title: INPUT - TSWT

description: alligned to mm9 reference genome

data_processing:
Using Bowtie v1.1.2 software reads were mapped to the mouse mm9 genome using parameters -v2 -m1.
Aligned reads were analyzed using Easeq v1.03. Peaks were called in each IP sample relative to input using the auto-detect window size and a p-value and FDR less than 1.0x10-5.
Signal was quantified at all genes in mouse mm9 referece genome from the TSS ± 10kb. (see supplemental file)
Genome_build: mouse mm9
Supplementary_files_format_and_content: .wig files show Aligned reads used to quantify signal at the TSS of all genes. The .txt file contains the quantified H2BK5Ac signal at the TSS ± 10kb for all genes.

extract_protocol:
Cells were fixed in 1% paraformaldehyde for 10 minutes, harvested, and the nuclei were isolated and lysed. The nuclear lysate was sonicated and underwent immunoprecipitation using 50 µl of dynabeads (Invitrogen) coupled to 5 µl of Active Motif α-H2BK5Ac antibody per sample. DNA-protein crosslinks were reversed overnight at 65C, and samples were ribonuclease and proteinase treated before DNA was purified using Min Elute columns (Qiagen).
Preparation of libraries was performed using 50 ng of ChIP or TSWT input DNA and the KAPA HyperPrep kit with Illumina TruSeq indexed adapters. Dual SPRI size selection was performed after 18 cycles of amplification according to the manufacturer’s protocol. The average library size was ~300 bp. 12-plex libraries were sequenced (1 X 75 bp) using an Illumina NextSeq500 ranging from 7.1-8.9 X 107 reads per sample.

tag: antibody


title: Jersey_14_C

status: Public on Mar 07 2017

type: SRA

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

library_source: transcriptomic

data_processing:
Reads were aligned to the genome assembly Bos taurus UMD3.1 using STAR: ultrafast universal RNA-Seq aligner STAR_2.3.0
Gene expression counts were computed using HTSeq-count
Genome_build: Bos taurus UMD3.1
Supplementary_files_format_and_content: Text files (.txt) containing the Ensembl gene IDs and raw counts (Note: last five rows are general statistics). One file for each sample (38 samples)

molecule: total RNA

organism: Bos taurus

source_name: Liver tissue

extract_protocol:
liver biopsies were collected ,preserved in RNA later,and stored at -80 degree Celcius. mRNA was extracted from the liver tissue samples using the Qiazol, RNeasy® Mini Kit and MaXtract High Density for further RNA-Sequencing.
Illumina TruSeq Stranded mRNA Kit was used with 0.4 ug of total RNA for the construction of sequencing libraries.

tag: breed

value: Jersey

value: High

tag: diet

value: Control (Low Concentrate)

tag: tissue

value: liver


title: Jersey_10_C


title: H2BK5Ac - TSKI4 HDAC6 sh2

city: Memphis

first: Amy

last: Abell

state: TN

address: 3774 Walker Ave

department: Biological Sciences

country: USA

institute: The University of Memphis

description: alligned to mm9 reference genome

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Trophoblast Stem Cells

growth_protocol: Cells were cultured in the absence of feeders in 30% TS media (RPMI 1640, 20% fetal bovine serum, 1% penicillin and streptomycin, 1% L-glutamine, 1% sodium pyruvate, and 100 µM β-mercaptoethanol) and 70% MEF-conditioned TS cell media. For maintenance of the stem cell state, TS medium was supplemented with FGF4 (37.5 ng/ml) and Heparin (1 mg/ml).

value: H2BK5Ac Active Motif

tag: knock-in

value: MAP3K4 K1361R

tag: shRNA

value: HDAC6 shRNA

tag: strain


title: Holstein_15_C

value: Holstein

value: Low


title: Holstein_9_C


title: Moz WT Rep 1

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Sample name: KJ7WT9

data_processing:
Reads were aligned to the mouse genome using Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using Rsubread's featureCounts function and NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

molecule: polyA RNA

source_name: Germinal Center B cells

extract_protocol:
RNA extraction protocol not provided.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Germinal Center B cells

tag: background strain

tag: genotype

value: AID-cre T/+

tag: timepoint post-immunisation

value: Day 7

tag: number of pooled mice

value: 5 males, 1 female

tag: date of experiment


title: c-Myb WT Plasmablasts Rep 2

description: Sample name: KJSECWT7

source_name: Plasmablasts

value: Plasmablasts

value: Myb fl/fl (no cre)

value: Day 5 post-sec

value: 3 males, 4 females


title: Moz WT Rep 2

description: Sample name: MozAID-WT-d7

value: 3 males, 2 males


title: H2BK5Ac - TSKI4

description: alligned to mm9 reference genome

value: pLKO vector


title: H2BK5Ac - TSWT

description: alligned to mm9 reference genome


title: c-Myb WT Plasmablasts Rep 1

description: Sample name: KJSECWT5

value: 3 males, 3 females


title: Jersey_8_C

value: Jersey

value: High

value: Control (Low Concentrate)

value: liver


title: Jersey_8_HC


title: Jersey_10_HC


title: Control H3k27me3 sample2

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling were done using the Illumina Pipeline (v.1.8.2).
Alignment to the mm9 genome was performed using Bowtie.
BAM files were created from bowtiefiles using samtools.
Enriched domains were called using hiddenDomains and MACSv2 using the input and each replicate for control and mutant using default parameters.
bigWig files were created using samtools to count the number of reads (for normalization), bedtools to make bedGraph files and bedGraphToBigWig to convert the bedGraph to bigWig.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bed files are tab-delimited text files.
Supplementary_files_format_and_content: bigWig files are a binary file format.

source_name: spermatogenic cells, control, H3k27me3 ChIP

extract_protocol:
Testes were collected from 6-week-old mice and digested with collagenase, trypsin, and DNaseI. Percoll solution and cell strainers were applied to separate somatic cells from spermatogenic cells. The isolated cells were examined under differential interference contrast optics and 90% of them were spermatogenic cells.
ChIP-seq libraries were prepared according to Illumina instructions and sequenced on Illumina's HiSeq2000 instrument.

tag: strain/background

value: mixed background

tag: genotype/variation

tag: age

value: 6 weeks

value: spermatogenic cells

tag: chip antibody

value: H3K27me3 (ab6002; Abcam)


title: c-Myb KO Plasmablasts Rep 1

description: Sample name: KJSECKO6

value: Myb fl/fl CD23-cre T/+

value: 3 males, 2 females


title: KO_input_s22

city: La Jolla

first: Shujuan

last: Chen

state: CA

address: 9500 Gilman Drive

department: Pharmacology

institute: University of California, San Diego

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the transgenic genome assembly (mm9 plus 250kb human UGT1A1 gene ) using Bowtie 2 version 2.2.9 with default configuration.
Peaks were called using MACS2  version 2.1.1 with the default and broad peak ( -- broad   --broad-cutoff 0.1) configurations
Peak annotation and motif finding done using HOMER version 3.12
Genome_build: mm9+human UGT1A1 gene
Supplementary_files_format_and_content: MACS2-peaks files, bedgraphs  files were generated using  HOMER software version 3.12

source_name: Jejunum

extract_protocol:
IECs were isolated with a modified method (Goodyear AW, et al. J Immunol Methods 2014;405:97-108). Dissociated IECs were collected by centrifugation.
IECs were freshly isolated from both DIECUN and F/FUN neonates at P12 and were subjected to ChIP (MAGnify ChIP system, ThermoFisher). After reverse cross-linking, library preparation was carried out by using the MicroPlex Library Preparation Kit V2 (Diagenode, C05010012). Cluster generation and 50 cycles of single end sequencing were carried out on an Illumina Nexseq 500. Sequence tags were aligned (mapped) to the unmasked mouse (mm9) or human (hg19) reference genome.

value: NCoR1 deletion KO

value: intestinal epithelial cells

tag: chip antibodies

tag: mice strain


title: Moz KO Rep 2

description: Sample name: MozAID-KO-d7

value: Germinal Center B cells

value: Moz fl/fl AID-cre T/+

value: Day 7

value: 6 males, 2 females


title: WT_input_s21

value: WT


title: c-Myb KO Plasmablasts Rep 2

description: Sample name: KJSECKO8

value: Plasmablasts

value: Day 5 post-sec

value: 1 male, 3 females


title: c-Myb KO B Cells Rep 2

description: Sample name: KJ12KO4

value: Day 12

value: 3 females


title: Holstein_7_HC

tag: breed

value: Holstein

value: Low

tag: diet

value: liver


title: Holstein_7_C

value: Control (Low Concentrate)

tag: tissue


title: c-Myb KO B Cells Rep 1

description: Sample name: KJ12KO2

value: Myb fl/fl CD23-cre T/+

value: 2 females


title: Moz KO Rep 1

description: Sample name: KJ7KO10

value: 5 males, 1 female


title: c-Myb WT B Cells Rep 1

description: Sample name: KJ12WT1

value: Germinal Center B cells

value: Myb fl/fl (no cre)

value: 1 male, 2 females


title: Holstein_6_C

value: High


title: Jersey_5_HC

value: Jersey


title: KO_H3K27me3

value: NCoR1 deletion KO

value: intestinal epithelial cells

value: H3K27me3 (Active Motif, AM61017)


title: WT_R2

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

description: Retinas from 2 female and 2 male animals

data_processing:
Reads were aligned to the mm9 transcriptome with TopHat v1.4.1
Transcript/gene abundances were estimated with Cufflinks v1.3.0
Differential expression analysis was conducted with Cuffdiff within Cufflinks v1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and gene_differential_expression

source_name: Retina

extract_protocol:
Retinas were dissected in cold sterile HBSS with Ca and Mg (Gibco) and stored at -80 ⁰C. Total RNA was extracted with TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) with on-column DNaseI digestion (Qiagen).
Polyadenylated mRNA was selected from total RNA using Dynabeads (Invitrogen). The mRNA was fragmented and reverse-transcribed to double-stranded cDNA using random hexamers, blunt-ended, 3’-adenylated, and ligated to sequencing adapters. Ligated fragments were amplified for 12 cycles with primers to incorporate unique sample barcodes. Samples were pooled and subjected to 1x50bp sequencing on one lane of Illumina HiSeq 2000.

value: 3 weeks

value: WT

tag: number of retinas


title: WT_input_s1


title: Holstein_6_HC

value: Holstein


title: Jersey_5_C


title: rd7_R2

tag: strain

value: Nr2e3 mutant


title: Jersey_4_HC

value: Low

value: liver


title: T45_3

city: Beijing

first: Lijun

last: Wang

address: No.20 Nanxincun, Xiangshan, Beijing 100093, China

country: China

institute: IBCAS

description: Treated at 45 ℃

data_processing:
Base-calling were performed using RTA and CASAVA.
The quality of sequencing data was estimated using FastQC (v0.11.3). Then adaptors and low quality bases were removed using Trimmomatic (v0.33).
Clean reads from all samples were pooled together and feeded to de novo RNA-seq assembly software Trinity (v2.0.6) with default parameters.
The expression of assembled transcripts and genes were quantified using RSEM (v1.2.19).
Genome_build: vitis28
Supplementary_files_format_and_content: identified alternative splicing events + counts

organism: Vitis vinifera

source_name: T45 leaves

growth_protocol: One-year old ‘Jingxiangyu’ (Vitis vinifera L.) grapevines were planted in pots, then grown in a greenhouse at 70-80% relative humidity at 18-25°C, with the maximum photosynthetically active radiation (PAR) at approximately 1,000 μmol photons m−2 s−1.

extract_protocol:
Total RNAs from leaves were extracted using Trizol (Invitrogen, 15596-018) according to the manufacturer’s instructions. Highly purified and intact mRNAs were enriched from total RNAs using Dynabeads® mRNA purification kit (Ambion, 61006). RNAs were fragmented into ~ 300 nt fragments by 1 min incubation at 94℃ in fragmentation buffer (10 mM ZnCl2, 10 mM Tris-HCl, pH 7.0). The fragmentation reaction was stopped with 50 mM EDTA, followed by standard ethanol precipitation and collected for sequencing and expression validation.
For the strand-specific RNA-seq, fragmented RNAs were re-suspended in H2O and used for library generation with mRNA sequencing kit (Illumina Inc. San Diego, CA). Sequencing was carried out on Illumina HiSeq 4000 sequencer (Illumina Inc. San Diego, CA) according to the manufacturer’s instructions and 150 nt paired-end sequencing reads were generated.

treatment_protocol: When the sixth leaves (from base to apex) of grapevines became mature, all grapevines were divided into four groups and acclimated for two days in a controlled environment room (70% average relative humidity, 25/18 (12 h/12 h) day/night cycle and PAR at 800 μmol m−2 s−1). On day 3, the grapevines were subjected to the following treatments: (1) the plants of the control group were maintained at the optimal day/night temperature (25°C/18°C) in the above growth room; (2) the plants of the treatment groups were exposed to 35°C, 40°C or 45°C from 11:30 to 13:30 (the conditions were the same as the control, except for temperature). The fourth to sixth leaves (from base to apex) of each plant were detached at 13:30 (the end of the heat stress treatment). Each biological replicate included three plants, and three replicates were used for both the three treatments and the control. Leaves were frozen in liquid nitrogen immediately and stored at −80°C for further analysis.

value: leaf

tag: induction stage


title: WT_R1


title: Jersey_4_C

value: Control (Low Concentrate)


title: rd7_R1


title: T45_1

description: Treated at 45 ℃


title: T45_2

description: Treated at 45 ℃


title: T40_3

description: Treated at 40 ℃

source_name: T40 leaves


title: c-Myb WT B Cells Rep 2

description: Sample name: KJ12WT3

tag: cell type

tag: background strain

value: Day 12

value: 2 females


title: Jersey_3_HC


title: KO_input_s2


title: Holstein_2_HC


title: T35_3

description: Treated at 35 ℃

source_name: T35 leaves


title: T40_2

description: Treated at 40 ℃


title: Jersey_3_C


title: Holstein_2_C


title: Sall4 ko EAF oocyte, replicate 1 [RRBS-seq]

city: Shanghai

first: Shaorong

last: Gao

address: No. 1239, Siping Road

institute: Tongji University

data_processing:
RRBS sequencing reads were mapped to a combined genome with mm9 using bsmap(v 2.89) with parameter "-D C-CGG -w 100 -s 12 -v 0.1 -m 32 -x 1000 -R".
Methylation level of each CpG site was estimated using mcall(v 1.3.0) with default parameters.
Genome_build: mm9

source_name: early antrum follicle stage oocyte

extract_protocol:
Single oocyte harvested from Sall4fl/fl;Zp3-Cre and Sall4fl/fl female mice at P12.5 and P17.5
The DNA from the nuclei of the oocytes were extracted, with digestion of nuclear proteins. The DNA was further treated with MspI digestion (Fermentas), end-repair, dA-tailing, adaptor-ligation, and bisulfite-conversion in a one-tube reaction. The MethylCode Bisulfite Conversion Kit (Invitrogen, MECOV-50) was used for bisulfite-conversion and purification. Unmethylated lambda DNA (Fermentas) was added to the gDNA sample before MspI digestion to monitor the bisulfite conversion rate. The converted libraries were further purified with Agencourt AMPure XP beads (Beckman A63881) and amplified by 2-round PCR enrichment. After amplification, size-selection was performed on the 12% native polyacrylamide TBE gel to obtain the 200–500 bp DNA fragments.

value: Sall4 ko

tag: development stage

value: early antrum follicle

value: oocyte


title: Sall4 wt EAF oocyte, replicate 3 [RRBS-seq]

value: wild type


title: Sall4 wt EAF oocyte, replicate 4 [RRBS-seq]


title: Sall4 ko EAF oocyte, replicate 2 [RRBS-seq]


title: Sall4 wt EAF oocyte, replicate 2 [RRBS-seq]


title: T35_2

description: Treated at 35 ℃


title: Holstein_1_C

value: High


title: Holstein_1_HC


title: T35_1

description: Treated at 35 ℃


title: Sall4 wt EAF oocyte, replicate 1 [RRBS-seq]


title: Sall4 ko SF oocyte, replicate 5 [RRBS-seq]

source_name: secondary follicle stage oocyte

value: secondary follicle


title: Sall4 ko SF oocyte, replicate 4 [RRBS-seq]


title: T25_1

description: Treated at 25 ℃

source_name: T25 leaves


title: WT_H3K9me3

value: intestinal epithelial cells

value: H3K9me3 (Abcam, ab8898)


title: Sall4 ko SF oocyte, replicate 2 [RRBS-seq]


title: KO_H3K9me3

value: NCoR1 deletion KO


title: KO_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: Sall4 wt SF oocyte, replicate 7 [RRBS-seq]


title: Sall4 ko SF oocyte, replicate 1 [RRBS-seq]


title: Sall4 wt SF oocyte, replicate 6 [RRBS-seq]


title: WT_H3K27ac

value: WT


title: Sall4 wt SF oocyte, replicate 4 [RRBS-seq]


title: KO_H3K9ac

value: H3K9ac (Active Motif, AM39137)


title: Sall4 wt SF oocyte, replicate 5 [RRBS-seq]


title: Sall4 wt SF oocyte, replicate 3 [RRBS-seq]


title: WT_H3K9ac


title: T40_1

description: Treated at 40 ℃


title: T25_3

description: Treated at 25 ℃


title: T25_2

description: Treated at 25 ℃


title: Sall4 wt SF oocyte, replicate 1 [RRBS-seq]


title: Sall4 wt SF oocyte, replicate 2 [RRBS-seq]


title: WT_H3K27me3

value: H3K27me3 (Active Motif, AM61017)


title: experimental group oocyte, replicate 3 [RNA-seq]

data_processing:
Tophat(v 1.3.3) was used for sequencing read alignment with the parameters “tophat -p 8 --mate-inner-dist 0 --mate-std-dev 20 -o ./ -G mm9_refSeq.gtf mm9 Sample.1.fq Sample.2.fq” relative to input samples.
Gene expression for each sample were quantified to FPKM using Cufflinks(v 1.2.0) with the parameters "cufflinks -G mm9_refSeq.gtf --output-dir ./ accepted_hits.bam" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking files are generated using Cufflinks and FPKM represent expected number of fragments per kilobase of transcript sequence per million base pairs sequenced.

source_name: experimental group oocyte

extract_protocol:
secondary and early antral follicle oocytes were obtained from Sall4fl/fl;Zp3-Cre (Sall4 KO) and Sall4fl/fl ovaries of P12.5 and P17.5 female mice. In the microinjection experiments, we detached secondary follicles from P10.5 WT female mice ovaries.
Reverse transcription was performed directly on the cytoplasmic lysate. Terminal deoxynucleotidyl transferase was then used to add a poly(A) tail to the 3’ end of the first-strand cDNAs. The total cDNA library of the single cell was then amplified by 18- 20 cycles for the library construction. The amplified cDNA was fragmented using Covaris sonicator (Covaris S220). To generate the sequence libraries, the TruSeq® Library Prep Pooling kit (Illumina 15042173) or NEBNext Ultra DNA Library Prep Kit (New England Biolabs E7370) was used following the manufacturer’s instructions.

value: Kdm5b OE, Kdm6a/6b si-RNA

value: P10.5 oocyte, after 7 days in vitro culture


title: experimental group oocyte, replicate 1 [RNA-seq]


title: Sall4 ko SF oocyte, replicate 3 [RRBS-seq]


title: WT_H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: WT_H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: input_TSA_16h_rep1

city: Neuherberg/munich

first: Christian

last: Lindermayr

state: Bavaria

address: Ingolstädter Landstrasse 1

department: Biochemical plant pathology

country: Germany

institute: Helmholtz-Zentrum munich

data_processing:
Filtering of uniquely mappable reads using the clc genomics workbench (version 8.5.1, Quiagen)
Mapping of reads to the Arabidopsis genome (TAIR10) using the clc genomics workbench and default settings. PCR duplicates were also filtered out.
Peak calling using a P-value threshold of 0.05. For each sample the appropriate input control was considered. Peak calling was done with the clc genomics workbench
Removal of low quality samples (RSC values < 0.8)
Computation of differential H3K9/14ac sites using DiffBind software: chromosomic peaks outside the centromeric region that occurred in at least six samples were used in the differential analysis with the edgeR method, and log2 fold changes as well as raw and FDR-adjusted p-values were recorded for each treatment-versus-control comparison.
Identification of NO-regulated H3K9/14ac sites by comparison of the GSNO and GSNO/cPTIO treatment
Genome_build: TAIR9
Supplementary_files_format_and_content: Peak files contain the chromosomal coordinates of the peaks in .bed format. DiffBind output files contain log2(fold changes) (treatment - control), P-values, FDRs of all peaks tested in tab delimited text format (.txt)

organism: Arabidopsis thaliana

source_name: liquid grown seedlings

growth_protocol: Approximately 20 µL of seeds (dry volume) were grown in sterile 1x MS supplemented with 1% sucrose under moderate shaking (120 rpm) and short-day conditions (10h light/ 14h dark, light intensity 130 µmol s-1 m-2)

extract_protocol:
Chromatin was isolated, sheared and subjected to immunoprecipitation using the Plant ChIP-seq Kit (Diagenode, C01010150) according to the manual.
Libraries were prepared using the MicroPlex Library Preparation kit v2 (Diagenode, C05010014) according to the manual. 1 ng of each sample and input was used for library preparation, 11 amplification cycles were applied to amplify the libraries. All libraries were prepared in parallel. 10 µL of each indexed library were pooled and the final library was purified using AMPure resin.

treatment_protocol: 250 µM GSNO, 250 µM GSH, 250 µM GSNO / 500 µM cPTIO, 5 µM TSA for 3h and 16h

value: 7 days

value: anti-H3K9/14ac (Diagenode, C15410200)

tag: ecotype


title: experimental group oocyte, replicate 2 [RNA-seq]

value: oocyte


title: KO_H3K4me1


title: control group oocyte, replicate 5 [RNA-seq]

source_name: control group oocyte

value: wild type


title: input_GSNO_cPTIO_16h_rep1


title: control group oocyte, replicate 4 [RNA-seq]


title: input_GSNO_cPTIO_16h_rep2


title: control group oocyte, replicate 3 [RNA-seq]


title: input_GSH_16h_rep2


title: control group oocyte, replicate 2 [RNA-seq]


title: KO_H3K4me3


title: input_GSH_16h_rep1


title: input_GSNO_16h_rep1


title: input_TSA_16h_rep2


title: input_water_16h_rep2


title: Sall4 ko EAF oocyte, replicate 2 [RNA-seq]

value: Sall4 ko

value: early antrum follicle


title: Sall4 ko EAF oocyte, replicate 3 [RNA-seq]


title: input_water_16h_rep1


title: Sall4 ko EAF oocyte, replicate 1 [RNA-seq]


title: Sall4 wt EAF oocyte, replicate 3 [RNA-seq]


title: input_TSA_3h_rep2


title: input_TSA_3h_rep1


title: input_GSNO_cPTIO_3h_rep2


title: input_GSNO_cPTIO_3h_rep1


title: Sall4 ko SF oocyte, replicate 2 [RNA-seq]

value: secondary follicle


title: Sall4 ko SF oocyte, replicate 3 [RNA-seq]


title: input_GSH_3h_rep1


title: Sall4 wt EAF oocyte, replicate 1 [RNA-seq]


title: input_GSH_3h_rep2


title: input_GSNO_3h_rep1


title: Sall4 wt SF oocyte, replicate 1 [RNA-seq]


title: input_GSNO_3h_rep2


title: Sall4 wt SF oocyte, replicate 2 [RNA-seq]


title: input_GSNO_16h_rep2


title: control group oocyte, replicate 1 [RNA-seq]


title: input_water_3h_rep2


title: Dgcr8KO2d5_B

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

description: reverse-stranded protocol

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using STAR v2.4.2a allowing up to 2 mismatches
FeatureCounts V1.4.5-p1 was used to summarize reads for each gene, using -s 2 (reversely stranded) and ignoring multiple-hit reads
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count

source_name: Embyronic stem cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 129/Ola background

value: Blastocyste

value: Passage 7

tag: genotype

value: Dgcr8 knockout


title: DicerKO2

description: reverse-stranded protocol

value: Passage 4

value: Dicer knockout


title: input_water_3h_rep1


title: Sall4 wt EAF oocyte, replicate 2 [RNA-seq]


title: ChIP_TSA_16h_rep1


title: CHIP_GSNO_cPTIO_16h_rep1


title: Sall4 ko SF oocyte, replicate 1 [RNA-seq]


title: ChIP_GSH_16h_rep2


title: E14_P33

description: reverse-stranded protocol


title: ChIP_GSH_16h_rep1


title: E14_P42

description: reverse-stranded protocol


title: persistent_group_time_2_subject_7

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

description: Ion Torrent PGM with the Ion 316 Chip v2

data_processing:
Sequencing reads were generated and initially processed by Ion Torrent Suite software version 4.4.2.
Low quality reads and polyclonal sequences were filtered from sequencing data, then raw data was trimmed to 22 base pairs from 5’ end and profiles were generated by aligning sequences to hg19 with BWA; then, we quantified using miRDeep2 v2.0.0.7 and annotated based on miRBase v20.
Differential expression analysis was conducted on DESeq2 with Benjamini and Hochberg multiple testing correction applied.
Target prediction and analysis was conducted using the miRWalk2.0 database.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

source_name: Blood

extract_protocol:
Blood samples were collected into PAXgene blood RNA tubes and processed with PAXgene blood miRNA kit (Qiagen, Valencia, CA) for miRNA extraction. Quality and quantity of extracted RNA was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and the Agilent Bioanalyzer 2100 Small RNA assay (Agilent Technologies, Inc., Santa Clara, CA). All samples were enriched for miRNA using standard recommendations for preparation of small RNA libraries protocol.
Barcoded libraries were prepared with an input of 1-5ng of enriched small RNA using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA). Template-positive Ion PGM™ Ion Sphere™ Particles were prepared for sequencing using Ion PGM™ Template OT2 200 Template Kit v2 with pooled libraries optimized to 14pM.

tag: time

value: 90 days


title: persistent_group_time_2_subject_9


title: persistent_group_time_2_subject_10


title: ChIP_GSNO_16h_rep2


title: ChIP_GSNO_16h_rep1


title: ChIP_water_16h_rep2


title: persistent_group_time_2_subject_6


title: persistent_group_time_2_subject_8


title: persistent_group_time_2_subject_5


title: Dgcr8KO2d5_A

description: reverse-stranded protocol


title: ChIP_water_16h_rep1


title: ChIP_TSA_3h_rep2


title: ChIP_TSA_3h_rep1


title: persistent_group_time_2_subject_2


title: persistent_group_time_2_subject_3


title: DicerKO1

description: reverse-stranded protocol


title: persistent_group_time_2_subject_1


title: CHIP_GSNO_cPTIO_3h_rep2


title: ChIP_TSA_16h_rep2


title: CHIP_GSNO_cPTIO_16h_rep2


title: CHIP_GSNO_cPTIO_3h_rep1


title: persistent_group_time_1_subject_10

value: baseline


title: ChIP_GSH_3h_rep2


title: persistent_group_time_1_subject_9


title: ChIP_GSH_3h_rep1


title: persistent_group_time_1_subject_8


title: ChIP_GSNO_3h_rep2


title: ChIP_GSNO_3h_rep1


title: ChIP_water_3h_rep1


title: ChIP_water_3h_rep2


title: persistent_group_time_1_subject_2


title: persistent_group_time_1_subject_5


title: persistent_group_time_1_subject_6


title: persistent_group_time_1_subject_3


title: persistent_group_time_1_subject_7


title: persistent_group_time_1_subject_1


title: persistent_group_time_2_subject_4


title: persistent_group_time_1_subject_4


title: improved_group_time_2_subject_4


title: improved_group_time_2_subject_1


title: improved_group_time_2_subject_2


title: improved_group_time_1_subject_4


title: improved_group_time_2_subject_3


title: improved_group_time_1_subject_5


title: improved_group_time_1_subject_3


title: improved_group_time_1_subject_1


title: improved_group_time_1_subject_2


title: control_group_time_2_subject_8


title: control_group_time_2_subject_7


title: control_group_time_2_subject_9


title: control_group_time_2_subject_6


title: control_group_time_2_subject_5


title: control_group_time_2_subject_2


title: control_group_time_2_subject_3


title: control_group_time_2_subject_4


title: control_group_time_2_subject_1


title: control_group_time_1_subject_9


title: improved_group_time_2_subject_5


title: control_group_time_1_subject_8


title: control_group_time_1_subject_6


title: control_group_time_1_subject_7


title: tcdd2_20dpf

city: Raleigh

first: AtLee

last: Watson

state: North Carolina

address: Campus Box 7633

institute: North Carolina State University

data_processing:
The resulting reads were trimmed to remove adaptor sequences and low quality base-calls, and were aligned to the Oryzias latipes (Medaka) genome (Version 75; www.ensembl.org) using Bowtie 2.2.6.
Differentially expressed genes were identified using Cuffdiff2, whereas principal component analysis was performed with DESeq2 in R.
Genome_build: Ensembl, Version 75  ftp://ftp.ensembl.org/pub/release-75/gtf/oryzias_latipes/
Supplementary_files_format_and_content: Tab delimited text files for each sample were generated reporting FPKMs for each sampleand log2 fold change between DMSO- and TCDD-treated cohorts.

organism: Oryzias latipes

source_name: axial tissue (including bone, fat, muscle, dermis)

growth_protocol: Following DMSO or TCDD exposure, embryos were cultured in 1X ERM at 26-27 °C with static media renewal every other day until hatch. Hatched individuals were transferred to plastic containers containing 100 mL of 1X ERM, were fed 1-2 mg of ground Otohime B1 larval diet (Reed Mariculture, Campbell, CA) daily, and media was renewed every other day until tissue dissection and RNA isolation at 20 dpf.

extract_protocol:
Larval medaka were euthanized at 20 dpf in 0.125% tricaine/ERM solution and replicates were pooled to ensure 15-25 individuals per RNA sample. Specimen were transferred to Leibowitz’s media (L-15) containing 10% Fetal Bovine Serum. Dechorionated embryos or hatched larvae were passed through a 20-22 gauge hypodermic needle and 3-ml syringe several times to isolate the axial skeleton from craniofacial and abdominal viscera. Sheared tissue was collected on 105-μm nylon mesh and transferred to fresh L-15/10% FBS media. Under a dissecting light microscope axial tissue was inspected and trimmed of any remaining craniofacial or abdominal tissue. Samples were immediately flash frozen in liquid nitrogen. Tissues were homogenized in TRI Reagent® and total RNA was isolated according to the TRI Reagent manufacturer’s protocol. Finally, total RNA was quantified using Agilent 2100 Bioanalyzer and 2100 Expert Software package (Agilent Technologies). RNA samples with RNA Integrity numbers (RINs) of 9.9 or greater were used for RNA-Seq library generation.
Whole transcriptome libraries were prepared using Ion Total RNA-Seq Kit v2 (Ion Torrent, Life Technologies, Carlsbad, CA) for the Ion PGM sequencing platform as described by the manufacturer. Briefly, polyA mRNA was purified for each sample from 2 μg of denatured total RNA with oligo(dT)25 Dynabeads®.  Adaptors from Ion Adaptor Mix v2 were ligated to poly(A) RNA, and each sample was reverse transcribed to form cDNA, and then amplified using Platinum® PCR Supermix High Fidelity, Ion Xpress™ RNA 3’ Barcode Primers, and a different Ion Xpress® RNA-Seq BC Primer (BC#11-16) for each sample to form a barcoded library. The library was then pooled with equimolar amounts from each of the 6 barcoded samples.  The pooled library was amplified of the pooled library using the Ion OneTouch™ 200 and Ion PGM Template OT2 200 Kit. The solution containing template-positive ISPs was enriched on the Ion OneTouch™ ES according to the manufacturer’s protocol. Sequencing primers were annealed to the template-positive ISPs, Ion PGM™ Sequencing 200 v2 Polymerase was added to the ISP solution, and incubated at room temperature for 5 minutes. Finally, the template-positive ISPs + Sequencing Polymerase mixture were carefully loaded into the Ion 318™ chip and sequenced overnight on the Ion PGM™ System.

treatment_protocol: Medaka embryos were treated with DMSO or 0.3 nM TCDD at Stages 8-9 (approximately 4 hours post fertilization) for 1 hour. Embryos were subsequently washed four times with 1X ERM and transferred to a

value: Orange-red Hd-dR

value: 20 days post fertilization

tag: chemical

value: 0.3 nM TCDD


title: tcdd3_20dpf

tag: age

value: axial tissue (including bone, fat, muscle, dermis)


title: control_group_time_1_subject_4


title: tcdd1_20dpf


title: dmso3_20dpf

value: 0.1% DMSO


title: control_group_time_1_subject_3


title: dmso1_20dpf


title: Mt

first: Jing

address: Medical Building  C121

department: School of Lifesciences

institute: Tsinghua University

data_processing:
HCS3.3.20, RTA 2.5.2 and bcl2fastq2-v2.16 were used for basecalling.
Sequenced reads were remove reads with adaptors, and remove reads in which unknown bases are more than 10%, remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters  -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200  to map clean reads to reference gene, and use BWA with parameters  -o 1 -e 50 -i 50 -L -k 2 -l 31 -t 4 -q 10 to reference genome Danio_rerio.GRCz10.dna.toplevel.fa .
RSEM is a quantification tool that computed  Maximum likelihood  abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model . FPKM (fragment Per Kilobase of gene per Megabase of library size) method is used in calculated expression level.
Genome_build: Zv10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: kdrl:GFP+ Endothelial cells

extract_protocol:
Morphologically normal siblings and mutant embryos from crosses of Tg(kdrl:GFP); gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single-cell suspension. Then, kdrl:GFP+ ECs were sorted by flow cytomer (FACSAria (BD) and MoFlo XDP (BeckMan)) and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit (QIAGEN).
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo (dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM  2000 or other sequencer when necessary.

tag: genetic background

value: tsu3994;Tg(kdrl;GFP) cross

tag: genotype/variation

value: Morphologically mutant embryo

tag: Stage

value: 44 hpf (hour post fertilization)

value: Endothelial cells


title: Sib

value: Morphologically normal siblings embryo


title: control_group_time_1_subject_1


title: Nugen, replicate 2, hour 20

city: Houston

first: Rafael

last: Rosengarten

state: Texas

address: 2520 Robinhood St #603

institute: Genialis, Inc

description:
rRNA-depleted total RNA
Nu_rep2_hr20

data_processing:
The data was mapped to the D. discoideum genome using TopHat version 2.0.13. Only uniquely mapped reads were permitted and the reference transcript annotation was supplied (--GTF --report-secondary-alignments --max-multihits 1 --mate-inner-dist 100).
Transcripts were assembled using Cufflinks (v2.2.1) with the option --GTF-guide to guide the reference annotation based transcript (RABT) assembly. The transcript annotation files from cufflinks were then merged using Cuffmerge (v2.2.1) to obtain a final transcriptome assembly.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the reads mapped to the chrR (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked. All DDB_G* IDs will be available on dictybase.org and dictyexpress.org although are not present on these websites at the time of accessioning these data in GEO.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names (DDB_G ids, CUFF ids) and the second its expression. Files ending with "_raw.txt" contain raw expression values while files ending with "_nor.txt" contain normalized expression values.
Supplementary_files_format_and_content: File_S3 contains the entire set of of CUFF models (and previously defined coding genes) with their genomic coordinates. This file also contains the normalized  expression values for all samples.
Supplementary_files_format_and_content: File_S4 contains the DDB_G assignments to the confident subset of those CUFF models.

organism: Dictyostelium discoideum

source_name: Cells developing on nitrocellulose filters

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5) to mid-log phase prior to collection for development.

extract_protocol:
TriZol (Life Sciences) -- Cells were scraped (filter) or pelleted (suspension) and disrupted in TriZol. Total RNA was extracted by phenol/chloroform as per manufacturer's instructions.
Ribosomal RNA was depleted using either the InDA-C method (Ovation, Nugen) or RiboZero "Plant root & seed" reagents, following manufacturer's instructions.

tag: growth media

tag: treatment

value: Development on 5 cm nitrocellulose filters, InDA-C rRNA depletion

tag: time point (hour)

tag: replicate


title: Nugen, replicate 2, hour 24

description:
rRNA-depleted total RNA
Nu_rep2_hr24

tag: strain


title: Nugen, replicate 2, hour 14

description:
rRNA-depleted total RNA
Nu_rep2_hr14


title: Nugen, replicate 2, hour 06

description:
rRNA-depleted total RNA
Nu_rep2_hr06


title: Nugen, replicate 2, hour 08

description:
rRNA-depleted total RNA
Nu_rep2_hr08


title: Nugen, replicate 2, hour 18

description:
rRNA-depleted total RNA
Nu_rep2_hr18


title: Nugen, replicate 2, hour 10

description:
rRNA-depleted total RNA
Nu_rep2_hr10


title: control_group_time_1_subject_5


title: 14dpi RNAseq rep2

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
RNAseq reads were aligned to the transcriptome of the zebrafish genome (GRCz10, gene model annotation release 80) using TopHat version 2.0.13 with default parameters
Reads mapping to genes were counted using HTseq-count version 0.5.4p3 with parameters ‘-s no -a 10’
Differential expression analysis of the RNAseq was done using the DESeq tool
Genome_build: GRCz10 zebrafish genome
Supplementary_files_format_and_content: normalized counts, fold changes and significance of changes in gene expression are given for each gene (A: uninjured, B: 14dpi)

source_name: undergoing regeneration 14 days after genetic ablation, whole heart - ventricle

growth_protocol: Wild-type or transgenic male and female zebrafish of the outbred Ekkwill (EK) strain were used for all experiments, with adults ranging in age from 4 to 6 months. Water temperature was maintained at 26°C for animals .

extract_protocol:
Whole ventricles from 20-30 fish were extracted with trizol. RNAseq libraries were made from polyA enriched toRNA.
Libraries were prepared as described in the Illumina RNAseq cloning kit

treatment_protocol: Fish were incubated in .4 uM tamoxifen for 18 hrs. Hearts were dissected 14 days later.

tag: expression

value: transgenic

value: (Z-CAT)pd36 ; (CreER)pd10

value: .4 uM tamoxifen 18 hrs

value: 14 days post incubation

tag: tissue

value: whole heart - ventricle

value: cardiomyocytes


title: Nugen, replicate 2, hour 04

description:
rRNA-depleted total RNA
Nu_rep2_hr04


title: 14dpi RNAseq rep1

tag: cell type


title: nascent_RNA seq_A7_replicate2

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description:
nascent RNA
combined.read.count.dm3.gene.sense.txt,combined.read.count.dm3.gene.antisense.txt

data_processing:
Sequencing reads were aligned to the fly genome fb5_22 using Bowtie v.0.12.7 with the unique option enabled (Langmead et al. 2009).
Consistency of replicates was checked by genome-wide correlation analysis and by visual inspection.
For ChIP-seq data, the aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function.
The smoothed fold enrichment profiles at log2 scale were calculated using the get.smoothed.enrichment.mle function (window size = 150 bp for the Gaussian kernel function and step size = 20 bp) in the SPP R package.
For RNA-seq data, read counts per each genes were calculated using bedtools multiBamCov function, strand-specifically. The read count info was used for differential expression analysis between conditions.
Genome_build: dm3
Supplementary_files_format_and_content: tdf (wig) and IP fold enrichment profile compared to input at log2 scale for ChIP-seq data; text and read counts per gene (rows) for each samples and conditions (columns), sense and antisense separately.

organism: Drosophila melanogaster

source_name: Embryo-derived cell-line

growth_protocol: S2 wild-type and upSET mutant cells were maintained in Schneider's media supplemented with 10% FBS and 1% antibiotic/antimycotic. The yw; UpSET-BioTAP/+; DsRed+{ΔupSET}/DsRed+{ΔupSET} line was maintained on cornmeal agar at 20-25C; late embryos were collected on molasses agar egg lay plates at 25C

extract_protocol:
RNA-SEQ: Nascent-RNA sequencing was done using a urea-based method similar to NET-seq (CHURCHMAN AND WEISSMAN 2011; CHURCHMAN AND WEISSMAN 2012), and essentially as reported elsewhere (ALEKSEYENKO et al. 2015).  In short, 1x107 S2 cells were collected by centrifugation at 300 x g at 4°C, and homogenized in CKS buffer + SUPERase•In RNase inhibitor (Ambion AM2696) + ProteaseArrest (G-Biosciences 786-108) with 3 strokes through a 25G needle.  Nuclei were collected by centrifugation and resuspended in CF buffer + RNasin.  NUN buffer was added and samples were vortexed ~30sec until a wispy, filamentous precipitate was apparent.  This precipitate was spun down and washed 3 times with NUN buffer.  Samples were then treated with proteinaseK in CF buffer + 0.5% SDS at 55°C for 30 min.  Samples were then passed through a 25G needle 5 times to disrupt the chromatin, and incubated an additional 30 min at 55°C.  Samples were extracted twice with 25:24:1 phenol:chloroform:isoamyl alcohol, once with 24:1 chloroform:isoamyl alcohol, and ethanol precipitated overnight in the presence of glycogen (Ambion AM9510).  Resulting nucleic acids were treated with RNase-free TURBO DNase (Ambion AM2238) for 30 min at 37°C, with proteinaseK +SDS for an additional 5min at 37°C, and then extracted once each with 25:24:1 phenol:chloroform:isoamyl alcohol and 24:1 chloroform:isoamyl alcohol.  Nascent-RNA was ethanol precipitated overnight except without the addition of glycogen.  Illumina sequencing libraries were constructed using the NEBNext Ultra Directional RNA Library kit (NEB 7420). ChIP-SEQ: Using a protocol essentially described elsewhere (ALEKSEYENKO et al. 2008), 0.1 grams of embryos were collected and disrupted using a motorized pestle.  Formaldehyde was added to 1% final concentration and incubated for 15min at room temperature.  Following quenching of the reaction with glycine and washing, fixed material was sonicated in RIPA buffer using a Bioruptor, 4 cycles of 30s on/ 30s off on the high setting.  Sonicated material was supplemented with TritonX-100 to 1%, Sodium DOC to 0.1%, and NaCl to 140mM, and debris was cleared by centrifugation.  Chromatin was aliquoted and stored at -80°C until IP.  For ChIP, 20-30uL of IgG agarose slurry per IP were washed in RIPA buffer and incubated with chromatin overnight.  Bound immunocomplexes were washed 5x with RIPA (140mM NaCl, 10mM Tris pH8, 1mM EDTA pH8, 1% Triton, 0.1% SDS, 0.1% sodium deoxycholate), once with LiCl buffer(250mM LiCl, 10mM Tris pH8, 1mM EDTA pH8, 0.5% NP40, 0.5% sodium deoxycholate), twice with TE, and finally resuspended in TE.  Input and IPs were treated for 30min with RNase at 37°C, then overnight with the addition of proteinase K and SDS (0.5% final), and crosslinks were reversed for 6hrs at 65°C.  IP samples were supplemented with NaCl to 140mM final, and both IP and input samples were extracted with an equal volume of 25:24:1 phenol:chloroform:isoamyl alcohol.  To maximize recovery in IPs, the organic fraction was extracted with TEN140 (TE+140mM NaCl) and pooled with the initial aqueous phase.  All samples were then extracted with an equal volume of 24:1 chloroform:isoamyl alcohol, and precipitated overnight at -80°C with sodium acetate and ethanol, in the presence of glycogen.  The entirety of the precipitated IP-DNA and ~200ng of input DNA were used to create high-throughput sequencing Illumina libraries using the NEBNext ChIP-seq kit (NEB 6240).  Prior to library amplification, size selection was achieved using a 2% agarose gel (Lonza 50111).
Libraries for sequencing were prepared using standard Illumina protocols.

value: Embryo-derived cell-line

tag: developmental stage

value: Late embryonic stage

value: 2x7bp near start codon, resulting in frameshift after 2-3aa WT


title: Uninjured RNAseq rep2

source_name: uninjured, whole heart - ventricle


title: Nugen, replicate 2, hour 00

description:
rRNA-depleted total RNA
Nu_rep2_hr00


title: dmso2_20dpf

value: Orange-red Hd-dR

value: 20 days post fertilization

value: axial tissue (including bone, fat, muscle, dermis)


title: Nugen, replicate 2, hour 02

description:
rRNA-depleted total RNA
Nu_rep2_hr02


title: Uninjured RNAseq rep1


title: 14dpi H3K27Ac ChIP

description: Mnased chromatin

data_processing:
ChIP-seq reads were aligned to the GRCz10 zebrafish genome assembly using Bowtiewith with parameters “-M 5 -k 1 -I 50 -X 500 --solexa-quals –best”
The positions with anomalously high read counts are potential amplification artifacts and were removed from consideration
Peaks in the ChIP-Seq fragments distribution were identified using the SPP software package with default parameters
Genome_build: GRCz10 zebrafish genome
Supplementary_files_format_and_content: peak files were generated using spp; scores show the enrichment

source_name: undergoing regeneration 14 days after genetic ablation, whole heart - ventricle, ChIP

extract_protocol:
Whole ventricles from 20-30 fish were grinded up and nuclei were extracted using digitonin. Chromatin was then solubilized using micrococcal nuclease. ChIP was performed using the Active Motif H3K27Ac antibody (39136)
Libraries were preapred as described in Bowman et al. BMC Genomics 14:466 (2013)

value: .4 uM 18 hrs

tag: chip antibody

value: H3K27Ac antibody (Active Motif, 39136)


title: nascent_RNA seq_G3_replicate2

tag: genotype

value: 67bp deletion removing 5'UTR and start ATG+10bp CDS


title: nascent_RNA seq_B2_replicate2

value: 1bp deletion resulting in frameshift after 367aa WT


title: Nugen, replicate 1, hour 24

description:
rRNA-depleted total RNA
Nu_rep1_hr24

value: Development on 5 cm nitrocellulose filters, InDA-C rRNA depletion


title: nascent_RNA seq_S2_replicate2

value: wild type


title: control_group_time_1_subject_2

tag: time

value: baseline


title: Nugen, replicate 1, hour 22

description:
rRNA-depleted total RNA
Nu_rep1_hr22


title: Uninjured H3K27Ac ChIP

description: Mnased chromatin

source_name: uninjured, whole heart - ventricle, ChIP

value: transgenic


title: nascent_RNA seq_A7_replicate1


title: nascent_RNA seq_B2_replicate1


title: Nugen, replicate 1, hour 20

description:
rRNA-depleted total RNA
Nu_rep1_hr20


title: Nugen, replicate 1, hour 18

description:
rRNA-depleted total RNA
Nu_rep1_hr18


title: nascent_RNA seq_G3_replicate1


title: 7dpt chip rep2

source_name: proliferating 7 days after Nrg1 stimulated hyperplasia, cardiomyocyte, chromatin pulldown

extract_protocol:
Whole ventricles from 20-30 fish were grinded up and nuclei were extracted using digitonin. Chromatin was then solubilized using micrococcal nuclease.
Libraries were preapred as described in Bowman et al. BMC Genomics 14:466 (2013)

tag: chromatin pulldown

value: streptavidin

value: 4 uM tamoxifen 24 hrs

value: 7 days post incubation

value: cardiomyocyte


title: NMWT3

city: London

first: Ming-Shi

last: Li

state: Greater London

address: Norfolk Place

department: Medicine/Paediatrics

country: United Kingdom

institute: Imperial College London

description: MC58 (wild type)

data_processing:
base calling: Illumina Casava1.7 software
data filtering: base composition analysis for QC; Remove reads with adapters; Remove reads in which unknown bases are more than 10%; Remove low quality reads (the percentage of low quality bases is over 20% in a read, we define the low quality base to be the base whose sequencing quality is no more than 40).
Read alignment: SOAPaligner/SOAP2 with cut off at 5 mismatches
Expression level: The gene expression level is calculated using RPKM (Mortazavi et al., 2008, Nat methods)
Screening of differentially expressed genes (DEGs) was perform using algorithm developed by BGI based on “The significance of digital gene expression profiles” (Audic and Claverie, 1997, Genome Res) and “false discovery rate in multiple testing” (Benjamini and Yekutieli, 2001, The Annals of Statistics)
Genome_build: MC58 (GeneBank:  AE002098.2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values

organism: Neisseria meningitidis MC58

source_name: bacterial isolate

growth_protocol: Neisseria meningitidis was initially cultured on BHI agar plate supplemented with 10% FBS and then subcultured in RPMI1640 with 10% FBS to 0.5 - 0.7 of OD (600)

extract_protocol:
FastRNA Pro Blue kit and FastPrep-24 (MP Biochemicals)
based on RNA fragmentation and standard Illumina protocol

treatment_protocol: Rnase-protect (QIAGEN)


title: NMWT2

description: MC58 (wild type)


title: nascent_RNA seq_S2_replicate1

value: Embryo-derived cell-line

value: Late embryonic stage


title: Nugen, replicate 1, hour 16

description:
rRNA-depleted total RNA
Nu_rep1_hr16


title: UpSET-BioTAP_embryos_input_ChIPseq_replicate2

description: 10_upSET-BioTAP_C_IP_S10.log2.chip.input.tdf

source_name: Developmental Stage Embryo 12-24h

value: Developmental Stage Embryo 12-24h

value: Embryo 12-24h

tag: antibody


title: 7dpt chip rep1


title: 7dpt input

description: Mnased chromatin

source_name: proliferating 7 days after Nrg1 stimulated hyperplasia, whole heart, input

value: none (input)

value: whole heart


title: NMWT1

description: MC58 (wild type)


title: UpSET-BioTAP_embryos_input_ChIPseq_replicate1

description: 9_upSET-BioTAP_A_IP_S9.log2.chip.input.tdf


title: 0419M3

description: MC58 (ΔNMB0419::Kan)

source_name: isogenic mutant


title: Nugen, replicate 1, hour 14

description:
rRNA-depleted total RNA
Nu_rep1_hr14


title: 14dpi chip rep2

source_name: undergoing regeneration 14 days after genetic ablation, cardiomyocyte, chromatin pulldown

value: (cmlc2:H3.3-bio)pd185 ; (Z-CAT)pd36 ; (CreER)pd10

value: .4 uM tamoxifen 18 hrs

value: 14 days post incubation


title: 14dpi chip rep1


title: Nugen, replicate 1, hour 10

description:
rRNA-depleted total RNA
Nu_rep1_hr10

value: Development on 5 cm nitrocellulose filters, InDA-C rRNA depletion


title: UpSET-BioTAP_embryos_IP_ChIPseq_replicate1

value: UpSET


title: Nugen, replicate 1, hour 08

description:
rRNA-depleted total RNA
Nu_rep1_hr08


title: UpSET-BioTAP_embryos_IP_ChIPseq_replicate2


title: coi1_2_Al6h

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

data_processing:
By base calling, the original image data produced by the sequencer is transferred into sequences, which are defined as "raw reads"(or "raw data") and saved as ".fastq" files. As the raw reads may contain low quality reads and or adaptor sequences, preprocessing is necessary before starting further analysis. Normally, data cleaning (or data filtering) is performed to obtain "clean reads" (or "clean data") for further analysis.
As there are some adaptor sequences and/or low quality reads present in the raw reads, data filtering is carried out to obtain high quality reads as the clean reads (clean data). The procedure include following steps: 1. Remove reads with adaptor sequences. 2. Remove reads in which the percentage of unknown bases (N) is greater than 10%. 3. Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, we define this read as low quality
The gene expression level is calculated by using RPKM[Mortazavi et al. (2008). Nature Methods. 5(7): 621-8] method (Reads Per kb per Million reads),
Genome_build: Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2[Li R et al. (2009) Bioinformatics, 25 (15). 1966-1967.]. No more than 2 mismatches were allowed in the alignment
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: roots_with Al

growth_protocol: The seedlings were pre-grown in 2% modified MGRL solution for 6 d at pH 5.0 in a growth chamber with a 16/8 h light/dark cycle at 22 oC.

extract_protocol:
Total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN GmbH, Qiagen, GmbH, Hilden, Germany) following the manufacturer’s protocol.  RNA libraries were prepared for sequencing using standard Illumina protocols
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.

treatment_protocol: Approximately 500 seedlings (6-d-old) of both the wild-type Col and coi1-2 mutant line were exposed to a 2% MGRL solution containing 0 or 10 μM AlCl3 (pH 5.0). After 6 h, the roots were sampled for RNA isolation.

value: root

tag: age

value: six days

tag: treament

value: with Al


title: 14dpi input

description: Mnased chromatin

source_name: undergoing regeneration 14 days after genetic ablation, whole heart, input

value: transgenic


title: Uninjured chip rep3

source_name: uninjured, cardiomyocyte, chromatin pulldown

value: streptavidin

value: 7 days post incubation


title: WT2

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Peptoclostridium difficile R20291 whole genome sequence using bowtie v1.0.1 with parameter -k 2000
MAP2COV was used for counting genes with parameters -t RNA -b YES
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied on each strand coverage count with the WT as a reference
Genome_build: Peptoclostridium difficile R20291 (FN545816.1)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts (∆tcdR, WT), Normalized Counts (∆tcdR, WT), Statistics (FC, pvalue, significant)

organism: Clostridioides difficile

source_name: Wild type strain R20291

growth_protocol: Strains were grown aerobically in TY 18h at 37°C

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

tag: subsp.

value: strain

value: wild type


title: Uninjured chip rep2

value: cardiomyocyte


title: coi1_2_Al0h

source_name: roots_without Al

tag: genotype/variation

value: without Al


title: Nugen, replicate 1, hour 06

description:
rRNA-depleted total RNA
Nu_rep1_hr06

source_name: Cells developing on nitrocellulose filters

tag: growth media

tag: treatment


title: Nugen, replicate 1, hour 04

description:
rRNA-depleted total RNA
Nu_rep1_hr04

tag: time point (hour)

tag: replicate


title: Uninjured chip rep1

tag: expression


title: Nugen, replicate 1, hour 02

description:
rRNA-depleted total RNA
Nu_rep1_hr02

tag: strain


title: tcdR2

source_name: Mutant tcdR of strain R20291

value: Mutant tcdR


title: Uninjured input

description: Mnased chromatin

source_name: uninjured, whole heart, input

value: none (input)

tag: cell type

value: whole heart


title: Col_Al0h

tag: tissue

value: Col


title: Nugen, replicate 1, hour 00

description:
rRNA-depleted total RNA
Nu_rep1_hr00


title: tcdR1


title: 0419M2

description: MC58 (ΔNMB0419::Kan)


title: WT1


title: stv-1 Rep1

status: Public on Mar 06 2017

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: small RNA

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with trimmed mean of M values (TMM) normalization method. Robinson and Oshlack Genome Biology 2010.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is MicroRNA gene IDs and the second column is normalized reads counts

source_name: flowers and flower buds

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol: Illumina small RNA library protocol

value: flowers and flower buds


title: stv-1  Rep2

description: small RNA


title: Wild type Rep1

description: small RNA


title: Wild type  Rep2

description: small RNA


title: 0419M1

description: MC58 (ΔNMB0419::Kan)


title: b13_HR

city: Sherbrooke

first: Jean-Francois

last: Lucier

state: Quebec

address: 2500, boulevard de l'Université

department: Département de Biologie

country: Canada

institute: Université de Sherbrooke

description: processed data file: HR1_vs_control_1_gene_exp.diff.gz

data_processing:
The quality of the raw reads was confirmed using FastQC (v0.10, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by alignment on the TAIR10 assembly of A. thaliana Col-0 genome using TopHat (v2.0.8) (Trapnell et al., 2009) with default parameters “q10”. CuffDiff (v2.1.1) (Trapnell et al., 2013) was then used with parameters frag-bias-correct, multi-read-correct and the genome annotations file from NCBI 2013-03-06
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values of triplicate control or defense samples together with differential expression analysis (Log2FC, FDR)

source_name: DEX treatment_ribosome IP

growth_protocol: Arabidopsis thaliana Avr/L18 transgenic line was grown in soil under 16 hours light-8 hours dark cycles at 22°C

extract_protocol:
Cellular extracts of Arabidopsis Avr/L18 at 2h after spraying with DEX (30μM) or water (control) were prepared for ribosome IP followed by RNA purification as previously described (Mustroph et al., 2009a; Zanetti et al., 2005). Total RNA was purified from the same extract in parallel using QIAgen RNA purification kit.
RNAseq libraries were constructed as described elsewhere (Carraro et al., 2014).

treatment_protocol: DEX 30 uM or Mock treatment (Water) for 2h

value: 4 week old

tag: treated with

value: DEX 30 uM for 2 hrs

value: leaves

tag: molecule subtype

value: ribosome IP, rRNA-depleted RNA


title: b14_HR

tag: genotype


title: b11_control

source_name: control_ribosome IP

value: water (mock control) for 2hr


title: b12_HR


title: b9_control


title: b4_HR

description: processed data file: HR2_vs_control_2_gene_exp.diff.gz

source_name: DEX treatment_total RNA

value: total RNA, rRNA depleted


title: b5_HR


title: b6_HR


title: b3_control

source_name: control_total RNA


title: Col_Al6h

value: root

value: six days

value: with Al


title: b1_control


title: b2_control


title: NAMEC5 ITGB4lo rep 3 lane 6

city: Cambridge

first: Brian

last: Bierie

address: 455 Main St

institute: Whitehead Institute

description:
mRNA
NAMEC5_6

data_processing:
RNA-Seq reads from Illumina 1.5 encoding were aligned using TopHat (v 2.0.13) to the human genome (GRCh37) with Ensembl annotation (GRCh37.75) in gtf format: default parameters were used, except for base encoding.
HTSeq-count was used to obtain counts with intersection-strict mode and strand=reverse.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.htseqcount.new.txt: Raw counts from HTSeq-count.

source_name: Mammary epithelial cells

growth_protocol: NAMEC cell lines were grown in complete MEGM medium, MDA-MB231 cells were grown in DMEM + 10% FBS, and SUM159 cells were grown in F12 + 5% IFS + 5ug/ml insulin + 1ug/ml hydrocortisone.

extract_protocol:
Total RNA was prepared using a modified TRIzol protocol. To prepare total RNA, 1ml of TRIzol reagent was added to a sub-confluent 10cm dish of cells, scraped, then placed in a microfuge tube. Microfuge tubes were flash frozen on dry ice. Samples were then thawed and 200ul of chloroform was added to each tube, shaken vigorously by hand for 15 seconds, and incubated at room temperature for 3 minutes then centrifuged at 13,000g for 15 minutes. The aqueous phase was removed and placed into a gDNA elimination column from the RNeasy Plus kit (Qiagen). The eluate was mixed at a 1:1 ratio with 70% RNase-free EtOH and purified following the remaining steps outlined in the RNeasy Plus kit. Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling were done using the Standard Illumina pipeline, and then demultiplexed into fastq files.
RNA-seq libraries were prepared using the TruSeq stranded polyA mRNA kits as described by the manufacturer (Illumina RS-122-2101).

treatment_protocol: RNA was collected 48 hours after seeding cells in their respective normal growth medium.

tag: cell line

value: Mammary epithelial cells

tag: itgb4 level

value: lo


title: Nugen, replicate 1, hour 12

description:
rRNA-depleted total RNA
Nu_rep1_hr12

value: Development on 5 cm nitrocellulose filters, InDA-C rRNA depletion


title: NAMEC5 ITGB4lo rep 2 lane 6

description:
mRNA
NAMEC5_5


title: NAMEC5 ITGB4lo rep 3 lane 5

description:
mRNA
NAMEC5_3


title: NAMEC5 ITGB4lo rep 1 lane 6

description:
mRNA
NAMEC5_4


title: NAMEC1 ITGB4lo rep 3 lane 6

description:
mRNA
NAMEC1_6


title: b10_control

tag: age


title: NAMEC5 ITGB4lo rep 1 lane 5

description:
mRNA
NAMEC5_1


title: NAMEC1 ITGB4lo rep 1 lane 6

description:
mRNA
NAMEC1_4


title: NAMEC1 ITGB4lo rep 3 lane 5

description:
mRNA
NAMEC1_3


title: NAMEC1 ITGB4lo rep 2 lane 6

description:
mRNA
NAMEC1_5


title: NAMEC1 ITGB4lo rep 1 lane 5

description:
mRNA
NAMEC1_1


title: MDA231 ITGB4lo rep 3 lane 4

description:
mRNA
2514_231_lo

source_name: Mammary carcinoma cells

value: Mammary carcinoma cells


title: NAMEC1 ITGB4lo rep 2 lane 5

description:
mRNA
NAMEC1_2


title: MDA231 ITGB4lo rep 2 lane 4

description:
mRNA
2499_231_lo


title: MDA231 ITGB4hi rep 2 lane 4

description:
mRNA
2500_231_hi

value: hi


title: MDA231 ITGB4hi rep 1 lane 4

description:
mRNA
2480_231_hi


title: MDA231 ITGB4lo rep 1 lane 4

description:
mRNA
2479_231_lo


title: SUM159 ITGB4hi rep 3 lane 3

description:
mRNA
2065_159_hi


title: SUM159 ITGB4lo rep 2 lane 3

description:
mRNA
2052_159_lo


title: SUM159 ITGB4lo rep 3 lane 3

description:
mRNA
2064_159_lo


title: SUM159 ITGB4hi rep 1 lane 3

description:
mRNA
2020_159_hi


title: NAMEC8 ITGB4hi rep 3 lane 2

description:
mRNA
N8_hi_6


title: NAMEC5 ITGB4lo rep 2 lane 5

description:
mRNA
NAMEC5_2


title: NAMEC8 ITGB4hi rep 1 lane 2

description:
mRNA
N8_hi_4


title: NAMEC8 ITGB4hi rep 2 lane 2

description:
mRNA
N8_hi_5


title: NAMEC8 ITGB4lo rep 2 lane 2

description:
mRNA
N8_lo_5


title: NAMEC8 ITGB4hi rep 2 lane 1

description:
mRNA
N8_hi_2


title: NAMEC8 ITGB4lo rep 1 lane 2

description:
mRNA
N8_lo_4


title: NAMEC8 ITGB4hi rep 3 lane 1

description:
mRNA
N8_hi_3


title: NAMEC8 ITGB4lo rep 3 lane 1

description:
mRNA
N8_lo_3


title: SUM159 ITGB4lo rep 1 lane 3

description:
mRNA
2021_159_lo


title: NAMEC8 ITGB4hi rep 1 lane 1

description:
mRNA
N8_hi_1


title: NAMEC8 ITGB4lo rep 2 lane 1

description:
mRNA
N8_lo_2


title: NAMEC8 ITGB4lo rep 3 lane 2

description:
mRNA
N8_lo_6


title: NAMEC8 ITGB4lo rep 1 lane 1

description:
mRNA
N8_lo_1


title: ZNF90

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

institute: EPFL

data_processing:
Raw sequences were filtered according to the Purity flag using Illumina CASAVA-1.8 FASTQ Filter software before further processing.
Reads from each KRAB-ZNF library were mapped on GRCh37g1k (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/) using Bowtie2 (version 2.2.1) with the “very-sensitive-local” setting. Mapped reads were compressed in BAM files and indexed using SAMtools version 1.18.
We used MACS (version 1.4.2.1) with the “keep-dup all” parameter, which is recommended for ChIP-exo as genuine reads can accumulate on a few positions following exonuclease digestion.  We devised a strategy based on random sampling of few reads from all ChIP-exo to build a composite total input, and verified that regions yielding very high signal for any one particular KRAB-ZNF were not enriched in our composite total input. An extensive filtering strategy was put in place as we found MACS to be prone to call peaks in various problematic regions of the human genome. Briefly, we filtered out peaks that would meet either of those criteria: MACS score < 80 (equivalent to a p-value of 1x10-8); within the blacklist of regions prone to false positives devised by ENCODE; ratio of forward vs. reverse strand reads greater than 4; less than 20 reads over 500 bp per 15 million reads; normalized read count was less than 2 fold over the control.
Genome_build: GRC h37 g1k
Supplementary_files_format_and_content: BED files from MACS after filtering to remove common artifacts

source_name: transduced 293T cell line

growth_protocol: Human embryonic kidney-derived 293T cells  were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2. Human embryonic stem cells (Line H1) were cultured in mTeSR1 medium (Stem Cell Technologies) on Matrigel (BD Biosciences) and in the presence of ROCK inhibitor (Y-27632, Stem Cell Technologies).

extract_protocol:
Chromatin was prepared by resuspending 3x107 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follow: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
ChIP-exo was performed on bead-bound chromatin as described (Rhee and Pugh, 2011), with adaptations for use in 96-well plates and Illumina sequencing (detailed protocol available in Supplemental Information of the manuscript associated with this GEO entry).

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/mL) for 7 days and induced using doxycyclin (1 ug / mL) for a few days before fixation with formaldehyde (1% for 10 min).

tag: host cell line

value: HEK 293T

tag: tagged protein


title: ZNF8


title: ZNF93


title: ZNF880


title: MDA231 ITGB4hi rep 3 lane 4

description:
mRNA
2513_231_hi


title: ZNF891


title: SUM159 ITGB4hi rep 2 lane 3

description:
mRNA
2051_159_hi


title: ZNF879


title: ZNF860


title: ZNF85


title: ZNF823


title: ZNF816


title: ZNF81


title: ZNF808


title: ZNF805


title: ZNF7


title: ZNF79


title: ZNF799


title: ZNF793-replicate 2


title: ZNF793


title: ZNF786


title: ZNF792


title: ZNF790


title: ZNF791


title: ZNF785


title: ZNF789


title: ZNF780A


title: ZNF846


title: ZNF84


title: ZNF766


title: ZNF777


title: ZNF776


title: ZNF778


title: ZNF77


title: ZNF75D-replicate 2


title: ZNF764


title: ZNF765


title: ZNF75D


title: ZNF74


title: ZNF737


title: ZNF749


title: ZNF736


title: ZNF783


title: ZNF708


title: ZNF707


title: ZNF716


title: ZNF714


title: ZNF730


title: ZNF705G


title: ZNF69


title: ZNF782


title: ZNF682-replicate 2


title: ZNF684


title: ZNF695


title: ZNF680-replicate 2


title: ZNF681


title: ZNF680


title: ZNF669


title: ZNF667


title: ZNF674


title: ZNF662


title: ZNF671


title: ZNF649


title: ZNF641


title: ZNF626


title: ZNF621


title: ZNF619


title: ZNF701


title: ZNF682


title: Control CD1a+ replicate 3

city: Duarte

first: chintan

last: parekh

state: California

address: 1500 east duarte

department: Pediatrics

institute: Children's Hospital Los Angeles

description: Sample 10

data_processing:
Read alignment: Tophat v2.0.14 was used to align paired end reads to the human transcriptome and genome (hg 19)
Estimation of gene level counts: HTseq v0.6.1p1, whole genome annotation file of protein coding and long non-coding RNA genes published in Casero et al, Nature Immunology 2015 (PMID: 26502406) was used for the Htseq analysis.
Differential expression analysis: DESeq2, experiment identifier (experiment number 1, 2 or 3) was used as a covariate
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts for genes (HTseq output)

source_name: Control CD1a+

growth_protocol: CD34+ cord blood (CB) cells were transduced with knockdown or scrambled control shRNA (multiplicity of Infection [MOI]=10) lentivirus. CD34+GFP+lin- CB cells were sorted (fluorescence activation cell sorting, FACS) and then co-cultured with OP9DLL1. The medium for OP9DLL1 co-cultures medium consisted of alpha-MEM (ThermoFisher), 20% fetal bovine serum (FBS, Hyclone, lot no. AXF42576), L-glutamine (2 mM, Cellgro, Manassas, VA), Pencillin-streptomycin (0.5X, CellGro), IL-7 (5 ng/ ml), and Flt3 ligand (5 ng/ml). On day 14 of co-culture, CD45+GFP+CD7+CD1a- and CD45+GFP+CD7+CD1a+ T-cell precursors were isolated from control and knockdown co-cultures  by FACS and analyzed by RNA-Seq to determine the effect of BCL11B knockdown on the transcriptome of T-cell precursors.

extract_protocol:
The Trizol method (Mirneasy RNA extraction mini kit, Qiagen, Valencia, CA) was used to extract total RNA from  CD45+GFP+CD7+CD1a- and CD45+GFP+CD7+CD1a+ T-cell precursors isolated by FACS on day 14 of cord blood cells-OP9DLL1 co-cultures .
The Ovation Human FFPE RNA‑Seq System (NuGen) was used to convert 25 ng of total RNA from T-cell precursors into amplified cDNA libraries. The cDNA was sheared using a S220 focused ultrasonicator (Covaris, Woburn, MA) to generate an average fragment size of 300 base pairs. twenty cycles of PCR were used to ampify the libraries.
Libraries were sequenced on Illumina Nextseq500 (paired end 75 base pair sequencing)

treatment_protocol: CD34+ enriched cord blood cells (enriched by magnetic activated cell sorting) were cultured for 16 hours in 100 microliters of transduction medium (X-Vivo 15 [Lonza, Walkersville, MD], thrombopoietin [50ng/ml], FLT3 ligand (50 ng/ ml], Stem cell factor [50 ng/ ml], and l-glutamine [2 mM, Cellgro, Manassas, VA]) on retronectin (50 ng/ ml, Clontech) coated non tissue culture treated 48 well plates (100,000 cells/ well). ShRNA Lentiviral supernatant (multiplicity of infection=10) along with additional transduction medium (to achieve a 1:1 volume ratio for supernatant and transduction medium) was then added. 125 microliters of transduction medium was added 24 hours after the dose of lentivirus. After 48 hours of exposure to lentivirus, CD34+GFP+lin(CD3, CD4, CD8,CD19)- cells were sorted for co-culture with OP9DLL1 stroma.

value: Cord blood CD34+ cells

tag: transduced with

value: scrambled control shRNA lentivral vector containing a GFP reporter

tag: cell populatione

value: CD45+GFP+CD7+CD1a+ T-cell precursors

tag: experiment number


title: ZNF616


title: Knockdown CD1a+ replicate 3

description: Sample 12

source_name: Knockdown CD1a+

value: BCL11B knockdown shRNA lentivral vector containing a GFP reporter


title: ZNF613


title: Knockdown CD1a+ replicate 2

description: Sample 8


title: Control CD1a- replicate 3

description: Sample 9

source_name: Control CD1a-

value: CD45+GFP+CD7+CD1a- T-cell precursors


title: Knockdown CD1a- replicate 3

description: Sample 11

source_name: Knockdown CD1a-


title: ZNF614


title: ZNF675


title: ZNF611


title: Control CD1a- replicate 2

description: Sample 5


title: ZNF610


title: ZNF615


title: ZNF605


title: Knockdown CD1a+ replicate 1

description: Sample 4


title: Knockdown CD1a- replicate 1

description: Sample 3


title: Control CD1a+ replicate 1

description: Sample 2


title: ZNF587


title: ZNF585A


title: ZNF620


title: ZNF627


title: Control CD1a- replicate 1

description: Sample 1


title: ZNF584


title: ZNF582


title: CD34- cells-replicate 2-control

data_processing:
Read alignment: Bowtie2 (version 2.2.6) was used to align reads to the human genome (hg 19).
Peak calling: MACS2 version 2.1.0 (BAMPE mode, default q value cutoff of 0.01 ), peaks for each IP sample called relative to its corresponding control. Reads with a mapping quality below 30 were removed prior to inputting reads into MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: thymus

growth_protocol: CD34+ and CD34- cells were isolated from human thymuses using the magnetic activated cell sorting (MACS) system. The CD34+ fraction showed >85% purity for CD34+ cells when measured by FACS. Two biological replicates were sequenced for each cell type. One replicate was derived from  cells pooled from two thymuses. The other replicate was derived from cells from a separate  thymus.

extract_protocol:
CD34+ (19-29×106 cells) or CD34- (60×106 cells) cells were treated with 1% formaldehyde for 10 minutes, which was followed by chromatin shearing with micrococcal nuclease to an average size of 150 base pairs.  An aliquot of precleared chromatin was incubated with 1µg of anti-Bcl11b (IP) or 1µg of isotype control (control) antibody (antibodies from Cell Signaling) followed by hybridization to 30μl of Protein G Magnetic Beads for 3 hours. The protein-DNA complexes were eluted, and incubated with proteinase K to digest protein. The eluate was reverse crosslinked by incubation at 65°C for 2 hours. DNA was purified with a DNA purification kit (Cell Signaling).
Libraries were made with the Next Ultra™ DNA Library Prep Kit (NEB) (input=5 ng of ChIP DNA)
Libraries were sequenced on Illumina Nextseq500 (paired end 75 base pair sequencing)

tag: chip antibody

value: Isotype control


title: CD34- cells-replicate 2-IP

treatment_protocol: CD34+ and CD34- cells were isolated from human thymuses using the magnetic activated cell sorting (MACS) system. The CD34+ fraction showed >85% purity for CD34+ cells when measured by FACS. Two biological replicates were sequenced for each cell type. One replicate was derived from  cells pooled from two thymuses. The other replicate was derived from cells from a separate  thymus.

tag: replicate


title: CD34+ cells-replicate 2-control


title: ZNF571


title: Knockdown CD1a- replicate 2

description: Sample 7


title: ZNF573


title: CD34+ cells-replicate 2-IP


title: ZNF570


title: Control CD1a+ replicate 2

description: Sample 6


title: CD34- cells-replicate 1-IP


title: ZNF567


title: ZNF566


title: CD34+ cells-replicate 1-IP


title: CD34+ cells-replicate 1-control


title: ZNF564


title: ZNF562


title: Control replicate 3

data_processing:
Read alignment: Tophat v2.0.14 was used to align paired end reads to the human transcriptome and genome (hg 19)
Estimation of gene level counts: HTseq v0.6.1p1, whole genome annotation file of protein coding and long non-coding RNA genes published in Casero et al, Nature Immunology 2015 (PMID: 26502406) was used for the Htseq analysis.
Differential expression analysis: DESeq2, experiment identifier (experiment number 1, 2 or 3) was used as a covariate
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: T-ALL cells

growth_protocol: Primagraft T-ALL cells (xenografted primary T-ALL cells) were generated by serial transplantations of deidentified bone marrow cells from a pediatric patient with relapsed T-ALL in NOD/SCID/IL2Rγ-/- mice. Primagraft T-ALL cells were cultured in alpha-MEM, 20% FBS, L-glutamine (2 mM), and Penicillin-streptomycin (0.5X). Primagraft cells at different passages of culture were transduced with a BCL11B expression or a control lentiviral vector (MOI=1), and 72 hours later, GFP+ cells were isolated by FACS for RNA-Seq.

extract_protocol:
The Trizol method (Mirneasy RNA extraction mini kit, Qiagen, Valencia, CA) was used to extract total RNA from  GFP+ T-ALL cells isolated by FACS at 72 hours post transduction.
The Ovation Human FFPE RNA‑Seq System (NuGen) was used to convert 25 ng of total RNA from GFP+ T-ALL cells into amplified cDNA libraries. The cDNA was sheared using a S220 focused ultrasonicator (Covaris, Woburn, MA) to generate an average fragment size of 300 base pairs. twenty cycles of PCR were used to ampify the libraries.
Libraries were sequenced on Illumina Nextseq500 (paired end 75 base pair sequencing)

treatment_protocol: T-ALL Cells were plated in 24 well tissue culture treated plates (300,000 cell/ well) in lentiviral supernatant (MOI=1) mixed with 300 microliters of culture medium/ well. After 24 hours an additional 300 microliters of culture medium was added. After 48 hours of exposure to lentivirus, the cells were washed with DPBS and then replated in 500 microliters of culture medium. After a further 24 hours, transduced (GFP+) cells were sorted for RNA-Seq (n=3 experiments).

tag: overexpressing or control

value: control

tag: passage


title: BCL11B replicate 3

value: overexpressing


title: BCL11B replicate 2


title: ZNF561


title: ZNF555


title: Control replicate 2


title: Control replicate 1


title: ZNF552


title: BCL11B replicate 1


title: ZNF550


title: SUZ12kd-gapmer_04

first: Caroline

middle: J.

last: Woo

state: Massachusetts

address: 200 Sidney Street

institute: RaNA Therapeutics Inc.

data_processing:
Fastq generation: bcl2fastq v2.17.1.14
Read quality and adapter trimming:  Trimmomatic (version 0.35) modules and settings: Crop, 150 bp; IlluminaClip 2 seed mismatches, paired end seed score of 30, single end seed score of 10, minimum adapter length of 2, and keeping both reads; SlidingWindow, window size of 10 bp, minimum average phred score of 15; reads discarded if length below 36 bases.
rRNA depletion: Trimmed reads were aligned against human rRNA sequences with bowtie2 v. 2.1.0, all reads that successfully aligned were removed
Alignment: STAR v. 2.5.1a performed alignment using a modified version of hg38 reference genome that had the SMN2 containing chromosomal segment duplication (chr5:69,924,952-70,129,737) masked
Raw gene count generation: HTseq-count version 0.6.1 counted reads that overlapped features in the Gencode v24 Homo sapiens primary assembly annotation gtf (ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_24/gencode.v24.primary_assembly.annotation.gtf.gz). Parameters: mode, intersection-nonempty; minaqual, 0; stranded, reverse
Gene expression filter: Raw counts were imported into R version 3.2.3 and converted into log2 counts per million. Lowly expressed genes across the samples were filtered using a mixture model from the SCAN.UPC R package version 2.12.1
Data normalization and transformation: After filtering, the TMM normalization was applied to the data (found in the edgeR package, v 3.12.0). Count data was then transformed using the voom transform found in limma v. 3.26.7
Differential expression: Limma v 3.26.7 was used to fit the normalized, transformed data to a linear model blocking time and comparing each treatment versus the mock samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files for each sample include raw paired end counts for each gene (gene identifiers are based on Gencode v24 gtf file at ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_24/gencode.v24.primary_assembly.annotation.gtf.gz)

source_name: GM09677 SMA fibroblasts, SUZ12kd-treated

growth_protocol: GM09677 fibroblasts were plated a 24-well tissue culture plate at 4 x 104 cells/well in DMEM containing 10% FBS and 1x non-essential amino acids. Cells were passaged every 2-3 days with 0.025% trypsin-EDTA to 50% confluency.

extract_protocol:
The cells were harvested with TRIzol (Life Technologies) at either day 2 or day 3 for RNA.
RNA-Seq libraries were prepared using Illumina's TruSeq mRNA Library Prep kit according to manufacturers LT (low-throughput) protocol. Briefly, mRNA was isolated from total template RNA using oligo-dT beads, first strand cDNA was synthesized using kit provided actinomycin-D mix with added SuperScript III reverse transcriptase (Invitrogen), followed by second strand synthesis using a marking mix that incorporates dUTP in place of dTTP. 3' ends of ds-cDNA were adenylated with a single 'A' nucleotide to serve as a complementary overhang for ligation of the single 'T' of indexed Illumina sequence adapters. Adapter ligated fragments were size selected using a double-sided SPRI bead clean-up (Ampure-XP, Beckman Coulter) to target fragments in the ~300 base pair range. Purified, size selected library fragments then underwent 15 cycles of PCR amplification before a final SPRI bead clean-up to remove primer dimers. Library fragments were sized using the DNA 1000 protocol for the BioAnalyzer 2100, and final library quantification was performed using the Kapa Library Quantification qPCR Kit for Illumina (Kapa Biosystems). Libraries were then pooled, and multiplex sequencing was performed on the Illumina NextSeq 500 using a 300 cycle high output kit according to manufacturers instructions. A total of two high output runs were performed using the same multiplexed library pool in order to achieve the desired quantity of reads per sample.

treatment_protocol: GM09677 fibroblasts were plated a 24-well tissue culture plate at 4 x 104 cells/well in DMEM containing 10% FBS and 1x non-essential amino acids. Cells were transfected the following day at 75% confluency with Lipo2000 (Life Technologies) with either no oligo, RN-0005, or SUZ12 gapmer at a final concentration of 15 nM.

tag: treatment

tag: time point

tag: batch

value: eye lens fibroblast culture

tag: gender

value: male


title: CD34- cells-replicate 1-control

tag: cell type


title: ZNF565


title: ZNF549


title: RN-0005_04

source_name: GM09677 SMA fibroblasts, RN-0005 treated

tag: cell line


title: ZNF549-replicate 2


title: ZNF548


title: ZNF543


title: RN-0005_03


title: SUZ12kd-gapmer_03


title: ZNF540


title: mock_03

source_name: GM09677 SMA fibroblasts, mock controls

value: mock


title: mock_04


title: ZNF558


title: SUZ12kd-gapmer_02


title: ZNF534


title: ZNF530


title: ZNF557


title: ZNF529


title: ZNF528


title: ZNF527


title: ZNF525


title: mock_01


title: mock_02


title: RN-0005_01


title: ZNF506


title: ZNF547


title: ZNF496


title: ZNF487


title: ZNF485


title: ZNF492


title: ZNF479


title: ZNF484


title: ZNF483


title: SUZ12kd-gapmer_01


title: ZNF468


title: ZNF480


title: RN-0005_02


title: ZNF44


title: ZNF441


title: ZNF443


title: ZNF442


title: ZNF454


title: ZNF45


title: WT_RNA_rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
For ChIP: reads aligned to reference using bowtie version 1.0.0 using parameters –best
For ChIP: bigWig files were generated by getting a ratio of IP over Input in 1 kb bins (H3, H3K9me3, PML) and consist of raw counts (H3.3 and H3K27me3)
For ChIP: peaks called using Enriched Domain Detector (H3, PML) and RSEG (H3.3, H3K27me3, H3K9me3)
For RNA: reads aligned with tophat v2.0.8b with parameter –-b2-very-sensitive and -G
For RNA: transcript abundance estimated with cufflinks v2.2.1 with parameter -–GTF -b and -u
For RNA: reference gtf with cuffmerge v2.2.1 with parameters -g, -s
For RNA: diffrential expression analysis with cuffdiff v2.2.1 with parameters -b, -u
For RNA: csv file created from cuffdiff output file genes.fpkm_tracking
Genome_build: mm10
Supplementary_files_format_and_content: [ChIP-Seq] bigWig files for viewing in Genome Browser; bed files with columns: Chromosome, Start, End, Score; or columns: Chromosome, Start, End, Name/Blank, Score; or columns: Chromosome, Start, End, Name/Blank, AverageCount, DomainScore, Strand
Supplementary_files_format_and_content: [RNA-Seq] .cvs file reports FPKMs

source_name: Mouse embryonic fibroblasts, wild-type

growth_protocol: MEFs isolated from wild-type and Pml-null mice (C57BL/6 background) were cultured in T175 flasks in DMEM/F12 supplemented with 10% fetal calf serum and 1% penicillin streptomycin. Cells were cultured to confluency prior to ChIP.

extract_protocol:
For ChIP-seq: Cells (10e7 cells/ChIP) were harvested and fixed with 1% formaldehyde for 10 min before quenching with 125 mM glycine. Cells were lysed for 30 min at 4C on a rotator in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% deoxycholate, 1 mM PMSF, protease inhibitor cocktail) adjusted to 1% SDS, and sonicated 3 times 15 min in a Bioruptor® (Diagenode). After sedimentation at 10,000 g for 10 min, the supernatant was collected and diluted 10x in RIPA buffer without SDS to constitute input chromatin. Chromatin was incubated overnight at 4oC on a rotator with antibodies coupled to magnetic Dynabeads Protein G. ChIP samples were washed 3 times in ice-cold RIPA buffer. Crosslinks were reversed and DNA eluted for 6 h at 37C in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS, 0.5 µg/ml RNase A, and 2 µg/ml Proteinase K added twice. DNA was purified and dissolved in H2O.For RNA-seq: 10e6 cells were cultured. Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation.
Sequencing library was prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 and NextSeq500 at the Norwegian Sequencing Center.

treatment_protocol: Cells were cultured under proliferating conditions until confluency. When confluent, cells  were harvested by trypsinization  and crosslinked for ChIP (H3K9me3, H3K27me3, PML). Cells were also collected and transfected using a nucleofector (Amaxa) with relevant plasmids (H3.3-Flag or H3.3-HA), with or without transfection with relevant siRNAs as described in the acompanying paper. After transfection(s), cells were reseeded and cultured as above prior to harvest and crosslinking for ChIP.  For RNA-seq experiments, only native cells (non-transfected) were used.

tag: strain

value: MEF

tag: genotype/variation

value: wild-type

tag: passages

value: Passage 10-15

tag: state/treatment

value: Proliferating, untreated


title: ZNF445

tag: host cell line

tag: tagged protein


title: ZNF440


title: WT_RNA_rep2


title: ZNF439


title: ZNF519


title: WT_RNA_rep1


title: ZNF486


title: ZNF433


title: WT_H33_HA

value: anti-HA (Abcam, catalog# ab-9110, lot# GR235874-8)


title: PMLKO_RNA_rep2

source_name: Mouse embryonic fibroblasts, PML knock-out

value: PML knock-out


title: PMLKO_RNA_rep3


title: ZNF430

value: HEK 293T


title: ZNF431


title: ZNF460


title: ZNF429


title: ZNF425


title: PMLKO_RNA_rep1


title: PMLKO_H33_HA


title: PMLKO_PML

value: anti-PML (Millipore, catalog# 05-718, lot# 2684855)


title: ZNF419


title: ZNF419-replicate 2


title: ZNF398


title: ZNF3


title: ZNF383


title: ZNF382


title: ZNF382-replicate 2


title: ZNF418


title: ZNF432


title: ZNF417


title: ZNF343


title: ZNF33B


title: ZNF33A-replicate 2


title: ZNF334


title: ZNF33A


title: ZNF354A


title: ZNF337


title: ZNF331


title: ZNF324


title: ZNF324B


title: ZNF320


title: ZNF333


title: total scnRNAs from wild-type cells @10.5 hpm [10992]

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
26-32-nt RNAs that map uniquely to the MIC genome were analyzed
Supplementary_files_format_and_content: Normalized numbers (RPKM) of RNAs that map the compiled Type-A or Type-B IESs (Noto et al. [2015] Mol. Cell 59, 229-242) are shown as histograms with 10-b bin
Supplementary_files_format_and_content: Normalized numbers (RPKM) of RNAs that map the MIC supercontigs (http://ciliate.org/index.php/home/downloads) are shown as histograms with 100-b bin

organism: Tetrahymena thermophila

source_name: Conjugating cells at 8 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol:
Total RNA was prepared using Tri-zol reagent
RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24


title: ZNF304


title: ZNF354B


title: MLL4 ChIPSeq_D7_in_3T3L1

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
ChIP-seq reads and FAIRE-seq reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Peaks of ChIP-seq and FAIRE-seq were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-seq of others: Windows (50), Gaps (50), FDR (1e-10); For FAIRE-seq: Windows (50), Gaps (50), E-value (1000)
Paired-end reads of RNA-seq are aligned to the mm9 genome assembly using TopHat (v2.0.10) with default parameters. Cufflinks (v1.0.3) was used to calculate the fragments per kilo base per million (FPKM) as expression measurements for each gene as annotated in RefSeq with default parameters.
For single-end RNA-seq, reads were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters  Aligned reads on exonic regions from RNA-Seq were used to calculate RPKM to measure the gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq data, wig files were generated using in-house script and the scores represent RPKM; For RNA-seq data, tab-delimited text files were generated to include FPKM/RPKM values for each gene.

source_name: 3T3L1 preadipocyte cell

growth_protocol: Primary brown preadipocytes were isolated from interscapular BAT of newborn Pparγf/f, Mll3-/-Mll4f/f, or Brd4f/f mice (Jackson no. 004584) and immortalized with SV40T-expressing retroviruses generated from the pBabepuro-large T plasmid

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. At D0, confluent cells were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin. At D2, D4, and D6, the cells were replenished with medium containing 10% FBS, 0.02 μM insulin, and 1 nM T3.

value: immortalized white preadipocytes

tag: stage of adipogenesis

value: Mature adipocytes (D7)

value: Anti-MLL4 #3 (Home-made)


title: ZNF30


title: Input_D7_in_3T3L1

tag: chip antibody


title: input_for_CBP_ChIPSeq_D7_rep

source_name: Brown preadipocyte cell

value: immortalized Brd4-flox/flox brown preadipocytes


title: ZNF302


title: RNA_D7_rep

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_D0_rep

value: Confluent (D0)


title: CBP_ChIPSeq_D7_rep

value: CBP (D6C5) Rabbit mAb (Cell Signaling Technology, Lot 7389S, Batch 1)


title: ZNF28


title: RNA_D-3_rep

value: Proliferating (D-3)


title: ZNF2


title: ZNF287


title: RNA_D2_rep

value: Immature adipocytes (D2)


title: ZNF300