in GSE98564


title: Control subject 6297 blood collection 11 [D8]

description:
C_6297_t11
Reanalysis of sample C_6297_t11 in GSE98564


title: Control subject 6296 blood collection 03 [D8]

description:
C_6296_t03
Reanalysis of sample C_6296_t03 in GSE98564


title: Control subject 6296 blood collection 02 [D8]

description:
C_6296_t02
Reanalysis of sample C_6296_t02 in GSE98564


title: Control subject 6231 blood collection 13 [D8]

description:
C_6231_t13
Reanalysis of sample C_6231_t13 in GSE98564


title: Control subject 6296 blood collection 04 [D8]

description:
C_6296_t04
Reanalysis of sample C_6296_t04 in GSE98564


title: Control subject 6296 blood collection 15 [D8]

description:
C_6296_t15
Reanalysis of sample C_6296_t15 in GSE98564


title: Control subject 6296 blood collection 10 [D8]

description:
C_6296_t10
Reanalysis of sample C_6296_t10 in GSE98564


title: Control subject 6296 blood collection 09 [D8]

description:
C_6296_t09
Reanalysis of sample C_6296_t09 in GSE98564


title: Control subject 6296 blood collection 14 [D8]

description:
C_6296_t14
Reanalysis of sample C_6296_t14 in GSE98564


title: Control subject 6296 blood collection 11 [D8]

description:
C_6296_t11
Reanalysis of sample C_6296_t11 in GSE98564


title: Control subject 6296 blood collection 12 [D8]

description:
C_6296_t12
Reanalysis of sample C_6296_t12 in GSE98564


title: Control subject 6296 blood collection 13 [D8]

description:
C_6296_t13
Reanalysis of sample C_6296_t13 in GSE98564


title: Control subject 6231 blood collection 14 [D8]

description:
C_6231_t14
Reanalysis of sample C_6231_t14 in GSE98564


title: Control subject 6231 blood collection 15 [D8]

description:
C_6231_t15
Reanalysis of sample C_6231_t15 in GSE98564


title: Control subject 6231 blood collection 12 [D8]

description:
C_6231_t12
Reanalysis of sample C_6231_t12 in GSE98564


title: Control subject 6231 blood collection 10 [D8]

description:
C_6231_t10
Reanalysis of sample C_6231_t10 in GSE98564


title: Control subject 6089 blood collection 15 [D8]

description:
C_6089_t15
Reanalysis of sample C_6089_t15 in GSE98564


title: Control subject 6231 blood collection 01 [D8]

description:
C_6231_t01
Reanalysis of sample C_6231_t01 in GSE98564


title: Control subject 6089 blood collection 12 [D8]

description:
C_6089_t12
Reanalysis of sample C_6089_t12 in GSE98564


title: Control subject 6231 blood collection 09 [D8]

description:
C_6231_t09
Reanalysis of sample C_6231_t09 in GSE98564


title: Control subject 6231 blood collection 04 [D8]

description:
C_6231_t04
Reanalysis of sample C_6231_t04 in GSE98564


title: Control subject 6231 blood collection 03 [D8]

description:
C_6231_t03
Reanalysis of sample C_6231_t03 in GSE98564


title: Control subject 6089 blood collection 03 [D8]

description:
C_6089_t03
Reanalysis of sample C_6089_t03 in GSE98564


title: Control subject 6089 blood collection 14 [D8]

description:
C_6089_t14
Reanalysis of sample C_6089_t14 in GSE98564


title: Control subject 6089 blood collection 13 [D8]

description:
C_6089_t13
Reanalysis of sample C_6089_t13 in GSE98564


title: Control subject 6231 blood collection 08 [D8]

description:
C_6231_t08
Reanalysis of sample C_6231_t08 in GSE98564


title: Control subject 6231 blood collection 02 [D8]

description:
C_6231_t02
Reanalysis of sample C_6231_t02 in GSE98564


title: Control subject 6068 blood collection 11 [D8]

description:
C_6068_t11
Reanalysis of sample C_6068_t11 in GSE98564


title: Control subject 6231 blood collection 11 [D8]

description:
C_6231_t11
Reanalysis of sample C_6231_t11 in GSE98564


title: Control subject 6068 blood collection 12 [D8]

description:
C_6068_t12
Reanalysis of sample C_6068_t12 in GSE98564


title: Control subject 6068 blood collection 13 [D8]

description:
C_6068_t13
Reanalysis of sample C_6068_t13 in GSE98564


title: Control subject 6089 blood collection 11 [D8]

description:
C_6089_t11
Reanalysis of sample C_6089_t11 in GSE98564


title: Control subject 6068 blood collection 08 [D8]

description:
C_6068_t08
Reanalysis of sample C_6068_t08 in GSE98564


title: Control subject 6068 blood collection 09 [D8]

description:
C_6068_t09
Reanalysis of sample C_6068_t09 in GSE98564


title: Control subject 6089 blood collection 02 [D8]

description:
C_6089_t02
Reanalysis of sample C_6089_t02 in GSE98564


title: Control subject 6089 blood collection 10 [D8]

description:
C_6089_t10
Reanalysis of sample C_6089_t10 in GSE98564


title: Control subject 6089 blood collection 01 [D8]

description:
C_6089_t01
Reanalysis of sample C_6089_t01 in GSE98564


title: Control subject 6089 blood collection 04 [D8]

description:
C_6089_t04
Reanalysis of sample C_6089_t04 in GSE98564


title: Control subject 6089 blood collection 08 [D8]

description:
C_6089_t08
Reanalysis of sample C_6089_t08 in GSE98564


title: Control subject 6068 blood collection 10 [D8]

description:
C_6068_t10
Reanalysis of sample C_6068_t10 in GSE98564


title: Control subject 6068 blood collection 02 [D8]

description:
C_6068_t02
Reanalysis of sample C_6068_t02 in GSE98564


title: Control subject 6089 blood collection 09 [D8]

description:
C_6089_t09
Reanalysis of sample C_6089_t09 in GSE98564


title: Control subject 6045 blood collection 14 [D8]

description:
C_6045_t14
Reanalysis of sample C_6045_t14 in GSE98564


title: Control subject 6068 blood collection 15 [D8]

description:
C_6068_t15
Reanalysis of sample C_6068_t15 in GSE98564


title: Control subject 6045 blood collection 13 [D8]

description:
C_6045_t13
Reanalysis of sample C_6045_t13 in GSE98564


title: Control subject 6068 blood collection 04 [D8]

description:
C_6068_t04
Reanalysis of sample C_6068_t04 in GSE98564


title: Control subject 6068 blood collection 03 [D8]

description:
C_6068_t03
Reanalysis of sample C_6068_t03 in GSE98564


title: Control subject 6045 blood collection 03 [D8]

description:
C_6045_t03
Reanalysis of sample C_6045_t03 in GSE98564


title: Control subject 6068 blood collection 01 [D8]

description:
C_6068_t01
Reanalysis of sample C_6068_t01 in GSE98564


title: Control subject 6045 blood collection 12 [D8]

description:
C_6045_t12
Reanalysis of sample C_6045_t12 in GSE98564


title: Control subject 6045 blood collection 08 [D8]

description:
C_6045_t08
Reanalysis of sample C_6045_t08 in GSE98564


title: Control subject 6045 blood collection 09 [D8]

description:
C_6045_t09
Reanalysis of sample C_6045_t09 in GSE98564


title: Control subject 6045 blood collection 11 [D8]

description:
C_6045_t11
Reanalysis of sample C_6045_t11 in GSE98564


title: Control subject 6045 blood collection 15 [D8]

description:
C_6045_t15
Reanalysis of sample C_6045_t15 in GSE98564


title: Sleep deprived subject 6341 blood collection 13 [D6]

description:
SD_6341_t13
Sample SD_6341_t13 in GSE98564

data_processing: Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6.


title: Control subject 6068 blood collection 14 [D8]

description:
C_6068_t14
Reanalysis of sample C_6068_t14 in GSE98564


title: Control subject 6045 blood collection 04 [D8]

description:
C_6045_t04
Reanalysis of sample C_6045_t04 in GSE98564


title: Control subject 6045 blood collection 02 [D8]

description:
C_6045_t02
Reanalysis of sample C_6045_t02 in GSE98564


title: Sleep deprived subject 6341 blood collection 03 [D6]

description:
SD_6341_t03
Sample SD_6341_t03 in GSE98564


title: Sleep deprived subject 6336 blood collection 12 [D6]

description:
SD_6336_t12
Sample SD_6336_t12 in GSE98564


title: Sleep deprived subject 6341 blood collection 02 [D6]

description:
SD_6341_t02
Sample SD_6341_t02 in GSE98564


title: Sleep deprived subject 6336 blood collection 11 [D6]

description:
SD_6336_t11
Sample SD_6336_t11 in GSE98564


title: Sleep deprived subject 6336 blood collection 10 [D6]

description:
SD_6336_t10
Sample SD_6336_t10 in GSE98564


title: Sleep deprived subject 6341 blood collection 15 [D6]

description:
SD_6341_t15
Sample SD_6341_t15 in GSE98564


title: Sleep deprived subject 6341 blood collection 14 [D6]

description:
SD_6341_t14
Sample SD_6341_t14 in GSE98564


title: Sleep deprived subject 6341 blood collection 12 [D6]

description:
SD_6341_t12
Sample SD_6341_t12 in GSE98564


title: Sleep deprived subject 6341 blood collection 08 [D6]

description:
SD_6341_t08
Sample SD_6341_t08 in GSE98564


title: Sleep deprived subject 6336 blood collection 08 [D6]

description:
SD_6336_t08
Sample SD_6336_t08 in GSE98564


title: Sleep deprived subject 6341 blood collection 11 [D6]

description:
SD_6341_t11
Sample SD_6341_t11 in GSE98564


title: Sleep deprived subject 6311 blood collection 15 [D6]

description:
SD_6311_t15
Sample SD_6311_t15 in GSE98564


title: Sleep deprived subject 6336 blood collection 14 [D6]

description:
SD_6336_t14
Sample SD_6336_t14 in GSE98564


title: Sleep deprived subject 6336 blood collection 04 [D6]

description:
SD_6336_t04
Sample SD_6336_t04 in GSE98564


title: Sleep deprived subject 6311 blood collection 14 [D6]

description:
SD_6311_t14
Sample SD_6311_t14 in GSE98564


title: Sleep deprived subject 6341 blood collection 09 [D6]

description:
SD_6341_t09
Sample SD_6341_t09 in GSE98564


title: Sleep deprived subject 6341 blood collection 01 [D6]

description:
SD_6341_t01
Sample SD_6341_t01 in GSE98564


title: Sleep deprived subject 6336 blood collection 15 [D6]

description:
SD_6336_t15
Sample SD_6336_t15 in GSE98564


title: Sleep deprived subject 6311 blood collection 12 [D6]

description:
SD_6311_t12
Sample SD_6311_t12 in GSE98564


title: Control subject 6045 blood collection 01 [D8]

description:
C_6045_t01
Reanalysis of sample C_6045_t01 in GSE98564


title: Sleep deprived subject 6336 blood collection 09 [D6]

description:
SD_6336_t09
Sample SD_6336_t09 in GSE98564


title: Sleep deprived subject 6336 blood collection 02 [D6]

description:
SD_6336_t02
Sample SD_6336_t02 in GSE98564


title: Sleep deprived subject 6311 blood collection 11 [D6]

description:
SD_6311_t11
Sample SD_6311_t11 in GSE98564


title: Sleep deprived subject 6341 blood collection 10 [D6]

description:
SD_6341_t10
Sample SD_6341_t10 in GSE98564


title: Sleep deprived subject 6311 blood collection 13 [D6]

description:
SD_6311_t13
Sample SD_6311_t13 in GSE98564


title: Sleep deprived subject 6311 blood collection 09 [D6]

description:
SD_6311_t09
Sample SD_6311_t09 in GSE98564


title: Sleep deprived subject 6311 blood collection 08 [D6]

description:
SD_6311_t08
Sample SD_6311_t08 in GSE98564


title: Sleep deprived subject 6311 blood collection 02 [D6]

description:
SD_6311_t02
Sample SD_6311_t02 in GSE98564


title: Sleep deprived subject 6336 blood collection 13 [D6]

description:
SD_6336_t13
Sample SD_6336_t13 in GSE98564


title: Sleep deprived subject 6311 blood collection 01 [D6]

description:
SD_6311_t01
Sample SD_6311_t01 in GSE98564


title: Sleep deprived subject 6307 blood collection 14 [D6]

description:
SD_6307_t14
Sample SD_6307_t14 in GSE98564


title: Sleep deprived subject 6307 blood collection 15 [D6]

description:
SD_6307_t15
Sample SD_6307_t15 in GSE98564


title: Sleep deprived subject 6307 blood collection 10 [D6]

description:
SD_6307_t10
Sample SD_6307_t10 in GSE98564


title: Sleep deprived subject 6307 blood collection 11 [D6]

description:
SD_6307_t11
Sample SD_6307_t11 in GSE98564


title: Sleep deprived subject 6307 blood collection 12 [D6]

description:
SD_6307_t12
Sample SD_6307_t12 in GSE98564


title: Sleep deprived subject 6336 blood collection 03 [D6]

description:
SD_6336_t03
Sample SD_6336_t03 in GSE98564


title: Sleep deprived subject 6307 blood collection 03 [D6]

description:
SD_6307_t03
Sample SD_6307_t03 in GSE98564


title: Sleep deprived subject 6307 blood collection 04 [D6]

description:
SD_6307_t04
Sample SD_6307_t04 in GSE98564


title: Sleep deprived subject 6311 blood collection 03 [D6]

description:
SD_6311_t03
Sample SD_6311_t03 in GSE98564


title: Sleep deprived subject 6307 blood collection 09 [D6]

description:
SD_6307_t09
Sample SD_6307_t09 in GSE98564


title: Sleep deprived subject 6307 blood collection 13 [D6]

description:
SD_6307_t13
Sample SD_6307_t13 in GSE98564


title: Sleep deprived subject 6307 blood collection 08 [D6]

description:
SD_6307_t08
Sample SD_6307_t08 in GSE98564


title: Sleep deprived subject 6307 blood collection 02 [D6]

description:
SD_6307_t02
Sample SD_6307_t02 in GSE98564


title: Sleep deprived subject 6311 blood collection 04 [D6]

description:
SD_6311_t04
Sample SD_6311_t04 in GSE98564


title: Sleep deprived subject 6307 blood collection 01 [D6]

description:
SD_6307_t01
Sample SD_6307_t01 in GSE98564


title: Sleep deprived subject 6291 blood collection 11 [D6]

description:
SD_6291_t11
Sample SD_6291_t11 in GSE98564


title: Sleep deprived subject 6291 blood collection 12 [D6]

description:
SD_6291_t12
Sample SD_6291_t12 in GSE98564


title: Sleep deprived subject 6291 blood collection 04 [D6]

description:
SD_6291_t04
Sample SD_6291_t04 in GSE98564


title: Sleep deprived subject 6291 blood collection 10 [D6]

description:
SD_6291_t10
Sample SD_6291_t10 in GSE98564


title: Sleep deprived subject 6291 blood collection 15 [D6]

description:
SD_6291_t15
Sample SD_6291_t15 in GSE98564


title: Sleep deprived subject 6234 blood collection 15 [D6]

description:
SD_6234_t15
Sample SD_6234_t15 in GSE98564


title: Sleep deprived subject 6291 blood collection 13 [D6]

description:
SD_6291_t13
Sample SD_6291_t13 in GSE98564


title: Sleep deprived subject 6291 blood collection 14 [D6]

description:
SD_6291_t14
Sample SD_6291_t14 in GSE98564


title: Sleep deprived subject 6291 blood collection 08 [D6]

description:
SD_6291_t08
Sample SD_6291_t08 in GSE98564


title: Sleep deprived subject 6291 blood collection 01 [D6]

description:
SD_6291_t01
Sample SD_6291_t01 in GSE98564


title: Sleep deprived subject 6291 blood collection 02 [D6]

description:
SD_6291_t02
Sample SD_6291_t02 in GSE98564


title: Sleep deprived subject 6291 blood collection 09 [D6]

description:
SD_6291_t09
Sample SD_6291_t09 in GSE98564


title: Sleep deprived subject 6291 blood collection 03 [D6]

description:
SD_6291_t03
Sample SD_6291_t03 in GSE98564


title: Sleep deprived subject 6234 blood collection 12 [D6]

description:
SD_6234_t12
Sample SD_6234_t12 in GSE98564


title: Sleep deprived subject 6234 blood collection 13 [D6]

description:
SD_6234_t13
Sample SD_6234_t13 in GSE98564


title: Sleep deprived subject 6234 blood collection 11 [D6]

description:
SD_6234_t11
Sample SD_6234_t11 in GSE98564


title: Sleep deprived subject 6234 blood collection 14 [D6]

description:
SD_6234_t14
Sample SD_6234_t14 in GSE98564


title: Sleep deprived subject 6212 blood collection 11 [D6]

description:
SD_6212_t11
Sample SD_6212_t11 in GSE98564


title: Sleep deprived subject 6234 blood collection 09 [D6]

description:
SD_6234_t09
Sample SD_6234_t09 in GSE98564


title: Sleep deprived subject 6212 blood collection 08 [D6]

description:
SD_6212_t08
Sample SD_6212_t08 in GSE98564


title: Sleep deprived subject 6212 blood collection 12 [D6]

description:
SD_6212_t12
Sample SD_6212_t12 in GSE98564


title: Sleep deprived subject 6212 blood collection 15 [D6]

description:
SD_6212_t15
Sample SD_6212_t15 in GSE98564


title: Sleep deprived subject 6212 blood collection 13 [D6]

description:
SD_6212_t13
Sample SD_6212_t13 in GSE98564


title: Sleep deprived subject 6212 blood collection 01 [D6]

description:
SD_6212_t01
Sample SD_6212_t01 in GSE98564


title: Sleep deprived subject 6234 blood collection 03 [D6]

description:
SD_6234_t03
Sample SD_6234_t03 in GSE98564


title: Sleep deprived subject 6212 blood collection 03 [D6]

description:
SD_6212_t03
Sample SD_6212_t03 in GSE98564


title: Sleep deprived subject 6212 blood collection 10 [D6]

description:
SD_6212_t10
Sample SD_6212_t10 in GSE98564


title: Sleep deprived subject 6207 blood collection 14 [D6]

description:
SD_6207_t14
Sample SD_6207_t14 in GSE98564


title: Sleep deprived subject 6207 blood collection 13 [D6]

description:
SD_6207_t13
Sample SD_6207_t13 in GSE98564


title: Sleep deprived subject 6234 blood collection 08 [D6]

description:
SD_6234_t08
Sample SD_6234_t08 in GSE98564


title: Sleep deprived subject 6212 blood collection 09 [D6]

description:
SD_6212_t09
Sample SD_6212_t09 in GSE98564


title: Sleep deprived subject 6207 blood collection 15 [D6]

description:
SD_6207_t15
Sample SD_6207_t15 in GSE98564


title: Sleep deprived subject 6207 blood collection 11 [D6]

description:
SD_6207_t11
Sample SD_6207_t11 in GSE98564


title: Sleep deprived subject 6234 blood collection 10 [D6]

description:
SD_6234_t10
Sample SD_6234_t10 in GSE98564


title: Sleep deprived subject 6207 blood collection 09 [D6]

description:
SD_6207_t09
Sample SD_6207_t09 in GSE98564


title: Sleep deprived subject 6212 blood collection 02 [D6]

description:
SD_6212_t02
Sample SD_6212_t02 in GSE98564


title: Sleep deprived subject 6212 blood collection 04 [D6]

description:
SD_6212_t04
Sample SD_6212_t04 in GSE98564


title: Sleep deprived subject 6234 blood collection 04 [D6]

description:
SD_6234_t04
Sample SD_6234_t04 in GSE98564


title: Sleep deprived subject 6234 blood collection 02 [D6]

description:
SD_6234_t02
Sample SD_6234_t02 in GSE98564


title: Sleep deprived subject 6207 blood collection 12 [D6]

description:
SD_6207_t12
Sample SD_6207_t12 in GSE98564


title: Sleep deprived subject 6207 blood collection 10 [D6]

description:
SD_6207_t10
Sample SD_6207_t10 in GSE98564


title: CiPSCs-6

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

description: genes_cpm_filter_expression_nonmerged.tsv

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

source_name: iPSCs

extract_protocol:
Total RNA was prepared with TRIzol. For quantitative PCR, cDNAs were synthesized with ReverTra Ace (Toyobo) and oligo-dT (Takara), and then analyzed by qPCR with Premix Ex Taq (Takara).
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: iPSCs


title: CiPSCs-5


title: Sleep deprived subject 6207 blood collection 08 [D6]

description:
SD_6207_t08
Sample SD_6207_t08 in GSE98564


title: CiPSCs-2


title: CiPSCs-4


title: CiPSCs-3


title: Sleep deprived subject 6207 blood collection 04 [D6]

description:
SD_6207_t04
Sample SD_6207_t04 in GSE98564


title: CiPSCs-1


title: Sleep deprived subject 6166 blood collection 15 [D6]

description:
SD_6166_t15
Sample SD_6166_t15 in GSE98564


title: 225: 4X choline female rep 2 (mRNA)

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
allSamples_gene_exp.diff: CH_2
allSamples_genes.read_group_tracking: CH_2
female_gene_exp.diff: CHF_1
female_genes.read_group_tracking: CHF_1

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited cuffdiff2 output text files including individual sample results (raw counts, FPKM values in read_groups_tracking files) and differential gene expression results (log2FC, p-values, and q-values [corrected for multiple hypothesis testing] in gene_exp.diff files)

source_name: Mouse placenta

growth_protocol: Prior to euthanization and tissue harvesting, the mice in this study had ad libitum access to the diet and water, and were housed in microisolator cages in an environmentally-controlled room (22-25°C, 70% humidity) with a 12-hour light-dark cycle.

extract_protocol:
Placenta tissues were removed from the mice after they were sacrificed at gestational day 15.5 and were immediately flash frozen in liquid nitrogen. RNA were extracted from the tissues using Trizol following the manufacturer's protocol.
RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Directional Ultra RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: Prior to euthanization and tissue harvesting, the mice in this study were fed the AIN-93G diet, with either 1X choline concentration (1.4g choline chloride/kg diet; Dyets Cat #103345) or 4X choline concentration (5.6g choline chloride/kg diet; Dyets Cat #103347).

value: non-Swiss Albino (NSA)

value: Placenta

tag: developmental stage

value: Gestational day 15.5

tag: fetal sex

value: Female

tag: diet treatment

value: 4X choline


title: 287: 4X choline female rep 3 (mRNA)

description:
allSamples_gene_exp.diff: CH_5
allSamples_genes.read_group_tracking: CH_5
female_gene_exp.diff: CHF_2
female_genes.read_group_tracking: CHF_2

tag: tissue


title: 198: 4X choline female rep 1 (mRNA)

description:
allSamples_gene_exp.diff: CH_0
allSamples_genes.read_group_tracking: CH_0
female_gene_exp.diff: CHF_0
female_genes.read_group_tracking: CHF_0


title: Sleep deprived subject 6207 blood collection 03 [D6]

description:
SD_6207_t03
Sample SD_6207_t03 in GSE98564

value: susceptible


title: Sleep deprived subject 6207 blood collection 02 [D6]

description:
SD_6207_t02
Sample SD_6207_t02 in GSE98564

value: Sleep Deprived


title: Sleep deprived subject 6166 blood collection 13 [D6]

description:
SD_6166_t13
Sample SD_6166_t13 in GSE98564


title: Sleep deprived subject 6166 blood collection 12 [D6]

description:
SD_6166_t12
Sample SD_6166_t12 in GSE98564


title: Sleep deprived subject 6166 blood collection 14 [D6]

description:
SD_6166_t14
Sample SD_6166_t14 in GSE98564


title: Sleep deprived subject 6166 blood collection 11 [D6]

description:
SD_6166_t11
Sample SD_6166_t11 in GSE98564


title: Sleep deprived subject 6207 blood collection 01 [D6]

description:
SD_6207_t01
Sample SD_6207_t01 in GSE98564


title: 252: 1X choline female rep 3 (mRNA)

description:
allSamples_gene_exp.diff: N_4
allSamples_genes.read_group_tracking: N_4
female_gene_exp.diff: NF_2
female_genes.read_group_tracking: NF_2

value: 1X choline


title: Sleep deprived subject 6166 blood collection 04 [D6]

description:
SD_6166_t04
Sample SD_6166_t04 in GSE98564

value: baseline


title: Sleep deprived subject 6166 blood collection 08 [D6]

description:
SD_6166_t08
Sample SD_6166_t08 in GSE98564


title: Sleep deprived subject 6166 blood collection 09 [D6]

description:
SD_6166_t09
Sample SD_6166_t09 in GSE98564


title: Sleep deprived subject 6166 blood collection 10 [D6]

description:
SD_6166_t10
Sample SD_6166_t10 in GSE98564


title: Sleep deprived subject 6166 blood collection 02 [D6]

description:
SD_6166_t02
Sample SD_6166_t02 in GSE98564