title: IL2-58

description: Mice dosed every 4 days for 28 days


title: IL2-50

status: Public on Feb 28 2017

type: SRA

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

country: USA

institute: Michigan State University

description: Mice dosed every 4 days for 28 days

library_source: transcriptomic

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.33
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat2 v2.1.0
Conversion to SAM format: SAMTools v1.2.0
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

molecule: total RNA

organism: Mus musculus

source_name: Ileal epithelium

extract_protocol:
Intestinal epithelium scrapings were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Ovation Mouse RNA-Seq System 1-16 sample preparation kit (NuGen, San Carlos, CA), with an additional DNase step. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

tag: strain

tag: Sex

value: Male

tag: age

value: Post natal day 56

tag: intestinal segment

value: Distal Ileum

tag: duration of treatment

value: 28 Days

tag: treatment

value: TCDD

tag: dose

tag: dose unit

value: µg/kg


title: IL2-51

description: Mice dosed every 4 days for 28 days


title: IL2-52

description: Mice dosed every 4 days for 28 days


title: JEJ-17

description: Mice dosed every 4 days for 28 days

data_processing:
Quality control: FASTQC v0.11.2
Removal of adaptors: Trimmomatic v0.32
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat2 v2.0.12
Conversion to SAM format: SAMTools v0.1.19
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Jejunum epithelium

value: Jejunum


title: IL2-26

description: Mice dosed every 4 days for 28 days


title: IL2-28

description: Mice dosed every 4 days for 28 days


title: IL2-35

description: Mice dosed every 4 days for 28 days


title: IL2-36

description: Mice dosed every 4 days for 28 days


title: IL2-27

description: Mice dosed every 4 days for 28 days


title: IL2-41

description: Mice dosed every 4 days for 28 days


title: IL2-18

description: Mice dosed every 4 days for 28 days


title: IL2-20

description: Mice dosed every 4 days for 28 days


title: IL2-43

description: Mice dosed every 4 days for 28 days


title: IL2-14

description: Mice dosed every 4 days for 28 days


title: IL2-17

description: Mice dosed every 4 days for 28 days


title: IL2-09

description: Mice dosed every 4 days for 28 days


title: Total input n MEFs Kap1 WT cells

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description: Total input of sample MEFWTk27 and MEFWTk9

library_source: genomic

data_processing:
Illumina pipeline Casava 1.82
For ChIP-seq: Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads); For RNA-seq: reads were aligned to the mm9 genome assembly using HISAT 2 with default parameters (--rna-strandness R was added when it applied)
For ChIP-seqs: Peaks were called using MACS v1.4
BigWigs files for the ChIP-seq experiments were generated using the Bedtools genomecov program followed by the bedGraphToBigWig program from the UCSC tools. The scaling factor option was set for each file in order to obtain a BigWig normalized to reads per 100 mio mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: MACS peaks; bw: bigWig files

molecule: genomic DNA

source_name: Total input n MEFs Kap1 WT cells

extract_protocol:
Cells were washed with PBS, fixed for 10 minutes at 1% formaldehyde, and quenched with glycine (at 125 mM final) for 5 minutes at room temperature. Cells were washed three times with ice-cold PBS, and harvested. The pellet was lysed, resuspended in 1 mL of sonication buffer (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.5% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 30 minutes, 5% duty cycle, 140W, 200 cycles). Chromatin was decrosslinked (RNAse A at 1μg/μL, 65°C overnight), purified and quantified by Nanodrop. Fragment size was assessed on a Bioanalyzer High Sensitivity chip (Agilent 2100). Immunoprecipitations were performed with 40 ug of chromatin (for KAP1 and SETDB1), or 20 ug of chromatin  (for histone modifications), with antibody-coupled magnetic beads (Dynabeads, ThermoFisher) in IP buffer (10 mM Tris at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 2% Triton X-100, and protease inhibitors) overnight. Chromatin was decrosslinked (Proteinase K at 400ng/μL, 65°C overnight) and DNA purified for analysis.
Illuminal ChIP-seq protocol

tag: strain background

tag: genotype/variation

value: WT

tag: developmental stage/age

value: embryonic

tag: tissue/cell type

value: Mouse embryonic fibroblast (MEF)


title: IL2-02

description: Mice dosed every 4 days for 28 days

value: Vehicle


title: Total input mESC E3, replicate 2

description: Total input of sample E3WT2

source_name: Total input mESC E3

value: WT Kap1fl/fl

value: adult

value: murine embryonic stem cell (mESC)


title: Total input Hepa 1.6 cells

description: Total input sample HepaKap1 and HekpaFR

source_name: Total input Hepa 1.6 cells

value: hepatoma

tag: cell line

value: Liver hepatoma (Derived from BW7756 tumour in a C57L mouse)


title: H3K9me3 ChIP-Seq in MEF WT cells

source_name: H3K9me3 ChIP-Seq in MEF WT cells

value: WT Kap1 loxP/loxP

tag: chip antibody

value: antiH3K9me3 (Diagenode, C15410056)


title: IL2-33

description: Mice dosed every 4 days for 28 days

value: Male

value: Post natal day 56


title: Total input mESC E3, replicate 1

description: Total input of sample es3_wt


title: H3K27ac ChIP-Seq in MEF WT cells

source_name: H3K27ac ChIP-Seq in MEF WT cells

value: antiH3K27ac (Abcam, ab4729)


title: H3K9me3 ChIP-Seq in MEFs Kap1 KO cells

source_name: H3K9me3 ChIP-Seq in MEFs Kap1 KO cells

value: Kap1 KO


title: H3K27ac ChIP-Seq in MEFs Kap1 KO cells

source_name: H3K27ac ChIP-Seq in MEFs Kap1 KO cells


title: SETDB1 ChIP-Seq in Hepa 1.6 cells

source_name: SETDB1 ChIP-Seq in Hepa 1.6 cells

value: Liver hepatoma(Derived from BW7756 tumour in a C57L mouse)

value: antiSETDB1 (Sripathy, Stevens et al. 2006)


title: KAP1 ChIP-Seq inHepa 1.6 cells

source_name: KAP1 ChIP-Seq inHepa 1.6 cells

value: WT

value: antiKAP1 (Trono laboratory, rabbit polyclonal S23470)


title: H3K9me3 ChIP-Seq of Liver Kap1 KO cells (female), MNase digested, replicate 2

value: Alb-Cre Kap1fl/fl

value: Liver


title: KAP1 ChIP-Seq in mESC E3, replicate 2

description: processed data file: e3_kap1_80cutoff_rep1_or_rep2.bed.gz

source_name: KAP1 ChIP-Seq in mESC E3

value: embryonic (E3)


title: KAP1 ChIP-Seq in mESC E3, replicate 1


title: IL2-04

description: Mice dosed every 4 days for 28 days

value: Distal Ileum

value: 28 Days

value: Vehicle

value: µg/kg


title: DUO-66

description: Mice dosed every 4 days for 28 days

source_name: Duodenal epithelium

tag: tissue

value: Duodenum

value: TCDD

tag: dose (µg/kg)


title: DUO-72

description: Mice dosed every 4 days for 28 days

value: Male


title: H3K9me3 ChIP-Seq of Liver Kap1 KO cells (female), MNase digested, replicate 1

value: adult

value: antiH3K9me3 (Diagenode, C15410056)


title: IL2-11

description: Mice dosed every 4 days for 28 days

value: Post natal day 56


title: RNA-seq of MEF Kap1 KO cells stably expressing a codon-optimized, full length, HA-tagged version of KAP1

extract_protocol:
Total RNA was extracted and DNase-I treated using a spin column-based RNA purification kit (Macherey-Nagel). cDNA was prepared with SuperScript II reverse transcriptase (Invitrogen).
Truseq Stranded RNA

value: Kap1 KO, overexpressing HA-KAP1

value: embryonic

value: Mouse embryonic fibroblast (MEF)


title: H3K9me3 ChIP-Seq of Liver WT cells (female), MNase digested, replicate 2

value: WT Kap1fl/fl


title: Total input n MEFs Kap1 KO cells

description: Total input of sample MEFKOk27 and MEFKOk9

source_name: Total input n MEFs Kap1 KO cells

value: Kap1 KO


title: IL2-03

description: Mice dosed every 4 days for 28 days


title: DUO-54

description: Mice dosed every 4 days for 28 days


title: DUO-56

description: Mice dosed every 4 days for 28 days


title: DUO-62

description: Mice dosed every 4 days for 28 days


title: DUO-68

description: Mice dosed every 4 days for 28 days


title: DUO-60

description: Mice dosed every 4 days for 28 days


title: DUO-49

description: Mice dosed every 4 days for 28 days


title: DUO-47

description: Mice dosed every 4 days for 28 days


title: DUO-45

description: Mice dosed every 4 days for 28 days


title: H3K9me3 ChIP-Seq of Liver WT cells (female), MNase digested, replicate 1

value: Liver


title: DUO-29

description: Mice dosed every 4 days for 28 days


title: DUO-40

description: Mice dosed every 4 days for 28 days


title: DUO-02

description: Mice dosed every 4 days for 28 days


title: DUO-36

description: Mice dosed every 4 days for 28 days


title: DUO-17

description: Mice dosed every 4 days for 28 days


title: DUO-25

description: Mice dosed every 4 days for 28 days


title: DUO-18

description: Mice dosed every 4 days for 28 days


title: DUO-10

description: Mice dosed every 4 days for 28 days


title: DUO-28

description: Mice dosed every 4 days for 28 days


title: DUO-34

description: Mice dosed every 4 days for 28 days


title: L-67

description: Mice dosed every 4 days for 28 days

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.33
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat v2.1.0
Conversion to SAM format: SAMTools v0.1.19
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions


title: L-52

description: Mice dosed every 4 days for 28 days


title: L-58

description: Mice dosed every 4 days for 28 days


title: L-50

description: Mice dosed every 4 days for 28 days


title: DUO-16

description: Mice dosed every 4 days for 28 days


title: DUO-21

description: Mice dosed every 4 days for 28 days


title: DUO-09

description: Mice dosed every 4 days for 28 days


title: L-68

description: Mice dosed every 4 days for 28 days


title: L-60

description: Mice dosed every 4 days for 28 days


title: L-66

description: Mice dosed every 4 days for 28 days


title: L-57

description: Mice dosed every 4 days for 28 days


title: L-42

description: Mice dosed every 4 days for 28 days


title: L-49

description: Mice dosed every 4 days for 28 days


title: L-41

description: Mice dosed every 4 days for 28 days


title: DUO-43

description: Mice dosed every 4 days for 28 days


title: L-36

description: Mice dosed every 4 days for 28 days


title: DUO-03

description: Mice dosed every 4 days for 28 days


title: DUO-05

description: Mice dosed every 4 days for 28 days


title: L-18

description: Mice dosed every 4 days for 28 days


title: L-28

description: Mice dosed every 4 days for 28 days


title: L-20

description: Mice dosed every 4 days for 28 days


title: L-17

description: Mice dosed every 4 days for 28 days


title: L-44

description: Mice dosed every 4 days for 28 days


title: L-25

description: Mice dosed every 4 days for 28 days


title: L-04

description: Mice dosed every 4 days for 28 days


title: L-26

description: Mice dosed every 4 days for 28 days


title: L-33

description: Mice dosed every 4 days for 28 days


title: PDGFB K27M T4

city: Copenhagen

first: Faizaan

last: Mohammad

state: Choose A State

address: Ole Maaloøs vej 5 Fourth Floor

country: Denmark

institute: BRIC

description: treatment: Untreated

data_processing:
After removal of Illumina adapter sequences with skewer, RNA-seq reads were mapped to the mouse genome (UCSC mm10) assembly using STAR with default parameters. The release vM8 of mouse transcript annotations were downloaded from the Gencode project (http://www.gencodegenes.org) and read counts per gene were computed using the featureCounts program.
Genome_build: mm10
Supplementary_files_format_and_content: Table of gene read counts made using featureCounts and Gencode vM8 annotations

molecule: polyA RNA

source_name: Mouse tumor derived from PDGF K27M Neural Stem Cells

extract_protocol:
RNA from tumours isolated from the mice were extracted using Rneasy plus kit (Qiagen).
500 ng of total RNA was used to make the library of polyA RNA using TruSeq RNA sample prep kit (Illumina) accordig to the protocol provided by the supplier. The libraries were sequenced using Illumina HiSeq2500 sequencer.

tag: cell type

tag: genotype


title: 3TBCN

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

country: China

institute: Kunming Institute of Zoology

data_processing:
Basecalls performed using CASAVA version 1.8
Data were filtered using GSQCToolkitv2.3.3 with parameters –pe -cutOffReadLen4HQ 70 –cutOffQualScore 20 N 5.
RNA-seq reads were aligned to the human genome assembly using Tophat-2.1.0 with read-mismatches=2.
The fragments per kilobase of transcript per million fragments (FPKM) of the genes were calculated using express cufflinks2.2.1, --max-multiread-fraction 0.75, Cuffnorm all samples from different stages, –library-norm-method is genometric. Then raw data was transform into logarithm, log2(FPKM +1).

organism: Homo sapiens

extract_protocol: The RNA sequencing libraries were constructed using the Illumina mRNA-Seq Prep Kit, and they were sequenced on the Illumina HiSeq 2000 platform in paired-end reads with 150 bp length

value: human glioblastoma stem cell

tag: tissue type

value: brain


title: 3CTR

source_name: control cells


title: L-11

description: Mice dosed every 4 days for 28 days

tag: strain

tag: Sex

tag: age

value: 28 Days


title: L-01

description: Mice dosed every 4 days for 28 days

tag: duration of treatment

tag: treatment

value: Vehicle


title: L-10

description: Mice dosed every 4 days for 28 days


title: L-09

description: Mice dosed every 4 days for 28 days


title: DUO-64

description: Mice dosed every 4 days for 28 days


title: L-34

description: Mice dosed every 4 days for 28 days


title: PDGFB K27M T2

description: treatment: Untreated

value: Mouse tumor derived from PDGF K27M Neural Stem Cells


title: L-02

description: Mice dosed every 4 days for 28 days


title: PDGF H3.3 Suz12

description:
treatment: DMSO
ChIP: Suz12 (Cell Signaling; catalog #  D39F6)

data_processing:
Reads were mapped to the mouse (UCSC mm10) genome assembly using bowtie (version 1.1.2) with default parameters except concerning multi-mapping reads which were discarded using option "-m1". For each library, mapped reads were de-duplicated by keeping a single read in each group of reads mapping to the exact same genomic sequence.
To generate ChIP-seq profiles, reads were extended to a total length of 180 bp starting from the 5' end, representing the average DNA fragment length in our libraries, and genomic coverage was computed at base pair resolution. For each library, coverage values were scaled according to the estimated Background Read Density (BRD, see the methods description in our study).
Regions locally enriched for H3K27me3, Suz12 and Ring1b were established with the SPP peak calling package using the broad enrichment procedure and IgG samples as control. We used default parameters except a z-threshold value of 6.85 and background weights corresponding to our estimated BRD scaling for the normalization between ChIP and IgG libraries.
Genome_build: mm10
Supplementary_files_format_and_content: BED files with SPP peaks, bigWig files with normalized ChIP-seq profiles

source_name: PDGF Neural Stem Cells

growth_protocol: Mouse cells were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. Glycine was added at a final concentration of 125 mM to quench the formaldehyde. Cells were then washed twice with PBS and harvested in SDS buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA). Cells were pelleted down, resuspended in Triton-X IP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin was sonicated to get the DNA fragments of <1000 bp with average DNA fragment size of 300 bp.
500 μg chromatin was used to perform chromatin immunoprecipitation (ChIP) and 10 ng of ChIP DNA was used to make library using NEBNext Ultra DNA library kit for illumine (E7370; New England Biolabs) according to supplier’s instructions. The libraries were sequenced using Illumina HiSeq2500 sequencer.

treatment_protocol: The cells were treated with either DMSO or Ezh2 inhibitor (EPZ6438, 3 uM) for 12 days.

value: PDGF Neural Stem Cells


title: PDGFB K27M T3

description: treatment: Untreated


title: PDGF K27M Ring1b

description:
treatment: DMSO
ChIP: Ring1b (in-house)


title: PDGF K27M Suz12


title: PDGF K27M EPZ me3 rep2

description:
treatment: EPZ
ChIP: H3K27me3 (Cell Signaling; catalog # C36B11)
replicate: R2


title: PDGFB K27M T1

description: treatment: Untreated


title: PDGF H3.3 DMSO IgG rep2

description:
treatment: DMSO
ChIP: IgG
replicate: R2


title: PDGF H3.3 Ring1b

description:
treatment: DMSO
ChIP: Ring1b (in-house)


title: PDGF H3.3 EPZ me3 rep2


title: PDGF K27M me3 rep2

description:
treatment: DMSO
ChIP: H3K27me3 (Cell Signaling; catalog # C36B11)
replicate: R2


title: PDGF H3.3 IgG rep1

description:
treatment: DMSO
ChIP: IgG
replicate: R1


title: PDGF K27M me3 rep1

description:
treatment: DMSO
ChIP: H3K27me3 (Cell Signaling; catalog # C36B11)
replicate: R1


title: PDGF H3.3 DMSO me3 rep2


title: PDGF H3.3 EPZ me3 rep1

description:
treatment: EPZ
ChIP: H3K27me3 (Cell Signaling; catalog # C36B11)
replicate: R1


title: PDGFB H3 EPZ I

description:
treatment: EPZ
replicate: I

data_processing:
Mouse transcript annotation version GRCm38.79 was downloaded from the Ensembl database (http://www.ensembl.org). Mapping and transcript pseudo-quantification were preformed using kallisto. Differential expression analysis was performed using sleuth according to the software manual.
Genome_build: mm10
Supplementary_files_format_and_content: Differential analysis results using kallisto and sleuth

extract_protocol:
RNA from in vitro cultured cells were extracted using Rneasy plus kit (Qiagen).
500 ng of total RNA was used to make the library of polyA RNA using TruSeq RNA sample prep kit (Illumina) accordig to the protocol provided by the supplier. The libraries were sequenced using Illumina HiSeq2500 sequencer.


title: PDGFB H3 EPZ II

description:
treatment: EPZ
replicate: II


title: PDGFB K27M EPZ III

description:
treatment: EPZ
replicate: III


title: PDGF K27M EPZ me3 rep1


title: PDGFB K27M DMSO II

description:
treatment: DMSO
replicate: II


title: PDGB K27M DMSO I

description:
treatment: DMSO
replicate: I


title: PDGFB K27M EPZ II

description:
treatment: EPZ
replicate: II


title: PDGFB K27M DMSO III

description:
treatment: DMSO
replicate: III


title: PDGFB H3 DMSO II

description:
treatment: DMSO
replicate: II


title: PDGFB K27M EPZ I

description:
treatment: EPZ
replicate: I


title: PDGF H3.3 me3 rep1


title: PDGFB H3 DMSO I

description:
treatment: DMSO
replicate: I


title: PDGFB H3 EPZ III

description:
treatment: EPZ
replicate: III


title: PDGFB H3 DMSO III

description:
treatment: DMSO
replicate: III


title: Stategra_Ikaros-ERt2 cells 18h 4-OHT Batch4

city: Valencia

first: Ana

last: Conesa

state: Valencia

address: C/ Eduardo Primo Yúfera 3

department: Computational Genomics Program

country: Spain

institute: Centro de Investigaciones Príncipe Felipe (CIPF)

description: 18h after Taxomifen induction in Ikaros/ERt2 cells

data_processing:
Trimming was applied to remove Illumina primers and low-quality nucleotides.; the very-sensitive mode only allowing a unique best mapping per fragment was used.
Tophat2 (Kim et al 2013) was used to map reads to the mm10 reference genome
Htseq-count (intersect option) was used to assign fragments to genes.
Counts were normalized with cqn (Hansen et al, 2012).
ComBat was used to reduce batch effect
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing mRNA quantification values for each Sample (matrix).

source_name: pre-B lymphocyte

extract_protocol:
Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS. RNA from all samples was extracted usng RNAbee (AMS Biotechnology (Europe) Ltd) and treated with Turbo DNase (Life Technologies). Agilent Bioanalyzer  was used to check the RNA integrity and samples were quantified using a Nanodrop
Total RNA with RNA Integrity number >8 (Agilent Bioanalyzer) was quantified using a Nanodrop. Stranded mRNA Libraries were prepared as follows, mRNA was isolated from 4 micrograms of total RNA using oligo dT beads, fragmented and cDNA was synthesised. 2nd strand cDNA was synthesised and labelled with dUTPs . This was followed by adapter ligation with barcoded Illumina adapters and 14 cycles of PCR amplification of adapter ligated DNA. Libraries were quantified using the Qubit Nano DNA quantification kit. Molar concentration of libraries was done with  the Kapa Illumina Quantification Kit. 14pM of pooled libraries was sequenced per lane on the HiSeq 2500 with paired end, 75 bp sequencing.

treatment_protocol: Cells containing inducible Ikaros were generated by transducing mouse pre-B cell line B3 with mouse stem cell virus (MSCV) retroviral vectors encoding a fusion protein of  haemagglutinin-tagged wild type Ikaros (HA-Ikaros) and the estrogen receptor hormone-binding domain (ERt2), followed by an internal ribosomal entry site (IRES) and GFP. B3 cells containing inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP)  were plated at a density of 0.5 million cells/ml in IMDM  medium containing 10% FCS and 1% penicillin-streptomycin. 0.5uM 4 hydroxy-tamoxifen was added to the cells 2h before collection. Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin.

tag: transfection

value: inducible Ikaros

tag: time

tag: #replicate

tag: #batch

tag: dose

value: pre-B lymphocyte


title: Stategra_Ikaros-ERt2 cells 6h 4-OHT Batch3

description: 6h after Taxomifen induction in Ikaros/ERt2 cells

tag: cell line


title: Stategra_Ikaros-ERt2 cells 18h 4-OHT Batch3


title: Stategra_Ikaros-ERt2 cells 6h 4-OHT Batch4


title: Stategra_Ikaros-ERt2 cells 24h 4-OHT Batch1

description: 24h after Taxomifen induction in Ikaros/ERt2 cells


title: Stategra_Ikaros-ERt2 cells 24h 4-OHT Batch4


title: Stategra_Ikaros-ERt2 cells 12h 4-OHT Batch1

description: 12h after Taxomifen induction in Ikaros/ERt2 cells


title: Stategra_Ikaros-ERt2 cells 18h 4-OHT Batch1


title: Stategra_Ikaros-ERt2 cells 24h 4-OHT Batch3


title: Stategra_Ikaros-ERt2 cells 2h 4-OHT Batch3

description: 2h after Taxomifen induction in Ikaros/ERt2 cells


title: Stategra_Ikaros-ERt2 cells 12h 4-OHT Batch3


title: Stategra_Ikaros-ERt2 cells 6h 4-OHT Batch1


title: Stategra_Ikaros-ERt2 cells 2h 4-OHT Batch4


title: Stategra_Ikaros-ERt2 cells 0h 4-OHT Batch4

description: 0h after Taxomifen induction in Ikaros/ERt2 cells


title: Stategra_Ikaros-ERt2 cells 0h 4-OHT Batch2


title: Stategra_Ikaros-ERt2 cells 0h 4-OHT Batch1


title: Stategra_Ikaros-ERt2 cells 2h 4-OHT Batch1


title: Stategra_Control cells 24h Batch4

description: 24h after Taxomifen induction in Control cells

value: control


title: 10203X4

city: Salt Lake City

first: Christopher

last: Gregg

state: Utah

address: 323 Wintrobe Bldg 530, 20 North 1900 East

department: Neurobiology and Anatomy

institute: University of Utah

data_processing:
HiSeq 101 Cycle Paired-End Sequencing v4  Sequencing libraries (25 pM) were chemically denatured are applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq instrument, a 101 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).
Make unique transcriptome index for each daughter based on parent genotyping
Novoalign to daughter specific transriptome index
Useq TranscriptomeParser
Count reads with custom pysam based python script
Genome_build: macFas5
Supplementary_files_format_and_content: bam files were generated with novoalign and USeq TranscriptomeParser

organism: Macaca fascicularis

source_name: Dorsal Raphe Nucleus

growth_protocol: Wake Forest

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold
HiSeq 101 Cycle Paired-End Sequencing v4  Sequencing libraries (25 pM) were chemically denatured are applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq instrument, a 101 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reage
Sequencing libraries (25 pM) were chemically denatured are applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq instrument, a 101 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reage

value: Dorsal Raphe Nucleus

value: female

tag: mother id

tag: father id


title: 10480X2

tag: tissue


title: 10480X4


title: 10480X1


title: 10203X3


title: Stategra_Control cells 24h Batch1

tag: cell type


title: 10203X2


title: 10203X5


title: Stategra_Control cells 18h R1 Batch4

description: 18h after Taxomifen induction in Control cells


title: Stategra_Control cells 24h Batch3


title: 10203X1


title: Mother 8076

data_processing:
Library strategy: wgs
HiSeq 101 Cycle Paired-End Sequencing v4  Sequencing libraries (25 pM) were chemically denatured are applied to an Illumina HiSeq v4 paired end flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).  Following transfer of the flowcell to an Illumina HiSeq instrument, a 101 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).
Realign with GATK
Genotyped with GATK
Genome_build: macFas5
Supplementary_files_format_and_content: bam files were generated with novoalign and GATK

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq DNA PCR-Free Sample Prep (550 bp mean insert size)
DNA samples (2 ug) were sheared using a Covaris S2 Focused-ultrasonicator and libraries were prepared using the Illumina TruSeq DNA PCR-Free Sample Preparation Kit (cat# FC-121-3001 and FC-121-3002) with an average insert size of 550 bp.  Adapter-ligated molecules were analyzed by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824) and the molarity of individual libraries were normalized to 10 nM in preparation for Illumina sequence analysis.


title: Father 7556

value: male


title: Mother 7870


title: Stategra_Ikaros-ERt2 cells 12h 4-OHT Batch4


title: Mother 7872


title: Father 7560


title: Stategra_Control cells 18h R1 Batch1


title: Stategra_Control cells 12h R1 Batch4

description: 12h after Taxomifen induction in Control cells


title: NA19160 CM

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
The reads were mapped to hg19 using subread align] allowing for two mismatches
The alignment were filtered to remove mapped reads with quality less than 10 using samtools -q 10
We used the WASP alignment strategy to filter read that may be mismapped owing to the human genome reference allele bias (pmid26366987)
We also used WASP to remove cofounding effect from sample-specific GC biases and read count differences to allow comparison between samples.
Genome_build: hg19
Supplementary_files_format_and_content: Each column represnets and individual and each row represnets a gene. This file contains raw counts.

source_name: Induced pluripotent stem cell derived cardiomyocyte

growth_protocol: iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media.

extract_protocol:
RNA was extracted from from frozen cell pellets using the Zymo ZR-Duet DNA/RNA MiniPrep kit, per manufacture specifications.
Libraries were prepared using Illumina TruSeq library preperation per manufacutre specifications.

treatment_protocol: When cells were 70-100% confluent E8 media was replaced with ‘heart media’ (RPMI (14-040-CM, Thermo Fisher Scientific) supplemented with B-27 Supplement, minus insulin (A1895601, Thermo Fisher Scientific), 2mM GlutaMAX (35050-061, Thermo Fisher Scientific), and 100mg/mL Pennicllin/Streptomycin (30002Cl, Corning)) with the addition of 1:100 Matrigel (35427, Corn- ing) and 12uM of the GSK-3 inhibitor CHIR99021 trihydrochloride (4953, Tocris,) which activates WNT signaling (day 0)4. ‘Heart media’ was replaced 24 hours later (day 1). After an additional 48 hours media was replaced with new ‘heart media’ containing 2uM of the WNT inhibitor Wnt-C59 (5148, Tocris)4 (day 3). Cells were cultured in the media with Wnt-C59 for 48 hours. Regular ‘heart media’ changes were performed from day 5 to day 14. Clusters of spontaneously beating cells were typically visible between 7 and 12 days. On day 14 heart media was replaced with ‘lactate media’ (RPMI without glucose (11879, Gibco), 75 mg/ml human recombinant albumin (A0237, Sigma), 213 ug/ml L-ascorbic acid 2-phosphate (sc228390, Santa Cruz Biotechnology), 5mM Sodium L-lactate (L7022, Sigma), and 100mg/mL Pennicillin/Streptomycin) 24930130. The ‘lactate media’ purifies cardiomyocytes using metabolic selection whereby the majority of non-cardiomyocyte cells cannot use lactate as their primary source of energy, leaving a culture significantly enriched for cardiomyocytes6. Every other day ‘lactate media’ changes were performed until day 20. By day 20 the cells had generally formed into large three-dimensional sheets of beating cells. To make a more uniform sheet of cells we dissociated the cultures using 0.05% trypsin (25-053-Cl, Thermo Fisher Scientific) and replated cells into six-well plates at a density of 1.5 million cells per well. Cells were then cultured in ‘galactose media’ (DMEM without glucose (A14430-01, Thermo Fisher Scientific), 1.7 mg/mL galactose (G5388, Sigma), 1mM Na pyruvate (11360-070, Gibco), 5mM HEPES (SH3023701, Thermo Fisher Scien- tific), 2mM GlutaMax, 10%FBS (4360-500, J R Scientific), and 100mg/mL Pennicillin/Streptomycin) to help to mature cardiomyocytes by forcing them to undergo aerobic metabolism7,8. Regular media changes with ‘galactose media’ continued for the duration of the experiment. After an additional five days (day 25) cells were moved to an incubator at physiological oxygen levels (10%). Two days later (day 27) cells were subjected to electrical stimulation at 6.6 V/cm, 2 ms and 1 Hz (C-PaceEP Cell Culture EP Stimulator, IonOptix) for four days to help further mature the cells.


title: Stategra_Control cells 12h R1 Batch1


title: Father 7893


title: NA19108 CM

value: Induced pluripotent stem cell derived cardiomyocyte


title: Stategra_Control cells 12h R1 Batch3


title: Stategra_Control cells 18h R1 Batch3


title: Stategra_Control cells 6h R1 Batch4

description: 6h after Taxomifen induction in Control cells


title: Father 7827


title: NA19116 CM


title: NA18912 CM


title: NA18870 CM


title: NA19128 CM


title: NA19101 CM


title: Mother 8091


title: NA19098 CM


title: Mother 7231


title: Stategra_Control cells 2h R1 Batch3

description: 2h after Taxomifen induction in Control cells


title: Stategra_Control cells 2h R1 Batch4


title: Stategra_Control cells 2h R1 Batch1


title: Mother 8077


title: Stategra_Control cells 6h R1 Batch1


title: Stategra_Control cells 6h R1 Batch3


title: NA18520 CM


title: NA18852 CM


title: Mother 7404


title: 10480X3


title: NA18511 CM


title: NA18505 CM


title: Father 7594


title: Mother 7883


title: Stategra_Control cells 0h Batch1

description: 0h after Taxomifen induction in Control cells


title: Stategra_Control cells 0h Batch2


title: MDAMB231_BETi211_2

city: Memphis

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

data_processing:
RTA version 1.18.66.3 (HCS  version 2.2.68 ) was used for basecalling
bcl2fastq version 2.17.1.14 was used for generation fastq files
Read alignment was done using Bowtie v0.12.8, with parameters “-k 100”.
Gene abundance estimation was done using rSeq v0.2.2, with parameters “-expression_analysis”.
Transcriptome annotation: GENCODE v24 basic.
Genome_build: NCBI GRCh38.p5
Supplementary_files_format_and_content: RPKM values of each cell line treated with DMSO, Thalidomide, BETi211and BETd246

growth_protocol: Cells were grown in RPMI 1640 medium containing 10% fetal bovine serum, 50 units/mL penicillin and 100 µg/mL streptomycin and incubated at 37°C with 5% CO2 .

extract_protocol:
Cells were collected at the end of treatment and total RNA was purified using RNeasy Mini Kit from Qiagen. RNA was assessed for quality using the TapeStation (Agilent). Samples with RINs (RNA Integrity Numbers) of 8 or greater were ribosomal RNA depleted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat)  (Illumina).
RNA libraries were prepared from the rRNA-depleted total RNA using TruSeq RNA Library Prep v2 kit (Illumina) following Illumina's standard protocol. Where the entire fraction of 0.1-3ug of rRNA depleted total RNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA were then adenylated and adapters were ligated.  One of the adapters that was ligated had a 6 nucleotide barcode that was unique for each sample which allowed us to sequence more than one sample in each lane of a HiSeq flow cell (Illumina). The products are purified and enriched by PCR to create the final cDNA library. Final libraries were checked for quality and quantity by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit (Kapa Biosystems) for Illumina Sequencing platforms.

treatment_protocol: Cells were seeded in 6-well culture plates at a density of around 50% and grown overnight. Cells at 80-90% confluence were treated with DMSO (0.05% v/v), thalidomide (1000 nmol/L), BETi-211 (1000 nmol/L) or BETd-246 (100 nmol/L) for 3 hours before collected for RNA isolation.

tag: cell source

value: mammary gland/breast

tag: genetic background

value: ERα-negative, PR-negative and absence of HER2 overexpression

tag: molecular subtype

value: basal

tag: treated with

value: BETi-211 (1000 nmol/L) for 3hr


title: MDAMB231_BETd246_2

value: BETd-246 (100 nmol/L) for 3 hr


title: MDAMB231_BETd246_1


title: Father 7756

tag: Sex


title: STATegra Ikaros cells 24h Batch4

data_processing:
The FASTQ sequence reads were generated using the Illumina Casava pipeline.
FASTQC quality control tool version 0.10.0
The paired end 100bp sequences reads were mapped using the Bismark package v0.10.1
Quality control for alignments using HTseq QA tool
Calling using the Bismark package v0.10.1
Calling using the MethylKit  R package
BedGraph and *.cov files were further considered and analyzed with the BiSeq package
Coverage was inspected before proceeding to smooth the methylation levels (between 0 and 1) per CpG site to avoid potential bias during the smoothing step
Methylation levels were smoothed  as described in Hebestreit, K. et al. Bioinformatics 29, 1647–1653 (2013).
M-values were obtained as M = log2(B/(1-B)), where B is the constrained methylation level
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing Methylation levels for each Sample (matrix)  formatted as chr_start_end (i.e. Chromosome number, Start position and End position).

extract_protocol:
B3 cells containing inducible Ikaros were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.  Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.
gDNA concentration was measured with Quant-it Picogreen dsDNA assay and 1 μg input was used in the Msp I digestion.  Following overnight incubation at 37°C, digestion reactions were terminated by adding 0.5 M EDTA and purified on a GeneJET PCR purification column. Libraries were prepped using the NEBNext Ultra DNA library preparation kit for Illumina and methylated adapters (Index primers Set 1). Subsequently, adapter ligated fragments were BS converted using the EZ DNA Methylation Gold kit (Zymo Research). 14 cycles of PCR were performed and the products were purified using AMPure XP beads. Quality of the final libraries was checked on a High sensitivity DNA chip (Agilent) and concentration was measured with qPCR. Sequencing was done on an Illumina HiSeq2500 PE 2x100bp.

treatment_protocol: Cells containing inducible Ikaros were generated by transducing mouse pre-B cell line B3 with mouse stem cell virus (MSCV) retroviral vectors encoding a fusion protein of  haemagglutinin-tagged wild type Ikaros (HA-Ikaros) and the estrogen receptor hormone-binding domain (ERt2), followed by an internal ribosomal entry site (IRES) and GFP. B3 cells containing inducible Ikaros (HA-Ikaros-ERt2-IRES-GFP)  were plated at a density of 0.5 million cells/ml in IMDM  medium containing 10% FCS and 1% penicillin-streptomycin. 0.5uM 4 hydroxy-tamoxifen was added to the cells 2h before collection.


title: NA18855 CM


title: STATegra Ikaros cells 24h Batch3


title: MDAMB231_BETi211_1


title: 10203X6


title: STATegra Ikaros cells 24h Batch1


title: MDAMB231_Thalidomide_2

value: Thalidomide (1000 nmol/L) for 3hr


title: STATegra Ikaros cells 18h Batch4


title: STATegra Ikaros cells 18h Batch3


title: MDAMB231_DMSO_2

value: DMSO for 3hr


title: Stategra_Control cells 0h Batch4


title: STATegra Ikaros cells 12h Batch4


title: MDAMB231_DMSO_1


title: STATegra Ikaros cells 18h Batch1


title: STATegra Ikaros cells 12h Batch3


title: MDAMB157_BETd246_1


title: MDAMB157_BETd246_2


title: STATegra Ikaros cells 12h Batch1


title: STATegra Ikaros cells 6h Batch4


title: MDAMB157_BETi211_2


title: STATegra Ikaros cells 6h Batch3


title: MDAMB157_BETi211_1


title: MDAMB157_Thalidomide_1


title: MDAMB157_Thalidomide_2


title: STATegra Ikaros cells 6h Batch1


title: STATegra Ikaros cells 2h Batch4


title: MDAMB157_DMSO_2


title: STATegra Ikaros cells 2h Batch3


title: MDAMB157_DMSO_1


title: MDAMB231_Thalidomide_1


title: STATegra Ikaros cells 0h Batch4


title: STATegra Ikaros cells 2h Batch1


title: MDAMB468_BETd246_2


title: unbiased_adult_dr_23

data_processing:
Make Cast/B6 Transcriptome Index with IUPAC codes to indicate SNPs that will be heterozygous in the offspring
Align to hybrid transcriptome index with Novoalign
Useq TranscriptomeParser
Count non-redundant maternal and paternal reads reads with custom pysam based python script.
Genome_build: mm9
Supplementary_files_format_and_content: bam files were generated with novoalign and TranscriptomeParser

extract_protocol:
Qiagen RNAeasy Kit
Illumina TruSeq RNASeq
50bp single end reads

tag: age

value: Adult


title: MDAMB468_BETd246_1


title: MDAMB468_BETi211_2


title: STATegra Ikaros cells 0h Batch2

tag: treatment


title: unbiased_adult_dr_19


title: MDAMB468_BETi211_1


title: STATegra Ikaros cells 0h Batch1

tag: transfection


title: STATegra Control cells 24h Batch3

tag: time


title: MDAMB468_Thalidomide_1


title: MDAMB468_Thalidomide_2


title: unbiased_adult_dr_16


title: STATegra Control cells 24h Batch4

tag: #replicate


title: unbiased_adult_dr_15


title: MDAMB468_DMSO_2


title: STATegra Control cells 24h Batch1

tag: #batch


title: unbiased_adult_dr_12


title: STATegra Control cells 18h Batch3

tag: dose


title: MDAMB468_DMSO_1

tag: cell line


title: Mother 8087


title: unbiased_adult_dr_13


title: unbiased_adult_dr_22


title: SF8628 DMSO IgG

description:
treatment: DMSO
ChIP: IgG

data_processing:
Reads were mapped to the Human (UCSC hg38) genome assembly using bowtie (version 1.1.2) with default parameters except concerning multi-mapping reads which were discarded using option "-m1". For each library, mapped reads were de-duplicated by keeping a single read in each group of reads mapping to the exact same genomic sequence.
To generate ChIP-seq profiles, reads were extended to a total length of 180 bp starting from the 5' end, representing the average DNA fragment length in our libraries, and genomic coverage was computed at base pair resolution. For each library, coverage values were scaled according to the estimated Background Read Density (BRD, see the methods description in our study).
Regions locally enriched for H3K27me3 were established with the SPP peak calling package using the broad enrichment procedure and IgG samples as control. We used default parameters except a z-threshold value of 6.85 and background weights corresponding to our estimated BRD scaling for the normalization between ChIP and IgG libraries.
Genome_build: hg38
Supplementary_files_format_and_content: BED files with SPP peaks, bigWig files with normalized ChIP-seq profiles

source_name: primary DIPG tumor cell line

growth_protocol: Three human DIPG cell lines (DIPG007, DIPG012 and SF7761) were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors). Another human DIPG cell line (SF8628) was cultured in DMEM with 10% FBS.

treatment_protocol: The cells were treated with DMSO for 12 days.

value: primary DIPG tumor cell line

tag: tumor sample

tag: genotype


title: unbiased_adult_dr_20

tag: tissue


title: unbiased_adult_dr_10


title: STATegra Control cells 18h Batch1

tag: cell type


title: unbiased_adult_dr_9


title: sir2Δhst1Δ-KO1 rep1

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

description: Sir2/Hst1 double knockout replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Saccharomyces cerevisiae whole genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: Saccharomyces cerevisiae
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: Overnight cultures grown in YPD were diluted to an OD of 0.3 in YPD. The cultures were incubated at 30C with shaking until an OD of 1

extract_protocol: 1 Completely resuspend cell pellet in 500 µl AE/SDS (10 volumes AE 1 volume 10% SDS).  Add 500 µl phenol equilibrated with citrate buffer (pH 4.7).  Vortex well.  2  Incubate sample 4 minutes at 65º.  3  Chill sample in dry ice until frozen solid, about ten minutes.  4  Spin in microcentrifuge for 10 minutes, or until fully thawed with separate phases.  5  Transfer aqueous phase (top layer) to fresh microcentrifuge tube containing 500 µl phenol/CHCl3.  Rock 5 minutes on rotator. Spin in microcentrifuge 5 min at maximum speed.   6  Transfer aqueous phase (top layer) to fresh microcentrifuge tube containing 50 µl 3M NaOAc and 950 µl 100% ethanol.  Mix by inverting.  7 Spin down RNA in microcentrifuge for 8 minutes at 4º.    8 Remove supernatant.  Gently add 100 µl 100% ethanol to pellet.  Spin 2 minutes.  9. Remove supernatant.  Resuspend pellet in 20 µl DEPC H20 for RT-PCR   RNA was then DNAse treated with  Promega DNAse (thermo scientific). The reaction was stopped using a phenol/chloroform extraction and the resulting RNA was run through a Qiagen RNA column.

treatment_protocol: 10 OD of cells were harvested by centrifugation and washed in AE buffer (50mM NaOAc pH 5.3 and 10mM EDTA).

tag: genotype/variation

tag: growth phase

value: exponentially growing yeast

value: MAT@  can1-100   his3-11   hst1D::KanMX   leu2-3,112  lys2D  sir2D::TRP1   trp1-1   ura3-1 hmrD::ura3


title: STATegra Control cells 12h Batch4

value: pre-B lymphocyte


title: SF7761 DMSO IgG

description:
treatment: DMSO
ChIP: IgG


title: WT_rep2

description: Wildtype replicate 2

value: Wild-type

value: ^MAT@   can1-100   his3-11   leu2-3,112   lys2D   trp1-1   ura3-1   ^GAL   hmr::ura3


title: unbiased_adult_dr_8

value: Dorsal Raphe Nucleus

value: female


title: sir2Δhst1Δ-KO1 rep2

description: Sir2/Hst1 double knockout replicate 2


title: SF8628 DMSO me3

description:
treatment: DMSO
ChIP: H3K27me3 (Cell Signaling; catalog # C36B11)


title: unbiased_adult_dr_17


title: STATegra Control cells 12h Batch3

value: control


title: WT_rep1

description: Wildtype replicate 1


title: SF7761 DMSO me3


title: unbiased_adult_dr_5


title: STATegra Control cells 6h Batch4


title: STATegra Control cells 18h Batch4


title: DIPG012 DMSO IgG

description:
treatment: DMSO
ChIP: IgG


title: unbiased_adult_dr_6


title: DIPG012 DMSO me3


title: unbiased_adult_dr_4


title: DIPG007 DMSO me3


title: unbiased_adult_dr_3


title: DIPG007 DMSO IgG

description:
treatment: DMSO
ChIP: IgG


title: STATegra Control cells 6h Batch3


title: unbiased_adult_dr_2


title: STATegra Control cells 6h Batch1


title: STATegra Control cells 2h Batch4


title: unbiased_adult_dr_1


title: unbiased_p15dr_14


title: Y-tun_slow_rep3

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

data_processing:
Demultiplex with bcl2fastq v.2 software (Illumina )
[Gene Prediction] Map to assembled genome with tophat v2.1.1, and the BAM files were used in BRAKER v1.9 for gene prediction.
[Gene expression] Map RNA-Seq to predicted transcriptome with bwa, and differentially gene expression analysis with DESeq2.
[Gene expression] Quantify TPM with Kallisto v0.42.4
Genome_build: nHd.3.0 for H. dujardini, Hashimoto et al. Nat. Com. 2016 for R. varieornatus.
Supplementary_files_format_and_content: A tabular file of the TPM expression of each gene of each condition/replicate.

organism: Ramazzottius varieornatus

source_name: Whole body

growth_protocol: The tardigrade Hypsibius dujardini Z151 was purchased from Sciento (Manchester, UK). H. dujardini Z151 and Ramazzottius varieornatus strain YOKOZUNA-1 were cultured as previously described. Briefly, tardigrades were fed Chlorella vulgaris (Chlorella Industry) on 2% Bacto Agar (Difco) plates prepared with Volvic water, incubated at 18 °C for H. dujardini and 22 °C for R. varieornatus under constant dark conditions. Culture plates were renewed every 7~8 days.

extract_protocol:
[1~30 Individuals]Specimens were thoroughly washed with Milli-Q water on a sterile nylon mesh (Millipore), immediately lysed in TRIzol reagent (Life Technologies) using three cycles of immersion in liquid nitrogen followed by 37°C incubation. Total RNA was extracted using the Direct-zol RNA kit (Zymo Research) following the manufacturer’s instructions, and RNA quality was checked using the High Sensitivity RNA ScreenTape on a TapeStation (Agilent Technologies). [10K individuals] RNA extraction with TRIzol reagent (Life Technologies) followed by RNeasy Plus Mini Kit (Qiagen) purification.
[30 individuals] mRNA was amplified using the SMARTer Ultra Low Input RNA Kit for Sequencing v.4 (Clontech), and Illumina libraries were prepared using the KAPA HyperPlus Kit (KAPA Biosystems). Purified libraries were quantified using a Qubit Fluorometer (Life Technologies), and the size distribution was checked using the TapeStation D1000 ScreenTape (Agilent Technologies). Libraries size selected above 200 bp by manually excision from agarose and purification with a NucleoSpin Gel and PCR Clean-up kit (Clontech) [10K individuals] Library preparation and sequencing was conducted at Beijing Genomics Institute.

treatment_protocol: Anhydrobiotic samples were prepared by placing adult samples in a chamber maintained at 85% relative humidity (RH) for 48 hr for H. dujardini, and 30% RH for 24 hr and additional 24 hr at 0% RH for slow-dried R. varieornatus, and 0% RH for 30 minutes on a moist paper towel, and additional 48 hours without for fast-dried R. varieornatus. Successful anhydrobiosis was assumed when >90% of the samples prepared in the same chamber recovered after rehydration.

tag: strain

value: adult

tag: #individuals


title: Y-tun_slow_rep1


title: STATegra Control cells 2h Batch3


title: STATegra Control cells 12h Batch1


title: unbiased_p15dr_13

tag: Sex


title: Y-tun_slow_rep2

tag: age


title: STATegra Control cells 2h Batch1

tag: treatment


title: STATegra Control cells 0h Batch4

tag: transfection


title: HG meso rep 1

city: Cincinnati

first: Aaron

middle: M

last: Zorn

state: OH

address: 3333 Burnet Ave

department: Develpomental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Quality check and trimming of raw reads was performed using FastQC and Trimmomatic, respectively at default parameters. Quality trimmed Reads were mapped to the X. laevis genome 9.1 and quantified using RSEM at default parameters.
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Matrix with genes and samples providing expression of genes in each sample in TPM(Transcripts per Million). File is in .xlsx format

organism: Xenopus laevis

extract_protocol:
Total RNA was extracted from two or three independent biological replicates using the Nucleo-spin RNA kit (Machery-Nagel).
Libraries were constructed with TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Small molecule inhibitors were dissolved in DMSO and embryos were cultured from stages NF12-20 with either DMSO vehicle in 0.1XMBS or 40 μM DMH1 (TOCRIS) or BIO (60 μM; TOCRIS). To activate the hsp:Dkk1GFP transgene, we gave a pulse of 30min in 37C followed by incubation at 13C.

tag: Stage

value: Hindgut endoderm explants

value: wild type


title: unbiased_p15dr_12


title: HG meso rep 2


title: HG endo rep 1


title: Y-active_slow_rep3


title: STATegra Control cells 0h Batch2

tag: time

tag: #replicate


title: FG meso rep 1

value: Foregut mesoderm explants


title: unbiased_p15dr_11


title: Y-active_slow_rep1


title: Y-active_slow_rep2


title: HG endo rep 2


title: Y-tun_fast_rep3


title: FG endo rep 2

value: Foregut endoderm explants


title: FG meso rep 2


title: unbiased_p15dr_9


title: Y-tun_fast_rep2


title: unbiased_p15dr_8


title: Y-tun_fast_rep1


title: HG HSdkk1 rep 2

value: Hindgut explants

value: Heatshock


title: unbiased_p15dr_7


title: Y-active_fast_rep3


title: HG HSdkk1 rep 1


title: unbiased_p15dr_6


title: Y-active_fast_rep2


title: unbiased_p15dr_5


title: Y-active_fast_rep1


title: HG noHS rep 2

value: no Heatshock


title: STATegra Control cells 0h Batch1

tag: #batch

tag: dose


title: Y_B1_rep3

value: Juvenile 1st day


title: unbiased_p15dr_10


title: HG noHS rep 1


title: FG HSdkk1 rep 2

value: Foregut explants


title: unbiased_p15dr_3


title: unbiased_p15dr_4


title: Y_B1_rep2


title: unbiased_p15dr_1


title: unbiased_p15dr_2


title: FG endo rep 1


title: unbiased_p5dr_14


title: FG HSdkk1 rep 1


title: FG noHS rep 2


title: Dorsal rep 3

source_name: Dorsal

value: Dorsal explant


title: Y_E5_rep3

value: Egg 5th day after laying


title: unbiased_p5dr_13


title: Dorsal rep 2


title: Y_E5_rep1


title: unbiased_p5dr_12


title: Y_E4_rep3

value: Egg 4th day after laying


title: Dorsal rep 1


title: unbiased_p5dr_11


title: HG BIO rep 2

value: BIO


title: Y_E4_rep2


title: Y_E4_rep1


title: HG BIO rep 3


title: Y_B1_rep1


title: unbiased_p5dr_9

value: Dorsal Raphe Nucleus


title: unbiased_p5dr_10

value: female


title: Y_E3_rep3

value: Egg 3rd day after laying


title: FG noHS rep 1


title: HG BIO rep 1


title: Y_E5_rep2


title: HG DMH1 rep 3


title: Y_E3_rep1


title: unbiased_p5dr_8


title: Y_E3_rep2


title: unbiased_p5dr_6


title: HG DMH1 rep 2


title: Y_E2_rep3

value: Egg 2nd day after laying


title: HG DMH1 rep 1


title: unbiased_p5dr_5


title: unbiased_p5dr_4


title: HG DMSO rep 3

value: DMSO


title: Y_E2_rep1


title: Y_E2_rep2


title: HG DMSO rep 1

value: wild type


title: HG DMSO rep 2


title: unbiased_p5dr_3


title: Y_E1_rep3

value: Egg 1st day after laying


title: unbiased_p5dr_2


title: unbiased_p5dr_1


title: Y_E1_rep1


title: unbiased_p5dr_7


title: FG BIO rep 3


title: Y_E1_rep2


title: FG BIO rep 2


title: Granulocyte MeCP2 ChIP-seq Replicate2

city: Camperdown

first: Dadi

last: Gao

address: RPA, Missenden Road

country: Australia

institute: Centenary Institute

description: Processed data file: Granulocyte_mecp2_fold.bed

data_processing:
bismark v0.9.0 was applied to map WGBS data with default settings
bowtie2 v2.1.0 was applied to map ChIP-seq data with default settings
MAC2 v2.0,10 was applied to call peaks
TopHat v2.2.2 was applied to map RNA-seq data with default settings
Genome_build: GRCm38.73; GRCh37.75
Supplementary_files_format_and_content: Processed bed files for both WGBS and ChIP-seq are provided. The 5th column indicates the percentage of DNA methylation of a CpG site covered by more than 5 reads for WGBS and indicates the fold change of a peak in ChIP against its background for ChIP-seq. respectively. The percentage of DNA methylation at a CpG site is calculated as: 100* number of reads supports cytosine / total number of reads covering the site

source_name: Granulocytes

extract_protocol:
Purelink Genomic DNA extraction kit
Illumina's Methyl C-seq WGBS and Chip-Seq protocols

value: Whole blood

value: Granulocytes

value: WT

value: MeCP2 antibody


title: FG BIO rep 1


title: Granulocyte MeCP2 ChIP-seq Replicate1


title: FG DMH1 rep 2


title: Granulocyte DNA Input Replicate1


title: FG DMH1 rep 3


title: Promyelocyte MeCP2 ChIP-seq Replicate2

description: Processed data file: Promyelocyte_cpg_count_cutoff_5_destrand.bed

source_name: Promyelocytes

value: Promyelocytes


title: dsxRNAi_F-BRN_S4

city: Bloomington

first: Cristina

last: Ledon-Rettig

state: IN

address: 915 E 3rd Street

department: Biology

institute: Indiana University

data_processing:
Trimming: Resulting read sequences were cleaned using Trimmomatic version 0.32 to remove adapter sequences and perform quality trimming using the following parameters, “2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18”.
Reverse Complement: The trimmed reads where then reversed complemented using FASTX-Toolkit version 0.0.13.2
Mapping: Reads were mapped against the Onthophagus taurus genome v0.5.3 gene models using TopHat2 version 2.1.0  with the parameters “–b2-very-sensitive–read-edit-dist”
Read counting: Read counting was done for each gene using htseq-count from the HTSeq package version 0.6.1p1
Normalization: A table containing counts normalized per kilobase of feature length per million mapped fragments (FPKM values) was generated using the R package DESeq2
Genome_build: 10.15482/USDA.ADC/1255153
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Onthophagus taurus

source_name: Brain

growth_protocol: Onthophagus taurus beetles were field collected near Bloomington, IN and Chapel Hill, NC, kept in a sand/soil mixture at a 16:8 h light:dark cycle at 25 °C, and fed homogenized cow manure twice a week. Animals used for experiments were generated by breeding 5 females and 3 males in a moist sand/soil mixture container with ad libitum food. After 8 days, brood balls produced by females were collected and larvae were transferred to 12-well plates.

extract_protocol:
After dissection, all tissue samples were immediately placed in ice-cold Trizol and stored at -80ºC. After thawing to 4ºC, tissues in Trizol were homogenized with disposable polypropylene RNase-free pellet pestles, and total RNA was extracted using a standard phenol-chloroform protocol followed by RNeasy Mini spin column purification including on-column DNAse I digestion. Total RNA was quality checked using RNA ScreenTape TapeStation System and quantified with a Quant-iT RiboGreen Assay Kit.
A total of 96 (2 treatments x 2 sexes x 4 tissues x 6 biological replicates) RNA Stranded RNA sequencing libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to manufacturer's instructions. Libraries were quantified using a Quant-iT DNA Assay Kit (Thermo Fisher), pooled in equal molar amounts, and sequenced as single-end reads using a 75 cycles, high output kit on the NextSeq500 platform (Illumina).

treatment_protocol: a pSC-A vector containing the OtdsxC construct was used as template in PCR reactions using M13 forward and reverse primers. The resulting PCR product was used as a template for in vitro transcription of forward and reverse RNA strands using MEGAscript T7 and T3 Kits (Life Technologies). After DNase I treatment, ssRNA was precipitated by lithium chloride, incubated at -20ºC for 1h, spun at 4ºC for 20 min, washed with 80% ethanol, and resuspended in water. After quantification, forward and reverse strands were mixed at a 1:1 ratio by weight, and annealed by heating to 80°C and then cooling slowly over 5h to 35ºC. The concentration of the annealed RNA was measured, confirmed by gel electrophoresis, and stored at −80°C until injection. Injections into Onthophagus larvae were carried out with doses of 0.5 μg of dsRNA diluted in injection buffer (5 mM KCl, 1 mM KPO4 pH 6.9) to a total of 3 μL and injected into larvae during the first 5 days of the final instar. Sham control injections were made exactly as described above, except that larvae were injected with 1 μg of control dsRNA derived from a 167-bp PCR product derived from a pBluescript SK vector.

value: dsxRNAi

value: supraesophageal ganglion (brain)


title: dsxRNAi_F-BRN_S6


title: dsxRNAi_F-BRN_S5


title: dsxRNAi_F-BRN_S3


title: Promyelocyte MeCP2 ChIP-seq Replicate1


title: FG DMSO rep 2

value: Foregut explants


title: Promyelocyte DNA iInput Replicate2


title: FG DMSO rep 1


title: Granulocyte WGBS

description: Processed data file: Granulocyte_cpg_count_cutoff_5_destrand.bed

value: Bisulphite treated


title: ctrlRNAi_M-GEN_S96

source_name: Genitalia

value: control

value: male

value: genital epithelium


title: Promyelocyte WGBS


title: ctrlRNAi_M-GEN_S95


title: p300_HG_BIO

description: processed data file: p300_FGHG_IDR_peaks.bed

data_processing:
Quality check and quality trimming of raw reads was performed using FastQC and Trimmomatic respectively at default parameters. Quality trimmed reads were mapped to the X. laevis genome assembly 9.1 using Bowtie2 at default parameters. Duplicate mapped reads and multi-mapped were removed using picard and samtools respectively. Uniquely mapped reads were used for peak calling. MACS2 was used for peak calling and differential peak analysis at default parameters. IDR ananlysis was performed using MACS2 peaks.
Genome_build: Xenopus laevis genome v9.1
Supplementary_files_format_and_content: Peak Files in BED format; direct output of IDR pipeline that is .regionPeak Format [UCSC Compatible]

source_name: Hindgut explants

extract_protocol:
ChIPed DNA fragments were purified with phenol:chloroform:isoamylalcohol and precipitated in ethanol.
Libraries were constructed with ThruPLEX® DNA-seq kit.

value: Wild Type

value: Hindgut explants

tag: treated with

value: BIO

tag: chip antibody


title: Input_for_p300_HG_BIO

tag: tissue


title: p300_HG_DMSO

value: DMSO


title: Granulocyte DNA Input Replicate2

tag: cell type

tag: genotype


title: FG DMH1 rep 1

tag: genotype/variation

value: wild type


title: dsxRNAi_F-BRN_S2

value: female


title: Input_for_p300_HG_DMSO


title: p300_FG_BIO

source_name: Foregut explants


title: FG DMSO rep 3


title: dsxRNAi_F-BRN_S1


title: Promyelocyte DNA Input Replicate1

value: Whole blood


title: Input_for_p300_FG_BIO


title: STATegra Ikaros cells 18h Batch3

description: 18h after Taxomifen induction in Ikaros/ERt2 cells

data_processing:
miRNA-seq data were trimmed and aligned to the mm10 reference (source miRbase) using Novoalign software
Counts were obtained using multiBamCov (Bedtools suite)
Prior to normalize the data, low count miRNAS were filtered out with CPM (counts per million) method in NOISeq R package
TMM method was used to normalize the data
ComBat was used to reduce batch effect
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing smallRNA quantification values for each Sample (matrix).

extract_protocol:
B3 cells containing inducible Ikaros were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.  Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.
Small-RNA Seq libraries were generated using TruSeq Small RNA Sample Preparation Kit following the manufacter’s instructions. In brief, the kit takes advantage of the hallmark 3’ hydroxyl group microRNAs have that result from the enzymatic cleavage by Dicer (and other RNA processing enzymes) and an adenylated 3’ adapter that specifically ligates to this end. By targeting the 3’ end of small RNAs, unwanted ligation to other transcripts is reduced allowing for specific sequencing of microRNAs and other 3’OH transcript species. The protocol involves: isolation of total RNA; ligation of the 3’ adapter; addition of the hairpin oligo to reduce adapter dimers; ligation of the 5’ adapter; annealing of the primer to the 3’ adapter and reverse transcription and PCR amplification and barcode addition.

value: inducible Ikaros

tag: cell line

value: pre-B lymphocyte


title: STATegra Ikaros cells 24h Batch1


title: STATegra Ikaros cells 24h Batch2


title: STATegra Ikaros cells 24h Batch3


title: ctrlRNAi_F-GEN_S90


title: p300_FG_DMSO


title: ctrlRNAi_M-GEN_S91


title: ctrlRNAi_M-GEN_S93


title: ctrlRNAi_M-GEN_S92


title: ctrlRNAi_F-GEN_S89


title: STATegra Ikaros cells 18h Batch1


title: STATegra Ikaros cells 18h Batch2


title: ctrlRNAi_M-GEN_S94


title: Input_for_p300_FG_DMSO


title: ctrlRNAi_F-GEN_S88


title: bcat_HG_BIO

description: processed data file: bcat_FGHG_IDR_peaks.bed

value: b-catenin (Life technologies 712700)


title: STATegra Ikaros cells 18h Batch13

description:
corresponding processed data file header: Ik18h_rep6
18h after Taxomifen induction in Ikaros/ERt2 cells
R6

data_processing:
Data were aligned to the mm10 reference using Bowtie
Capture narrow and broad chromatin elements using HOMER
Sort and merge with Bedtools software
Quantitate read counts over regions using coverageBed options (Bedtools)
Region counts were normalized with both RPKM and TMM methods
Unknown sources of variation were removed by using ARSyN method (Batch correction)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing DHS regions for each Sample (matrix) formatted as chr_start_end (i.e. Chromosome number, Start position and End position).

extract_protocol:
B3 cells containing inducible Ikaros were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Time point samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.  Control vector-ERt2 B3 cells were plated at a density of 0.5 million cells/ml in IMDM medium supplemented with 10% FCS and 1% penicillin/streptomycin. Samples were collected by 5 min centrifugation at 1200 rpm. Cell pellets were washed 2 times in PBS, frozen in liquid nitrogen and storaged at -80.
DNase-seq libraries were generatedas previously described (Myers protocol: http://myers.hudsonalpha.org/documents/Myers%20Lab%20Sequencing%20Library%20Protocol%20061508.pdf). Libraries were sequenced as 43bp paired-end on the NextSeq 500 Illumina platform. DNase-seq libraries were sequenced to a minimum depth of ~20 million reads per each biological replicate.


title: ctrlRNAi_F-GEN_S87


title: STATegra Ikaros cells 18h Batch12

description:
corresponding processed data file header: Ik18h_rep5
18h after Taxomifen induction in Ikaros/ERt2 cells
R5


title: STATegra Ikaros cells 24h Batch11

description:
corresponding processed data file header: Ik24h_rep4
24h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: STATegra Ikaros cells 12h Batch3

description: 12h after Taxomifen induction in Ikaros/ERt2 cells


title: STATegra Ikaros cells 24h Batch13

description:
corresponding processed data file header: Ik24h_rep6
24h after Taxomifen induction in Ikaros/ERt2 cells
R6


title: Input_for_bcat_HG_BIO


title: STATegra Ikaros cells 18h Batch11

description:
corresponding processed data file header: Ik18h_rep4
18h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: ctrlRNAi_F-GEN_S86


title: bcat_HG_DMSO


title: STATegra Ikaros cells 24h Batch12

description:
corresponding processed data file header: Ik24h_rep5
24h after Taxomifen induction in Ikaros/ERt2 cells
R5


title: STATegra Ikaros cells 12h Batch13

description:
corresponding processed data file header: Ik12h_rep6
12h after Taxomifen induction in Ikaros/ERt2 cells
R6


title: Input_for_bcat_HG_DMSO


title: dsxRNAi_M-GEN_S84

value: dsxRNAi


title: STATegra Ikaros cells 6h Batch3

description: 6h after Taxomifen induction in Ikaros/ERt2 cells


title: ctrlRNAi_F-GEN_S85


title: STATegra Ikaros cells 12h Batch1


title: STATegra Ikaros cells 12h Batch12

description:
corresponding processed data file header: Ik12h_rep5
12h after Taxomifen induction in Ikaros/ERt2 cells
R5


title: bcat_FG_BIO


title: dsxRNAi_M-GEN_S83


title: STATegra Ikaros cells 12h Batch11

description:
corresponding processed data file header: Ik12h_rep4
12h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: STATegra Ikaros cells 6h Batch2


title: Input_for_bcat_FG_BIO


title: STATegra Ikaros cells 6h Batch13

description:
corresponding processed data file header: Ik6h_rep6
6h after Taxomifen induction in Ikaros/ERt2 cells
R6


title: bcat_FG_DMSO


title: STATegra Ikaros cells 6h Batch12

description:
corresponding processed data file header: Ik6h_rep5
6h after Taxomifen induction in Ikaros/ERt2 cells
R5


title: STATegra Ikaros cells 2h Batch3

description: 2h after Taxomifen induction in Ikaros/ERt2 cells


title: dsxRNAi_M-GEN_S81


title: dsxRNAi_M-GEN_S80


title: Input_for_bcat_FG_DMSO


title: dsxRNAi_M-GEN_S79


title: STATegra Ikaros cells 6h Batch11

description:
corresponding processed data file header: Ik6h_rep4
6h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: STATegra Ikaros cells 2h Batch2


title: dsxRNAi_F-GEN_S78


title: Input_for_Smad1_WE

description: processed data file: Smad1_WE_IDR_peaks.bed

source_name: Whole embryos

value: Whole embryos


title: STATegra Ikaros cells 2h Batch1


title: Smad1_WE

value: Smad (Invitrogen 38-5400)


title: STATegra Ikaros cells 0h Batch6

description: 0h after Taxomifen induction in Ikaros/ERt2 cells


title: dsxRNAi_M-GEN_S82


title: p300_WE

description: processed data file: p300_WE_peaks.bed


title: STATegra Ikaros cells 0h Batch5


title: STATegra Ikaros cells 6h Batch1


title: dsxRNAi_F-GEN_S77


title: dsxRNAi_F-GEN_S75


title: STATegra Ikaros cells 2h Batch11

description:
corresponding processed data file header: Ik2h_rep4
2h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: STATegra Control cells 24h Batch3

description: 24h after Taxomifen induction in Control cells


title: H_tun_10k_rep3

organism: Hypsibius dujardini

tag: strain

value: adult

tag: #individuals


title: STATegra Ikaros cells 2h Batch13

description:
corresponding processed data file header: Ik2h_rep6
2h after Taxomifen induction in Ikaros/ERt2 cells
R6


title: STATegra Ikaros cells 0h Batch13

description:
corresponding processed data file header: Ik0h_rep6
0h after Taxomifen induction in Ikaros/ERt2 cells
R6


title: dsxRNAi_F-GEN_S76

tag: Sex


title: STATegra Ikaros cells 2h Batch12

description:
corresponding processed data file header: Ik2h_rep5
2h after Taxomifen induction in Ikaros/ERt2 cells
R5

tag: treatment


title: Input_for_p300_WE

description: processed data file: p300_WE_peaks.bed


title: STATegra Ikaros cells 0h Batch4

tag: transfection


title: dsxRNAi_F-GEN_S74


title: STATegra Ikaros cells 0h Batch11

description:
corresponding processed data file header: Ik0h_rep4
0h after Taxomifen induction in Ikaros/ERt2 cells
rep4


title: STATegra Ikaros cells 0h Batch12

description:
corresponding processed data file header: Ik0h_rep5
0h after Taxomifen induction in Ikaros/ERt2 cells
R5


title: H_tun_10k_rep2

tag: age


title: H_tun_10k_rep1


title: dsxRNAi_F-GEN_S73


title: ctrlRNAi_M-CHE_S72

source_name: Head horns

value: control

value: cephalic horn epithelium (head horns)


title: STATegra Control cells 24h Batch12

description:
corresponding processed data file header: CT24h_rep5
24h after Taxomifen induction in Control cells
R5

tag: time


title: H_active_10k_rep3


title: ctrlRNAi_M-CHE_S71

value: male


title: ctrlRNAi_M-CHE_S70


title: STATegra Control cells 24h Batch1

tag: #replicate


title: H_active_10k_rep2


title: STATegra Control cells 18h Batch3

description: 18h after Taxomifen induction in Control cells

tag: #batch


title: STATegra Control cells 24h Batch11

description:
corresponding processed data file header: CT24h_rep4
24h after Taxomifen induction in Control cells
rep4

tag: dose


title: H_active_10k_rep1


title: STATegra Control cells 18h Batch1


title: STATegra Control cells 12h Batch3

description: 12h after Taxomifen induction in Control cells


title: ctrlRNAi_M-CHE_S69


title: STATegra Control cells 24h Batch13

description:
corresponding processed data file header: CT24h_rep6
24h after Taxomifen induction in Control cells
R6


title: STATegra Control cells 18h Batch12

description:
corresponding processed data file header: CT18h_rep5
18h after Taxomifen induction in Control cells
R5


title: ctrlRNAi_M-CHE_S68


title: STATegra Control cells 24h Batch2


title: STATegra Control cells 18h Batch11

description:
corresponding processed data file header: CT18h_rep4
18h after Taxomifen induction in Control cells
rep4


title: STATegra Control cells 6h Batch3

description: 6h after Taxomifen induction in Control cells


title: ctrlRNAi_M-CHE_S67


title: STATegra Control cells 12h Batch13

description:
corresponding processed data file header: CT12h_rep6
12h after Taxomifen induction in Control cells
R6


title: STATegra Control cells 18h Batch13

description:
corresponding processed data file header: CT18h_rep6
18h after Taxomifen induction in Control cells
R6


title: ctrlRNAi_F-CHE_S65


title: 45581-SET-4(DP268);EAK-7;AKT-1-10

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
QC: We checked the quality of the raw reads data for each sample using FastQC [1] (version 0.10.1) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content, etc.).  We trimmed reads based on quality scores using CutAdapt with default parameters.
Aligment: We used the software package Tuxedo Suite for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference transcriptome using TopHat (version 2.0.9) and Bowtie (version 2.1.0.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
QC: We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Normalization and Quantitation: We used Cufflinks/CuffDiff (version 2.1.1) for expression quantitation, normalization, and differential expression analysis, using WBcel235 as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund package.
Differential Expression: We used locally developed scripts to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ ± 1.5.
Genome_build: WBcel235
Supplementary_files_format_and_content: .txt table of normalized expression values for each gene for each sample

organism: Caenorhabditis elegans

source_name: whole organisim

growth_protocol: greater than 200 gravid adults laid eggs on plates for 6 hrs at 20C, after which eggs were transferred to 25C for 24 hrs. Larvae were then collected and processed for RNA

extract_protocol:
RNA was extracted using chloroform extraction from Trizol, after which RNA was further purified using the DirectZol RNA miniprep kit (Zymo Research)
mRNA was isolated from 100 ng total RNA by polyA selection, fragmented and reverse-transcribed into cDNA. Adapters were ligated to individual samples to allow multiplexing samples (8-9/lane).

treatment_protocol: larvae grown at 25C (dauer-inducing conditions)

tag: developmental stage

value: dpEA

value: whole organisim


title: 45582-EAK-7;AKT-1 DPY-21-10


title: ctrlRNAi_F-CHE_S66


title: 45580-SET-4(N4600);EAK-7;AKT-1-10

value: nEA


title: STATegra Control cells 12h Batch12

description:
corresponding processed data file header: CT12h_rep5
12h after Taxomifen induction in Control cells
R5


title: ctrlRNAi_F-CHE_S63


title: STATegra Control cells 6h Batch2


title: STATegra Control cells 12h Batch11

description:
corresponding processed data file header: CT12h_rep4
12h after Taxomifen induction in Control cells
rep4


title: 45583--EAK-7;AKT-1;DAF-12-6


title: 45579-EAK-7;AKT-1-10

value: EA


title: ctrlRNAi_F-CHE_S64


title: STATegra Control cells 12h Batch1


title: 45578-EAK-7;AKT-1;DAF-12-10


title: 45576-WT-10

value: WT


title: STATegra Control cells 6h Batch12

description:
corresponding processed data file header: CT6h_rep5
6h after Taxomifen induction in Control cells
R5


title: STATegra Control cells 12h Batch2


title: STATegra Control cells 6h Batch1


title: 45577-DAF-16;EAK-7;AKT-1-10


title: STATegra Control cells 2h Batch3

description: 2h after Taxomifen induction in Control cells


title: ctrlRNAi_F-CHE_S62

value: female


title: STATegra Control cells 2h Batch1


title: STATegra Control cells 6h Batch13

description:
corresponding processed data file header: CT6h_rep6
6h after Taxomifen induction in Control cells
R6


title: STATegra Control cells 2h Batch2


title: STATegra Control cells 2h Batch13

description:
corresponding processed data file header: CT2h_rep6
2h after Taxomifen induction in Control cells
R6


title: STATegra Control cells 2h Batch12

description:
corresponding processed data file header: CT2h_rep5
2h after Taxomifen induction in Control cells
R5


title: STATegra Control cells 0h Batch5

description: 0h after Taxomifen induction in Control cells


title: dsxRNAi_M-CHE_S60


title: STATegra Control cells 0h Batch4


title: dsxRNAi_M-CHE_S59


title: 45574-SET-4(DP268);EAK-7;AKT-1-6


title: dsxRNAi_M-CHE_S58


title: STATegra Control cells 0h Batch6


title: STATegra Control cells 2h Batch11

description:
corresponding processed data file header: CT2h_rep4
2h after Taxomifen induction in Control cells
rep4


title: 45573-EAK-7;AKT-1 DPY-21-9


title: STATegra Control cells 0h Batch13

description:
corresponding processed data file header: CT0h_rep6
0h after Taxomifen induction in Control cells
R6


title: 45572-SET-4(DP268);EAK-7;AKT-1-9


title: 45575-EAK-7;AKT-1 DPY-21-6


title: STATegra Control cells 6h Batch11

description:
corresponding processed data file header: CT6h_rep4
6h after Taxomifen induction in Control cells
rep4


title: 45571-SET-4(N4600);EAK-7;AKT-1-9


title: 45570-EAK-7;AKT-1-9


title: STATegra Control cells 18h Batch2

description: 18h after Taxomifen induction in Control cells


title: STATegra Control cells 0h Batch12

description:
corresponding processed data file header: CT0h_rep5
0h after Taxomifen induction in Control cells
R5


title: STATegra Control cells 0h Batch11

description:
corresponding processed data file header: CT0h_rep4
0h after Taxomifen induction in Control cells
rep4


title: dsxRNAi_M-CHE_S55


title: 45569--EAK-7;AKT-1;DAF-12-9


title: dsxRNAi_F-CHE_S54


title: dsxRNAi_M-CHE_S57


title: dsxRNAi_M-CHE_S56


title: 45568-DAF-16;EAK-7;AKT-1-9


title: dsxRNAi_F-CHE_S53


title: 45567-WT-9


title: primed_t0_2_2

city: Nashville

first: Ann

last: Tate

address: 465 21st Ave., MRBIII Room 4270

department: Biological Sciences

institute: Vanderbilt University

description: experiment (TS) 2

data_processing:
The program FASTQC was used to perform quality filtering
The Galaxy Fastx-Toolkit barcode_splitter_enhanced was used to split barcodes and sort reads by sample with one mismatch allowed
TopHat2 in Galaxy was used to map raw reads to the T. castaneum genome assembly using default parameters except with microexon search
The python program in Galaxy, Htseq-count, was used to assign and count mapped reads associated with gene features using the "union" function
Count data was analysed using DESeq2 in R
Genome_build: Tcas3 (Ensembl Metazoa 28)
Supplementary_files_format_and_content: htseq-count tabular files - raw gene counts; Please note that the first half of the identifier before the colon is the ensembl metazoa feature file version (e.g. TCOGS2), and the part after the colon (e.g. TC000001) is the metazoa ensembl gene stable id (http://metazoa.ensembl.org/biomart/martview/d209d108b0c374cad0147aa32cf0deab) for Tribolium castaneum. Ensembl metazoa has a new feature version up for T. castaneum (Tcas3). However, a command like sapply(strsplit(rownames(ddspnru),  split = "\\+"),"[",1)  can be used in R to split the gene stable id into a new column of the data frame before using it to query other feature  attributes through biomart.

organism: Tribolium castaneum

source_name: primed_0h post infection

extract_protocol:
larvae were flash frozen in liquid nitrogen and stored at -80C until RNA extractions, which was accomplished with the Rneasy blood and tissue mini kit (Qiagen)
mRNA was extracted from total RNA using oligo-dT beads, and libraries were processed according to the Illumina TruSeq v2 library prep kit directions. Individual barcodes were adapted onto each sample.

treatment_protocol: offspring of primed and uprimed mothers were infected with an LD50 dose of Bt and sacrificed along a time series over 12 hours

tag: priming treatment

value: primed

tag: time point (hr)

value: 0h post infection

tag: id w/in treatment_time pair

value: whole organism


title: primed_t0_1_2

description: experiment (TS) 2

tag: tissue


title: ctrlRNAi_F-CHE_S61


title: primed_t0_3_2

description: experiment (TS) 2


title: unprimed_t0_3_2

description: experiment (TS) 2

source_name: unprimed_0h post infection

value: unprimed


title: dsxRNAi_F-CHE_S51

value: dsxRNAi


title: 45566-SET-4(N4600);EAK-7;AKT-1-6

tag: genotype/variation


title: dsxRNAi_F-CHE_S52


title: 45564-EAK-7;AKT-1 DPY-21-8


title: 45565-EAK-7;AKT-1-6


title: dsxRNAi_F-CHE_S49


title: unprimed_t0_2_2

description: experiment (TS) 2


title: dsxRNAi_F-CHE_S50


title: 45563-SET-4(DP268);EAK-7;AKT-1-8


title: primed_t8_3_2

description: experiment (TS) 2

source_name: primed_8h post infection

value: 8h post infection


title: ctrlRNAi_M-THE_S47

source_name: Thoracic horn

value: thoracic horn epithelium


title: ctrlRNAi_M-THE_S48


title: 45562-SET-4(N4600);EAK-7;AKT-1-8


title: primed_t8_2_2

description: experiment (TS) 2


title: unprimed_t0_1_2

description: experiment (TS) 2


title: 45561-EAK-7;AKT-1-8


title: ctrlRNAi_M-THE_S46


title: 45559-DAF-16;EAK-7;AKT-1-8


title: H_active_30_rep2

value: adult


title: H_tun_30_rep1


title: ctrlRNAi_M-THE_S44

value: control


title: primed_t8_1_2

description: experiment (TS) 2


title: ctrlRNAi_M-THE_S45


title: primed_t6_4_2

description: experiment (TS) 2

source_name: primed_6h post infection

value: 6h post infection


title: 45558-WT-8


title: 45557-DAF-16;EAK-7;AKT-1-6


title: H_active_30_rep1


title: H_tun_30_rep3


title: H_B7_rep3

value: Juvenile 7th day


title: primed_t2_3_2

description: experiment (TS) 2

source_name: primed_2h post infection

value: 2h post infection


title: primed_t6_3_2

description: experiment (TS) 2


title: H_tun_30_rep2

source_name: Whole body


title: STATegra Ikaros cells 12h Batch2

description: 12h after Taxomifen induction in Ikaros/ERt2 cells

source_name: pre-B lymphocyte

value: inducible Ikaros

tag: cell line

tag: cell type

value: pre-B lymphocyte


title: primed_t6_1_2

description: experiment (TS) 2


title: 45560-EAK-7;AKT-1;DAF-12-8

value: whole organisim


title: primed_t2_2_2

description: experiment (TS) 2


title: primed_t2_1_2

description: experiment (TS) 2


title: H_B7_rep2

tag: strain

tag: #individuals


title: 45554-SET-4(DP268);EAK-7;AKT-1-7

value: dpEA


title: H_B7_rep1


title: ctrlRNAi_F-THE_S40

tag: treatment

tag: Sex

value: female


title: ctrlRNAi_F-THE_S42


title: ctrlRNAi_F-THE_S41


title: H_active_30_rep3

tag: age


title: ctrlRNAi_M-THE_S43

value: male


title: unprimed_t8_3_2

description: experiment (TS) 2

source_name: unprimed_8h post infection


title: ctrlRNAi_F-THE_S39


title: 45551-EAK-7;AKT-1;DAF-12-7


title: 45556-WT-6

value: WT


title: H_B5_rep3

value: Juvenile 5th day


title: 45553-SET-4(N4600);EAK-7;AKT-1-7

value: nEA


title: ctrlRNAi_F-THE_S37


title: unprimed_t8_2_2

description: experiment (TS) 2

value: unprimed

value: whole organism


title: unprimed_t6_4_2

description: experiment (TS) 2

source_name: unprimed_6h post infection


title: H_B6_rep2

value: Juvenile 6th day


title: 45555-EAK-7;AKT-1 DPY-21-7


title: H_B6_rep1


title: 45550-DAF-16;EAK-7;AKT-1-7


title: ctrlRNAi_F-THE_S38

value: thoracic horn epithelium


title: H_B5_rep2


title: unprimed_t6_2_2

description: experiment (TS) 2


title: 45552-EAK-7;AKT-1-7

value: EA


title: dsxRNAi_M-THE_S36

value: dsxRNAi


title: dsxRNAi_M-THE_S35


title: H_B5_rep1


title: H_B6_rep3


title: dsxRNAi_M-THE_S33


title: dsxRNAi_M-THE_S34


title: H_B4_rep2

value: Juvenile 4th day


title: unprimed_t6_1_2

description: experiment (TS) 2

value: 6h post infection


title: unprimed_t8_1_2

description: experiment (TS) 2

value: 8h post infection


title: H_B4_rep3


title: unprimed_t2_3_2

description: experiment (TS) 2

source_name: unprimed_2h post infection

value: 2h post infection


title: 45549-WT-7

value: whole organisim


title: 6Month-2

city: Beijing

first: Fangming

last: Kan

address: Dongdansantiao

institute: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences

data_processing:
libraries with different indices were multiplexed and loaded on an Illumina HiSeq instrument  according to manufacturer’s instructions (Illumina, San Diego, CA, USA).Sequencing was carried out  using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the  HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument
pass filter data of fastq format were processed by  Trimmomatic (v0.30) to be high quality clean data.
reference genome sequences and gene model annotation files of relative species were downloaded  from genome website,ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index  reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2  (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed  properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data.Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative  binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false  discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Genome_build: mm9
Supplementary_files_format_and_content: exl files include RPKM values for all genes and the P-value of differentially expressed genes compared with HBV(-)mouse

source_name: liver tissue

extract_protocol:
The total RNA of each sample was extracted using a RNeasy Mini Kit (Qiagen).1μg of total RNA with a RIN value above 7 was used for following the library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AAV8-HBV1.2 vector was diluted into phosphate-buffered saline (PBS), and then 200 µl of rAAV8-HBV 1.2 vector [2×1011 vector genome equivalents (vg)] was injected into the mice via the tail vein. The control group was injected with the same volume of PBS.  Liver tissues were collected at 1, 3 and 6-months post injection, and were frozen in liquid nitrogen.

value: Liver


title: 6Month-3


title: dsxRNAi_M-THE_S32


title: H_B4_rep1


title: unprimed_t2_1_2

description: experiment (TS) 2


title: 6Month-1


title: primed_t12_7_1

description: experiment (TS) 1

source_name: primed_12h post infection

value: primed

value: 12h post infection


title: dsxRNAi_M-THE_S31

value: male


title: 3Month-2


title: 3Month-3


title: dsxRNAi_F-THE_S30

value: female


title: H_B3_rep2

value: Juvenile 3rd day


title: 3Month-1


title: dsxRNAi_F-THE_S29


title: primed_t12_3_1

description: experiment (TS) 1


title: H_B3_rep1


title: 1Month-3


title: primed_t12_6_1

description: experiment (TS) 1


title: H_B2_rep3

value: Juvenile 2nd day


title: unprimed_t2_2_2

description: experiment (TS) 2

value: unprimed

value: whole organism


title: dsxRNAi_F-THE_S28

value: thoracic horn epithelium


title: 1Month-2


title: dsxRNAi_F-THE_S27


title: primed_t6_6_1

description: experiment (TS) 1


title: dsxRNAi_F-THE_S26


title: 1Month-1


title: H_B2_rep2


title: primed_t6_3_1

description: experiment (TS) 1


title: dsxRNAi_F-THE_S25


title: H_B2_rep1


title: H_B3_rep3


title: primed_t2_5_1

description: experiment (TS) 1


title: HBV(-) mouse 2

value: PBS


title: ctrlRNAi_M-BRN_S23

source_name: Brain

value: control

value: supraesophageal ganglion (brain)


title: H_B1_rep3

value: Juvenile 1st day


title: HBV(-) mouse 3


title: primed_t2_3_1

description: experiment (TS) 1


title: ctrlRNAi_M-BRN_S24


title: HBV(-) mouse 1


title: ctrlRNAi_M-BRN_S22


title: primed_t2_2_1

description: experiment (TS) 1


title: H_B1_rep2


title: H_B1_rep1


title: H_E5_rep3

value: Egg 5th day after laying


title: ctrlRNAi_M-BRN_S21


title: primed_t0_3_1

description: experiment (TS) 1

value: 0h post infection


title: ctrlRNAi_M-BRN_S20


title: primed_t0_4_1

description: experiment (TS) 1


title: primed_t6_1_1

description: experiment (TS) 1

value: 6h post infection


title: ctrlRNAi_M-BRN_S19


title: ctrlRNAi_F-BRN_S17


title: H_E4_rep3

value: Egg 4th day after laying


title: H_E5_rep1


title: unprimed_t12_7_1

description: experiment (TS) 1

source_name: unprimed_12h post infection


title: H_E5_rep2


title: H_E4_rep2


title: ctrlRNAi_F-BRN_S18


title: unprimed_t12_1_1

description: experiment (TS) 1


title: H_E3_rep3

value: Egg 3rd day after laying


title: ctrlRNAi_F-BRN_S15


title: unprimed_t6_6_1

description: experiment (TS) 1


title: H_E4_rep1


title: primed_t0_6_1

description: experiment (TS) 1

value: primed


title: unprimed_t12_2_1

description: experiment (TS) 1

value: 12h post infection


title: ctrlRNAi_F-BRN_S13

value: female


title: H_E3_rep2


title: unprimed_t2_6_1

description: experiment (TS) 1

value: 2h post infection


title: ctrlRNAi_F-BRN_S14


title: H_E3_rep1


title: unprimed_t6_7_1

description: experiment (TS) 1


title: H_E2_rep3

value: Egg 2nd day after laying


title: dsxRNAi_M-BRN_S11

value: dsxRNAi

value: male


title: dsxRNAi_M-BRN_S12


title: unprimed_t2_4_1

description: experiment (TS) 1

value: unprimed

value: whole organism


title: unprimed_t2_5_1

description: experiment (TS) 1


title: unprimed_t0_6_1

description: experiment (TS) 1


title: dsxRNAi_M-BRN_S8


title: siUPF1

status: Public on Feb 27 2017

city: Seoul

first: younseo

last: Oh

address: 222, Wangsimni-ro, Seongdong-gu, Seoul, Republic of Korea

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: human neuroblastoma cell line

growth_protocol: SH-SY5Y cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: growth media

value: 10% fetal bovine serum (FBS), 1% penicillin/streptomycin


title: ctrlRNAi_F-BRN_S16

value: control

value: supraesophageal ganglion (brain)


title: Nondifferentiation

value: 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, 50 μM of retinoic acid


title: unprimed_t0_7_1

description: experiment (TS) 1

value: 0h post infection


title: H_E1_rep1

value: Egg 1st day after laying


title: Differentiation


title: unprimed_t6_5_1

description: experiment (TS) 1

value: 6h post infection


title: H_E2_rep2


title: H_E1_rep2


title: unprimed_t0_1_1

description: experiment (TS) 1


title: dsxRNAi_M-BRN_S7


title: siSTAU1


title: dsxRNAi_M-BRN_S9


title: DUIV_shSUZ12_rep1

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.1.0.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate. RNAseq bigwigs are split by strand.

source_name: DIPG_SU_IV (H3.1K27M)

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Treatment with JQ1 or DMSO was administrated only once

value: Diffuse Intrinsic Pontine Glioma (DIPG)

tag: passages

value: Low passages (6-10)

tag: chip antibody

tag: agent

value: Cells lentiviral infected with SUZ12 specific shRNA vector


title: DUIV_shSUZ12_rep2


title: siControl


title: DUIV_CTRL_rep1

value: Cells lentiviral infected with control vector


title: SF8628_shSUZ12_rep2


title: H_E2_rep1


title: DUIV_CTRL_rep2


title: SU_DIPG_IV_JQ1_300nM_24h_rep2

tag: time point


title: SF8628_CTRL_rep2


title: dsxRNAi_M-BRN_S10


title: H_E1_rep3


title: B6_iWAT_12w_HFD_rosi

city: Philadelphia

first: Raymond

last: Soccio

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Bowtie or GSNAP with default parameters
Peak bedGrpah was generated by HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph or bigWig

source_name: iWAT

extract_protocol:
DNA was isolated using phenol/chloroform extraction and  NaCl/EtOH precipitated  with  20 μg  glycogen  carrier
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina

value: iWAT


title: 129_iWAT_12w_HFD_control


title: B6_eWAT_12w_LFD_PPARg_5

source_name: eWAT

value: eWAT