title: Malignant bone and soft tissue tumor [SH59W21_Cell3]


title: Malignant bone and soft tissue tumor [SH59W19_Cell4]

status: Public on Feb 14 2019

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals of miRNAs over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.). Total RNA was also obtained from the FFPE sections using the Arcturus® Paradise® Extraction and Isolation kit (Life Technologies) in accordance with the manufacturer's instructions.

tag: tissue

value: Serum

tag: patient diagnosis

value: Malignant bone and soft tissue tumor

tag: gender

value: Female

tag: tumor stage

value: StageIB

tag: age


title: Malignant bone and soft tissue tumor [SH59W19_Cell3]

value: Male

value: StageIV


title: Malignant bone and soft tissue tumor [SH59W19_Cell2]

value: StageIII


title: Malignant bone and soft tissue tumor [SH59W18_Cell4]


title: Intermediate bone and soft tissue tumor [SH59W19_Cell1]

value: Intermediate bone and soft tissue tumor

value: StageIA


title: Malignant bone and soft tissue tumor [SH59W21_Cell1]


title: Malignant bone and soft tissue tumor [SH59W18_Cell3]


title: Malignant bone and soft tissue tumor [SH59W24_Cell1]


title: Malignant bone and soft tissue tumor [SH59W18_Cell1]


title: Malignant bone and soft tissue tumor [SH59W17_Cell3]


title: Malignant bone and soft tissue tumor [SH59W17_Cell2]


title: Malignant bone and soft tissue tumor [SH59W17_Cell1]

value: StageIIA


title: Malignant bone and soft tissue tumor [SH59W22_Cell1]


title: Malignant bone and soft tissue tumor [SH59W16_Cell2]


title: Malignant bone and soft tissue tumor [SH59W16_Cell1]


title: Malignant bone and soft tissue tumor [SH59W18_Cell2]


title: Malignant bone and soft tissue tumor [SH59W15_Cell1]


title: Malignant bone and soft tissue tumor [SH59W15_Cell2]


title: Malignant bone and soft tissue tumor [SH59W15_Cell4]


title: Malignant bone and soft tissue tumor [SH59W14_Cell4]


title: Malignant bone and soft tissue tumor [SH59W15_Cell3]


title: Malignant bone and soft tissue tumor [SH59W14_Cell3]


title: Malignant bone and soft tissue tumor [SH59W14_Cell2]


title: Malignant bone and soft tissue tumor [SH59W14_Cell1]


title: Malignant bone and soft tissue tumor [SH59W13_Cell4]


title: Malignant bone and soft tissue tumor [SH59W13_Cell1]


title: Malignant bone and soft tissue tumor [SH59W13_Cell2]


title: Malignant bone and soft tissue tumor [SH59W13_Cell3]


title: Malignant bone and soft tissue tumor [SH59W17_Cell4]


title: Malignant bone and soft tissue tumor [SH59W12_Cell3]


title: Malignant bone and soft tissue tumor [SH59W12_Cell2]


title: Malignant bone and soft tissue tumor [SH59W16_Cell3]


title: Malignant bone and soft tissue tumor [SH59W12_Cell1]


title: Malignant bone and soft tissue tumor [SH59W11_Cell3]


title: Malignant bone and soft tissue tumor [SH59W11_Cell4]


title: Malignant bone and soft tissue tumor [SH59W11_Cell2]


title: Malignant bone and soft tissue tumor [SH59W11_Cell1]


title: Malignant bone and soft tissue tumor [SH59W10_Cell4]


title: Malignant bone and soft tissue tumor [SH59W09_Cell4]


title: Malignant bone and soft tissue tumor [SH59W10_Cell1]


title: Malignant bone and soft tissue tumor [SH59W10_Cell2]


title: Malignant bone and soft tissue tumor [SH59W09_Cell2]


title: Malignant bone and soft tissue tumor [SH59W09_Cell1]


title: Malignant bone and soft tissue tumor [SH59W07_Cell4]


title: Malignant bone and soft tissue tumor [SH59W06_Cell3]


title: Malignant bone and soft tissue tumor [SH59W12_Cell4]


title: Malignant bone and soft tissue tumor [SH59W06_Cell4]


title: Malignant bone and soft tissue tumor [SH59W06_Cell1]


title: Malignant bone and soft tissue tumor [SH59W04_Cell3]


title: Malignant bone and soft tissue tumor [SH59W04_Cell2]


title: Malignant bone and soft tissue tumor [SH59W10_Cell3]


title: Malignant bone and soft tissue tumor [SH59W07_Cell1]


title: Malignant bone and soft tissue tumor [SH59W05_Cell1]


title: Malignant bone and soft tissue tumor [SH59W06_Cell2]


title: Malignant bone and soft tissue tumor [SH59W09_Cell3]


title: Malignant bone and soft tissue tumor [SH59W05_Cell2]


title: Malignant bone and soft tissue tumor [SH59W05_Cell3]


title: Malignant bone and soft tissue tumor [SH59W03_Cell4]


title: Malignant bone and soft tissue tumor [SH59W07_Cell3]


title: Malignant bone and soft tissue tumor [SH59W03_Cell3]


title: Malignant bone and soft tissue tumor [SH59W02_Cell4]


title: Malignant bone and soft tissue tumor [SH59W04_Cell4]


title: Malignant bone and soft tissue tumor [SH59W02_Cell3]

value: StageIIB


title: Malignant bone and soft tissue tumor [SH59W03_Cell1]


title: Malignant bone and soft tissue tumor [SH59W03_Cell2]


title: Malignant bone and soft tissue tumor [SH59W02_Cell2]


title: Malignant bone and soft tissue tumor [SH59W02_Cell1]


title: Malignant bone and soft tissue tumor [SH59W01_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q64_Cell4]


title: Malignant bone and soft tissue tumor [SH59W01_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q64_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q63_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q64_Cell2]

value: StageIVB


title: Malignant bone and soft tissue tumor [SH59Q63_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q63_Cell2]


title: Malignant bone and soft tissue tumor [SH59W01_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q62_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q62_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q62_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q61_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q60_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q59_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q60_Cell1]

value: StageX


title: Malignant bone and soft tissue tumor [SH59Q62_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q61_Cell3]

value: StageIVA


title: Intermediate bone and soft tissue tumor [SH59Q58_Cell4]


title: Intermediate bone and soft tissue tumor [SH59Q58_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q61_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q64_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q58_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q60_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q57_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q57_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q59_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q57_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q57_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q55_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q60_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q55_Cell3]


title: Intermediate bone and soft tissue tumor [SH59Q59_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q55_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q55_Cell2]


title: Intermediate bone and soft tissue tumor [SH59Q59_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q54_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q53_Cell3]


title: Malignant bone and soft tissue tumor [SH59Q53_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q54_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q53_Cell4]


title: Intermediate bone and soft tissue tumor [SH59Q52_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q61_Cell2]


title: Intermediate bone and soft tissue tumor [SH59Q50_Cell4]


title: Intermediate bone and soft tissue tumor [SH59Q51_Cell3]


title: Intermediate bone and soft tissue tumor [SH59Q52_Cell3]


title: Intermediate bone and soft tissue tumor [SH59Q50_Cell1]


title: Intermediate bone and soft tissue tumor [SH59Q50_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q52_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q53_Cell1]


title: Malignant bone and soft tissue tumor [SH59Q51_Cell4]


title: Pancreatic Cancer [SH51T31_Cell1]

value: Pancreatic Cancer

value: uncertain


title: Malignant bone and soft tissue tumor [SH59Q54_Cell2]


title: Intermediate bone and soft tissue tumor [SH59Q50_Cell3]


title: Pancreatic Cancer [SH51T27_Cell4]


title: Pancreatic Cancer [SH51T29_Cell1]


title: Pancreatic Cancer [SH51T25_Cell3]


title: Pancreatic Cancer [SH51T23_Cell1]


title: Pancreatic Cancer [SH51T23_Cell4]


title: Malignant bone and soft tissue tumor [SH59Q52_Cell1]


title: Pancreatic Cancer [SH51T15_Cell4]


title: Pancreatic Cancer [SH51T15_Cell1]


title: Pancreatic Cancer [SH51T11_Cell1]


title: Pancreatic Cancer [SH51T22_Cell2]


title: Pancreatic Cancer [SH51T21_Cell2]


title: Pancreatic Cancer [SH51Q65_Cell4]


title: Pancreatic Cancer [SH51Q63_Cell1]


title: Pancreatic Cancer [SH51Q63_Cell2]


title: Pancreatic Cancer [SH51Q57_Cell2]


title: Pancreatic Cancer [SH51Q57_Cell4]


title: Pancreatic Cancer [SH51Q49_Cell2]


title: Pancreatic Cancer [SH51Q45_Cell4]


title: Pancreatic Cancer [SH51T26_Cell1]


title: Pancreatic Cancer [SH51T26_Cell2]


title: Pancreatic Cancer [SH51Q16_Cell2]


title: Pancreatic Cancer [SH51Q16_Cell1]


title: Pancreatic Cancer [SH51Q09_Cell4]


title: Lung Cancer [SH58L01_Cell3]

value: Lung Cancer


title: Lung Cancer [SH57Y55_Cell1]

value: Serum


title: Lung Cancer [SH57Y51_Cell3]


title: Pancreatic Cancer [SH51Q17_Cell4]


title: Pancreatic Cancer [SH51Q55_Cell4]


title: Pancreatic Cancer [SH51Q09_Cell2]


title: Pancreatic Cancer [SH51T03_Cell2]


title: Pancreatic Cancer [SH51Q37_Cell2]


title: Lung Cancer [SH59Q46_Cell1]


title: Lung Cancer [SH59X33_Cell1]


title: Lung Cancer [SH59X32_Cell2]


title: Lung Cancer [SH59Q46_Cell4]


title: Lung Cancer [SH59Q48_Cell1]


title: Lung Cancer [SH59X34_Cell1]


title: Pancreatic Cancer [SH51P61_Cell4]


title: Pancreatic Cancer [SH51P65_Cell1]


title: Lung Cancer [SH59Q45_Cell4]


title: Lung Cancer [SH59Q42_Cell3]


title: Lung Cancer [SH59Q45_Cell3]


title: Lung Cancer [SH59X33_Cell2]


title: Lung Cancer [SH59Q41_Cell1]


title: Lung Cancer [SH59Q40_Cell4]


title: Lung Cancer [SH59Q39_Cell1]


title: Lung Cancer [SH59Q39_Cell3]


title: Lung Cancer [SH59Q38_Cell2]


title: Lung Cancer [SH59Q38_Cell1]


title: Lung Cancer [SH59Q49_Cell4]


title: Lung Cancer [SH59Q36_Cell3]


title: Lung Cancer [SH59Q36_Cell1]


title: Lung Cancer [SH59Q40_Cell2]


title: Lung Cancer [SH57Y51_Cell2]


title: Lung Cancer [SH59Q39_Cell4]


title: Lung Cancer [SH59Q33_Cell1]


title: Lung Cancer [SH59Q32_Cell3]


title: HCC [SH55T41_Cell2]

value: HCC


title: HCC [SH55T41_Cell1]


title: Lung Cancer [SH59Q32_Cell2]


title: Lung Cancer [SH59Q28_Cell4]


title: HCC [SH55T38_Cell2]


title: HCC [SH55T38_Cell4]


title: HCC [SH55T28_Cell1]


title: HCC [SH55T36_Cell1]


title: HCC [SH55T26_Cell2]


title: HCC [SH55T26_Cell1]


title: Lung Cancer [SH59Q48_Cell2]


title: HCC [SH55T33_Cell2]


title: HCC [SH54N57_Cell2]


title: HCC [SH55T23_Cell1]


title: HCC [SH55T25_Cell3]


title: HCC [SH54N55_Cell3]


title: HCC [SH54N51_Cell1]


title: HCC [SH54N41_Cell3]


title: HCC [SH56964_Cell1]


title: HCC [SH54N45_Cell2]


title: HCC [SH54N43_Cell3]


title: HCC [SH54N40_Cell1]


title: HCC [SH54N33_Cell3]


title: HCC [SH54N38_Cell2]


title: HCC [SH54N38_Cell1]


title: HCC [SH54N33_Cell2]


title: HCC [SH54N32_Cell1]


title: HCC [SH54N33_Cell1]


title: HCC [SH54N34_Cell1]


title: HCC [SH54N29_Cell1]


title: HCC [SH54N29_Cell4]


title: Glioma [SH51P04_Cell3]

value: Glioma


title: Glioma [SH51P08_Cell2]


title: Glioma [SH51D42_Cell4]


title: Glioma [SH51L49_Cell2]


title: Glioma [SH51G66_Cell3]


title: Glioma [SH51M67_Cell2]


title: Glioma [SH51P02_Cell1]


title: Glioma [SH51952_Cell4]


title: Glioma [SH51D23_Cell4]


title: Glioma [SH51G66_Cell2]


title: Glioma [SH51G66_Cell1]


title: Glioma [SH51939_Cell2]


title: Glioma [SH51941_Cell2]


title: Glioma [SH51938_Cell1]


title: Glioma [SH4ZJ50_Cell4]


title: Glioma [SH4ZJ50_Cell1]


title: Glioma [SH4ZP65_Cell3]


title: Glioma [SH51933_Cell4]


title: Glioma [SH51934_Cell1]


title: Glioma [SH51924_Cell4]


title: Glioma [SH51933_Cell1]


title: Glioma [SH51925_Cell2]


title: Glioma [SH51934_Cell2]


title: Glioma [SH51921_Cell4]


title: Glioma [SH51919_Cell2]


title: Gastric Cancer [SH59Y54_Cell4]

value: Gastric Cancer


title: Glioma [SH51919_Cell1]


title: Glioma [SH51914_Cell3]


title: Gastric Cancer [SH59Y51_Cell2]


title: Glioma [SH51916_Cell1]


title: Gastric Cancer [SH59Y51_Cell4]


title: Gastric Cancer [SH59Y57_Cell1]


title: Glioma [SH51914_Cell2]


title: Gastric Cancer [SH59Y49_Cell4]


title: Gastric Cancer [SH59Y45_Cell2]


title: Malignant bone and soft tissue tumor [SH59Q54_Cell3]

value: Malignant bone and soft tissue tumor

value: Male


title: Gastric Cancer [SH59Y52_Cell4]


title: Gastric Cancer [SH59Y53_Cell1]


title: Gastric Cancer [SH59Y56_Cell1]


title: Gastric Cancer [SH59Y48_Cell4]


title: HCC [SH54N36_Cell3]


title: Gastric Cancer [SH59Y44_Cell3]


title: Gastric Cancer [SH59Y44_Cell2]


title: Gastric Cancer [SH59Y43_Cell1]


title: Gastric Cancer [SH59Y41_Cell4]


title: Gastric Cancer [SH59Y45_Cell1]


title: Gastric Cancer [SH59Y40_Cell3]


title: Gastric Cancer [SH59Y40_Cell1]


title: Gastric Cancer [SH59Y41_Cell2]


title: Gastric Cancer [SH59Y42_Cell3]


title: Gastric Cancer [SH59Y35_Cell3]


title: Gastric Cancer [SH59Y42_Cell4]


title: Gastric Cancer [SH59Y34_Cell3]


title: Gastric Cancer [SH59Y44_Cell4]


title: Gastric Cancer [SH59Y34_Cell4]


title: Gastric Cancer [SH59Y33_Cell2]


title: Gastric Cancer [SH59Y33_Cell3]


title: Gastric Cancer [SH59Y43_Cell3]


title: Gastric Cancer [SH59Y34_Cell1]


title: Esophageal Cancer [SH57N09_Cell1]

value: Esophageal Cancer


title: Esophageal Cancer [SH57M65_Cell4]


title: Esophageal Cancer [SH57M60_Cell4]


title: Gastric Cancer [SH59Y32_Cell2]


title: Esophageal Cancer [SH57M53_Cell4]


title: Esophageal Cancer [SH57N07_Cell1]


title: Esophageal Cancer [SH57M53_Cell2]


title: Esophageal Cancer [SH57M46_Cell2]


title: Esophageal Cancer [SH57M53_Cell1]


title: Esophageal Cancer [SH56F21_Cell2]


title: Esophageal Cancer [SH57M46_Cell3]


title: Esophageal Cancer [SH57M46_Cell4]


title: Gastric Cancer [SH59Y33_Cell4]


title: Esophageal Cancer [SH57M60_Cell2]


title: Esophageal Cancer [SH56F21_Cell1]


title: Esophageal Cancer [SH56F15_Cell1]


title: Esophageal Cancer [SH56F13_Cell2]


title: Esophageal Cancer [SH56F16_Cell4]


title: Esophageal Cancer [SH56F15_Cell3]


title: Esophageal Cancer [SH56F05_Cell4]


title: Esophageal Cancer [SH56F07_Cell1]


title: Esophageal Cancer [SH56F03_Cell3]


title: Esophageal Cancer [SH56B68_Cell4]


title: Glioma [SH51926_Cell2]


title: Esophageal Cancer [SH56B63_Cell3]


title: Esophageal Cancer [SH56B63_Cell1]


title: Colorectal Cancer [SH52T19_Cell2]

value: Colorectal Cancer


title: Esophageal Cancer [SH56F17_Cell3]


title: Esophageal Cancer [SH56B62_Cell1]


title: Colorectal Cancer [SH52T16_Cell4]


title: Colorectal Cancer [SH52T16_Cell3]


title: Esophageal Cancer [SH56F03_Cell4]


title: Esophageal Cancer [SH56F13_Cell3]


title: Colorectal Cancer [SH52T21_Cell2]


title: Colorectal Cancer [SH52T16_Cell1]


title: Colorectal Cancer [SH52T06_Cell3]


title: Colorectal Cancer [SH52T14_Cell4]


title: Colorectal Cancer [SH52T09_Cell2]


title: Colorectal Cancer [SH52T09_Cell1]


title: Esophageal Cancer [SH56F17_Cell1]


title: Colorectal Cancer [SH52T05_Cell2]


title: Colorectal Cancer [SH52T01_Cell1]


title: Colorectal Cancer [SH52R25_Cell3]


title: Colorectal Cancer [SH52T22_Cell3]


title: Colorectal Cancer [SH52R31_Cell3]


title: Colorectal Cancer [SH52R13_Cell4]


title: Colorectal Cancer [SH52T02_Cell1]


title: Esophageal Cancer [SH56B68_Cell1]


title: Colorectal Cancer [SH52T22_Cell4]


title: Colorectal Cancer [SH52R13_Cell2]


title: Colorectal Cancer [SH52T05_Cell1]


title: Esophageal Cancer [SH56F16_Cell1]


title: Colorectal Cancer [SH52109_Cell1]


title: Colorectal Cancer [SH52Q29_Cell4]


title: Colorectal Cancer [SH52Q29_Cell3]


title: Colorectal Cancer [SH4ZA67_Cell1]


title: Colorectal Cancer [SH52T06_Cell2]


title: HCC [SH55T35_Cell2]


title: Colorectal Cancer [SH52Q09_Cell1]


title: Colorectal Cancer [SH52Q05_Cell4]


title: NC6

type: SRA

city: Wuhan

first: LI

last: LI

state: Hubei

address: 185 Donghu Road

country: China

institute: wuhan university school of basic medical sciences

library_source: transcriptomic

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version: 0.36), low-quality reads were discarded and adaptor sequences were trimmed
Reads mapped to the exon regions of each gene were counted by featurecouts (Subread-1.5.1; Bioconductor) and RPKMs were calculated. Genes differential expressed between groups were identified using the edgeR package
A corrected P-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: CD4+ T cells

extract_protocol:
CD4+ T cells were further purified from PBMCs using anti-CD4 antibody-coated magnetic beads,Total RNAs were extracted from samples using TRIzol (Invitrogen) following the methods by Chomczynski
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: CD5+ T cells purified from PBMCs

value: blood

tag: genotype/variation

value: HIV unfected

tag: molecule subtype

value: rRNA depletion RNA


title: H9

value: CD4+ T cells purified from PBMCs

value: HIV infected


title: Colorectal Cancer [SH52R03_Cell4]


title: M2G_2_0D

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

country: USA

institute: Indiana University

data_processing:
Library strategy: Ribo-Seq
Reads were subtracted of rRNA/tRNA using bowtie 0.12.8, then unmapped reads were mapped to the Caulobacter NA1000 genome (CP001340) using bowtie 0.12.8.
Ribosome profiling: The position of each alignment is distributed into several nucleotides in the center of the footprint. For each footprint read, the center residues that are at least 12 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)][Li et al,. Nature 484, 538 (2012)].
Genome_build: CP001340
Supplementary_files_format_and_content: Each line in the processed file has three columns: Col 1: Genomic coordinate based on CP001340, Col 2: Strand, Col 3: Total read weight assigned to the coordinate, Only genomic coordinates with non-zero read weight are included in the text file, Reads aligning to rRNA, tRNA and non-coding RNA are not included.

organism: Caulobacter vibrioides

source_name: C. crescentus M2G mid-log

growth_protocol: Caulobacter crescentus NA1000 were innoculated at OD600 0.05 and grown to OD600 0.5 at 28C at 200RPM.

extract_protocol:
Cells were lysed by mixer mill using 6 cycles of 3 min at 15Hz. In between cycles, the chamber was resuspended in liquid nitrogen to keep frozen. Ribosome protected mRNA fragments were size selected via gel purification.
mRNA fragments were ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, rRNA fragments removed using biotinylated DNA probes, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].

treatment_protocol: Cells were incubated with 100ug/mL Chloramphenicol for 2 min and rapidly collected by centrifugation. Cells were resuspended in lysis buffer and dripped into liquid nitrogen.

tag: strain


title: M2G_1_3D


title: M2G_3_0D


title: Colorectal Cancer [SH52Q25_Cell1]


title: Colorectal Cancer [SH52Q01_Cell3]


title: Colorectal Cancer [SH52Q10_Cell2]


title: PBMC_Control_DayOrientedSchedule_RelTime_24.2_Subject_T19 [re-analysis]

city: Montreal

first: Laura

last: Kervezee

state: Quebec

address: 6875 LaSalle Boulevard

department: Douglas Mental Health University Institute

country: Canada

institute: McGill University

description: reanalysis of GSM2870797, PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group

hyb_protocol: After fragmentation and labeling, 2.8 µg DNA target was hybridized on Clariom™S HT, Human (ThermoFisher Scientific-Affymetrix).

scan_protocol: Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1).

label: Biotin

label_protocol: Sense-strand cDNA was synthesized from 10 ng of total RNA, and fragmentation and labeling were performed to produce ds-cDNA with the GeneChip® Pico Reagent Kit according to manufacturer’s instructions (ThermoFisher Scientific-Affymetrix).

growth_protocol: An indwelling catheter was inserted in a forearm vein at least 4 hours prior to the start of each 24-hour measurement period.

extract_protocol: Extraction of RNA was performed by addition of chloroform in order to separate organic and aqueous components. Isopropanol and subsequent ethanol washes were used to precipitate and purify the RNA. RNA was dissolved in RNase-free H2O (Qiagen, Toronto, ON, Canada). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation for 30 minutes at 1600rpm on a density gradient (Histopaque-1077, Sigma Aldrich, Oakville, ON, Canada). PBMCs were washed 3 times in phosphate-buffered saline (PBS), lysed in TRIzol (Life Technologies, Burlington, ON, Canada) and stored at -80°C until further processing.

tag: subject

tag: experimentalgroup

value: Control

tag: condition

value: DayOrientedSchedule

tag: relclocktime


title: PBMC_Control_DayOrientedSchedule_RelTime_24.2_Subject_T15 [re-analysis]

description: reanalysis of GSM2870794, PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_24.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870793, PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_36.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870805, PBMC sample taken at 36.3 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group

value: NightOrientedSchedule


title: PBMC_Control_NightOrientedSchedule_RelTime_42.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870798, PBMC sample taken at 42.2 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_24.4_Subject_T13

description: PBMC sample taken at 24.4 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group

value: BrightLight


title: PBMC_Control_NightOrientedSchedule_RelTime_42.1_Subject_T18 [re-analysis]

description: reanalysis of GSM2870796, PBMC sample taken at 42.1 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_20.3_Subject_T13

description: PBMC sample taken at 20.3 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: PBMC_Control_DayOrientedSchedule_RelTime_24.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870799, PBMC sample taken at 24.3 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_14.4_Subject_T22 [re-analysis]

description: reanalysis of GSM2870801, PBMC sample taken at 14.4 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_42.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870800, PBMC sample taken at 42.2 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_18.2_Subject_T17 [re-analysis]

description: reanalysis of GSM2870795, PBMC sample taken at 18.2 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_42.2_Subject_T13

description: PBMC sample taken at 42.2 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: PBMC_Control_DayOrientedSchedule_RelTime_17.2_Subject_T23 [re-analysis]

description: reanalysis of GSM2870802, PBMC sample taken at 17.2 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_42.3_Subject_T10

description: PBMC sample taken at 42.3 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group


title: PBMC_Control_DayOrientedSchedule_RelTime_6.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870792, PBMC sample taken at 6.2 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_24.4_Subject_T11

description: PBMC sample taken at 24.4 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group


title: PBMC_Control_DayOrientedSchedule_RelTime_24.2_Subject_T23 [re-analysis]

description: reanalysis of GSM2870804, PBMC sample taken at 24.2 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_20.2_Subject_T23 [re-analysis]

description: reanalysis of GSM2870803, PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_42.3_Subject_T11

description: PBMC sample taken at 42.3 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: M2, Mature_stage RNA-Seq

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

data_processing:
Illumina Casava software used for basecalling.
High quality reads were filtered using the Trimmomatic tool
A quality check was performed with FastQC
Filtered reads were mapped to the Arabidopsis genome TAIR10 using STAR. Read counting was carried out with HTSeq.
Counts normalization was performed with DESeq2 to normalize the raw reads
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

organism: Arabidopsis thaliana

source_name: Mature stage embryo

extract_protocol:
Embryo isolation was performed as described in Xiang et al. 2011. Total RNA was extracted from embryos corresponding to the seven developmental stages for two biological replicates at each stage, following the RNAqueous-Micro kit protocol (Ambion, Catalog# 1927).  The mRNA amplification was conducted according to the protocol provided in the MessageAmp aRNA kit (Ambion, Catalog# 1750).
Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit (ver. 1, rev A) according to the manufacturer's instructions.

value: whole embryo

tag: Stage

value: Mature stage

tag: ecotype


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_32.1_Subject_T10

description: PBMC sample taken at 32.1 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group


title: M1, Mature_stage RNA-Seq


title: PBMC_Control_NightOrientedSchedule_RelTime_26.2_Subject_T23 [re-analysis]

description: reanalysis of GSM2870789, PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_30.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870790, PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_22.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870788, PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870786, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_18.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870787, PBMC sample taken at 18.3 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_34.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870791, PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_8.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870785, PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: B2, Bent stage RNA-Seq

source_name: Bent stage embryo

value: Bent stage


title: B1, Bent stage RNA-Seq


title: T1, Torpedo stage RNA-Seq

source_name: Torpedo stage embryo

value: Torpedo stage


title: T2, Torpedo stage RNA-Seq


title: H2, Heart stage RNA-Seq

source_name: Heart stage embryo

value: Heart stage


title: O2, Octant stage RNA-Seq

source_name: Octant stage embryo

value: Octant stage


title: H1, Heart stage RNA-Seq


title: G1, Globular stage RNA-Seq

source_name: Globular stage embryo

value: Globular stage


title: Z2, Zygote stage RNA-Seq

source_name: Zygote stage embryo

value: Zygote stage


title: Z1, Zygote stage RNA-Seq


title: PBMC_Control_DayOrientedSchedule_RelTime_0.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870783, PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_38.8_Subject_T22 [re-analysis]

description: reanalysis of GSM2870782, PBMC sample taken at 38.8 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: G2, Globular stage RNA-Seq


title: O1, Octant stage RNA-Seq


title: SS13BN_2

city: Milwaukee

first: Mingyu

last: Liang

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

library_source: genomic

data_processing:
Basecalls performed with Casava 1.8
Only one read of read pair, which was verified to contain the forward ren proximal promoter primer (TGTGAGGCCCCTGAGAATTC), was analyzed.  The 5' read end was trimmed of Illumina 5' adapter, genomic DNA including the renin proximal promoter primer sequence through primary EcoRI site.   Read was mapped to a fragend (Rn5 genome segmented by EcoRI) with Burrows-Wheeler Aligner with q > 13.  Reads reads that could not be uniquely mapped were filtered out.
Read counts at each fragend were binarized.  Frequency of observed reads in small windows (2 to 200 fragends on chr13, 501 fragends in rest of genome) and expected frequencies in large windows (3001 fragends on chr13, whole chromosome for rest of genome) were calcuated, and z-scores were calculated at each fragend comparing the observed to the expected.  This data is in the bed file and bigWig file
Significant fragends  were called with a False discovery rate (FDR) < 0.01. FDR was calculated by simulating 200 randomly generated genomes using the measured binomial frequency of each chromosome, calculating the z-scores at each position on the simulated dataset, and determining the threshold z-score where FDR = 0.01.
The region within 2Mb of the Renin viewpoint, reads were normalized to a power law distribution using the algorithm of Thongjuea et al. R/Bioconductor package for the discovery of long-range genomic interactions from chromsome conformation capture and next-generation sequencing data. Nucleic Acids Research 41: e132-e132, 2013.
Genome_build: Rn5
Supplementary_files_format_and_content: bed files contain calcuated Z-scores representing measured frequency of contact at each location in the genome relative to the background rate.  The background rate is the chromosome mean for all chromosomes except chromsome 13, where the background rate is a larger window.  bigWig files were generated from bed graphs using bedGraphToBigWig from UCSC tool archive and rn5.chrom.sizes

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Cardiac endothelial cells

growth_protocol: Cells grown on geletan coated plates in MCDB131 media with 10% heat inactivated FBS, and Bovine brain extract, hEGF and GA-1000 from Lonza EGM-MV Bullet Kit

extract_protocol:
4C-seq experiments were conducted using EcoRI according to previously published protocol (Stadhoulders, R. et al. Multiplexed chromatin conformation capture sequencing for rapid genome-scale high-resolution detection of long-range interactions. Nature Protocols 8:509-524, 2013.).
Libraries were prepared for sequencing using Illumina compatible protocol (Li, Y. et al. Base-resolution maps of 5-methylcytosine and 5-hydroxymethylcytosine in Dahl S rats: effects of salt and genomic sequence. Hypertension 63: 827-838, 2014.).
4C-seq

tag: passages

tag: Sex

value: pooled male and female

value: 2% formaldehyde, 10 min, room temp


title: SS13BN_1


title: PBMC_Control_DayOrientedSchedule_RelTime_4.3_Subject_T23 [re-analysis]

description: reanalysis of GSM2870784, PBMC sample taken at 4.3 h after habitual wake time during day-oriented schedule in Subject T23 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_20.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870776, PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_34.3_Subject_T22 [re-analysis]

description: reanalysis of GSM2870781, PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_0.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870772, PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_12.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870775, PBMC sample taken at 12.2 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: SS_3

value: SS/JrHsdMcwi


title: PBMC_Control_NightOrientedSchedule_RelTime_22.3_Subject_T22 [re-analysis]

description: reanalysis of GSM2870778, PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: SS_2


title: PBMC_Control_NightOrientedSchedule_RelTime_18.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870777, PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_26.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870779, PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_30.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870780, PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T22 in the Control group


title: SS13BN_3


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T22 [re-analysis]

description: reanalysis of GSM2870773, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_8.3_Subject_T22 [re-analysis]

description: reanalysis of GSM2870774, PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T22 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_34.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870770, PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_26.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870768, PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_22.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870767, PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: iPS-HSCs overexpressing LHX2 vs control iPS-HSCs

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description: normalized log2 ratio (iLHX2 Mes Dox Pos/iLHX2 Mes Dox Neg)

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: iLHX2-HSCs Mes Dox Neg

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Human iPS cells were seeded on 12 or 24 well plates at a density of ~6x10e4 cells/cm2. The cells were incubated in DMEM/F12 supplemented with 2% B-27 supplement (B27), 1% N-2 supplement (N2), 10 mM CHIR99012, 10 ng/ml recombinant human bFGF, 30 ng/ml recombinant human BMP-4, and 10 ng/ml recombinant activin A from days 1 to 3. Next, the cells were cultured in DMEM/F12 supplemented with 2% B27, 1% N2, 100 ng/ml bFGF and 50 ng/ml BMP-4 from days 4 to 6. Medium was changed daily from days 1 to 6. Harvested cells at day 6 were termed iPS-HSCs, and were passaged on fibronectin-coated plates.

extract_protocol: Total RNA was extracted using RNeasy mini or micro kits according to the manufacturer’s protocols.

treatment_protocol: The CytoSelectTM 24-well Cell Co-culture System was used following the manufacturer’s protocol with slight modifications. Briefly, iPS-HSCs or iLHX2-HSCs were dissociated using 0.05% trypsin/0.5 mM EDTA, and 2.0x10e5 cells were seeded into fibronectin-coated wells. The next day, 1.0x10e5 tdTOMATO-labeled iPS-HPCs derived from the PB001 cell line were seeded into the iPS-HSC-seeded wells, and incubated for 1 day. Both cells were cultured in Hepatocyte Culture Medium without EGF for 6 days (with or without Dox), and the medium was changed every other day. Co-cultured cells were dissociated using 0.05% trypsin/0.5 mM EDTA and were sorted using FACS. Sorted cells were then analyzed.

tag: cell line source

value: induced pluripotent stem cell-derived hepatic stellate-like cells (iPS-HSCs)

value: overexpressing LHX2

tag: treatment

value: vehicle

source_name: iLHX2-HSCs Mes Dox Pos

value: Dox


title: SS_1


title: PBMC_Control_NightOrientedSchedule_RelTime_38.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870771, PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group

value: Control

value: NightOrientedSchedule


title: PBMC_Control_NightOrientedSchedule_RelTime_30.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870769, PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870763, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group

value: DayOrientedSchedule


title: PBMC_Control_DayOrientedSchedule_RelTime_16.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870764, PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: iSCA3-2-iPSC 1

city: Taipei

first: Ching-Yu

last: Chuang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

hyb_protocol: Hybridized to the Affymetrix Human Genome U133 plus 2.0 array

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: GeneSpring X software

source_name: dermal fibroblast

label_protocol: biotin-labeled cRNA

growth_protocol: For neuronal differentiation, iPSCs were dissociated with 1 mg/ml dispase (Sigma), and then left to form embryoid bodies (EBs) in ultra-low attachment dishes (Corning, Corning, NY, USA) for 4 d, in 20% knockout serum replacement media, consisting of DMEM/F12, 20% knockout serum replacement, 1% NEAA, and 2 mM L-glutamine with 100 mM 2-mercaptoethanol, and containing 10 μM SB431542 and 100 nM LDN193189. EBs were then switched to N2 media, consisting of NeuroBasal medium, 1X N2 supplement, 1 mM sodium pyruvate, 2 mM L-glutamine, and 20 ng/mL bFGF (all purchased from Life Technologies), for another 2 d. Next, EBs were plated on Matrigel (BD Biosciences, Franklin Lakes, NJ, USA) coated tissue culture dishes (Corning) in N2 media until neural rosettes appeared. Rosettes were manually picked and cultured as spherical aggregates in N2 medium for 4 to 6 d. Afterward, neurospheres were attached to Matrigel-coated dishes in N2 medium until day 30, then switch to B27 media (NeuroBasal medium, 1X B27 supplement, 1% NEAA, 1 mm sodium pyruvate, 2 mM L-glutamine, 20 ng/ml bFGF and 300 ng/ml cAMP) for further neuronal maturation.

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

tag: gender

value: Female


title: PBMC_Control_DayOrientedSchedule_RelTime_8.5_Subject_T21 [re-analysis]

description: reanalysis of GSM2870762, PBMC sample taken at 8.5 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: iSCA2-2-iPSC 2

source_name: PBMC


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870761, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: iSCA3-1-iPSC 1


title: iSCA3-1-iPSC 2


title: PBMC_Control_DayOrientedSchedule_RelTime_20.3_Subject_T21 [re-analysis]

description: reanalysis of GSM2870765, PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_0.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870760, PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T21 in the Control group


title: iSCA2-1-iPSC 1

value: Male


title: PBMC_Control_NightOrientedSchedule_RelTime_18.2_Subject_T21 [re-analysis]

description: reanalysis of GSM2870766, PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T21 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_30.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870757, PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group


title: iSCA3-2-iPSC 2


title: rsd2 late

city: London

first: Peter

last: Sarkies

address: Du Cane Road

department: MRC Clinical Sciences Centre

country: United Kingdom

institute: Imperial College London

description: RNA 18-33nt

data_processing:
Adapter trimming using fastx_clipper
fastq to fasta file conversion using custom script in Perl 5.18.2
collapsing fasta file using fastx_collapser
selection of small RNAs 18-33 nucleotides in length using custom script in Perl 5.18.2
Supplementary_files_format_and_content: fasta w/ counts

organism: Caenorhabditis elegans

growth_protocol: C. elegans was maintained at 25C on nematode growth medium and E. coli OP50

extract_protocol:
RNA was extracted using trizol according to manufacturer's instructions
Illumina truseq small RNA according to manufacturer's instructions

value: Young adult

tag: mutant

tag: generation

value: late


title: PBMC_Control_NightOrientedSchedule_RelTime_38.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870759, PBMC sample taken at 38.2 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group


title: iSCA2-2-iPSC 1

tag: age


title: spr5 early

description: RNA 18-33nt

value: early


title: PBMC_Control_NightOrientedSchedule_RelTime_34.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870758, PBMC sample taken at 34.2 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group


title: spr5 late

description: RNA 18-33nt


title: rsd2 early

description: RNA 18-33nt


title: NGP_HBP1virus_replicate2

city: Ghent

first: Shana

last: Claeys

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics Ghent

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum, 1% glutamin, 1% kanamycin, 1% penicilin/streptomycin and HEPES (25mM).

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: NGP cells were transduced with an HBP1 overexpression construct.

tag: cell line

value: NGP

tag: cell type

value: neuroblastoma cells

tag: transduced with

value: HBP1 overexpression construct


title: CTRL-3-iPSC

source_name: foreskin fibroblast

value: newborn


title: n2 wild type early

description: RNA 18-33nt

value: WT


title: iSCA2-1-iPSC 2


title: CTRL-2-iPSC


title: NGP_HBP1virus_replicate1


title: gsp2 late

description: RNA 18-33nt


title: gsp2 early

description: RNA 18-33nt


title: NGP_parental_replicate1

value: none (parental control)


title: LPS Irs2LyzM-/- Rep2

first: Sanjay

middle: Padmakar

last: Khadayate

institute: MRC London Institute of Medical Sciences

description:
LPS
Sample 22

data_processing:
Illumina Casava1.8.2  software used for basecalling.
Sequenced reads were mapped to mm9 genome using tophat v2.0.8 with parameters -p 8 -r 130.
Gene Based read counts were obtained with HTSeq counts module v0.5.4p3
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample …

organism: Mus musculus

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow cells were flushed from bone marrow and were cultured on 10 cm sterile petri dishes in  DMEM-F12 + glutamax medium containing 10%Hyclone FBS, 1%PS and  25% of macrophage differentiation media ( L929 media).

extract_protocol:
Macrophages were differentiated from bone marrow cells  of 8 weeks old male mice. After treatment, cells were harvested and total RNA isolated using Trizol reagent.
Using a TruSeq RNA Sample Prep v2 kit (Illumina), poly-A tailed RNA (mRNA) was purified from total RNA using an oligo dT magnetic bead pull-down. The resulting mRNA was fragmented using metal ion-catalyzed hydrolysis and random priming used to synthesis double-stranded cDNA.  End repair was performed with a combination of fill-in reactions and exonuclease activity to produce blunt ends. A single “A” base was added to blunt ends followed by ligation to Illumina Paired-End Sequencing adapters containing unique index sequences, allowing samples to be pooled. The resulting libraries were amplified through 10 cycles of PCR using KAPA Hifi Polymerase, products were pooled based on a post-PCR Agilent Bioanalyzer, then the pool was size-selected using the LabChip XT Caliper (200-500 bp range).

treatment_protocol: when cells were fully differentiated, they were trypsined and plated in 6 cm cell culture dishes.  Cells were  treated with either vehicle, LPS or IL-4 for 24 hours before harvest.

tag: strain

value: 8 weeks

value: male


title: LPS Irs2LyzM-/- Rep3

description:
LPS
Sample 24


title: LPS Irs2LyzM-/- Rep1

description:
LPS
Sample 21


title: LPS Control Rep4

description:
LPS
Sample 20


title: PBMC_Control_NightOrientedSchedule_RelTime_26.3_Subject_T19 [re-analysis]

description: reanalysis of GSM2870756, PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group

tag: subject

tag: experimentalgroup


title: PBMC_Control_NightOrientedSchedule_RelTime_22.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870755, PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group

tag: condition

tag: relclocktime


title: NGP_parental_replicate2


title: n2 wild type late

description: RNA 18-33nt

tag: Stage


title: LPS Control Rep3

description:
LPS
Sample 19


title: LPS Control Rep2

description:
LPS
Sample 18


title: CTRL-1-iPSC


title: PBMC_Control_DayOrientedSchedule_RelTime_20.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870753, PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_18.3_Subject_T19 [re-analysis]

description: reanalysis of GSM2870754, PBMC sample taken at 18.3 h after habitual wake time during night-oriented schedule in Subject T19 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_16.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870752, PBMC sample taken at 16.2 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group


title: LPS Control Rep1

description:
LPS
Sample 17


title: IL-4 Irs2LyzM-/- Rep3

description:
IL-4
Sample 16


title: IL-4 Irs2LyzM-/- Rep2

description:
IL-4
Sample 14


title: IL-4 Irs2LyzM-/- Rep1

description:
IL-4
Sample 13


title: IL-4 Control Rep3

description:
IL-4
Sample 11


title: IL-4 Control Rep4

description:
IL-4
Sample 12


title: IL-4 Control Rep1

description:
IL-4
Sample 9


title: PBMC_Control_DayOrientedSchedule_RelTime_8.3_Subject_T19 [re-analysis]

description: reanalysis of GSM2870750, PBMC sample taken at 8.3 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group


title: IL-4 Control Rep2

description:
IL-4
Sample 10


title: Vehicle treated  Irs2LyzM-/- Rep3

description:
Vehicle treated
Sample 8


title: BMDM_4_Hepcidin

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
Gene expression data from BMDM with Hepcidin
JM_8

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were RMA normalized with package affy_1.36.1 of Bioconductor (BiocInstaller_1.8.3)

source_name: Primary mouse bone marrow-derived macrophages

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Bone marrow-derived macrophages (BMDMs) were obtained from bone marrow (BM) precursor cells. In brief, total BM was obtained from 8-10 week old WT by flushing femur and tibiae BM with Dulbecco’s modified Eagle’s medium (DMEM). Cells were cultured in plastic tissue culture dishes (150 mm) in 25 ml of DMEM containing 20% FBS (Fetal Bovine Serum) and 30% L cell-conditioned medium as a source of M-CSF. They were then incubated at 37°C in a humidified 5% CO2 atmosphere. After 7 days of culture, a homogeneous population of adherent BMDMs was obtained. BMDMs were scrapped and seeded at 150 000 cells per well into 24-well plate in 0,5 ml of DMEM containing 15% L cell-conditioned medium and 10% FBS. The following day, hepcidin (Peptide International) was added to the wells at 10µg/ml. The BMDMs were incubated for one hour and lysed with Trizol.

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

treatment_protocol: Hepcidin (Peptide International) was added to the wells at 10µg/ml. The BMDMs were incubated for one hour and lysed with Trizol.

value: Hepcidin

value: BMDM


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T19 [re-analysis]

description: reanalysis of GSM2870751, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group

value: Control


title: BMDM_3_Hepcidin

description:
Gene expression data from BMDM with Hepcidin
JM_6


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T19 [re-analysis]

description: reanalysis of GSM2870749, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group

value: DayOrientedSchedule


title: BMDM_4_PBS

description:
Gene expression data from BMDM with PBS
JM_7

value: PBS


title: SW480-45-2

city: Beijing

first: Jin-Wen

last: Song

state: Beijing

address: No. 100, West Fourth Ring Road, Fengtai District

institute: Beijing 302 Hospital

data_processing:
base-calling: bcl2fastq, alignment, filtering, peak-calling, generation of normalized abundance measurements etc…
data-caleaning: NGSQC
alignment:HISAT2
differential expression analyses: DESeq2
functional annotation and enrichment analyses: KOBAS
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: colorectal cancer cell line

extract_protocol:
RNA was harvested using Trizol reagent.The NEBNext Ultra RNA Library Prep Kit for Illumina was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SW480 cells

tag: genotype/variation

value: HPSE-knockdown


title: BMDM_3_PBS

description:
Gene expression data from BMDM with PBS
JM_5


title: SW480-45-1


title: SW480-45-3


title: Vehicle treated  Irs2LyzM-/- Rep2

description:
Vehicle treated
Sample 6

tag: Sex


title: PBMC_Control_NightOrientedSchedule_RelTime_39.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870747, PBMC sample taken at 39.2 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group

value: NightOrientedSchedule


title: BMDM_2_Hepcidin

description:
Gene expression data from BMDM with Hepcidin
JM_4


title: BMDM_1_Hepcidin

description:
Gene expression data from BMDM with Hepcidin
JM_2


title: BMDM_2_PBS

description:
Gene expression data from BMDM with PBS
JM_3


title: PBMC_Control_DayOrientedSchedule_RelTime_0.3_Subject_T19 [re-analysis]

description: reanalysis of GSM2870748, PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T19 in the Control group


title: Vehicle treated  Control Rep4

description:
Vehicle treated
Sample 4


title: BMDM_1_PBS

description:
Gene expression data from BMDM with PBS
JM_1


title: Vehicle treated  Irs2LyzM-/- Rep1

description:
Vehicle treated
Sample 5


title: PBMC_Control_NightOrientedSchedule_RelTime_30.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870745, PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group


title: Vehicle treated  Control Rep3

description:
Vehicle treated
Sample 3


title: SW480-NC-3

value: control


title: Vehicle treated  Control Rep2

description:
Vehicle treated
Sample 2


title: SW480-NC-2


title: Vehicle treated  Control Rep1

description:
Vehicle treated
Sample 1


title: Tcf1/Lef1-deficient Treg rep2

city: Washington

first: Weiqun

last: Peng

state: DC

address: 1918 F Street, NW , DC

institute: The George Washington University

data_processing:
The sequencing quality of RNA-Seq libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
RNA-Seq libraries were mapped to mouse genome using Tophat (v2.1.0, Trapnell et al., Bioinformatics). UCSC genes for mouse mm10 from iGenome(http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Mapped reads were then processed by Cuffdiff (v2.2.1, Trapnell et al., Nature biotechnology) to estimate expression levels of all genes and identify differentially expressed genes (FDR = 0.05). The expression level of a gene is expressed as a gene-level Fragments Per Kilobase of transcripts per Million mapped reads (FPKM) value.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each sample and all DEGs. Wig files are available for each sample.

source_name: Treg cells

extract_protocol:
Regulatory CD4+ T cells  were sort-purified from the spleen and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

tag: genotype

tag: tissue

value: splenocytes

tag: cell phenotype

value: CD4+, Thy1.2+, Foxp3-Cre-GFP+


title: PBMC_Control_NightOrientedSchedule_RelTime_34.3_Subject_T18 [re-analysis]

description: reanalysis of GSM2870746, PBMC sample taken at 34.3 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group


title: SW480-NC-1


title: PBMC_Control_NightOrientedSchedule_RelTime_22.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870743, PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_26.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870744, PBMC sample taken at 26.2 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group


title: WT Treg rep2

value: wild type


title: Tcf1/Lef1-deficient Treg rep1


title: WT Treg rep1


title: Tcf1-deficient CD4 T cells

data_processing:
The sequencing quality of ChIP-Seq libraries was assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm10 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
For ChIP-Seq libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of enrichment of four-fold or more, a P value of < 1E-5 and false-discovery rate of < 5% and thus identified Tcf1 binding peaks.
Genome_build: mm10

source_name: all CD4 T cells

extract_protocol:
Conventional or regulatory CD4+  T cells were sort-purified from WT Foxp3-cre-GFP mice, and the Tcf1-deficient CD4+ T cells were sorted from CD4-Cre+ Tcf1 fl/fl mice. The cells were then fixed and sonicated to generate chromatin fragments, followed by immunoprecipitation with antiserum against Tcf1, which were then properly washed and immunoprecipitated DNA extracted.
The DNA segments from ChIP were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: Tcf1 deficient

value: effector CD4 T cells

value: TCRb+, CD4+

tag: antibody


title: control_293T_ATAC-Seq

city: New York

first: Yael

last: David

state: NY

address: 1275 York Ave

department: Chemical Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
basecalls performed by bcl2fastq v2.19
Read alignment to GRCh38.p12 by BWA-MEM v0.7.15 with default options
Reads that mapped within the ENCODE hg38 blacklist region were removed with bedtools intersect
Mitochondrial reads were removed with the removeChrom script from harvard informatics' ATAC-seq pipeline (https://github.com/harvardinformatics/ATAC-seq/blob/master/atacseq/removeChrom.py)
Duplicate reads were removed with Picard Tools v2.16.0 MarkDuplicates function with the REMOVE_DUPLICATES option
Read alignments were converted to BED intervals with the BAMtoBED script from harvard informatics' ATAC-seq pipeline using the -x option to extend unpaired reads to the average insert size.
Read peaks were identified using MACS2 using the broad peak option
Genome_build: GRCH38.p12
Supplementary_files_format_and_content: BAM files contain filtered and deduplicated reads aligned to GRCh38, broadPeak files contain peaks called by MACS2

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (Sigma-Aldrich) at 37C with 5% CO2.

extract_protocol:
50,000 fresh 293T cells (ATCC: CRL-3216) were washed in cold PBS and lysed. The transposition reaction was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004)
After transposition and DNA purification, material was amplified for 5 cycles. After evaluation by real-time PCR, 7-9 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio (as described in Buenrostro, et al 2013).

treatment_protocol: Once cells reached 75% confluence, culture media was replaced. Treated cells received fresh media supplemented with 0.5mM methylglyoxal. Control cells received fresh media with no additional supplement.

tag: treatment


title: regulatory T cell Tcf1 ChIP-Seq

source_name: regulatory CD4+ T cells

value: Treg Cells

value: TCRb+, CD4+, CD25+, Foxp3-Cre-GFP+


title: Blood_WD_Neu_20

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to hg38 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Genome_build: hg38
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

source_name: whole blood

extract_protocol:
DNA was isolated using the QIAamp DNA Mini Kit (Qiagen).
Diluted DNA was bisulfite converted using the EZ DNA Methylation Lightning kit (Zymo) according to the manufacturer’s instructions. WGBS libraries were prepared using the TruSeq DNA Methylation kit (Illumina) with indexed PCR primers and a 14-cycle PCR program.

tag: circumstances

value: blood draw

tag: diagnosis

value: Wilson disease - neurologic

value: Male

tag: age

tag: bmi


title: MGO_293T_ATAC-Seq

tag: cell line

value: Methylglyoxal


title: PBMC_Control_DayOrientedSchedule_RelTime_20.3_Subject_T18 [re-analysis]

description: reanalysis of GSM2870741, PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group

tag: subject

value: Control

value: DayOrientedSchedule


title: Blood_WD_Neu_18


title: PBMC_Control_DayOrientedSchedule_RelTime_16.3_Subject_T18 [re-analysis]

description: reanalysis of GSM2870740, PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group

tag: experimentalgroup


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T18 [re-analysis]

description: reanalysis of GSM2870739, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group

tag: condition


title: conventional CD4 T cell Tcf1 ChIP-Seq

source_name: conventional CD4+ T cells

value: TCRb+, CD4+, CD25-, Foxp3-Cre-GFP-


title: Blood_WD_Neu_19

value: Female


title: Blood_WD_Neu_17


title: Blood_WD_Neu_15


title: Blood_WD_Neu_14


title: Blood_WD_Neu_16


title: PBMC_Control_NightOrientedSchedule_RelTime_18.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870742, PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T18 in the Control group

value: NightOrientedSchedule

tag: relclocktime


title: Blood_WD_Neu_13


title: PBMC_Control_DayOrientedSchedule_RelTime_8.4_Subject_T18 [re-analysis]

description: reanalysis of GSM2870738, PBMC sample taken at 8.4 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_34.4_Subject_T17 [re-analysis]

description: reanalysis of GSM2870734, PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: A2780_parental_2

city: Okayama

first: Takahito

last: Miyake

address: 369-8 Ofuku, Minami-ku

institute: Miyake Clinic

description: replicate 2

hyb_protocol: 500ng of total RNA was used for hybridization to each chip and incubated for 12 hours. Hybridization assays were left at 65°C until ready for processing and did not exceed 30 hours.

scan_protocol: After sample processing and hybridization were completed, samples were inserted into the Illumina BeadArray Reader (DirectHyb Gene Expression) as manufacture's protocol.

data_processing:
The Digital Analyzer for data imaging and processing (GenomeStudio Gene Expression Module User Manual) and GenomeStudio for data analysis (nCounter Expression Data Analysis Guide).
A two-sided t-test was applied to determine significantly difference between samples.

source_name: Homo sapiens

label_protocol: 500 ng of total RNA was extracted from each cells and labeled using Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for the Illumina System as manufacture's protocol.

growth_protocol: Parental and SINE resistant A2780 ovarian cancer cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 0.1% gentamycin at 37°C in 5% CO2 and 95% air.

extract_protocol: After 24 hours culture with SINE, total RNA was extracted from cells using mirVana RNA isolation labeling kit (Ambion) as manufacture's protocol.

treatment_protocol: Twenty-four hours after seeding, SINE was added to the culture medium for 24 hours.

tag: cell type

value: human ovarian cancer cell


title: A2780_SINE_1

description: replicate 1


title: Blood_WD_Neu_12


title: A2780_SINE_2

description: replicate 2


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870737, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_30.3_Subject_T17 [re-analysis]

description: reanalysis of GSM2870733, PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_0.2_Subject_T18 [re-analysis]

description: reanalysis of GSM2870736, PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T18 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_38.2_Subject_T17 [re-analysis]

description: reanalysis of GSM2870735, PBMC sample taken at 38.2 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: A2780_SINE_3

description: replicate 3


title: A2780_parental_1

description: replicate 1


title: PBMC_Control_NightOrientedSchedule_RelTime_22.3_Subject_T17 [re-analysis]

description: reanalysis of GSM2870731, PBMC sample taken at 22.3 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: A2780_parental_3

description: replicate 3


title: PBMC_Control_NightOrientedSchedule_RelTime_18.9_Subject_T17 [re-analysis]

description: reanalysis of GSM2870730, PBMC sample taken at 18.9 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_26.3_Subject_T17 [re-analysis]

description: reanalysis of GSM2870732, PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T17 in the Control group


title: Blood_WD_Neu_10


title: Blood_WD_Neu_11


title: Blood_WD_Neu_08


title: PBMC_Control_DayOrientedSchedule_RelTime_20.2_Subject_T17 [re-analysis]

description: reanalysis of GSM2870729, PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_8.8_Subject_T17 [re-analysis]

description: reanalysis of GSM2870727, PBMC sample taken at 8.8 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: Blood_WD_Neu_07


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T17 [re-analysis]

description: reanalysis of GSM2870726, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_0.2_Subject_T17 [re-analysis]

description: reanalysis of GSM2870725, PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: Blood_WD_Neu_06


title: PBMC_Control_NightOrientedSchedule_RelTime_38.3_Subject_T15 [re-analysis]

description: reanalysis of GSM2870724, PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T17 [re-analysis]

description: reanalysis of GSM2870728, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group


title: Blood_WD_Neu_09


title: Blood_WD_Neu_05


title: PBMC_Control_NightOrientedSchedule_RelTime_34.4_Subject_T15 [re-analysis]

description: reanalysis of GSM2870723, PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: AKT058

type: genomic

city: Memphis

first: Tong

last: Lin

state: TN

address: 262 Danny Thomas Place

department: Biostatistics

institute: St. Jude Children's Research Hospital

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using BeadArray reader

data_processing: R library minfi

label: Cy5, Cy3

source_name: Xenograft

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

tag: source

value: Xenograft Tumor

tag: disease state

value: Wilms tumor


title: AKT053


title: AKT052


title: PBMC_Control_NightOrientedSchedule_RelTime_30.2_Subject_T15 [re-analysis]

description: reanalysis of GSM2870722, PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: AKT057


title: Blood_WD_Neu_04

tag: Sex


title: AKT054


title: AKT064


title: AKT050


title: AKT047


title: AKT056


title: Blood_WD_Neu_03


title: Blood_WD_Neu_02


title: PBMC_Control_NightOrientedSchedule_RelTime_26.5_Subject_T15 [re-analysis]

description: reanalysis of GSM2870721, PBMC sample taken at 26.5 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_22.2_Subject_T15 [re-analysis]

description: reanalysis of GSM2870720, PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: Blood_WD_Neu_01


title: AKT036


title: AKT051


title: PBMC_Control_NightOrientedSchedule_RelTime_19_Subject_T15 [re-analysis]

description: reanalysis of GSM2870719, PBMC sample taken at 19 h after habitual wake time during night-oriented schedule in Subject T15 in the Control group


title: AKT037


title: Genomic DNA from the patient's medulloblastoma

city: Paris

first: Julien

last: Masliah-Planchon

address: 26 rue d'Ulm

institute: Institut Curie

description: medulloblastoma tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: iScan Control Software

label: Cy5 and Cy3

source_name: medulloblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from frozen tumors using phenol-chloroform procedure

tag: tissue

value: medulloblastoma

tag: gender


title: Blood_WD_Hep_20

value: Wilson disease - hepatic


title: AKT059


title: AKT033


title: AKT030


title: AKT043


title: AKT045


title: AKT055


title: AKT048


title: AKT040


title: AKT035


title: Blood_WD_Hep_18


title: Blood_WD_Hep_19


title: Blood_WD_Hep_17


title: Blood_WD_Hep_16


title: Blood_WD_Hep_15


title: AKT022


title: AKT032


title: AKT028


title: AKT029


title: Blood_WD_Hep_13


title: PBMC_Control_DayOrientedSchedule_RelTime_22.2_Subject_T15 [re-analysis]

description: reanalysis of GSM2870718, PBMC sample taken at 22.2 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group

data_processing: Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1).

extract_protocol: Extraction of RNA was performed by addition of chloroform in order to separate organic and aqueous components. Isopropanol and subsequent ethanol washes were used to precipitate and purify the RNA. RNA was dissolved in RNase-free H2O (Qiagen, Toronto, ON, Canada). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).


title: AKT027


title: AKT039


title: Blood_WD_Hep_14


title: Blood_WD_Hep_12


title: PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T15 [re-analysis]

description: reanalysis of GSM2870716, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group


title: AKT031


title: PBMC_Control_NightOrientedSchedule_RelTime_38.3_Subject_T14 [re-analysis]

description: reanalysis of GSM2870713, PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_4.2_Subject_T15 [re-analysis]

description: reanalysis of GSM2870715, PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_30.3_Subject_T14 [re-analysis]

description: reanalysis of GSM2870711, PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_0.3_Subject_T15 [re-analysis]

description: reanalysis of GSM2870714, PBMC sample taken at 0.3 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_34.4_Subject_T14 [re-analysis]

description: reanalysis of GSM2870712, PBMC sample taken at 34.4 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_26.3_Subject_T14 [re-analysis]

description: reanalysis of GSM2870710, PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_16.3_Subject_T15 [re-analysis]

description: reanalysis of GSM2870717, PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T15 in the Control group


title: Blood_WD_Hep_11


title: AKT023


title: AKT021


title: Blood_WD_Hep_09


title: Blood_WD_Hep_08


title: Blood_WD_Hep_10


title: PBMC_Control_NightOrientedSchedule_RelTime_22.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870709, PBMC sample taken at 22.2 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_20.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870707, PBMC sample taken at 20.2 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_13.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870705, PBMC sample taken at 13.2 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_NightOrientedSchedule_RelTime_18.2_Subject_T14 [re-analysis]

description: reanalysis of GSM2870708, PBMC sample taken at 18.2 h after habitual wake time during night-oriented schedule in Subject T14 in the Control group


title: PBMC_Control_DayOrientedSchedule_RelTime_16.3_Subject_T14 [re-analysis]

description: reanalysis of GSM2870706, PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: AKT026


title: AKT024


title: PBMC_Control_DayOrientedSchedule_RelTime_0.5_Subject_T14 [re-analysis]

description: reanalysis of GSM2870703, PBMC sample taken at 0.5 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: Blood_WD_Hep_05


title: Blood_WD_Hep_06


title: Blood_WD_Hep_07


title: AKT075


title: AKT071


title: PBMC_Control_DayOrientedSchedule_RelTime_8.8_Subject_T14 [re-analysis]

description: reanalysis of GSM2870704, PBMC sample taken at 8.8 h after habitual wake time during day-oriented schedule in Subject T14 in the Control group


title: Blood_WD_Hep_04


title: AKT020


title: APT064

source_name: Tumor resection

value: Primary Tumor


title: APT059


title: APT057


title: Blood_WD_Hep_02


title: Blood_WD_Hep_03


title: APT058


title: AKT067


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_30.2_Subject_T13

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group

value: BrightLight


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_34.2_Subject_T13

description: PBMC sample taken at 34.2 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_26.3_Subject_T13

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: Blood_PSC_10

value: Primary sclerosing cholangitis


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_38.2_Subject_T13

description: PBMC sample taken at 38.2 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: APT050


title: AKT066


title: AKT025


title: Blood_PSC_09

value: blood draw


title: APT052


title: Blood_WD_Hep_01


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_18.3_Subject_T13

description: PBMC sample taken at 18.3 h after habitual wake time during night-oriented schedule in Subject T13 in the BrightLight group


title: APT054


title: APT047


title: APT053


title: Blood_PSC_08


title: Blood_PSC_07


title: AKT074


title: APT056


title: Blood_PSC_06


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_20.3_Subject_T13

description: PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_16.3_Subject_T13

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_12.2_Subject_T13

description: PBMC sample taken at 12.2 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: APT051


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_4.2_Subject_T13

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: Blood_PSC_05


title: APT040


title: Blood_PSC_04


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_8.2_Subject_T13

description: PBMC sample taken at 8.2 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: Blood_PSC_03


title: Blood_PSC_02


title: Blood_PSC_01


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_0.2_Subject_T13

description: PBMC sample taken at 0.2 h after habitual wake time during day-oriented schedule in Subject T13 in the BrightLight group


title: Blood_NAFLD_10

value: Non-alcoholic fatty liver disease


title: APT055


title: T7_Naive

first: Zhaochen

last: Luo

address: No.1 Shi-zi-shan Street

institute: Huazhong Agricultural University

data_processing:
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were  sequenced on an Illumina platform and 125 bp/150 bp paired-end reads were  generated
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: lymph node

extract_protocol:
Lymph nodes were removed, and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: lymph node

value: post natal day 49

tag: genotype


title: Blood_NAFLD_09

tag: circumstances

value: Male


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_38.3_Subject_T11

first: Laura

last: Kervezee

institute: McGill University

description: PBMC sample taken at 38.3 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_34.2_Subject_T11

description: PBMC sample taken at 34.2 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: APT039


title: APT048


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_26.3_Subject_T11

description: PBMC sample taken at 26.3 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: APT036


title: T7_SAD


title: Wt_Naive

value: wild type


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_21.8_Subject_T11

description: PBMC sample taken at 21.8 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: Blood_NAFLD_08

tag: diagnosis


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_18.9_Subject_T11

description: PBMC sample taken at 18.9 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: Wt_SAD

tag: age


title: Blood_NAFLD_07

tag: bmi


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_30.3_Subject_T11

description: PBMC sample taken at 30.3 h after habitual wake time during night-oriented schedule in Subject T11 in the BrightLight group


title: Blood_NAFLD_06


title: M5_90_3 from RAW264.7 cells infected with B. melitensis M5-90 for 4h

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

description: Fourteen differentially expressed miRNAs were found in the two groups

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

label_protocol: The assay started from 2 to 5 μg total RNA sample were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

tag: cell line

value: RAW264.7 cells

tag: infection condition

value: B. melitensis M5-90

tag: infection time


title: Blood_NAFLD_05


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_20.3_Subject_T11

address: 6875 LaSalle Boulevard

description: PBMC sample taken at 20.3 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group

tag: subject

tag: experimentalgroup

tag: condition

value: DayOrientedSchedule


title: M5_90_2 from RAW264.7 cells infected with B. melitensis M5-90 for 4h


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_12.3_Subject_T11

description: PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group

tag: relclocktime


title: Blood_NAFLD_04


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_16.3_Subject_T11

description: PBMC sample taken at 16.3 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group


title: M5_90_1 from RAW264.7 cells infected with B. melitensis M5-90 for 4h


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_8.2_Subject_T11

description: PBMC sample taken at 8.2 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group


title: APT037

tag: source

tag: disease state


title: Blood_NAFLD_03

tag: Sex

value: Female


title: per3 from RAW264.7 cells infected with B. melitensis M5-90 ∆per for 4h

value: B. melitensis M5-90 ∆per


title: APT033

value: Wilms tumor


title: APT043


title: Blood_NAFLD_02


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_4.2_Subject_T11

description: PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group


title: APT035


title: per2 from RAW264.7 cells infected with B. melitensis M5-90 ∆per for 4h


title: per1 from RAW264.7 cells infected with B. melitensis M5-90 ∆per for 4h


title: PBMC_BrightLight_DayOrientedSchedule_RelTime_0.4_Subject_T11

description: PBMC sample taken at 0.4 h after habitual wake time during day-oriented schedule in Subject T11 in the BrightLight group


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_39.2_Subject_T10

description: PBMC sample taken at 39.2 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group

value: NightOrientedSchedule


title: Blood_NAFLD_01


title: Blood_HC_12

value: Healthy control


title: Chimp_NPC_10X (scRNA-seq)

city: La Jolla

first: Fred

middle: H

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

description:
Chimp
Marchetto_Gage_sc_count.txt.gz

data_processing:
bulk RNA: trim raw FASTQ files, SolexaQA++
bulk RNA: alignment to hg19, STAR
bulk RNA: alignment to panTro4, STAR
bulk RNA: alignment to gorgor3, STAR
bulk RNA: alignment to rhemac2, STAR
bulk RNA: join all alignments for each sample and sort by read id
bulk RNA: select reads mapped uniquely to each genome (3mm same species, 5 mm different species)
bulk RNA: Count reads in genes corresponding to the hg19 transcriptome reference, HT-Seq
bulk RNA: Transform counts to TPM
single-cell RNA: cellranger v2.0.0
Genome_build: hg19 (grch37), pantro4 (CSAC 2.1.4), gorgor3 (gorGor3.1), and rhemac2(MGSC Merged 1.0)
Supplementary_files_format_and_content: tab-delimited text files report TPMs and counts.

molecule: polyA RNA

organism: Pan troglodytes

source_name: NPC

growth_protocol: Established iPSC colonies were kept in feeder-free conditions indefinitely and passed using mechanical dissociation. To obtain NPCs from iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with the addition of Noggin. Rosettes were collected after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10 ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were obtained after 1-2 passages with accutase under the same conditions.

extract_protocol:
Total cellular RNA was extracted from ~5x10e6 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
RNA-seq: PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit. scRNA: library was prepared according to the 10X protocol

treatment_protocol: No additional treatment was performed

tag: sample id

tag: gender

value: F

tag: cell type

value: iPS-derived neural progenitor cells (NPCs)


title: PBMC_BrightLight_NightOrientedSchedule_RelTime_30.2_Subject_T10

description: PBMC sample taken at 30.2 h after habitual wake time during night-oriented schedule in Subject T10 in the BrightLight group

value: BrightLight


title: Blood_HC_11

tag: circumstances

value: blood draw


title: CD_fasted_3

city: Ann Arbor

first: Monica

last: Dus

state: MI

address: 1150 N. University Ave.

department: Department of Molecular, Cellular and Developmental Biology

institute: The University of Michigan

data_processing:
Reads were aligned using STAR  (version: 020201). --quantMode GeneCounts
Convert .sam files to .bam files using samtools (version 1.4).
Determine differential RNA abundance using DeSeq2 (version 1.18.0). dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
Genome_build: BDGP6
Supplementary_files_format_and_content: HTSeq counts, text format, gene ID, union, intersection_strict, intersection_nonempty

organism: Drosophila melanogaster

source_name: central brains

growth_protocol: Male w1118CS flies were collected 2 days after eclosure and housed in vials of 25 until 7 days old

extract_protocol:
Four biological replicates for each experimental condition were used for sequencing, and each replicate consisted of ten brains. For dissections, flies were briefly anesthetized on ice and brains were rapidly dissected in cold PBS before being transferred and frozen to an Eppendorf tube on dry ice. All dissections and RNA extractions were performed on the same day. Fly brains were manually homogenized in 700uL TRIzol + 4uL RiboLock using a plastic pestle and vortexing. RNA was extracted to the aqueous phase by adding 200uL chloroform with vigorous shaking, followed by centrifugation at 10,000 x g for 10 minutes at 4C. A second extraction was performed by adding equal parts chloroform to the aqueous phase, followed by centrifugation at 10,000 x g for 10 minutes at 4C. RNA was precipitated by adding equal parts 100% isopropanol, followed by a 15 minute incubation at room temperature and finally centrifugation at 10,000 x g for 15 minutes at 4C to pellet RNA. Supernatant was removed and the pellet was washed three times in 75% ethanol followed by centrifugation at 7500 x g for 5 minutes after each wash. The pellet was air-dried, and RNA was eluted in 15uL of RNase-free water.
Samples were ribo-depleted, DNase treated, and libraries were prepared using the Nugen Ovation Model Organisms kit (0350) by the University of Michigan sequencing core facility. Library concentrations were determined by qPCR.

treatment_protocol: "Starved” and “refed” groups were wet-starved with a kimwipe soaked in 2mL of water at 5PM the day before dissections. At lights on (9AM), “refed” flies were flipped to vials containing 400mM D-glucose and allowed to freely feed for 2 hours. “Starved” flies were flipped to new vials with wet kimwipes at the same time and remained starved during dissections of the “refed” group, for a total starvation time of 20 hours. “Sated” flies were wet-starved for one hour before dissections to synchronize their feeding state.

tag: strain

tag: tissue

value: central brains

value: fasted

value: male