title: LDB2nsd_Liver_Control

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

description:
LDB2nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

data_processing:
RNA sequencing (RNA-seq) data were processed using the Illumina Pipeline Software version 1.82. All RNA-seq samples passed FastQC quality thresholds (version 0.10.1) and could thus be used in subsequent analysis.
Reads were mapped to MGSCv37/mm9 using the STAR splice aligner with the 2pass pipeline (Dobin et al, 2013). Count data was generated using htseq-count from the HTseq package using parameters ‘stranded=reverse’ and ‘mode=union’ (Anders et al, 2015).
Gene boundaries were extracted from the mm9/refseq/reflat dataset of the UCSC table browser.
EdgeR was then used to normalize read counts by library size. Genes with a mean raw read count below 10 were excluded from the analysis, and the raw read counts were normalized using the TMM normalization (Robinson & Oshlack, 2010) and converted to log counts per million (CPM).
Genome_build: MGSCv37/mm9
Supplementary_files_format_and_content: text file with gene expression in log2 Counts Per Million (CPM)

source_name: liver tissue

extract_protocol:
Mice were sacrificed by decapitation after being anesthetized with isoflurane, cerebral cortex and liver were collected immediately. The whole procedure took no more than 5 minutes per mouse. Cortex and liver were flash-frozen in liquid nitrogen immediately after dissection and were stored at -140°C until further use.
For RNA extraction, frozen samples were homogenized for 45 seconds in 1 ml of QIAzol Lysis Reagent (Qiagen; Hilden, Germany) in a gentleMACS M tube using the gentleMACSTM Dissociator (Miltenyi Biotec; Bergisch Gladbach, Germany). Homogenates were stored at -80°C until RNA extraction. Total RNA was isolated and purified from cortex using the automated nucleic acid extraction system QIAcube (Qiagen; Hilden, Germany) with the RNeasy Plus Universal Tissue mini kit (Qiagen; Hilden, Germany) and were treated with DNAse. Total RNA from liver was isolated and purified manually using the Qiagen RNeasy Plus mini kit (Qiagen; Hilden, Germany) which includes a step for effective elimination of genomic DNA. RNA quantity, quality, and integrity were assessed utilizing the NanoDrop ND-1000 spectrophotometer (Thermo scientific; Waltham, Massachusetts, USA) and the Fragment AnalyzerTM (Advanced Analytical).

tag: condition

value: Control

value: Liver


title: LDBnsd_Liver_Control

status: Public on Jun 26 2018

type: SRA

description:
LDBnsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: genotype

value: DBA/2J x C57/BL/J F1

tag: tissue


title: LDBsd_Liver_SleepDeprived

description:
LDBsd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: Sleep Deprived


title: LDB2sd_Liver_SleepDeprived

description:
LDB2sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: NATLX1_H3K4me1

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

description: H3K4me1 histone marks in NA-TLX1 positive murine thymus

library_source: genomic

data_processing:
Library strategy: ChIPmentation
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus Musculus (mm10), Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

molecule: genomic DNA

source_name: thymus

extract_protocol: all libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: chip antibody

value: Active motif - Cat# 39297, RRID:AB_2615075


title: WT-Thy-RUNX1

description: RUNX1 binding in murine wildtype thymus

value: Active Motif - Cat# 39000


title: WT-Thy-H3K4me1

description: H3K4me1 histone marks in murine wildtype thymus


title: NATLX1_RUNX1

description: RUNX1 binding in NA-TLX1 positive murine thymus


title: atxr_rep2

city: college station

first: Xiuren

last: Zhang

state: Texas

address: 2123 tamu

department: biochemistry & biophysics

country: USA

institute: texas a&m university

data_processing:
All reads were mapped using TopHat2 (ver. 2.1.1) to the Arabidopsis genomic sequences with default parameters.
Reads mapped to selected genomic features were counted by HTSeq (ver.0.6.1) with default parameters.
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: Tab-delimited text files include raw reads counts for each Sample.

organism: Arabidopsis thaliana

source_name: 10-day-old seedlings

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) reagent from 10-day-old seedlings.
Total RNA was extracted by RNeasy Plant Kit (Qiagen) with DNaseI treatment; and Ribosome depletion libraries were generated by Ribo-Zero Plant and TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s manual.

value: atxr

value: 10-day-old seedlings


title: LDB1nsd_Liver_Control

description:
LDB1nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: LBDnsd_Liver_Control

description:
LBDnsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: C57/BL/J x DBA/2J F1


title: HepG2_D0_rep1_RNA

type: RNA

city: Los Angeles

first: Gangning

last: Liang

state: CA

address: 925 W 34th St

institute: University of Southern California

description: Before SGI-110 treatment

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

organism: Homo sapiens

source_name: Untreated

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

growth_protocol: Human carcinoma cell lines were obtained from the American Type Culture Collection (ATCC; www.atcc.org) and cultured according to standard mammalian tissue culture protocols and sterile technique.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SNU398, SNU475 and HepG2 cells were purchased form the American Type Culture Collection (ATCC; www.atcc.org), and treated with three daily consecutive doses of SGI-110 (Astex Pharmaceuticals, Dublin, CA) at 100 nM (72 h total exposure). Cells were harvested at subsequent time points.

tag: cell line

tag: time point

value: untreated


title: CT Treg OX40+

city: Milano

first: valeria

last: ranzani

address: via Francesco Sforza 35

country: Italy

institute: INGM

description:
SAMPLE 8
Live CD14- CD4+ CD25high CD127low CD45RA- OX40+

hyb_protocol: Illumina's Direct Hybridization Whole-Genome Expression.

scan_protocol: iScan, BeadArray Reader

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Treg liver tissue infiltrating

label_protocol: Illumina® TotalPrepTM RNA Amplification Kit

extract_protocol: miRVANA RNA extraction kit

value: cirrhotic and tumor (hepatocellular carcinoma) liver

tag: cell type

value: Treg cells OX40 +

tag: cell markers


title: CT Treg OX40-

description:
SAMPLE 7
Live CD14- CD4+ CD25high CD127low CD45RA- OX40-

value: Treg cells OX40 -


title: LDB1sd_Liver_SleepDeprived

description:
LDB1sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: CT Tconv OX40-

description:
SAMPLE 5
Live CD14- CD4+ CD25- CD45RA- OX40-

source_name: T cells liver tissue infiltrating

value: conventional T cells OX40 -


title: PB Tconv OX40+

description:
SAMPLE 2
Live CD14- CD4+ CD25- CD45RA- OX40+

source_name: T cells peripheral blood

value: peripheral blood

value: conventional T cells OX40 +


title: CT Tconv OX40+

description:
SAMPLE 6
Live CD14- CD4+ CD25- CD45RA- OX40+


title: PB Treg OX40+

description:
SAMPLE 4
Live CD14- CD4+ CD25high CD127low CD45RA- OX40+

source_name: Treg peripheral blood


title: LBDsd_Liver_SleepDeprived

description:
LBDsd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L98sd_Liver_SleepDeprived

description:
L98sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 98


title: LB62nsd_Liver_Control

description:
LB62nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: Control


title: LB61nsd_Liver_Control

description:
LB61nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: Liver


title: PB Tconv OX40-

description:
SAMPLE 1
Live CD14- CD4+ CD25- CD45RA- OX40-


title: L98nsd_Liver_Control

description:
L98nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L97sd_Liver_SleepDeprived

description:
L97sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 65a (97)


title: LB62sd_Liver_SleepDeprived

description:
LB62sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: Sleep Deprived


title: L96sd_Liver_SleepDeprived

description:
L96sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 48a (96)


title: LB61sd_Liver_SleepDeprived

description:
LB61sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L90sd_Liver_SleepDeprived

description:
L90sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 90


title: L95sd_Liver_SleepDeprived

description:
L95sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 95


title: L97nsd_Liver_Control

description:
L97nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L89nsd_Liver_Control

description:
L89nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 89


title: L90nsd_Liver_Control

description:
L90nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L89sd_Liver_SleepDeprived

description:
L89sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L87sd_Liver_SleepDeprived

description:
L87sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 87


title: L87nsd_Liver_Control

description:
L87nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L83nsd_Liver_Control

description:
L83nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 83


title: L85sd_Liver_SleepDeprived

description:
L85sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 85


title: L85nsd_Liver_Control

description:
L85nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L83sd_Liver_SleepDeprived

description:
L83sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L81nsd_Liver_Control

description:
L81nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 81


title: L96nsd_Liver_Control

description:
L96nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L95nsd_Liver_Control

description:
L95nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L75nsd_Liver_Control

description:
L75nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 75


title: L79sd_Liver_SleepDeprived

description:
L79sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 79


title: L71nsd_Liver_Control

description:
L71nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 71


title: L73nsd_Liver_Control

description:
L73nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 73


title: L75sd_Liver_SleepDeprived

description:
L75sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L73sd_Liver_SleepDeprived

description:
L73sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L79nsd_Liver_Control

description:
L79nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L67sd_Liver_SleepDeprived

description:
L67sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 67


title: L71sd_Liver_SleepDeprived

description:
L71sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L67nsd_Liver_Control

description:
L67nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: Control


title: L70sd_Liver_SleepDeprived

description:
L70sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 70

value: Liver


title: L66nsd_Liver_Control

description:
L66nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 66


title: L84nsd_Liver_Control

description:
L84nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 84


title: L84sd_Liver_SleepDeprived

description:
L84sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: Sleep Deprived


title: L81sd_Liver_SleepDeprived

description:
L81sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L66sd_Liver_SleepDeprived

description:
L66sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L64sd_Liver_SleepDeprived

description:
L64sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 64


title: L65nsd_Liver_Control

description:
L65nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 65


title: L65sd_Liver_SleepDeprived

description:
L65sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L64nsd_Liver_Control

description:
L64nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L56sd_Liver_SleepDeprived

description:
L56sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 56


title: L61sd_Liver_SleepDeprived

description:
L61sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 61


title: BAT_cold11

city: Cologne

first: Jan-Wilhelm

last: Kornfeld

state: NRW

address: Gleueler Strasse 50

country: Germany

institute: Max-Planck-Institute for Metabolism Research

data_processing:
Quality control of the raw FASTQ files using FastQC_v0.10.1
Alignment of reads against reference genome using tophat-2.0.10.Linux_x86_64
Alignment of RNA-Seq reads with the STAR aligner
Call of FPKM values per transcript using cufflinks-2.2.1.Linux_x86_64
Differential expression analysis on gene level using DESeq2 (R-3.2.2)
Genome_build: GRCm38.p5; Ensmbl Build 87

source_name: brown adipose tissue

extract_protocol:
RNA was isolated using the mirVANA Kit (Thermo Fisher) according to manufacturer’s protocols for total RNA isolation and rRNA depleted using NEBNext rRNA depletion kit
Libraries were prepared according to NEB´s instructions accompanying the NEBNExt Ultra  II Directional RNA  Library Prep Kit (New England Biolabs).

value: brown adipose tissue

tag: treatment

value: exposure to 4°C for 24h


title: L61nsd_Liver_Control

description:
L61nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L55nsd_Liver_Control

description:
L55nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 55


title: L51sd_Liver_SleepDeprived

description:
L51sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 51


title: L70nsd_Liver_Control

description:
L70nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L49sd_Liver_SleepDeprived

description:
L49sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 49


title: L50sd_Liver_SleepDeprived

description:
L50sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 50


title: L49nsd_Liver_Control

description:
L49nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L50nsd_Liver_Control

description:
L50nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L51nsd_Liver_Control

description:
L51nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L44nsd_Liver_Control

description:
L44nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 44


title: L45nsd_Liver_Control

description:
L45nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 45

value: Control


title: L43sd_Liver_SleepDeprived

description:
L43sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 43

value: Liver


title: L43nsd_Liver_Control

description:
L43nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L48sd_Liver_SleepDeprived

description:
L48sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 48


title: L44sd_Liver_SleepDeprived

description:
L44sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: Sleep Deprived


title: L55sd_Liver_SleepDeprived

description:
L55sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L32sd_Liver_SleepDeprived

description:
L32sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/TyJ 32


title: L56nsd_Liver_Control

description:
L56nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L32nsd_Liver_Control

description:
L32nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: L45sd_Liver_SleepDeprived

description:
L45sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L29nsd_Liver_Control

description:
L29nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/TyJ 29


title: L103nsd_Liver_Control

description:
L103nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 73b (103)


title: L101nsd_Liver_Control

description:
L101nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 101


title: L100nsd_Liver_Control

description:
L100nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 100


title: L100sd_Liver_SleepDeprived

description:
L100sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: L05sd_Liver_SleepDeprived

description:
L05sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/TyJ 05


title: L05nsd_Liver_Control

description:
L05nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: DB2sd_Cortex_SleepDeprived

description:
DB2sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

source_name: cerebral cortex tissue

value: Cortex


title: DBnsd_Cortex_Control

description:
DBnsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: DBA/2J x C57/BL/J F1


title: DB1sd_Cortex_SleepDeprived

description:
DB1sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: DB1nsd_Cortex_Control

description:
DB1nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: L29tsd_Liver_SleepDeprived

description:
L29tsd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/TyJ 29t


title: L29tnsd_Liver_Control

description:
L29tnsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt


title: BDnsd_Cortex_Control

description:
BDnsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: C57/BL/J x DBA/2J F1


title: B62sd_Cortex_SleepDeprived

description:
B62sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: L29sd_Liver_SleepDeprived

description:
L29sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: B62nsd_Cortex_Control

description:
B62nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: L101sd_Liver_SleepDeprived

description:
L101sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt


title: B61nsd_Cortex_Control

description:
B61nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 98nsd_Cortex_Control

description:
98nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 98


title: 97sd_Cortex_SleepDeprived

description:
97sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 65a (97)


title: 98sd_Cortex_SleepDeprived

description:
98sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 96sd_Cortex_SleepDeprived

description:
96sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 48a (96)


title: 96nsd_Cortex_Control

description:
96nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: Control


title: BDsd_Cortex_SleepDeprived

description:
BDsd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 95sd_Cortex_SleepDeprived

description:
95sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 95


title: 90nsd_Cortex_Control

description:
90nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 90


title: 95nsd_Cortex_Control

description:
95nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: DB2nsd_Cortex_Control

description:
DB2nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: DBsd_Cortex_SleepDeprived

description:
DBsd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: Sleep Deprived


title: 89sd_Cortex_SleepDeprived

description:
89sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 89


title: 85sd_Cortex_SleepDeprived

description:
85sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 85


title: 87nsd_Cortex_Control

description:
87nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 87


title: 85nsd_Cortex_Control

description:
85nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 87sd_Cortex_SleepDeprived

description:
87sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 84sd_Cortex_SleepDeprived

description:
84sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 84


title: 97nsd_Cortex_Control

description:
97nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: L48nsd_Liver_Control

description:
L48nsd
htseq-count_summary.Liver.txt.NSD.log2CPM.txt

value: BXD/RwwJ 48

value: Liver


title: L103sd_Liver_SleepDeprived

description:
L103sd
htseq-count_summary.Liver.txt.SD.log2CPM.txt

value: BXD/RwwJ 73b (103)


title: 90sd_Cortex_SleepDeprived

description:
90sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: Cortex


title: 89nsd_Cortex_Control

description:
89nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 84nsd_Cortex_Control

description:
84nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 79nsd_Cortex_Control

description:
79nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 79


title: 75nsd_Cortex_Control

description:
75nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 75


title: 81nsd_Cortex_Control

description:
81nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 81


title: 81sd_Cortex_SleepDeprived

description:
81sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 83sd_Cortex_SleepDeprived

description:
83sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 83


title: 79sd_Cortex_SleepDeprived

description:
79sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 73nsd_Cortex_Control

description:
73nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 73


title: 75sd_Cortex_SleepDeprived

description:
75sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 71nsd_Cortex_Control

description:
71nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 71

value: Control


title: 73sd_Cortex_SleepDeprived

description:
73sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 66nsd_Cortex_Control

description:
66nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 66


title: 70nsd_Cortex_Control

description:
70nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 70


title: 65nsd_Cortex_Control

description:
65nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 65


title: 67nsd_Cortex_Control

description:
67nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 67


title: 83nsd_Cortex_Control

description:
83nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: B61sd_Cortex_SleepDeprived

description:
B61sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: Sleep Deprived


title: 66sd_Cortex_SleepDeprived

description:
66sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 61sd_Cortex_SleepDeprived

description:
61sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 61


title: 67sd_Cortex_SleepDeprived

description:
67sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 65sd_Cortex_SleepDeprived

description:
65sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 64sd_Cortex_SleepDeprived

description:
64sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 64


title: 64nsd_Cortex_Control

description:
64nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 71sd_Cortex_SleepDeprived

description:
71sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 61nsd_Cortex_Control

description:
61nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 70sd_Cortex_SleepDeprived

description:
70sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 56sd_Cortex_SleepDeprived

description:
56sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 56


title: 55sd_Cortex_SleepDeprived

description:
55sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 55


title: 56nsd_Cortex_Control

description:
56nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: Cortex


title: 50sd_Cortex_SleepDeprived

description:
50sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 50


title: 49nsd_Cortex_Control

description:
49nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 49


title: 50nsd_Cortex_Control

description:
50nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 48sd_Cortex_SleepDeprived

description:
48sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 48


title: 49sd_Cortex_SleepDeprived

description:
49sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 51sd_Cortex_SleepDeprived

description:
51sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 51


title: 51nsd_Cortex_Control

description:
51nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 48nsd_Cortex_Control

description:
48nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 55nsd_Cortex_Control

description:
55nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: 45sd_Cortex_SleepDeprived

description:
45sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 45


title: PB Treg OX40-

description:
SAMPLE 3
Live CD14- CD4+ CD25high CD127low CD45RA- OX40-

value: peripheral blood

value: Treg cells OX40 -


title: Gastroc_24M_RAD001_6

city: Cambridge

first: Jun

last: Shi

state: MA

address: 181 Massachusetts Avenue

institute: Novartis Institutes for Biomedical Research

data_processing:
The 76bp paired-end reads were mapped to rat genome rn5 using STAR 2.4.5a with default parameters.
A genome-wide transcription signal map was derived by counting reads coverage in 10 bp step after normalizing to 1 million total reads. Stranded information was used to separate counts from sense and antisense strand.
For gene annotation, we first clustered the Refseq transcripts based on the sharing of splicing sites to get a master set of gene loci representing all alternative isoforms.
Signal from sense-strand were averaged across the exonic regions for each gene locus to measure the transcription level. This measure is equivalent to the RPKM “reads per kilobase per million” in other RNAseq analyses.
Genome_build: rn5

organism: Rattus norvegicus

source_name: Gastroc

extract_protocol: Snap frozen kidneys, livers and gastrocnemius muscles were ground in liquid nitrogen by mortar and pestle and total RNA was extracted from ~30 mg of tissue powder using miRNeasy Micro Kit (Qiagen, 217084). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies, USA) and the integrity validated by the OD260/OD280 absorption ratio (>1.8) and by RIN score (>8) using Agilent 2100 Bioanalyzer, RNA 6000 Nano LabChip kit and Agilent 2100 Expert Software (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: RAD001 (Novartis) was formulated as a custom made microemulsion pre-concentrate at 2 % (w/w) and diluted to a final concentration prior to dosing per os. Rats were treated with RAD001 diluted in water, supplemented with 0.25% methylcellulose.  Microemulsion pre-concentrate (adequate to a dose) diluted in water with 0.25% methylcellulose served as a vehicle control. For RAD001 treatment, 22.5 m old rats received per os either a vehicle daily or RAD001 once a week  (seven doses of RAD001 in total) and vehicle daily for the rest of the week for 6 weeks.

tag: age

value: 24 months


title: Gastroc_24M_RAD001_9


title: Gastroc_24M_RAD001_7


title: Gastroc_24M_RAD001_8


title: 45nsd_Cortex_Control

description:
45nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: Control


title: 44nsd_Cortex_Control

description:
44nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 44


title: 44sd_Cortex_SleepDeprived

description:
44sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: Gastroc_24M_RAD001_3


title: 43sd_Cortex_SleepDeprived

description:
43sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 43


title: Gastroc_24M_RAD001_5


title: Gastroc_24M_RAD001_2


title: Gastroc_24M_RAD001_1


title: 43nsd_Cortex_Control

description:
43nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: Gastroc_24M_Vehicle_9

value: Vehicle


title: Gastroc_24M_Vehicle_8


title: Gastroc_24M_Vehicle_6


title: Gastroc_24M_Vehicle_7


title: v_PIMC_Rep2

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

data_processing:
RNA-seq reads were quality-filtered using FASTQ Quality Filter (-q 20 –p 75) from FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Ribosomal RNA reads were filtered out using SortMeRNA tool.
RNA-seq reads were aligned on GRCh38 (Ensembl release 91) using HISAT2 aligner (--score-min L,0,-0.5)
FeatureCounts tool from the Subread package was used to count reads to genomic features
Genome_build: GRCh38 (Ensembl release 91)
Supplementary_files_format_and_content: tabular files were generated with featureCounts and contain raw gene counts

molecule: polyA RNA

source_name: Unstable plaque inner mass cells

extract_protocol:
The first passage PIMC from two stable and two vulnerable atheromes were washed with PBS twice and detached from Petri dishes using 0.2 % collagenase type II in IMDM, centrifuged 10 min at 400 g, then 750 µL of Trizol reagent was added to the pellet and frozen at  80°C until RNA extraction. PIMCs in Trizol were thawed, mixed with 0.15 mL chloroform, vortexed for 15 s, and incubated at ambient temperature for 2 min. Thereafter, samples were centrifuged at 12,000g for 15 min at 4°C. Aqueous phase was transferred to a fresh tube and precipitated after adding 20 µg glycogen and 375 µL isopropanol. RNA samples were treated with RNase-free DNase I (Fermentas, Vilnius, Lithuania) and precipitated in 70 % ethanol, 0,3 М NaAc, 20 µg glycogen. The concentration of extracted RNA and RNA integrity number (RIN) and were tested using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent RNA 6000 Pico Kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were prepared for the sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit and were sequenced with the HiSeq 2500.

treatment_protocol: Plaque tissue samples with average size 12±1×4±1×6±1 millimeters and weight 300-500 mg were treated two times with at least 2 volumes (volume : weight) of lysis buffer (0,5% NP-40, 2 mM EDTA, 0,01 M Tris-HCl, pH=7,5) for 10 minutes at the room temperature. Then tissue samples were washed 5 times with PBS, minced finely into small pieces (1 mm3) by sterile scalpels with subsequent incubation in 0,2 % Collagenase type II (prepared in IMDM from 1 % collagenase II (Invitrogen) in Hanks’ solution (Sigma-Aldrich) for 24 hours at 37 °С, 5 % CO2. Hydrolyzed plaque fragments were centrifuged 10 min at 400 g, resuspended in 6 ml IMDM, 10 % FBS, 100 μg/ml penicillin and streptomycin (Invitrogen, Carlsbad, CA, USA) (IMDM-FBS), placed in the 10-mm tissue culture dishes and cultivated at 37 °C, 5 % CO2. After 3 days adherent PIMC were washed 3 times with IMDM to remove tissue fragments, fresh IMDM-FBS was added and cells were cultivated at 37 °C, 5 % CO2 with a medium change every 5 days for 20-25 days until about 80 % of confluent cell monolayer was formed. Cells were subcultured with the solution of 0.2 % collagenase type II in IMDM (30-40 minutes treatment at 37°С, with subsequent addition of 4 volumes of IMDM-FBS with 0,5 % gelatin).

value: Cells derived from inner mass of unstable carotid atherosclerotic plaque


title: s_PIMC_Rep2

source_name: Stable plaque inner mass cells

value: Cells derived from inner mass of stable carotid atherosclerotic plaque


title: s_PIMC_Rep1


title: v_PIMC_Rep1


title: 32sd_Cortex_SleepDeprived

description:
32sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/TyJ 32

value: Sleep Deprived


title: 29tnsd_Cortex_Control

description:
29tnsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/TyJ 29t

value: Cortex


title: Transfection control 2

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description:
Sample name: TSPAN8.con.2
SH-SY5Y cells grown for 72h at control conditions.

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: SH-SY5Y neuroblastoma cells (ECACC, Salisbury, UK) were cultivated in DMEM/F12 1:1 cell medium with 10% v/v fetal bovine serum (lifetechnologies, Darmstadt, GER) at 37°C and 5% v/v CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Plus Kit (Qiagen) according to the manufacturers’ protocol.

treatment_protocol: RNA interference in SH-SY5Y cells was performed using the Accell Delivery siRNA system (ThermoScientific, Braunschweig, GER) according to the manufacturers’ protocol; treatment/control cells were incubated for 72h before further analysis.

tag: genotype/variation

value: control


title: 32nsd_Cortex_Control

description:
32nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: IGROV-1_replicate2

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description: parental cells

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: parental cells

value: parental cells


title: 29tsd_Cortex_SleepDeprived

description:
29tsd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: 29sd_Cortex_SleepDeprived

description:
29sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/TyJ 29


title: IGROV-1/Pt1_replicate3

description: cisplatin-resistant cells

source_name: cisplatin-resistant cells

value: cisplatin-resistant cells


title: TSPAN8 knockdown 2

description:
Sample name: TSPAN8.KD.2
SH-SY5Y cells grown for 72h at TSPAN8 knockdown conditions.

value: TSPAN8 knockdown


title: IGROV-1_replicate3

description: parental cells


title: IGROV-1/Pt1_replicate1

description: cisplatin-resistant cells


title: IGROV-1_replicate1

description: parental cells


title: Transfection control 1

description:
Sample name: TSPAN8.con.1
SH-SY5Y cells grown for 72h at control conditions.


title: Gastroc_24M_Vehicle_5


title: IGROV-1/OHP_replicate2

description: oxaliplatin-resistant cells

source_name: oxaliplatin-resistant cells

value: oxaliplatin-resistant cells


title: TSPAN8 knockdown 1

description:
Sample name: TSPAN8.KD.1
SH-SY5Y cells grown for 72h at TSPAN8 knockdown conditions.


title: IGROV-1/Pt1_replicate2

description: cisplatin-resistant cells


title: IGROV-1/OHP_replicate3

description: oxaliplatin-resistant cells


title: IGROV-1/OHP_replicate1

description: oxaliplatin-resistant cells


title: Gastroc_24M_Vehicle_4

value: 24 months


title: Hs578T TET1_KO_3_1

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the hg19 genome assembly using the Star software suite
ht-seq-count  with default settings to generate counts of each gene
Cuffdiff to generate FPKM and fold change of each condition compared to control, we filtered for genes that had 0 reads across all samples
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first column is gene name.  The next 6 columns are the FPKMs of the individual samples.

source_name: Triple negative breast cancer cell line

growth_protocol: Hs578T cells were cultured in DMEM medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: gRNAs targeting exon 3 of TET1 were cloned into the Lenti CRISPR V2 plasmid.  Lentiviruses were generated using HEK293T cells by transfecting with packaging plasmid (psPAX2, Addgene 12260), envelope plasmid (pMD2.G, Addgene 12259) and lenti-CRISPR V2 plasmid (Addgene 52961).  Cells were transfected using Lipofectamine 2000.  Viral supernatant was collected at 48 and 72 hours, filtered with 0.45µm membrane and incubated on Hs578T cells for 7 hours in the presence of polybrene (6µg/mL, Millipore).  We puromycin selected (1µg/mL) the cells for three days, followed by single cell cloning using serial dilution in 96 well plates.  After selection, cells were maintained in normal media supplemented with 0.25 µg/mL puromycin.

value: adult

value: TET1 KO_3 single clone 13_D8 (gRNA targeting exon 3)


title: Hs578T TET1_KO_3_3


title: Hs578T TET1_KO_3_2


title: Hs578T Empty Vector_1

value: Empty vector single clone B5


title: 29nsd_Cortex_Control

description:
29nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: Control


title: Hs578T Empty Vector_3

value: Empty vector single clone D5


title: Gastroc_24M_Vehicle_10

value: Vehicle


title: Gastroc_24M_Vehicle_3


title: Gastroc_24M_Vehicle_1


title: Hs578T Empty Vector_2

value: Empty vector single clone C5


title: ALLSIL-ETS1

description: ETS1 binding in ALLSIL cell line

source_name: ALL-SIL cell line

value: ALL-SIL

value: Thermo Fischer Scientific - Cat# MA5-15609, RRID:AB_10978854


title: 101nsd_Cortex_Control

description:
101nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: BXD/RwwJ 101

value: Cortex


title: 103sd_Cortex_SleepDeprived

description:
103sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 73b (103)

value: Sleep Deprived


title: 100sd_Cortex_SleepDeprived

description:
100sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/RwwJ 100


title: 101sd_Cortex_SleepDeprived

description:
101sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt


title: TLX1_3

description: TLX1 knockdown with GapMer

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus Musculus (mm10), Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

extract_protocol:
Maxwell 16 LEV simplyRNA Cells Kit according to manufacturers instructions (Promega)
all libraries were prepared for sequencing using standard Illumina protocols


title: Gastroc_24M_Vehicle_2


title: Gastroc_6M_Vehicle_8

value: 6 months


title: Gastroc_6M_Vehicle_9


title: ALLSIL-RUNX1

description: RUNX1 binding in ALLSIL cell line

value: Active Motif - Cat# 39000


title: TLX1_1

description: TLX1 knockdown with GapMer


title: TLX1_2

description: TLX1 knockdown with GapMer


title: NC_3

description: control


title: Gastroc_6M_Vehicle_6


title: 05sd_Cortex_SleepDeprived

description:
05sd
htseq-count_summary.Cortex.txt.SD.log2CPM.txt

value: BXD/TyJ 05


title: 05nsd_Cortex_Control

description:
05nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt


title: Gastroc_6M_Vehicle_4


title: NC_2

description: control


title: NC_1

description: control


title: Gastroc_6M_Vehicle_3


title: bonemarrow_ko3

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

data_processing:
RNA sequencing reads were first trimmed to remove polyA and Illumina TruSeq adapter sequences using cutadapt, then aligned to the mouse reference GRCm38 (mm10) genome using the STAR aligner.
The number of counts were summarized at the gene level using featureCounts. The R software (version 3.1.0) was then used for subsequent statistical analyses. Gene expression values were computed from the RPKM (reads per kilobase per million) values produced by the rpkm function of the edgeR R package by adding a pseudocount of 1 and log2-transforming the results.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include log2 of (RPKM +1) values for each Sample.

source_name: RFX7 knock-out NK cells from the bone marrow – replicate 3

extract_protocol:
Bone marrow (BM) and spleen (SP) were collected, processed and red blood cells lysed. NK cells were enriched using the EasySep™ Mouse NK Cell Isolation Kit (STEMCELL Technologies) prior to FACS-sorting. BM-derived NK cells were sorted as NK1.1+CD122+CD3-CD19- cells, and SP-derived NK cells as NK1.1+ Ncr1+CD3-CD19- cells. Total RNA was extracted using the RNeasy plus mini kit (Qiagen) according to manufacturer's instructions.
Clontech RNA-seq libraries were prepared for the splenic NK cell preparations. Double stranded cDNA for RNA-seq library preparation was generated using SMART-Seq v4 Ultra Low Input RNA reagents (Catalog Number 634888, Clontech, Mountain View, California, USA) according to the protocol provided with the reagents beginning with 10ng of total RNA and using 9 cycles of PCR. 150 pg of the resulting cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (Catalog Number 15032354, Illumina, San Diego, California, USA) using the single cell RNA-seq library preparation protocol developed for the Fluidigm C1 (Fluidigm, South San Francisco, California, USA). TruSeq stranded mRNA-seq libraries were prepared for the bone marrow-derived NK cells. RNA-seq libraries were prepared using 400ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) according to the protocol supplied with the reagents and starting with 100ng of total RNA on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA) using a PerkinElmer-developed automated script. Library sequencing Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. Sequencing data were processed using the Illumina Pipeline Software version 1.82.

tag: strain/background

value: Rfx7 KO

value: bone marrow

value: natural killer (NK) cells


title: Gastroc_6M_Vehicle_5


title: 100nsd_Cortex_Control

description:
100nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

value: Control


title: bonemarrow_ko1

source_name: RFX7 knock-out NK cells from the bone marrow – replicate 1


title: Gastroc_6M_Vehicle_2


title: 21W_male_rep2

city: Shanghai

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

country: China

institute: Tongji University

data_processing:
DNase–seq reads (50 bp single-end) were first trimmed of low quality and adaptor using cutadapt (v1.12), and then mapped to human genome (hg38) using bowtie (v1.2) with the parameters: -v 1 -m 1 --mm --no-unal. Uniquely mapping reads were kept for further analysis using samtools (v1.6). Signal tracks (variable step bw files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC).
The DHS peaks from different reps in each sample were merged using ‘bedtools merge’ from bedtools (v2.27.0), only if the reads were overlap in these reps. The RPKM of each DHS was calculated as follows: First, using ‘multiBamSummary --centerReads’ from deeptools (2.5.4) to count the number of reads in each DHS for each sample, then normalizing them to the total number of uniquely mapped reads and to the length of DHS peaks. The Pearson correlation coefficient (r) of signal densities at genome-wide DHSs was calculated to measure the correlation between replicates and samples.
For identifying more sensitive DHS peaks in primordial germ cell, we used an additional stringent cutoff requirement: RPKM >=3. The RefSeq gene assembly (mm10 & hg38) from the UCSC Genome Browser database were used in genome-wide distribution analysis. The regions ±1 kb around the TSS were defined as promoters in this study.
The processed data can be veiwed from UCSC without downloading any files, using these urls:
peaks at:  http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://de.cyverse.org/anon-files/iplant/home/xiaoshen19930901/trackHub2/hub_human.txt
signal tracks at:  http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://de.cyverse.org/anon-files/iplant/home/xiaoshen19930901/trackHub/hub_human.txt
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include DHS peaks for each Sample

extract_protocol:
FACS sorted Cells were first washed in 0.5% bovine serum albumin in phosphate-buffered saline (BSAPBS, Sigma) solution to avoid potential contamination. After washing, fresh cells were collected in 1.5 ml tubes and resuspended in 45μl lysis buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 6 mM MgCl2, 6 mM CaCl2, 0.1% NP40) then incubated on ice for 5 min to release the nuclei. DNase I (10,000 U/ml, Roche, 04716728001) was added to the final concentration of 30 U/ml, and incubated at 37 °C for exactly 5 min. DNase I concentrations to achieve optimal smearing sizes may differ for each cell line and therefore should be determined empirically for each cell type. After DNase I digestion, the reaction was terminated immediately by adding 50μl Stop Buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% SDS, 10 mM EDTA) containing 1μl Proteinase K (20 mg/ml, Life Technologies). After incubation at 55 °C for 1h, DNA was purified by extraction with phenol–chloroform and precipitated by ethanol in the presence of glycogen (20 mg/ml, Roche, 10901393001) more than 3 hours at −20 °C.  The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer’s instructions. In order to evaluate the library complexity, we chose agarose gel electrophoresis instead of SPRI-beads based methods for size selection. Because DNase I hypersensitive sites are not binary, only the smearing pattern samples were ideal for generating high-quality DNase data. DNA fragments of 150-300bp were extracted from the agarose gel for a second PCR amplification. The DNA was eluted in 15μl of elution buffer (2.5 mM Tris, pH 7.6, 0.05 mM EDTA) and quantified by a Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32854) and Agilent High Sensitivity assay kit (Agilent Technologies). The libraries were sequenced on a Hiseq2500 with single-end 50bp reads (Illumina).
The sequence libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions. The libraries were sequenced on a Hiseq2500 with single-end 50bp reads (Illumina).

treatment_protocol: Human PGCs and gonadal somatic cells were isolated as previously described. In addition to isolating the CD117 (BD PharMingen #555714, clone YB5.B8) positive FGCs, we also collected the CD117 negative cells as gonadal somatic cells by FACS.

tag: gender

value: male

tag: development stage

value: wild type

value: primordial germ cell


title: bonemarrow_ko2

source_name: RFX7 knock-out NK cells from the bone marrow – replicate 2


title: 21W_male_rep1


title: 15W_female_soma_rep2

value: female

value: gonad somatic cell


title: Gastroc_6M_Vehicle_10

value: Vehicle


title: bonemarrow_wt3

source_name: RFX7 wild-type NK cells from the bone marrow – replicate 3

value: Rfx7 WT


title: bonemarrow_wt2

source_name: RFX7 wild-type NK cells from the bone marrow – replicate 2


title: Gastroc_6M_Vehicle_7


title: bonemarrow_wt1

source_name: RFX7 wild-type NK cells from the bone marrow – replicate 1


title: Gastroc_6M_Vehicle_1


title: spnk_ko3

source_name: RFX7 knock-out NK cells from the Spleen – replicate 3

value: spleen


title: Liver_24M_RAD001_9

source_name: Liver

value: 24 months


title: 15W_female_soma_rep1


title: spnk_ko2

source_name: RFX7 knock-out NK cells from the Spleen – replicate 2


title: Liver_24M_RAD001_8


title: EPN-PFA SAMPLE 216

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

tag: diagnosis

value: EPN-PFA

tag: Sex

value: F

tag: institute

tag: os

tag: OS status

tag: pfs

tag: pfs status


title: Liver_24M_RAD001_6


title: 103nsd_Cortex_Control

description:
103nsd
htseq-count_summary.Cortex.txt.NSD.log2CPM.txt

source_name: cerebral cortex tissue

tag: genotype

value: BXD/RwwJ 73b (103)

tag: condition

tag: tissue

value: Cortex


title: 15W_female_rep2

tag: cell type


title: Liver_24M_RAD001_7

tag: treatment


title: 21W_female_rep1


title: 15W_female_rep1


title: spnk_wt3

source_name: RFX7 wild-type NK cells from the Spleen – replicate 3


title: Liver_24M_RAD001_5

tag: age


title: spnk_wt2

source_name: RFX7 wild-type NK cells from the Spleen – replicate 2

tag: genotype/variation


title: 13W_male_soma_rep2


title: spnk_ko1

source_name: RFX7 knock-out NK cells from the Spleen – replicate 1

tag: strain/background

value: Rfx7 KO


title: 13W_male_soma_rep1

tag: gender


title: 13W_male_rep2

tag: development stage


title: 13W_male_rep1


title: L1210 S

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University medical school

data_processing:
Library strategy: DNA-seq
Sequencing reads were aligned to mouse genome (mm9) using bowtie2.  Unmapped or discordant pairs were removed.
Duplicates were removed using Picard markduplicates.
RT measurements were performed as described (Yehuda et al. 2017).  Every 200 G1 phase reads were binned in order to establish genomic windows. Corresponding S phase reads were counted in order to determine an S/G1 ratio for each window. Ratio data was normalized by subtracting the mean and dividing by the standard deviation. Continuous data was smoothed and interpolated using the Matlab csaps function (10e-16) at a resolution of 100kb (approximate average size of the windows). Continuous segments containing under 15 informative windows were removed from the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files containing normalized replication timing data

growth_protocol: L1210 were cultured in L-15 medium (BI) supplemented with penicillin, streptomycin, L-Glutamine and 10% v/v heat-inactivated (56°C, 30 min) FBS (BI).

extract_protocol:
Cells were sorted by FACS into S and G1 phase portions
Library preparation was done similar to Blecher-Gonen et al. (Blecher-Gonen et al. 2013) with some changes. Briefly, Sonicated DNA was subjected to a 50µl end repair reaction using 1µl End repair mix (E6050L, NEB), cleaned by 1.8X AmpureXP beads, followed by a 50µl A-tail reaction using 2µl Klenow fragment exo- (M0212L, NEB). The products were cleaned by 1.8X beads and were ligated by 2µl quick ligase (M2200, NEB) to 0.75µM illumina compatible forked indexed adapters. Ligation products were size selected by 0.7X PEG (considering the PEG in the ligation buffer) in order to remove free adaptors. 12-19 cycles of amplification were performed by PFU Ultra II Fusion DNA polymerase (600670, Agilent) with the following Primers:   P7 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC 3’,   P5 5' CAAGCAGAAGACGGCATACGAGAT 3’.   Amplified DNA was size selected for 300-700bp fragments by taking the supernatant after using 0.5X beads (which removed fragments greater than 700bp) followed by a 1.0X beads cleaning (which removed remaining primers and adapter dimers). The final quality of the library was assessed by Qubit and TapeStation. Libraries were pooled and sequenced on NextSeq (illumina) for 75 bp paired-end sequencing, generating 10M reads per each library (60M per experiment for triplicates of G1 and S).

tag: phase

value: S


title: Liver_24M_RAD001_3


title: Liver_24M_RAD001_2


title: 12W_female_rep2


title: L1210 G1


title: spnk_wt1

source_name: RFX7 wild-type NK cells from the Spleen – replicate 1

value: natural killer (NK) cells


title: Liver_24M_RAD001_1


title: Liver_24M_Vehicle_8


title: Liver_24M_Vehicle_9


title: E14.5_male_input

data_processing:
ChIP–seq reads (50 bp single-end) were first trimmed of low quality and adaptor using cutadapt (v1.12), and then mapped to the mouse genome (mm10) using the bowtie (v1.2) with the parameters: -v 1 -m 1 --mm --no-unal. Uniquely mapping reads were kept for further analysis using samtools (v1.6). Signal tracks (variable step bw files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC) The RPKM of histone modification in different region was calculated by the same method in DNase-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks (variable step bigwig files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC)

treatment_protocol: For mouse PGCs, male mice homozygous for Oct4-EGFP transgene on an inbred C57BL/6J background were crossed with wild-type C57BL/6 females. Noon of the day when a copulatory plug was evident was counted as E0.5. For E12.5 experiments, embryos were genotyped to conﬁrm sex, and then gonads of each sex were pooled for ﬂow cytometry. For E13.5 and E14.5 experiments, male and female gonads were identiﬁed by the presence or absence of testicular cords, and gonads of each sex were pooled. Gonads were treated with 0.25% Trypsin-EDTA for 10 min at 37 °C, and trypsin was inactivated by addition of 15% Fetal Bovine Serum (FBS)/ DMEM. Cells were filtered through 40 µm cell strainers to obtain single cell suspension for FACS sorting (FACS Aria II SORP, BD Bioscience).

tag: strain

tag: chip antibody


title: Liver_24M_Vehicle_7


title: 11W_male_soma_rep1


title: E14.5_male_H3K27me3_rep1


title: 12W_female_rep1


title: E14.5_female_input


title: Liver_24M_Vehicle_6


title: 10W_female_soma_rep2


title: Liver_24M_Vehicle_5


title: Liver_24M_Vehicle_4


title: E14.5_female_H3K4me3_rep1

value: H3K4me3, Cell signaling Technology, #9727


title: 10W_female_rep2


title: E14.5_female_H3K27me3_rep2


title: 10W_female_rep1


title: Liver_24M_Vehicle_3


title: 10W_female_soma_rep1


title: 8W_male_soma_rep2

value: male


title: E14.5_female_H3K27me3_rep1


title: Liver_24M_Vehicle_2


title: Liver_24M_Vehicle_10


title: Liver_24M_Vehicle_1


title: 8W_male_soma_rep1

value: wild type


title: EpiLC_rep2

data_processing:
DNase–seq reads (50 bp single-end) were first trimmed of low quality and adaptor using cutadapt (v1.12), and then mapped to the mouse genome (mm10) using bowtie (v1.2) with the parameters: -v 1 -m 1 --mm --no-unal. Uniquely mapping reads were kept for further analysis using samtools (v1.6). Signal tracks (variable step bw files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC).
The DHS peaks from the DNase-seq data were identified by the Hotspot program (v4) with FDR < 0.01. The DHS peaks from different reps in each sample were merged using ‘bedtools merge’ from bedtools (v2.27.0), only if the reads were overlap in these reps. The RPKM of each DHS was calculated as follows: First, using ‘multiBamSummary --centerReads’ from deeptools (2.5.4) to count the number of reads in each DHS for each sample, then normalizing them to the total number of uniquely mapped reads and to the length of DHS peaks. The Pearson correlation coefficient (r) of signal densities at genome-wide DHSs was calculated to measure the correlation between replicates and samples.
For identifying more sensitive DHS peaks in primordial germ cell, we used an additional stringent cutoff requirement: RPKM >=3. The RefSeq gene assembly (mm10 & hg38) from the UCSC Genome Browser database were used in genome-wide distribution analysis. The regions ±1 kb around the TSS were defined as promoters in this study.
processed data can be viewed from UCSC without downloading any files, using these urls:
peaks at: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&hubUrl=https://de.cyverse.org/anon-files/iplant/home/xiaoshen19930901/trackHub2/hub_mouse.txt
signal tracks at: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&hubUrl=https://de.cyverse.org/anon-files/iplant/home/xiaoshen19930901/trackHub/hub_mouse.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DHS peaks for each Sample

growth_protocol: The R1 ESCs were cultured on mitomycin-C-treated MEFs in ES medium containing DMEM supplemented with 15% (v/v) fetal bovine serum, 1 mM l-glutamine, 0.1mM mercaptoethanol, 1% nonessential amino acid stock, penicillin/streptomycin, nucleosides and 1,000U/ml LIF. The EpiLCs were induced by plating 1.0×105 ESCs on a well of a 12-well plate coated with human plasma fibronectin (16.7 mg/ml) in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), and KSR (1%).

extract_protocol:
FACS sorted Cells were first washed in 0.5% bovine serum albumin in phosphate-buffered saline (BSAPBS, Sigma) solution to avoid potential contamination. After washing, fresh cells were collected in 1.5 ml tubes and resuspended in 45μl lysis buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 6 mM MgCl2, 6 mM CaCl2, 0.1% NP40) then incubated on ice for 5 min to release the nuclei. DNase I (10,000 U/ml, Roche, 04716728001) was added to the final concentration of 30 U/ml, and incubated at 37 °C for exactly 5 min. DNase I concentrations to achieve optimal smearing sizes may differ for each cell line and therefore should be determined empirically for each cell type. After DNase I digestion, the reaction was terminated immediately by adding 50μl Stop Buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% SDS, 10 mM EDTA) containing 1μl Proteinase K (20 mg/ml, Life Technologies). After incubation at 55 °C for 1h, DNA was purified by extraction with phenol–chloroform and precipitated by ethanol in the presence of glycogen (20 mg/ml, Roche, 10901393001) more than 3 hours at −20 °C.
The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer’s instructions. In order to evaluate the library complexity, we chose agarose gel electrophoresis instead of SPRI-beads based methods for size selection. Because DNase I hypersensitive sites are not binary, only the smearing pattern samples were ideal for generating high-quality DNase data. DNA fragments of 150-300bp were extracted from the agarose gel for a second PCR amplification. The DNA was eluted in 15μl of elution buffer (2.5 mM Tris, pH 7.6, 0.05 mM EDTA) and quantified by a Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32854) and Agilent High Sensitivity assay kit (Agilent Technologies). The libraries were sequenced on a Hiseq2500 with single-end 50bp reads (Illumina).

value: mouse epiblast like cell (EpiLC)


title: 8W_male_rep2

value: primordial germ cell


title: 8W_male_rep1


title: EpiLC_rep1


title: Liver_6M_Vehicle_9

value: 6 months


title: ESC_rep2

value: mouse embryonic stem cell (ESC)


title: E14.5_female_H3K4me3_rep2

value: female


title: Liver_6M_Vehicle_6

value: Vehicle


title: ESC_rep1


title: Liver_6M_Vehicle_7


title: 11W_male_soma_rep2

value: gonad somatic cell


title: BVSC_ESC_rep1


title: BVSC_ESC_rep2


title: E16.5_male_soma_rep2

tag: strain background

value: gonad  somatic cell


title: Liver_6M_Vehicle_4


title: Liver_6M_Vehicle_2


title: Liver_6M_Vehicle_5


title: Liver_6M_Vehicle_3


title: E16.5_male_rep2


title: E16.5_male_soma_rep1


title: Liver_6M_Vehicle_10


title: Liver_6M_Vehicle_1


title: E16.5_female_rep1


title: Kidney_24M_RAD001_9

source_name: Kidney

value: 24 months


title: Kidney_24M_RAD001_7


title: E16.5_female_rep2


title: E14.5_male_rep2


title: E14.5_male_rep1


title: Kidney_24M_RAD001_6


title: E14.5_female_rep2


title: E14.5_female_rep1


title: Kidney_24M_RAD001_3


title: Liver_6M_Vehicle_8


title: Kidney_24M_RAD001_5


title: Kidney_24M_RAD001_2


title: E16.5_male_rep1


title: Kidney_24M_Vehicle_9


title: Kidney_24M_RAD001_1


title: Kidney_24M_Vehicle_8


title: E13.5_male_rep2


title: E14.5_male_H3K27me3_rep2


title: Kidney_24M_Vehicle_6


title: E13.5_male_rep1


title: E13.5_female_rep2


title: Kidney_24M_RAD001_8


title: E12.5_male_rep2


title: E12.5_male_soma_rep1


title: E12.5_male_rep1


title: E12.5_female_soma_rep1


title: E12.5_female_rep2


title: Kidney_24M_Vehicle_5


title: Kidney_24M_Vehicle_4


title: Kidney_24M_Vehicle_3


title: E12.5_female_rep1


title: Kidney_24M_Vehicle_2


title: Kidney_24M_Vehicle_10


title: E10.5_rep2


title: E10.5_rep1


title: E13.5_female_rep1


title: Kidney_24M_Vehicle_1


title: E9.5_rep1


title: Kidney_6M_Vehicle_8


title: Kidney_6M_Vehicle_9


title: Kidney_6M_Vehicle_6


title: Kidney_6M_Vehicle_5


title: Kidney_6M_Vehicle_7


title: Kidney_6M_Vehicle_2


title: Kidney_6M_Vehicle_3


title: Kidney_6M_Vehicle_4


title: Kidney_6M_Vehicle_10


title: 53C

first: Abbas

last: Jariani

address: Gaston Geenslaan 1, box 2471

department: KU Leuven - VIB Centre for Microbiology

institute: KU Leuven - VIB

description:
fpm_RNAseq_data.csv
53C

data_processing:
map fastq to bam using tophat
convert bam files to sam using samtools
Number of reads covering each gene was calculated using HTSeq
Number of reads mapped to each gene was normalized to the total number of reads in the given sample
Genome_build: S288C_reference_genome_R64-2-1
Supplementary_files_format_and_content: CSV file containing one column for each sample and one row for each gene. The values are fragment per million (fpm).

organism: Saccharomyces cerevisiae

growth_protocol: growth in YPglu5% or YPmal10%

extract_protocol:
MasterPure Yeast kit
Illumina TruSeq kit

tag: growth media

value: maltose


title: 63C

description:
fpm_RNAseq_data.csv
63C


title: 59B

description:
fpm_RNAseq_data.csv
59B


title: 61C

description:
fpm_RNAseq_data.csv
61C


title: 47B

description:
fpm_RNAseq_data.csv
47B


title: 63B

description:
fpm_RNAseq_data.csv
63B


title: 59C

description:
fpm_RNAseq_data.csv
59C


title: 41C

description:
fpm_RNAseq_data.csv
41C


title: 61B

description:
fpm_RNAseq_data.csv
61B


title: E9.5_rep2


title: 57C

description:
fpm_RNAseq_data.csv
57C


title: Kidney_24M_Vehicle_7


title: 55B

description:
fpm_RNAseq_data.csv
55B


title: 51C

description:
fpm_RNAseq_data.csv
51C


title: 51B

description:
fpm_RNAseq_data.csv
51B


title: Kidney_6M_Vehicle_1


title: 41B

description:
fpm_RNAseq_data.csv
41B


title: 55C

description:
fpm_RNAseq_data.csv
55C


title: 45C

description:
fpm_RNAseq_data.csv
45C


title: 45B

description:
fpm_RNAseq_data.csv
45B


title: 53B

description:
fpm_RNAseq_data.csv
53B


title: 31C

description:
fpm_RNAseq_data.csv
31C


title: 31B

description:
fpm_RNAseq_data.csv
31B


title: 37B

description:
fpm_RNAseq_data.csv
37B


title: 43C

description:
fpm_RNAseq_data.csv
43C


title: 49C

description:
fpm_RNAseq_data.csv
49C


title: 35C

description:
fpm_RNAseq_data.csv
35C


title: 57B

description:
fpm_RNAseq_data.csv
57B


title: 27C

description:
fpm_RNAseq_data.csv
27C


title: 35B

description:
fpm_RNAseq_data.csv
35B


title: 47C

description:
fpm_RNAseq_data.csv
47C


title: 27B

description:
fpm_RNAseq_data.csv
27B


title: 34C

description:
fpm_RNAseq_data.csv
34C

value: glucose


title: 21B

description:
fpm_RNAseq_data.csv
21B


title: 39C

description:
fpm_RNAseq_data.csv
39C


title: mSVF WAT siH19_3 d0 2

source_name: epididymal adipose tissue

growth_protocol: Isolated BAT or WAT SVFs were  resuspended in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 4.5 g/l glucose, 20 % fetal calf serum (FCS), 20 mM HEPES, sodium pyruvate, L-glutamine, non-essential amino acids and 1 % gentamycin and cultured at 37° C with 5 % CO2. Media was changed every day until cells had reached 80 % confluency.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s protocols for total RNA isolation
Libraries were prepared according to NEB´s instructions accompanying the NEBNExt Ultra  II Directional RNA  Library Prep Kit (Part# E7760S). 20ng of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA followed by 14 cycles of PCR. Sequencing was performed using 1,3pM hybridization to a 2x100 paired end flow cell.

treatment_protocol: Short interfering RNAs (siRNAs; siH19, non-targeting Control, siCtrl) were delivered into  BAT or WAT SVFs by Amaxa nucleofection (Lonza Bioscience) according to manufacturer‘s recommendations. Cells were utilized 48–72 h after transfection. To induce commitment of SVFs into mature adipocytes, freshly prepared 0.05 % Insulin, 0.005 % Dexmethasone, 0.001 % Rosiglitazone and 0.05 % 3-Isobutyl-1-methylxanthin (IBMX; WAT and BAT) or 0.1 % Indomethazine, 0.001 % Triiodothyronine (BAT) in growth medium (induction medium) were added to confluent cells. After 48 h of induction, differentiation was replaced with freshly prepared 0.001 % Rosiglitazone (WAT) or 0.001 % Triiodothyronine (BAT) in growth medium (differentiation medium). RNA was iisolated at day3 of differentiation.

value: epididymal adipose tissue

value: stromal vascular fraction

tag: sirna

value: H19-targeting siRNA


title: mSVF WAT siH19_3 d0 1


title: mSVF WAT siKO d0 3

value: non-targeting control siRNA


title: mSVF_WAT_siH19_3_d3 2


title: mSVF WAT siH19_3 d0 3


title: 37C

description:
fpm_RNAseq_data.csv
37C


title: mSVF WAT siKO d3 1


title: 39B

description:
fpm_RNAseq_data.csv
39B


title: 29B

description:
fpm_RNAseq_data.csv
29B


title: mSVF_WAT_siH19_3_d3 3


title: 23C

description:
fpm_RNAseq_data.csv
23C


title: 29C

description:
fpm_RNAseq_data.csv
29C


title: 49B

description:
fpm_RNAseq_data.csv
49B


title: 19C

description:
fpm_RNAseq_data.csv
19C


title: mSVF WAT siKO d0 1


title: 19B

description:
fpm_RNAseq_data.csv
19B


title: mSVF WAT siKO d0 2


title: mSVF_BAT_siH19_3_d3 2

source_name: brown adipose tissue

value: brown adipose tissue


title: mSVF_BAT_siH19_3_d3 3


title: 21C

description:
fpm_RNAseq_data.csv
21C


title: 43B

description:
fpm_RNAseq_data.csv
43B


title: 15C

description:
fpm_RNAseq_data.csv
15C


title: mSVF_WAT_siH19_3_d3 1


title: mSVF WAT siKO d3 3


title: mSVF WAT siKO d3 2


title: 34B

description:
fpm_RNAseq_data.csv
34B


title: mSVF_BAT_siH19_3_d3 1


title: 15B

description:
fpm_RNAseq_data.csv
15B


title: mSVF BAT siH19_3 d0 3


title: 9C

description:
fpm_RNAseq_data.csv
9C


title: mSVF BAT siKO d3 3


title: 7B

description:
fpm_RNAseq_data.csv
7B


title: 9B

description:
fpm_RNAseq_data.csv
9B


title: 7C

description:
fpm_RNAseq_data.csv
7C


title: 5C

description:
fpm_RNAseq_data.csv
5C


title: 5B

description:
fpm_RNAseq_data.csv
5B


title: mSVF BAT siKO d3 1


title: mSVF BAT siKO d0 3


title: 25C

description:
fpm_RNAseq_data.csv
25C


title: mSVF BAT siKO d0 2


title: IGROV-1/Pt1_replicate3

description: cisplatin-resistant cells

source_name: cisplatin-resistant cells

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

tag: cell line

value: cisplatin-resistant cells


title: IGROV-1_replicate3

description: parental cells

source_name: parental cells

value: parental cells


title: mSVF BAT siKO d0 1


title: 17C

description:
fpm_RNAseq_data.csv
17C


title: 25B

description:
fpm_RNAseq_data.csv
25B


title: IGROV-1/Pt1_replicate2

description: cisplatin-resistant cells


title: mSVF BAT siH19_3 d0 2


title: IGROV-1/Pt1_replicate1

description: cisplatin-resistant cells


title: mSVF BAT siH19_3 d0 1


title: IGROV-1/OHP_replicate3

description: oxaliplatin-resistant cells

source_name: oxaliplatin-resistant cells

value: oxaliplatin-resistant cells


title: 17B

description:
fpm_RNAseq_data.csv
17B


title: LP leukemic5

city: Peoria

first: Peter

last: Gyarmati

state: IL

address: 1 Illini Drive

institute: University of Illinois

data_processing:
Base calling using bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Demultiplexing using bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Alignment to GRCm38.p6 using Bowtie
Normalization using EdgeR
Statistical evaluation of differential gene expression using EdgeR
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab delimited files include logFC, logCPM, LR, p-values for differential expression

source_name: lamina propria

extract_protocol:
Total RNA was extracted using Zymo Quick RNA
Libraries were prepared using Nugen´s Ovation solo RNA-seq system

tag: phenotype

value: leukemic

value: lymphoid cell

value: Nod/SCID gamma

value: lamina propria


title: LP leukemic4


title: mSVF BAT siKO d3 2


title: 3C

description:
fpm_RNAseq_data.csv
3C


title: 3B

description:
fpm_RNAseq_data.csv
3B


title: LP leukemic2


title: IGROV-1_replicate2

description: parental cells


title: 1C

description:
fpm_RNAseq_data.csv
1C


title: LP leukemic3


title: IGROV-1/OHP_replicate2

description: oxaliplatin-resistant cells


title: LP control6

value: control


title: LP control5


title: IGROV-1_replicate1

description: parental cells


title: 23B

description:
fpm_RNAseq_data.csv
23B


title: LP control4


title: LP control3


title: 19: Chronic Periodontitis

city: Belo Horizonte

first: Sérgio

last: Amaral

state: Mg

address: Av. Antonio Carlos

country: Brazil

institute: Universidade Federal de Minas Gerais

description: Each sample was divided and processed in duplicate (Megaplex™ primer pools A & B and miRNA reverse transcription kit, Applied Biosystems, Foster City, CA, USA). cDNA resulting from the previous step was amplified before the real-time PCR reaction (Megaplex™ PreAmp pools A & B primer pool and TaqMan® PreAmp master mix solution, Applied Biosystems, Foster City, CA, USA). Amplified cDNA was then diluted and added to PCR mix (TaqMan® OpenArray® Real-Time PCR master mix, Applied Biosystems, Foster city, CA, USA) on a 384-wells plaque. Following this, plaques containing miRNA panel (TaqMan® OpenArray® Human MicroRNA panel, Applied Biosystems, Foster City, CA, USA) were loaded (AccuFill™ system, Applied Biosystems, Foster City, CA, USA) and then real-time PCR reactions were performed (QuantStudio ™ 12K Flex Real-Time PCR System, Applied Biosystems, Foster City, CA, USA).

data_processing: The analysis of the results was performed with statistical software (Applied Biosystems® Analysis Software, v.1.0, Watham, MA, USA), assuming global normalization and correction of Benjamini and Hochberg for false positive findings in the volcano plot analysis (Benjamini & Hochberg, 1995). Minimal fold change threshold was defined as 2 and statistical significance was established at p ≤ 0.05 (student t-test).

source_name: Gingival tissue

label_protocol: RNA samples obtained from the extraction procedure were digested with DNAse (Invitrogen Life Technologies, Carlsbad, CA, USA). Then, 1.5μg of RNA from each sample was used for reverse transcription reaction (Superscript First-Strand Synthesis Kit, Invitrogen Life Technologies, Carlsbad, CA, USA) according to the manufacturer's protocol.

extract_protocol: Total RNA was obtained using the miRNA isolation kit (Ambion mirVana™ miRNA Isolation Kit, Life Tecnologies, Vilvius, LT, USA) according to the manufacturer's instructions. Tissue samples were macerated and then placed in a 1.5ml eppendorf containing 1ml of lysis / binding buffer for each 0.1g of tissue. After homogenization, 1/10 of miRNA homogenate additive volume was added and incubated on ice for 10 minutes. Afterwards, the same volume of lysis / binding buffer of acid phenol: chloroform was added. The contents were mixed for 60s and centrifuged for 5 min at 10000xg. Supernatant solutions were then transferred to another eppendorf with the addiction of 1.25 of the volume of 100% ethanol. Hence, the solutions were placed in filter catridge, according to the manufacturer's protocol for total RNA extraction.   Next, samples were quantified (NanoDrop 2000, ThermoFisher Scientific, Wilmington, DE, USA) and RNA quality was assessed (Bioanalyser 2100 RNA 6000 Nano Kit, Agilent Technologies, Waldbronn, Germany). RNA with an A260/A280 ratio≥ 1.8 and an RNA Integrity Number (RIN) between 6.5 and 10 were the quality parameters pursued for starting material (Fleige & Pfaffl, 2006).

value: Gingival tissue

value: 54 Years

tag: Sex

value: Male

tag: diagnosis

value: Chronic Periodontitis


title: 23: Chronic Periodontitis

tag: tissue

value: 50 Years


title: 11: Chronic Periodontitis

value: 36 Years

value: Female


title: 18: Chronic Periodontitis

value: 48 Years


title: LP control1

tag: cell type


title: 10: Chronic Periodontitis

tag: age

value: 51 Years


title: LP control2


title: IGROV-1/OHP_replicate1

description: oxaliplatin-resistant cells

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: Amostra 9: Chronic Periodontitis

value: 39 Years


title: Amostra 8: Chronic Periodontitis


title: Amostra 7: Chronic Periodontitis

value: 62 Years


title: IEL leukemic4

source_name: intraepithelial lymphocytes

value: lymphocyte

value: intraepithelium


title: Amostra 5: Chronic Periodontitis

value: 57 Years


title: IEL leukemic5

value: leukemic

value: Nod/SCID gamma


title: IEL leukemic1


title: IEL leukemic3


title: MRE_KO2_3T9_12h

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

data_processing:
FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Read Counts were obtained for each gene using FeatureCounts
Raw Read Counts were normalized to TPM (transcript per million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing TPM for each gene

source_name: 3T9 fibroblast

growth_protocol: cells were kept in absence of serum for 72 hours to induce quiescence (0h samples). Then, cells were stimulated with serum at collected at different time-points (8hrs and 12hrs)

extract_protocol:
Total RNA  was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare RNA libraries following the Illumina TruSeq Library Preparation Kit instructions

value: 3T9 fibroblast

tag: time

tag: treatment

value: Serum-Stimulated MRE-KO2 cells at 12 hours


title: 26: Agressive Periodontitis

value: Gingival tissue

value: 45 Years

value: Agressive Periodontitis


title: 1B

description:
fpm_RNAseq_data.csv
1B

value: maltose


title: IEL control6

value: control


title: LP leukemic1

value: lymphoid cell

value: lamina propria


title: IEL leukemic2


title: 25: Agressive Periodontitis

value: 42 Years

value: Male


title: 24: Agressive Periodontitis

value: 34 Years

value: Female


title: MRE_KO1_3T9_12h

value: Serum-Stimulated MRE-KO1 cells at 12 hours


title: IEL control5

value: lymphocyte

value: intraepithelium


title: Parental_3T9_12h

value: Serum-Stimulated Parental cells at 12 hours


title: 12: Agressive Periodontitis

value: 43 Years


title: 15: Agressive Periodontitis

value: 27 Years


title: 13: Agressive Periodontitis

value: Gingival tissue

value: 36 Years


title: MRE_KO2_3T9_8h

value: 3T9 fibroblast

value: Serum-Stimulated MRE-KO2 cells at 8 hours


title: Parental_3T9_8h

value: Serum-Stimulated Parental cells at 8 hours


title: IEL control4

value: control

value: Nod/SCID gamma


title: MRE_KO1_3T9_8h

value: Serum-Stimulated MRE-KO1 cells at 8 hours


title: IEL control2


title: Omega76_0.25xMBC_2

city: Bangalore

first: Deepesh

last: Nagarajan

state: Karnataka

address: FB-04, B-wing, Department of Biochemistry, New Biology Building, IISc

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

description: Gene expression after 12hr growth in LB broth (0.25x MBC omega76).

hyb_protocol: Agilent’s In situ Hybridization kit 5188-5242.

scan_protocol: Standard Agilent scanning protocol.

data_processing: Samples were background corrected using the normexp() function in the Limma package in R. This was followed by quantile normalization and log2 transformation.

organism: Acinetobacter baumannii

source_name: bacterial pellet

label_protocol: Samples were labeled using the Agilent Quick-Amp labeling Kit. QC was performed using NanoDrop.

growth_protocol: All cultures were grown in 10 ml LB broth at 37C/180rpm for 12 hours and flash-frozen with liquid nitrogen.

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit Cat#74106.

tag: media

value: LB broth

value: 0.25X omega76


title: Omega76_0.5xMBC_1

description: Gene expression after 12hr growth in LB broth (0.5x MBC omega76).

value: 0.5X omega76


title: IEL control3


title: 4: Agressive Periodontitis

value: Female

value: Agressive Periodontitis


title: Omega76_0.5xMBC_2


title: MRE_KO2_3T9_0h

value: Serum Starved MRE-KO2 cells


title: IEL control1

value: lymphocyte

value: intraepithelium


title: MRE_KO1_3T9_0h

value: Serum Starved MRE-KO1 cells


title: Amostra 02: Agressive Periodontitis

value: Gingival tissue

value: 35 Years


title: Amostra 01: Agressive Periodontitis

value: Male


title: Parental_3T9_0h

value: 3T9 fibroblast

value: Serum Starved Parental cells


title: Omega76_0.25xMBC_1


title: Omega76_0.1xMBC_2

description: Gene expression after 12hr growth in LB broth (0.1x MBC omega76).

value: 0.1X omega76


title: Omega76_0.1xMBC_1


title: Control_1

description: Gene expression after 12hr growth in LB broth (untreated).


title: Control_2


title: RNA-seq CLL14

status: Public on Jun 25 2018

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

description: This RNA-seq experiment was performed only to verify the IpA events.

data_processing:
Low-quality 3'-seq reads were trimmed by FASTQ Quality Trimmer: fastq_quality_filter Q33 -I input.fastq
Adaptors were trimmed by FASTX Clipper from FASTX-Toolkit (fastx_clipper).
Stretch of A's at the 3' end of reads were also trimmed. Reads with minimum length 21 were used for alignment.
3'-seq reads were aligned using BWA aligner: bwa aln -t 24 -l 100000 -n 0.04 -q 0
RNA-seq reads were aligned using STAR aligner.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ipa_tpm.txt: Tab-delimited text file includes tpm values.
Supplementary_files_format_and_content: counts_rnaseq.txt: Tab-delimited text file includes raw counts.

source_name: Peripheral blood mononuclear cells

extract_protocol:
Total RNA is isolated using Tri-reagent (Ambion) and DNase-treated (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease status

value: chronic lymphocytic leukemia (CLL)

value: B cells CD5+ CD19+

tag: patient id


title: RNA-seq CLL11


title: RNA-seq CLL7

description: processed data file: counts_rnaseq.txt


title: RNA-seq CLL12


title: RNA-seq CLL6

description: processed data file: counts_rnaseq.txt


title: RNA-seq CLL15


title: RNA-seq CLL7_2


title: RNA-seq CLL5

description: processed data file: counts_rnaseq.txt


title: RNA-seq CLL2

description: processed data file: counts_rnaseq.txt


title: RNA-seq CLL4

description: processed data file: counts_rnaseq.txt


title: RNA-seq NB5_2

source_name: Tonsil

value: healthy

value: Naive B cells CD19+ CD27-


title: 3'-seq CLL13

description: processed data file: ipa_tpm.txt

data_processing:
Library strategy: 3'-Seq
Low-quality 3'-seq reads were trimmed by FASTQ Quality Trimmer: fastq_quality_filter Q33 -I input.fastq
Adaptors were trimmed by FASTX Clipper from FASTX-Toolkit (fastx_clipper).
Stretch of A's at the 3' end of reads were also trimmed. Reads with minimum length 21 were used for alignment.
3'-seq reads were aligned using BWA aligner: bwa aln -t 24 -l 100000 -n 0.04 -q 0
RNA-seq reads were aligned using STAR aligner.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ipa_tpm.txt: Tab-delimited text file includes tpm values.
Supplementary_files_format_and_content: counts_rnaseq.txt: Tab-delimited text file includes raw counts.

extract_protocol:
Total RNA is isolated using Tri-reagent (Ambion) and DNase-treated (Ambion).
An oligo(dT) primer containing a VN-anker, a uridine, the sequence of the sequencing adapter and biotin (/5BiosG/CAGACGTGTGCTCTTCCGATCTTTTTTTTrUTTTTTTTTVN) is attached to streptavidin-coated magnetic beads (M280, Invitrogen). Total RNA is incubated for 5 min at 65°C, followed by incubation with the coated magnetic beads for 10 min at 45°C. First strand synthesis is carried out using Superscript III reverse transcriptase (Invitrogen) at 50°C. The enzyme is inactivated by incubation at 70°C for 15 min. Second strand synthesis is carried out using Second stand synthesis buffer (Invitrogen), dNTPs, DNA polymerase I (NEB), E. coli ligase (NEB) and RNase H (Invitrogen). To exchange the buffers and to remove enzymes from the previous step, we treat the samples with Pronase (Roche). We introduce a nick at the position of the uridine with RNase HII (NEB). Then, nick translation is carried out with DNA polymerase I (NEB) and dNTPs for 8 min at 8°C. The reaction is stopped by the addition of EDTA. At the new position of the nick we create a blunt end using T7 exonuclease, mung bean nuclease (NEB) and Klenow enzyme (NEB). Previously annealed Illumina TruSeq sequencing adapters (Ad1: 5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT; Ad2: 5'- AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT) are then blunt- end ligated. The magnetic beads are suspended in 39 ul H2O. 5 ul of beads are used in a PCR reaction. 10-13 cycles of PCR are carried out with Phusion polymerase (NEB), a forward primer (5'-AATGATACGGCGACCACCGAGATC) and one of the Illumina TruSeq barcode reverse primers. For preparation of the library, 6 PCR reactions are performed, run on 8% TBE gels (Invitrogen) and the smear between 160 bp and 220 bp is cut out, gel-extracted, ethanol-precipitated, analyzed by Bioanalyzer (Agilent) and sequenced on Illumina Hi-seq machines.


title: RNA-seq CLL1

description: processed data file: counts_rnaseq.txt


title: 3'-seq CLL12

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL11

description: processed data file: ipa_tpm.txt


title: RNA-seq CLL4_2


title: 3'-seq CLL5

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL4

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL3

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL6

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL10

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL8

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL1

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL2

description: processed data file: ipa_tpm.txt


title: 3'-seq CLL7

description: processed data file: ipa_tpm.txt


title: RNA-seq NB4_2


title: Amplicon_BS_Serum_300

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

description: library strategy: Bisulfite-Seq amplicon-Seq

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
The first 8 bp of Read 2, representing unique molecular identifiers (UMIs), were removed and written into the sequence IDs reads instead. The reads were then subjected to adapter and quality trimming using Trim Galore (v0.4.2; default parameters) and aligned to the mouse genome (build GRCm38) using Bismark (v0.16.3, parameters: --non_directional). After mapping reads were deduplicated using the UMI-mode of deduplicate_bismark (options --bam --barcode).
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

source_name: E14 ESC

growth_protocol: Naïve ESCs were cultured in serum free media with 2i inhibitors (Neurobasal, N2, B27, 103 U/ml LIF, 1 μM Mek inhibitor PD0325901 and 3 μM Gsk3β inhibitor CHIR99021) without feeders at 37°C and 5% CO2. Primed ESCs were cultured in serum containing media (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1 mM nonessential amino acids, 50 μM β-mercaptoethanol, and 103 U/ml LIF ESGRO) without feeders at 37°C and 5% CO2.

extract_protocol:
Cells were lysed by removing media from culture dishes and adding 200ul of RLT plus buffer (Qiagen) supplemented with 0.5mM 2-mercaptoethanol. . Total nucleic acid was purified from cell lysates with RNAdvance magnetic beads (Beckman Coulter, A32649) using a Bravo Workstation pipetting robot (Agilent Technologies) following the manufacturers protocol. RNA was subsequently purified by treating the total nucleic acid with DNase I.
KAPA HiFi Uracil+ Master Mix (Kapa Biosystems) was used to amplify regions of interest using 30nM primers (Table S3), with the reverse primer including an 8N unique molecular identifier (UMI). The PCR program was: 95C 5min; 35 repeats of 98C 20s, 60C 15s, 72C 60s; 72C 10min. Amplicons were pooled for each sample and purified using Ampure XP beads (Agencourt), before a second round of PCR was used to incorporate Illumina Adaptor sequences and index samples. The PCR reaction included 11ul pooled amplicons, 200nM indexed PE1.0 (Table S5) and iPCRTag primers (Quail et al., 2012), and KAPA HiFi Master Mix (Kapa Biosystems). The PCR program was: 98C 45s; 5 repeats of 98C 15s, 65C 30s, 72C 30s; 72C 5min. Samples were then pooled and purified before library QC and sequencing was performed with up to 144 samples included on a 150bp paired-end MiSeq run.

value: Embryonic stem cell

value: E14 ESC

tag: strain


title: Amplicon_BS_Serum_410


title: Amplicon_BS_Serum_380


title: Amplicon_BS_Serum_40


title: Amplicon_BS_Serum_430


title: Amplicon_BS_Serum_390


title: Amplicon_BS_Serum_450


title: Amplicon_BS_Serum_80


title: Amplicon_BS_Serum_70


title: Amplicon_BS_Serum_60


title: Amplicon_BS_Serum_440


title: Amplicon_BS_Serum_400


title: Amplicon_BS_Serum_460


title: Amplicon_BS_Serum_90


title: Amplicon_BS_Serum_50


title: Amplicon_BS_Serum_370


title: Amplicon_BS_Serum_350


title: Amplicon_BS_Serum_330


title: Amplicon_BS_Serum_310


title: Amplicon_BS_Serum_30


title: Amplicon_BS_Serum_320


title: Amplicon_BS_Serum_180


title: Amplicon_BS_Serum_140


title: Amplicon_BS_Serum_230


title: Amplicon_BS_Serum_150


title: Amplicon_BS_Serum_240


title: Amplicon_BS_Serum_290


title: Amplicon_BS_Serum_170


title: Amplicon_BS_Serum_20


title: Amplicon_BS_Serum_250


title: Amplicon_BS_Serum_420


title: Amplicon_BS_Serum_340


title: NA16595_rep2

city: Palo Alto

first: Bo

last: Zhou

address: 3165 Porter Drive, Rm 2260

department: Psychiatry

institute: Stanford University

hyb_protocol: Hybridization was performed by Macrogen (Rockville, MD)

scan_protocol: Scan was performed by Macrogen (Rockville, MD)

data_processing: Raw probe intensity data were normalized and processed by Illumina’s GenomeStudio software to export the log R ratio (LRR) and B allele frequency (BAF) for all markers. Genotyping coordinates were based on hg19.  QuantiSNP (Colella et al. 2007) was used to call CNVs. Only CNVs with probes > 10 and Max. Log BF > 10 were included in the analysis.

label: C-Bio and A-DNP

source_name: DNA from Coriell

label_protocol: Labelling was performed by Macrogen (Rockville, MD)

extract_protocol: DNA ordered from Coriell

tag: gender

value: Female

value: B-Lymphocyte


title: Amplicon_BS_Serum_360


title: 3'-seq CLL9

description: processed data file: ipa_tpm.txt


title: Amplicon_BS_Serum_270


title: Amplicon_BS_Serum_0


title: Amplicon_BS_Serum_200


title: Amplicon_BS_Serum_220


title: Amplicon_BS_Serum_100


title: Amplicon_BS_2i_60


title: Amplicon_BS_2i_80


title: Amplicon_BS_Serum_260


title: Amplicon_BS_Serum_280


title: Amplicon_BS_Serum_160


title: Amplicon_BS_2i_460


title: NA16595_rep1


title: Amplicon_BS_Serum_1440


title: RNA-seq CLL3

description: processed data file: counts_rnaseq.txt


title: Amplicon_BS_Serum_210


title: Amplicon_BS_2i_430


title: Amplicon_BS_Serum_190


title: Amplicon_BS_Serum_130


title: Amplicon_BS_Serum_120


title: Amplicon_BS_2i_40


title: Amplicon_BS_Serum_110


title: Amplicon_BS_Serum_10


title: Amplicon_BS_2i_50


title: Amplicon_BS_2i_450


title: Amplicon_BS_2i_420


title: Amplicon_BS_2i_70


title: Amplicon_BS_2i_410


title: Amplicon_BS_2i_370


title: Amplicon_BS_2i_360


title: Amplicon_BS_2i_400


title: Amplicon_BS_2i_390


title: Amplicon_BS_2i_440


title: Amplicon_BS_2i_290


title: Amplicon_BS_2i_30


title: Amplicon_BS_2i_270


title: Amplicon_BS_2i_380


title: Amplicon_BS_2i_340


title: Amplicon_BS_2i_230


title: Amplicon_BS_2i_320


title: Amplicon_BS_2i_310


title: Amplicon_BS_2i_330


title: Amplicon_BS_2i_260


title: Amplicon_BS_2i_250


title: Amplicon_BS_2i_280


title: Amplicon_BS_2i_220


title: Amplicon_BS_2i_200


title: Amplicon_BS_2i_210


title: Amplicon_BS_2i_160


title: Amplicon_BS_2i_180


title: Amplicon_BS_2i_300


title: Amplicon_BS_2i_1440


title: Amplicon_BS_2i_20


title: Amplicon_BS_2i_350


title: Amplicon_BS_2i_170


title: Amplicon_BS_2i_190


title: Amplicon_BS_2i_140


title: Amplicon_BS_2i_110


title: Amplicon_BS_2i_150


title: Amplicon_BS_2i_120


title: Amplicon_BS_2i_130


title: Amplicon_BS_2i_240


title: Amplicon_BS_2i_100


title: Amplicon_BS_2i_10


title: Amplicon_BS_2i_0


title: mouse_OPC_H3K4me3chIP-seq_Chd8cKO

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
RNA-seq: Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 whole genome by Tophat with default options
RNA-seq: Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
ChIP-seq: Sequenced reads were trimmed for adaptor sequence.
ChIP-seq: Reads mapped to rn5(mm10) whole genome by Bowtie2 with default options
ChIP-seq: Use samtools to delete the duplicate reads
ChIP-seq: Peak calling was performed using MACS1.4 with a default p value cut off.
ATAC-seq: Adaptor sequence were trimmed by cutadapt.
ATAC-seq: Reads mapped to mm10 whole genome by Bowtie2 with default options
ATAC-seq: Use Picard to delete the duplicate reads
ATAC-seq: Convert bam to wig by bam2wig
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: wig

source_name: mouse OPC

growth_protocol: Chip-seq: Briefly, mixed glial cells were initially cultured in DMEM-F12 medium supplied with 15% FBS, then switched to B104 conditioned medium for 2 days before isolating OPCs by mechanical detachment in an orbital shaker. Isolated rat OPCs were grown in Sato growth medium supplemented with mitogens 10 ng/ml PDGF-AA and 10 ng/ml bFGF, and differentiated in OL Differentiation Medium (Sato medium supplemented with 15 nM T3 and 10 ng/ml ciliary neurotrophic factor).

extract_protocol:
RNA-seq: Total RNA was extracted per the Trizol (Life Technologies) protocol and cleanup using Rneasy kit (Qiagen).
Chip-seq: In brief, chromatin was cross-linked and sheared with a Covaris S220 sonicator from primary oligodendrocyte cultures of newborn rat or mouse cortex. Immunoprecipitation was overnight at 4°C using antibodies directed against or control immunoglobulins in the presence of protein A/G Sepharose CL-4B beads (Life Technologies) pretreated with BSA. Rabbit anti-CHD8 (ab114126) antibodies were used for immunoprecipitation. After reverse crosslink, proteinase K treatment, the precipitated chromatin DNA was purified.
RNA-seq: RNA-seq libraries from control and mutant OPC cells were prepared using Illumina RNA-Seq Preparation Kit and sequenced using a HiSeq 2500 sequencer.
Chip-seq: libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB cat # E6240L), and then to sequence on the Illumina sequencer HS2500.
ATAC-seq: ATAC-seq assays were performed as previously described (Buenrostro et al., 2013). Briefly, we isolated nuclei of 30,000 sorted cells from the mouse cortex in a cold lysis buffer. Immediately after the nuclei preparation, we performed the transposase reaction for 30 min at 37 °C. The samples were purified using a Qiagen MinElute kit. Following purification, we amplified library fragments using 1× NEBnext PCR master mix.

treatment_protocol:
RNA-seq: For mouse OPC sorting, single cell suspension was prepared from control and Chd8 cKO mouse cortices with papain dissociation and cells were re-suspended in PBS with 2 mM EDTA and 0.5% BSA and incubated with rat anti- CD140a/PDGFRa and O4+ primary monoclonal antibody.
ATAC-seq: For mouse OPC sorting, single cell suspension was prepared from control and Chd8 cKO mouse cortices with papain dissociation and cells were re-suspended in PBS with 2 mM EDTA and 0.5% BSA and incubated with rat anti- CD140a/PDGFRa and O4+ primary monoclonal antibody.

tag: strain background

value: mixed

tag: genotype/variation

value: FACS sorted PDGFRa+/O4+

tag: chip antibody

value: H3K4me3 antibody:Millipore; # 07-473; 2207275


title: mouse_OPC_H3K4me3chIP-seq_control

value: control


title: mouse_OPC_RNA-seq_Chd8cKO2


title: mouse_OPC_RNA-seq_control1


title: mouse_OPC_ATAC-seq_control


title: mouse_OPC_RNA-seq_Chd8cKO1


title: mouse_OPC_RNA-seq_control2