title: Wild-type Kidney cortex area_R1

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The sequences obtained were mapped to the reference mouse genome using STAR (v2.3). Reads were then quantified using HTSeq-count and analyzed for differential expression using EdgeR. Genes that showed a corrected FDR < 0.05 were used for clustering and pathway analysis.
Genome_build: mm9
Supplementary_files_format_and_content: RNA Seq Count text file generates gene count after normalized abundance measure

source_name: Wildtype

growth_protocol: Wild-type, and Vhl F/F;Pbrm1 F/F;Ksp mice were fed normal diet and raised until animals were ~1 year old

extract_protocol:
RNA was extracted using All prep DNA/RNA mini kit (Cat. # 80204). RNA was further treated for DNase digestion using On column Dnase digestion kit from Qiagen.
MSKCC Core Facility processed the total RNA by using TruSeq RNA Sample Prep kit according to the manufacturer’s recommendation. Briefly, cDNA libraries were prepared from polyA selected RNA after end repair, A-tailing, ligation of the adaptors, and PCR enrichment. Libraries were later sequenced using Illumina HiSeq 2500 platform with 50 bp paired end reads and the total of 40 million reads per sample.

tag: tissue

value: Renal cortex (normal kidney)


title: ZNF317

status: Public on Mar 06 2017

type: SRA

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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: ZNF285


title: VhlF/FPbrm1F/FKsp-Cre tumor area_R5

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Double mutant

tag: strain

value: mixed genetic background (C57BL/6, BALB/c, and 129)

value: Renal cortex (kidney tumor)


title: Wild-type Kidney cortex area_L1


title: Wild-type Kidney cortex area_L2


title: Wild-type Kidney cortex area_R2


title: ZNF284


title: ZNF283


title: ZNF282


title: VhlF/FPbrm1F/FKsp-Cre tumor area_R4


title: ZNF311


title: ZNF282-replicate 2


title: ZNF274


title: ZNF273


title: VhlF/FPbrm1F/FKsp-Cre tumor area_R3


title: VhlF/FPbrm1F/FKsp-Cre tumor area_R2


title: ZNF267


title: VhlF/FPbrm1F/FKsp-Cre tumor area_L4


title: ZNF266


title: ZNF26


title: ZNF264


title: ZNF263


title: Cko-ST-04

city: Stanford

first: Calvin

last: Kuo

state: CA

address: 265 Campus Drive

department: Medicine

institute: Stanford University School of Medicine

description: Sample 24

data_processing:
Reads per kilobase per million (RPKM) were calculated for RefSeq transcripts using an customized R script
Reads were aligned to the mouse genome (build mm10)
Differential expression analysis of RNA-seq data were performed using edgeR
Transcripts were defined as differentially expressed if they showed a fold-change value higher than 1.5 and p-value lower than 0.05
Genome_build: mm10
Supplementary_files_format_and_content: text file with rpkm values

molecule: polyA RNA

source_name: Stroke hemisphere after 1-hr MCAO 1-d reperfusion

extract_protocol:
Sample 1-24: total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) and mRNA was selected by poly-A selection. Sample 25-29: total RNA was extracted using the Qiagen RNeasy Kit followed by DNaseI treatment.
Sample 1-24: 3' end of poly A transcripts were amplified by PCR using NuGen Ovation 3'-DGE System Kit and libraries were prepared using NuGen Ovation SP+ Ultralow DR Multiplex System. Sample 25-29: cDNA libraries were generated using the Nugen Ovation RNA-Seq system V2 and libraries were generated using the NEBNext Ultra RNA Library prep kit for Illumina.

treatment_protocol: Brains were removed from adult mice and cut into pieces with razor blades. After digestion with Collagenase IV + Dispase + DNase I, single cell suspensions were subjected to FACS sort to isolate live CD45-CD31+PDGFRb- endothelial cells.

value: brain

tag: developmental stage

value: Adult 12-20 weeks

tag: cell type

value: FACS sorted CD31+PDGFRb- brain endothelial cells

tag: genotype

value: Gpr124 flox/-; ROSA-CreER+

tag: gender

value: Male


title: Cko-ST-02

description: Sample 22

value: Female


title: ZNF254


title: ZNF25


title: ZNF248


title: ZNF257


title: Cko-NS-03

description: Sample 19

source_name: Non-stroke hemisphere after 1-hr MCAO 1-d reperfusion


title: Cko-ST-03

description: Sample 23


title: Cko-NS-02

description: Sample 18


title: Cko-ST-01

description: Sample 21


title: Cko-NS-04

description: Sample 20


title: ZNF235


title: Cko-NS-01

description: Sample 17


title: WT-ST-04

description: Sample 16

value: Gpr124 flox/+; ROSA-CreER+


title: WT-ST-03

description: Sample 15


title: ZNF223


title: ZNF225


title: WT-ST-02

description: Sample 14


title: WT-ST-01

description: Sample 13


title: WT-NS-03

description: Sample 11


title: WT-NS-04

description: Sample 12


title: ZNF214


title: ZNF212


title: ZNF211


title: WT-NS-01

description: Sample 9


title: WT-NS-02

description: Sample 10


title: ZNF205


title: ZNF202


title: ZNF224


title: ZNF189


title: ZNF19


title: ZNF197


title: ZNF18


title: PMLKO_RNA

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, PML knock-out

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.

value: MEF

tag: genotype/variation

value: PML knock-out

tag: passages

value: Passage 10-15

tag: state/treatment

value: Proliferating, untreated


title: WT_H33

source_name: Mouse embryonic fibroblasts, wild-type

value: wild-type

tag: chip antibody

value: anti-Flag (Sigma, catalog# F-1804, lot# 124K6106)


title: ZNF222


title: WT_PML

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


title: WT_H3K27me3

value: anti-H3K27me3 (Diagenode, catalog# 056-050, lot# A299-00242)


title: ZNF184

value: HEK 293T


title: WT_RNA


title: PMLKO_H3K27me3


title: ZNF181


title: PMLKO_H3K9me3

value: anti-H3K9me3 (Diagenode, catalog# 068-050, lot# A1675-001P)


title: WT_H3K9me3


title: ZNF180


title: WT_H3

value: anti-H3 (Abcam, catalog# ab1791)


title: ZNF182


title: ZNF211-replicate 2


title: PMLKO_H33


title: Flutamide+PPC_2

city: London

first: Marco

middle: Paolo

last: Licciardello

address: 15 Cotswold Road

country: United Kingdom

institute: The Institute of Cancer Research

description: 6 hours treatment

data_processing:
Reads were aligned with tophat (v2.0.4) with the --no-novel-juncs --no-novel-indels options
Gene expression was calculated as Reads Per Kb per Millions of reads (RPKMs) using RPKM_count.py from the RSeQC package and the NCBI RNA reference sequences collection (RefSeq) downloaded from UCSC
Genome_build: hg38
Supplementary_files_format_and_content: cufflinks outputs including RPKM values for indicated samples, log2 values of the fold change and statistical analysis

source_name: LNCaP cells

growth_protocol: LNCaP cells were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Cells were lysed and RNA isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. The amount of total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System
RNA-Seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit using Sciclone and Zephyr liquid handling robotics. Library amount was quantified using the Qubit 2.0 Fluorometric Quantitation system and the size distribution was assessed using Experion Automated Electrophoresis System

treatment_protocol: LNCaP cells were treated with DMSO, 15 μM flutamide, 35 μM PPC or the combination for 6 hours

value: prostate

tag: cell line

value: LNCaP


title: ZNF17


title: Flutamide+PPC_1

description: 6 hours treatment


title: PMLKO_H3


title: ZNF169-replicate 2


title: PPC_2

description: 6 hours treatment


title: PPC_1

description: 6 hours treatment


title: ZNF169


title: Flutamide_2

description: 6 hours treatment


title: DMSO_2

description: 6 hours treatment


title: Tumor 5 H3K27ac

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 51bp reads for ERa ChIP-seq and 65bp reads for H3K27ac) and processed with the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7. DFilter was run with bs=50, ks=30, refine, nonzero.
No peak calling was performed on H3K27ac data. Aligned reads were examined and quantified (using coverageBed from bedtools) in the corresponding ERa peaks.
Genome_build: hg19
Supplementary_files_format_and_content: peak

source_name: Endometrial tumor of a non-tamoxifen-user 5

extract_protocol:
Fresh Frozen tumor was crosslinked with 1% formaldehyde for 20 minutes, quenched with 2 M Glycin for 5 minutes, and washed twice with PBS. Nuclei were isolated and sonicated. ChIP was performed with ERa (sc-543; Santa Cruz), and H3K27ac (39133; Active Motif), which were coupled to Dynabeads prot A. Samples were washed with RIPA buffer and reverse crosslinked at 65 C O/N. Samples were treated with RNAse A and prot K and DNA was isolated by alcohol precipitation.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (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 cycles and library fragments of ~250 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: endometrial primary tumor tissue that contained of at least 50% tumor were cryosectioned, 30x 30um sections were used

value: endometrioid adenocarcinoma

value: H3K27ac (39133; Active motif)

tag: procedure

value: Chromatin IP against H3K27ac


title: DMSO_1

description: 6 hours treatment


title: Tumor 4 H3K27ac

source_name: Endometrial tumor of a non-tamoxifen-user 4


title: Flutamide_1

description: 6 hours treatment


title: ZNF157


title: Tumor 3 H3K27ac

source_name: Endometrial tumor of a non-tamoxifen-user 3


title: Tumor 2 H3K27ac

source_name: Endometrial tumor of a non-tamoxifen-user 2


title: Pdd1p ChIP from JMJ1 KO new MACs [39426_ChIP]

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
The first 36-nt sequences of the reads that map the micronuclear genome were used in downstream analyses
The numbers of normalized sequence reads (RPMs) from the ChIP sample that uniquely mapped to MIC supercontigs were divided by the numbers of reads from the Input sample.
Supplementary_files_format_and_content: histograms of mapped normalized sequence read numbers

organism: Tetrahymena thermophila

source_name: New MACs @ 12 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30⁰C overnight. To induce conjugation, exponentially growing cells (~3-5x 105/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 105/ml) at 30°C.

extract_protocol: Chromatin immunoprecipitation was performed with the new MACs only when their purity was above 80%. Chromatin from the new MACs was sheared into 150-500 bp fragments (peak ~300 bp) in Sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS, 1x complete protease inhibitor cocktail, 1 mM PMSF) using a probe sonicator. For ChIP, 20 mg of Protein A Sepharose CL-4B beads (GE Healthcare) was washed with TE twice and with ChIP buffer (25 mM Tris-HCl pH 8.0, 167 mM NaCl, 5 mM EDTA, 0.05% SDS, 1% Triton X-100, 1x complete protease inhibitor cocktail, 1 mM PMSF) 3 times and was then pre-incubated with 90 µl of ChIP buffer containing 10 µl of 10 mg/ml BSA (NEB) (total ~200 µl suspension) at 4°C for 1 h. The fragmented chromatin from 2 million new MACs in Sonication buffer was diluted with an equal volume of 2x ChIP dilution buffer (334 mM NaCl, 2% Triton X-100, 1x complete protease inhibitor cocktail), adjusted to 1 ml with ChIP buffer and incubated with a 25 µl suspension of the beads at 4°C for 2 h for the pre-absorption. To couple an antibody to the beads, the 10 µl suspension of the beads pre-incubated with BSA was incubated with an antibody (20 µg anti-H3K9me3, 30 µg anti-H3K27me3, 50 µl anti-Coi6p, 50 µl anti-Coi7p, 50 µl anti-Lia5p, or 5 µg anti-Pdd1p) in 0.5 ml of ChIP buffer at 4°C for 2 h and was then washed with ChIP buffer 3 times. The pre-absorbed chromatin was incubated with the antibody-coupled beads at 4°C overnight. The beads were washed once with Low-salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and twice each with High-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), LiCl wash buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% sodium deoxycholate, 1% NP-40) and TE. The immunoprecipitated chromatin was eluted with Elution buffer (0.1 M NaHCO3, 1% SDS). For cross-linking reversal, the NaCl concentration of the sample was adjusted to 200 mM, and the sample was incubated at 65°C for ~12 h. The DNA was extracted, and DNA libraries were generated from the immunoprecipitated DNA and 20 ng of the fragmented chromatin DNA without immunoprecipitation (Input) using the NEBNext DNA Library Prep Reagent Set for Illumina (NEB) and the KAPA Real-Time Library Amplification Kit (KAPA Biosystems). The libraries were sequenced using the HiSeq2000 platform (Illumina) with 50-nt single-end reads.

treatment_protocol: Nuclei from cells at 12 hpm were dissociated and stained with DAPI in TMSN buffer (0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.016% NP-40, 1 mM PMSF, 1x complete proteinase inhibitor cocktail (Roche), 0.1 µg/ml DAPI) using a dounce homogenizer with 15 strokes. The nuclear fraction was collected by centrifugation at 4,500 g at 4°C for 5 min and then washed with TMSN buffer once and with TMSN(-) buffer (TMSN buffer without complete proteinase inhibitor cocktail) twice. The nuclei were fixed with 1.25 mg/ml Di(N-succinimidyl) glutarate (Sigma) in PBSN buffer (PBS with 0.016% NP-40) at room temperature for 30 min, collected by centrifugation at 9,000 g at 4°C for 5 min, and washed with PBSN buffer twice. The DSG-fixed nuclei were re-fixed with 1% paraformaldehyde (Sigma) in PBSN buffer at room temperature for 10 min. The paraformaldehyde was quenched with 0.25 M glycine at room temperature for 5 min. The nuclei were washed with PBSN buffer containing 0.1 µg/ml DAPI twice and then with PBSN(+) buffer (PBSN with 1x complete proteinase inhibitor cocktail and 0.1 µg/ml DAPI) once, and the nuclear pellet was stored at -80°C. The nuclei were resuspended in PBSN(+), and the new MACs were collected according to their size and DAPI intensity using a FACSAria III (BD Biosciences). The purity of the collected new MACs was assessed by immuno-DNA-FISH using a Cy3-labeled probe against Tlr1 and an anti-Pdd1p antibody (Abcam) for wild-type, JUB1 KO, WT-rescue and MIM22 cells or an anti-H3K4me3 (Abcam) antibody for PDD1 KO cells: Tlr1-negative nuclei were counted as parental (old) MACs; Tlr1-positive, and Pdd1p- or H3K4me3-positive nuclei were counted as new MACs; Tlr1-positive but Pdd1p- or H3K4me3-negative nuclei were counted as MICs. Contamination of the parental MACs was rare (<2%), and most of the contaminants in our new MAC preparations were MICs.

value: JMJ1 KO

tag: antibody


title: H3K9me3 ChIP from JMJ1 KO new MACs [39427_ChIP]


title: Coi6p ChIP from JMJ1 KO new MACs [39425_ChIP]


title: ZNF141


title: ZNF154


title: ZNF135


title: ZNF136


title: Tumor 1 H3K27ac

source_name: Endometrial tumor of a non-tamoxifen-user 1


title: Tumor 6 H3K27ac

source_name: Endometrial tumor of a non-tamoxifen-user 6


title: Tumor K H3K27ac

source_name: Tamoxifen-associated endometrial tumor K


title: 72 h PE AGO1 CLIP-seq FB

city: Riverside

first: Alexander

last: Raikhel

address: 338 Entomology Building

department: Entomology

institute: University of California-Riverside

description: processed data file: Findpeaks output for 6 libraries of AGO1 CLIP-seq.xlsx

data_processing:
library strategy: AGO1 CLIP-seq library
Small RNA library: Adaptor trimming sequence: TGGAATTCTCGGGTGCCAAGG (kept length: 18-32 nt)
Small RNA library: R version 3.1.2
Small RNA library: Thomas Girke. systemPipeR: NGS workflow and report generation environment, 28 June 2014. URL https://github.com/tgirke/systemPipeR.
Small RNA library: bowtie2/2.2.3 -k 5 --non-deterministic
Small RNA library: summarizeOverlaps-IntersectionStrict
Small RNA library: miRDeep2 default parameter settings for novel miRNA prediction
AGO1 CLIP-seq library: fastx_toolkit/0.0.13 -Q 33
AGO1 CLIP-seq library: Adaptor trimming sequence: GTGTCAGTCACTTCCAGCGG (length minimal: 20 nt)
AGO1 CLIP-seq library: bowtie2/2.2.3 -f -p 6
AGO1 CLIP-seq library: tophat/2.0.14 -p 6 --no-novel-juncs --transcriptome-only --transcriptome-max-hits 1
AGO1 CLIP-seq library: bedtools/2.17.0
AGO1 CLIP-seq library: FindPeaks(version 4) -dist_type 3 -subpeaks 0.5 -trim 0.1
Genome_build: AaegL3
Supplementary_files_format_and_content: Raw and normalized expressions of 124 mature Aedes aegypti miRNAs in miRBase v21.xlsx: Expression table of raw (sheet 1) and normalized (sheet 2) read counts for 124 mature Aedes aegypti miRNAs
Supplementary_files_format_and_content: Findpeaks output for 6 libraries of AGO1 CLIP-seq.xlsx: Findpeaks output from 6 libraries, assembled similarly like BED format
Supplementary_files_format_and_content: novel miRNA prediction from small RNA libraries.xlsx: Output of miRDeep2 for novel miRNA identification

organism: Aedes aegypti

source_name: fat body tissue

growth_protocol: Ae. aegypti mosquitoes were maintained under laboratory conditions.

extract_protocol:
For small RNA libraries, total RNAs were extracted with TRIZOL. For AGO1 CLIP-seq libraries, tissues were finely sliced, irradiated to 900 mJ/cm2 under UV, lysed and immunoprecipitated by AGO1 antibody.
Small RNA libraries were prepared with Illumina TruSeq Small RNA library Preparation kit. AGO1 CLIP-seq libraries were prepared following established protocol in Karginov FV & Hannon GJ (2013) Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates. Gene Dev 27(14):1624-1632.

treatment_protocol: Three or four days post eclosion, mosquitoes are treated as 72 h PE. Samples were collected and mosquitoes within the same cage were provided a blood meal. Fat body samples were collected at 6 h, 24 h, 36 h and 48 h PBM.

value: UGAL/Rockefeller

value: female mosquito adult

tag: time points

value: 72 h post eclosion

value: fat body tissue

tag: molecule subtype

value: AGO1-miRNA-mRNA complex


title: Input for ChIP (Sample 18, 19) from JMJ1 KO new MACs [39421_ChIP]


title: 24 h PBM AGO1 CLIP-seq FB

value: 24 h post blood meal

tag: tissue


title: ZNF133

tag: host cell line


title: 48 h PBM SmRNA FB

description: processed data file: Raw and normalized expressions of 124 mature Aedes aegypti miRNAs in miRBase v21.xlsx

data_processing:
library strategy: Small RNA library
Small RNA library: Adaptor trimming sequence: TGGAATTCTCGGGTGCCAAGG (kept length: 18-32 nt)
Small RNA library: R version 3.1.2
Small RNA library: Thomas Girke. systemPipeR: NGS workflow and report generation environment, 28 June 2014. URL https://github.com/tgirke/systemPipeR.
Small RNA library: bowtie2/2.2.3 -k 5 --non-deterministic
Small RNA library: summarizeOverlaps-IntersectionStrict
Small RNA library: miRDeep2 default parameter settings for novel miRNA prediction
AGO1 CLIP-seq library: fastx_toolkit/0.0.13 -Q 33
AGO1 CLIP-seq library: Adaptor trimming sequence: GTGTCAGTCACTTCCAGCGG (length minimal: 20 nt)
AGO1 CLIP-seq library: bowtie2/2.2.3 -f -p 6
AGO1 CLIP-seq library: tophat/2.0.14 -p 6 --no-novel-juncs --transcriptome-only --transcriptome-max-hits 1
AGO1 CLIP-seq library: bedtools/2.17.0
AGO1 CLIP-seq library: FindPeaks(version 4) -dist_type 3 -subpeaks 0.5 -trim 0.1
Genome_build: AaegL3
Supplementary_files_format_and_content: Raw and normalized expressions of 124 mature Aedes aegypti miRNAs in miRBase v21.xlsx: Expression table of raw (sheet 1) and normalized (sheet 2) read counts for 124 mature Aedes aegypti miRNAs
Supplementary_files_format_and_content: Findpeaks output for 6 libraries of AGO1 CLIP-seq.xlsx: Findpeaks output from 6 libraries, assembled similarly like BED format
Supplementary_files_format_and_content: novel miRNA prediction from small RNA libraries.xlsx: Output of miRDeep2 for novel miRNA identification

value: 48 h post blood meal


title: Tumor D H3K27ac

source_name: Tamoxifen-associated endometrial tumor D


title: Lia5p ChIP from wild-type new MACs [30218_ChIP]

value: wild-type


title: ZNF132

source_name: transduced 293T cell line

value: HEK 293T

tag: tagged protein


title: Tumor I H3K27ac

source_name: Tamoxifen-associated endometrial tumor I


title: H3K27me3 ChIP from  JMJ1 KO new MACs [39428_ChIP]


title: Input for ChIP (Sample 21, 22) from JMJ1 KO new MACs [39422_ChIP]


title: 36 h PBM SmRNA FB

tag: strain

value: 36 h post blood meal


title: 24 h PBM SmRNA FB

tag: developmental stage


title: Tumor H H3K27ac

source_name: Tamoxifen-associated endometrial tumor H


title: Tumor G H3K27ac

source_name: Tamoxifen-associated endometrial tumor G


title: ZNF12


title: ZNF124


title: 6 h PBM SmRNA FB

value: 6 h post blood meal


title: ZNF114


title: Input for ChIP (Sample 14) from COI6 KO new MACs [14934_ChIP]

value: COI6 KO


title: 72 h PE SmRNA FB


title: ZNF10


title: H3K9me3 ChIP from COI6 KO new MACs [30215_ChIP]


title: Pdd1p ChIP from COI6 KOnew MACs [14935_ChIP]


title: H3K27me3 ChIP from COI6 KO new MACs [30216_ChIP]


title: Tumor 6 ERa

value: ERa (SC-543; Santa Cruz)

value: Chromatin IP against ERa


title: Tumor 5 ERa

value: endometrioid adenocarcinoma


title: ZNF101


title: ZNF100-replicate 3


title: Pdd1p ChIP from wild-type new MACs [14931_ChIP]


title: Coi7p ChIP from wild-type new MACs [30219_ChIP]


title: ZNF100-replicate 2


title: Tumor 4 ERa


title: DFL_HH27_WT_Hoxd13VP

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Library strategy: 4C-seq
De-multiplexing, mapping and 4C analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the galGal4 chicken genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “-n 2 --best -strata -m 5”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads.
Fragments scores are normalized to the mean score of fragments falling into a region defined as the bait coordinated ± 1Mb and the data was smoothed by using a running mean with window size of 11 fragments. During the procedure, fragments at chr7: 15,807,716-15,815,518 at Hoxd11 viewpoint and those at chr7: 15,828,450-15,833,591 at Hoxd13 viewpoint were excluded from the analysis, respectively.
Genome_build: galGal4
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph)

organism: Gallus gallus

source_name: Forelimb buds

extract_protocol:
Distal-anterior or distal-posterior forelimb buds at HH20, proximal or distal forelimbs at HH27, distal-anterior limb mesenchymal cultured cells for 38 hours and distal forelimb at HH25-26 from Ozd mutant were dissociated with collagenase (Sigma Aldrich) and filtered through cell strainer to obtain single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 8 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. Hoxd11_inverse_forward: 5’-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGAGTCGCCGGCTCTTTCTATG-3’; Hoxd11_inverse_reverse: 5’-CAAGCAGAAGACGGCATACGAAGGACTTTGGCGTGCAGAC-3’; Hoxd13_inverse_forward: 5’-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGAAATTCACATTTCAAAGGGTTGAC-3’; Hoxd13_inverse_reverse: 5’-CAAGCAGAAGACGGCATACGAGACGAAGTTTACTCAGTTGCTCCT-3’

value: wild type

tag: age

value: Distal forelimb


title: DFL_HH25-26_Ozd_Hoxd13VP

value: Ozd mutant


title: WFS38h_Hoxd13VP

tag: cell type

value: Cultured distal-anterior mesenchymal cells from chick forelimb buds at HH20-21

tag: hours of incubation

tag: treatment

value: WNT3A /FGF8/SHH


title: PFL_HH27_WT_Hoxd13VP

value: Proximal forelimb


title: Tumor 3 ERa


title: Input for ChIP (Sample 9, 15) from wild-type new MACs [14929_ChIP]

tag: genotype/variation


title: Tumor F H3K27ac

source_name: Tamoxifen-associated endometrial tumor F (same patient as tumor B)

value: H3K27ac (39133; Active motif)

value: Chromatin IP against H3K27ac


title: ZNF100


title: Tumor 2 ERa


title: DPFL_HH20_WT_Hoxd13VP

value: Distal-posterior mesenchyme from forelimb


title: Input for ChIP (Sample 11, 12) from COI6 KO new MACs [30213_ChIP]


title: Tumor 1 ERa


title: ZKSCAN5


title: DAFL_HH20_WT_Hoxd13VP

value: Distal-anterior mesenchyme from forelimb


title: Tumor K ERa


title: WFS38h_Hoxd11VP


title: Tumor J ERa

source_name: Tamoxifen-associated endometrial tumor J


title: H3K9me3 ChIP from wild-type new MACs [12996_ChIP]

value: wild-type


title: ZKSCAN3

value: HEK 293T


title: DFL_HH25-26_Ozd_Hoxd11VP


title: ZIM3


title: ZKSCAN2


title: ZIM2_1


title: DFL_HH27_WT_Hoxd11VP


title: Input for ChIP (Sample 4) from COI6 KO new MACs [21219_ChIP]


title: ZIK1


title: Coi6p ChIP from wild-type new MACs [14275_ChIP]


title: Input for ChIP (Sample 6, 7) from wild-type new MACs [12992_ChIP]


title: Tumor I ERa


title: Coi6p ChIP from COI6KO new MACs [21220_ChIP]


title: PFL_HH27_WT_Hoxd11VP


title: H3K27me3 ChIP from wild-type new MACs [12997_ChIP]


title: DPFL_HH20_WT_Hoxd11VP


title: Input for ChIP (Sample 2, 16) from wild-type new MACs [14272_ChIP]


title: Tumor G ERa


title: ZFP90


title: Tumor F ERa


title: DAFL_HH20_WT_Hoxd11VP


title: total scnRNAs from JIJ1 KO cells @10.5 hpm [18880]

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

source_name: Conjugating cells at 10.5 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

value: JMI1 KO


title: ZFP69


title: ZFP69B


title: total scnRNAs from LIA5 KO cells @10.5 hpm [29029]

value: LIA5 KO


title: total scnRNAs from COI7 mutant cells @10.5 hpm [23983]

value: COI7 mutant (COI7fs1/fs2)


title: WFS12h_input

data_processing:
Illumina Casava1.8.2 software used for basecalling. Demultiplexed ChIP-seq reads were mapped onto the modified ICGSC Gallus_gallus-4.0 (galGal4) using Bowtie (Galaxy Tool Version 1.1.2) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al., 2014).
The coordinates “chr2 --start=32915240 --end=33195168” of galGal4 were masked to take away the second and third copy of the HoxA cluster.
Both unmapped regions containing adaptors and contamination, and PCR duplicates were removed from mapped reads. Three fastq files from W, WF and WFS input data were concatenated and used for further analysis.
These analyses were performed on the public server of the Galaxy Project (https://usegalaxy.org/) (Hillman-Jackson et al., 2012).
By using bamCompare (Galaxy Tool Version 2.4.1.0) from the Galaxy deepTools2 webserver (http://deeptools.ie-freiburg.mpg.de/), ChIP and merged input data were normalized and compared to compute the log2 of the number of reads ratio (Ramirez et al., 2014, 2016).
Genome_build: customized galGal4
Supplementary_files_format_and_content: bedGraph of log2 of the normalized number of reads ratio histone marks ChIP versus concatenated Input.

source_name: Cultured limb mesenchymal cells

growth_protocol: Tissues from the distal-anterior portion of 170 forelimb buds were dissected from  HH21. After dissection, limb buds were incubated in 0.25% trypsin/PBS for 10 minutes at room temperature to loosen attached ectodermal tissue. Then, tissues were transferred to 10% FBS/DMEM to quench trypsin reaction. Loosened ectodermal tissues were removed and remaining mesenchyme was mechanically dissociated with pipetting. The cell suspension was evenly divided into four tubes and centrifuged at 2,000 rpm for 5 min. After removal of supernatants, the cells were resuspended with 500 μl of DMEM/F12 containing W (250 ng/ml of Wnt3a, R&D system), WF (Wnt3a and 120 ng/ml Fgf8b, R&D system), WS (Wnt3a and 1 ng/ μl of N-terminal fragment of Shh, R&D system), or WFS (Wnt3a, Fgf8b and Shh). 100 μl of cell suspension were plated in each well of 96-well plates (5x10^6 cells/ml), and cultured for 12 hrs at 37°C. After rinsing with PBS, the cultured cells were trypsinized for 5 min at 37°C, and were harvested.

extract_protocol:
Harvested cells were fixed in 1% formaldehyde/PBS for 15 minutes at room temperature, and the cross-link reaction was quenched by adding Glycine, followed by washing with cold PBS containing proteinase inhibitor. Samples were stored at -80°C before use. The ChIP experiment was performed according to (Beccari et al., 2016) using 3 µg of H3K27ac (ab4729, Abcam).
For ChIP-seq, at least 5 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 100 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: Cultured distal-anterior mesenchymal cells from chick forelimb buds at HH21


title: WF12h_input

value: WNT3A /FGF8


title: Tumor H ERa

value: endometrioid adenocarcinoma

value: ERa (SC-543; Santa Cruz)

value: Chromatin IP against ERa


title: total scnRNAs from COI6 KO cells @10.5 hpm [20629]

value: COI6 KO


title: ZFP1


title: WF12h_H3K27ac

value: wild type


title: WS12h_H3K27ac


title: WFS12h_H3K27ac

value: WNT3A /FGF8/SHH


title: total scnRNAs from COI6 KO cells @8 hpm [20628]

source_name: Conjugating cells at 8 hpm


title: ZFP14


title: total scnRNAs from COI6 KO cells @12 hpm [20630]

source_name: Conjugating cells at 12 hpm


title: total scnRNAs from COI6 KO cells @6 hpm [20627]

source_name: Conjugating cells at 6 hpm


title: total scnRNAs from COI6 KO cells @3 hpm [20626]

source_name: Conjugating cells at 3 hpm


title: RBAK

value: RBAK


title: total scnRNAs from JIJ1 KO cells @12 hpm [28012]


title: HKR1


title: PRDM9


title: WT-02_12-20weeks

description: Sample 29

source_name: Normal condition

value: brain

value: Adult 12-20 weeks

value: FACS sorted CD31+PDGFRb- brain endothelial cells

tag: genotype

value: Ctnnb1 +/+; Cdh5-CreER+

tag: gender

value: Male


title: WT-01_12-20weeks

description: Sample 28


title: Total input 293T - sampled

value: HEK 293T


title: ZFP57-replicate 2


title: total scnRNAs from wild-type cells @12 hpm [27417]

value: wild-type


title: W12h_input


title: Bcat-03

description: Sample 27

value: Ctnnb1 lox(ex3)/+; Cdh5-CreER+


title: total scnRNAs from wild-type cells @8 hpm [20930]


title: ZFP57


title: total scnRNAs from wild-type cells @6 hpm [20926]


title: Bcat-01

description: Sample 25


title: total scnRNAs from wild-type cells @3 hpm [15493]


title: W12h_H3K27ac

value: Cultured distal-anterior mesenchymal cells from chick forelimb buds at HH21


title: H3K4me3_suppl_ChIP-seq

status: Public on Mar 04 2017

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

data_processing:
Reads were aligned using bowtie2 v.2.2.4
Alignment was sorted using samtools v.0.1.19
Peaks were called using  MACS2 v.2.1.0.20151222 with the --broad parameter
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 broadPeaks in bed format

source_name: Nalm6 ALL leukemia cells

growth_protocol: 10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in  2x10^5 to 1x10^6

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample Kit . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (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 18 cycles and library fragments of 200-400bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The resulted library was validated by using Agilent Technologies 2100 Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (Illumina GA2) following the manufacturer's protocols.

value: pre-B ALL leukemia cells

tag: culture condition

value: 10% FBS RPMI1640 in 5% CO2, 37°C

tag: chip antibodies

value: Abcam, ab8580


title: H3K27me3_suppl_ChIP-seq

value: Millipore, 07-449


title: daily 3

city: Chicago

first: Mattia

last: Quattrocelli

state: IL

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

data_processing:
Reads from each sample were aligned with TopHat v2.1.0 to the mm10 genome assembly (grcm38, version 78).
Transcripts were assessed and raw read counts per gene were quantified with HTseq.
Reads Per Kilobase of transcript per Million mapped reads (RPKM) and fold-changes between groups were calculated using EdgeR from the Bioconductor package.
Differentially expressed genes were identified by adjusted P-value <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: .csv file with RPKM values of candidate genes (muscle repair, atrophy, ergogenesis) per samples
Supplementary_files_format_and_content: .csv file with RPK for all genes

source_name: skeletal muscle

extract_protocol:
Total RNA was isolated from ~30mg muscle tissue (quadriceps muscles from treated and control DBA/2J-mdx male 6 month-old mice) with the RNeasy Protect Mini Kit as per manufacturer’s instructions. RNA was quantitated at the Qubit fluorometer and quality-controlled at a 2100 Bioanalyzer.
Libraries were prepared from approximately 1ug RNA/sample by means of TruSeq Stranded Total RNA Library Prep Kit. Libraries were sequenced through the Illumina NextSeq 500 System (high-throughput, paired-end 150bp fragment sequencing.

treatment_protocol: Weekly: 1mg/kg/dose prednisone i.p., 1x week, accompanied by 6x week vehicle (dmso) injection. Daily: 1mg/kg/dose prednisone i.p., 7x week. Vehicle: 1mg/kg/dose (dmso) i.p., 7x week

value: quadriceps

tag: age (at analysis)

value: ~ 7 months


title: daily 2


title: daily 5


title: weekly 5


title: daily 1


title: weekly 4


title: weekly 1


title: weekly 2


title: weekly 3


title: KO3

city: Wuerzburg

first: Alireza

last: Paikari

address: Biocenter

country: Germany

institute: Wuerzburg University

description:
8_S32
mRNA

data_processing:
kallisto used for quantifying abundances of transcripts from RNA-Seq data.
sleuth used for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include TPM (transcripts per million) values for each Sample.

source_name: Placenta, miR-290 KO

extract_protocol:
miRNeasy micro columns (Qiagen).
KAPA stranded mRNA-Seq Kit.

tag: strain/background

value: miR-290 knockout

value: Placenta


title: WT3

description:
12_S36
mRNA

source_name: Placenta, WT


title: KO4

description:
13_S37
mRNA


title: vehicle 5


title: vehicle 4


title: KO2

description:
7_S31
mRNA


title: vehicle 2


title: WT2

description:
2_S26
mRNA


title: Bcat-02

description: Sample 26

value: brain


title: KO1

description:
6_S30
mRNA


title: KAP1 H1 embryonic stem cells

source_name: H1 embryonic stem cells

tag: cell line

value: H1 hES


title: vehicle 3

tag: tissue


title: WT1

description:
1_S25
mRNA


title: 144sR Wild Type - Postnatal Day 28

status: Public on Mar 03 2017

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

data_processing:
Basecalling and demultiplexing performed using CASAVA version 1.8.2
Alignments to reference assembly mm10 and known splice junctions found in the RefSeq database performed using ELAND v2e
Read counting for each gene and normalization to RPKM values performed using in-house tools.
Small RNA data analysis performed using Small RNA v1.0.0.0 (Illumina) configured with the following dependencies: Isis 2.5.52.11, SAMtools 0.1.19-isis-1.0.2, Bowtie 0.12.8, miRDeep 3.2, and miRBase v21.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (RPKM values) for the standard RNA-seq analysis are reported in the Excel file mRNA_Expression_Results.xlsx for all 12 replicates. Read counts for each IsomiR found on a known precursor are reported in the Excel file smallRNA_Expression_Results.xlsx for all 12 replicates.

source_name: Visual cortex

growth_protocol: normal rearing

extract_protocol:
RNA was extracted by the addiction of Phenol/guanidine-based QIAzol Lysis Reagent.
RNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 and the TruSeq Small RNA Sample PrepGuide (Illumina).

value: 10 days

value: wild type


title: 158sR Wild Type - Postnatal Day 28


title: 152R Wild Type - Postnatal Day 28

value: 28 days


title: daily 4


title: 144R Wild Type - Postnatal Day 28


title: 158R Wild Type - Postnatal Day 28


title: 146sR Wild Type - Postnatal Day 28


title: 079R miR-132/212 null mice - Postnatal Day 28


title: 088sR miR-132/212 null mice - Postnatal Day 28


title: 088R miR-132/212 null mice - Postnatal Day 28


title: 030R miR-132/212 null mice - Postnatal Day 28


title: 099sR Wild Type - Postnatal Day 10


title: 030sR miR-132/212 null mice - Postnatal Day 28


title: 129R miR-132/212 null mice - Postnatal Day 28


title: 117sR Wild Type - Postnatal Day 10


title: vehicle 1


title: 103sR Wild Type - Postnatal Day 10


title: 111R Wild Type - Postnatal Day 10


title: 103R Wild Type - Postnatal Day 10


title: 099R Wild Type - Postnatal Day 10


title: wild type HSP90 inhibition rep2

city: Cambridge

first: David

last: Housman

state: MA

address: 500 Main St

department: Biology

institute: MIT

data_processing:
Basecalls with HiSeq Control Software 1.5.15.1 and RTA 1.13.48
Reads were mapped to the mm9 build using the Bowtie alignment program with setting --best.
Raw counts that mapped to constitutive exons were recorded and summed for each gene.
Gene counts were used to estimate fold changes in expression levels with the DEseq2 pipeline.
Genome_build: mm9
Supplementary_files_format_and_content: text file of raw counts; all samples in one file

source_name: wild type HSP90 inhibition

extract_protocol:
TRIZOL total RNA isolation; polyA selection in first step of library construction
Illumina, strand-specific, paired end RNA-Seq protocol.

treatment_protocol: HSP90 Inhibition: Mice were dosed with 12 mg/kg NVP-HSP990. HSP990 was formulated in 0.2% methyl cellulose in 0.9% saline solution. The HSP990 mixture was sonicated in a water bath to create a uniform suspension with very small particle size. The drug was freshly prepared for each round of treatment and administered by oral gavage.

tag: strain background

value: CBA x C57BL/6 F1 (B6CBAF1/OlaHsd, Harlan Olac, Bicester, UK).

value: 12 wks

tag: treatment group

value: HSP90 Inhibition

tag: time post treatment

value: 4 hours

value: quadriceps femoris muscle


title: wild type vehicle HSP90 inhibition rep1

source_name: wild type vehicle HSP90 inhibition

treatment_protocol: Control HSP90 Inhibition: Vehicle (0.9% saline solution) was administered by oral gavage.

value: Control HSP90 Inhibition


title: wild type HSP90 inhibition rep1


title: wild type vehicle HSP90 inhibition rep2


title: R6/2 HSP90 inhibition rep1

source_name: R6/2 HSP90 inhibition


title: R6/2 vehicle HSP90 inhibition rep2

source_name: R6/2 vehicle HSP90 inhibition


title: R6/2 HSP90 inhibition rep2


title: 079sR miR-132/212 null mice - Postnatal Day 28

tag: strain


title: R6/2 vehicle HSP90 inhibition rep1

tag: age


title: 146R Wild Type - Postnatal Day 28


title: 129sR miR-132/212 null mice - Postnatal Day 28


title: SW480_KD

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

country: China

institute: Second Military Medical University

data_processing:
Adapters were removed by flexbar v2.5 with parameters -ae LEFT_TAIL -q 30 -m 100.
Pair-end reads were mapped to Ensembl human genome by tophat v2.1.0.
FPKM were calculated by cufflinks v2.2.1.
Genome_build: GRCh38.82
Supplementary_files_format_and_content: Output of cuffdiff, tab-delimited text files include FPKM values for each cell line.

source_name: SW480 cell line with SLC25A25-AS1 knocked down

growth_protocol: All cell lines were maintained in Dulbecco’s Modified Eagle Medium (Hyclone, Thermo Fisher Scientific, Pittsburgh, PA, USA) supplemented with 10% heat-inactivated fetal bovine serum (GIBCO, Grand Island, Life Technologies, NY, USA), 100 units/ml penicillin and 100mg/ml streptomycin at 37℃ in a 5% CO2 humidified atmosphere.

extract_protocol:
The purity and concentration of total RNA were assessed using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientiﬁc)
Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the RNA-Seq sample preparation kit (Illumina, San Diego, USA). And then we performed the paired-end sequencing (2*125 bp) on an Illumina Hiseq2500 following the vendor’s recommended protocol.

treatment_protocol: shRNA was inserted into the lentiviral vector pGreenPuro (pGP)by BamH I and EcoR Idigestion. The nonsilencing sequence was used as a negative control. The shRNA-pGPlentiviral vectors were constructed and packed by Holly Lab (Shanghai, China). CRC cells SW480 and HT29 were incubated with virus-containing medium supplemented with 5μg/ml polybrene (Sigma-Aldrich) for 8 hours. Then changed the medium with fresh DMEM and keptincubating for 96 hours. Stable SLC25A25-AS1-knockdown cells were selected in the presence of 3.5 mg/ml puromycin (Sigma-Aldrich) for 7 days.

tag: cell type

value: Colorectal carcinoma

tag: group

value: Knockdown


title: SW480_CN

source_name: Normal SW480 cell line

value: Control


title: Hsf1-/- HSP90 inhibition rep1

source_name: Hsf1-/- HSP90 inhibition

value: 8 wks


title: Hsf1-/- HSP90 inhibition rep2


title: 111sR Wild Type - Postnatal Day 10


title: Hsf1-/- vehicle HSP90 inhibition rep2

source_name: Hsf1-/- vehicle HSP90 inhibition


title: Hsf1-/- vehicle HSP90 inhibition rep1


title: 117R Wild Type - Postnatal Day 10


title: HT29_KD

source_name: HT29 cell line with SLC25A25-AS1 knocked down


title: wild type heat shock rep2

source_name: wild type heat shock

treatment_protocol: Heat shock: Animals were anesthetized with isoflurane and the whole body excluding the head was wrapped in a heating pad set at 41.5°C ± 0.2°C. Warm up period was in the range of 5 to 6 minutes to reach 41.5°C. During the 15 minute heat shock the core body temperature was maintained at 41.5°C ± 0.2°C for 15 minutes, and was constantly monitored by a rectal probe. Following heat shock, animals were cooled, revived, and returned to their home cage.

value: Heat shock


title: HT29_CN

source_name: Normal HT29 cell line


title: patient 1 [SLX-8966.N712_N501]

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

institute: University of Cambridge

description: processed data file: patient1.txt

data_processing:
Illumina basecalling
Sequenced reads were trimmed for Nextera Transposase Sequence,
Trimmed reads were mapped to Human GRCh38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Quality control of the cells were performed by looking at the  number of detected genes. Cells expressing low counts were removed for the following step
Gene expression count matrix were calculated with seqmonk
Genome_build: GRCh38-77
Supplementary_files_format_and_content: Space separated raw counts. Rows are genes, columns are cells.

source_name: haematopoietic stem and progenitor cells

extract_protocol:
CD90+, CD34+, CD38-, CD45RA- cells were flow sorted and subjected to Smart-Seq 2
Smart-Seq2 and Nextera XP

value: hameatopoietic stemand progenitor cells

tag: protocol

tag: subject id

value: patient 1

tag: disease state

value: myeloprolifertive disease


title: wild type heat shock rep1

tag: genotype/variation


title: siZC3H18 repC

first: Edouard

last: Bertrand

address: 1919 Route de Mendes

department: SERANAD

institute: CNRS

description: rRNA-depleted total RNA

data_processing:
Illumina RTA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then align with TopHat v2.0.12(with Bowtie 2.2.3) on hg19 (UCSC)
Counts were normalized using edgeR pseudo-counts
and used in genomecov -scale option
Genome_build: hg19
Supplementary_files_format_and_content: sum of normalised replicat were used to calculate logratio. Bedgraph and bigwig were generated

source_name: HeLa cells

growth_protocol: HeLa cells were grown in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% Penicilin/Streptavidin, at 37°C, 5% CO2

extract_protocol:
RNAs  were prepared using TRIzol (Thermo Fisher), and rRNA were removed using the RiboMinus Eukaryotes kit (Thermo Fisher A10837-08)
Libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation kit

treatment_protocol: Cells were transfected with PHAX, ZC3H18 or control FFL siRNAs using JetPrime (PolyPlus), and cells were harvested 48h later.  the PHAX siRNAs were 5′-UAGUAUCAGCGAGGAACAAAUUAdTdT and 5′-AAGAGUAUAUAGCACAGGAUUUAdTdT; the ZC3H18 siRNAs was 5' GGAAUGAAUUGUAGGUUUAdTdT; the control FFL siRNAs was CUUACGCUGAGUACUUCGAdTdT

value: HeLa

tag: sirna treatment


title: patient 1 [SLX-8966.N711_N508]

description: processed data file: patient1.txt


title: wild type control heat shock rep2

source_name: wild type control heat shock

treatment_protocol: Control heat shock: Animals were anesthetized with isoflurane and the whole body excluding the head was wrapped in a heating pad set at 36.9°C ± 0.2°C for 21 minutes. Following the mock heat shock, animals were revived and returned to their home cage.

value: wild type

value: Control heat shock


title: patient 1 [SLX-8966.N711_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N505]

description: processed data file: patient1.txt


title: wild type control heat shock rep1

value: CBA x C57BL/6 F1 (B6CBAF1/OlaHsd, Harlan Olac, Bicester, UK).


title: R6/2 heat shock rep2

source_name: R6/2 heat shock

value: 12 wks


title: patient 1 [SLX-8966.N708_N507]

description: processed data file: patient1.txt


title: siPHAX repC

description: rRNA-depleted total RNA

value: siPHAX


title: siPHAX repB

description: rRNA-depleted total RNA


title: siZC3H18 rep1

description: rRNA-depleted total RNA


title: R6/2 control heat shock rep2

source_name: R6/2 control heat shock

value: 4 hours


title: patient 1 [SLX-8966.N706_N504]

description: processed data file: patient1.txt


title: siPHAX repA

description: rRNA-depleted total RNA


title: R6/2 control heat shock rep1

value: quadriceps femoris muscle


title: patient 1 [SLX-8966.N704_N501]

description: processed data file: patient1.txt


title: R6/2 heat shock rep1


title: patient 1 [SLX-8966.N703_N503]

description: processed data file: patient1.txt


title: 152sR Wild Type - Postnatal Day 28

source_name: Visual cortex

value: 10 days


title: Hsf1-/- heat shock rep2

source_name: Hsf1-/- heat shock

value: 10 wks


title: siFFL repA

description: rRNA-depleted total RNA

value: siFFL


title: Hsf1-/- heat shock rep1


title: Hsf1-/- control heat shock rep2

source_name: Hsf1-/- control heat shock


title: siFFL repC

description: rRNA-depleted total RNA


title: patient 1 [SLX-8966.N702_N507]

description: processed data file: patient1.txt


title: siZC3H18 rep2

description: rRNA-depleted total RNA


title: siFFL rep2

description: rRNA-depleted total RNA


title: siFFL repB

description: rRNA-depleted total RNA


title: Halofuginone 3

city: Collegeville

first: Pu

last: Qin

address: 1250 S Collegeville Rd

institute: GSK

data_processing:
HCS 2.0.12/RTA 1.17.21.3 Basecalling
bcl2fastq Conversion Software v1.8.4
ArrayStudio v7 with OmicSoft Aligner
ArrayStudio v7 FPKM Quantification
Genome_build: Human NCBI build 37.3
Supplementary_files_format_and_content: fpkm

source_name: Normal human cardiac fibroblast-ventricle

growth_protocol: Cells were passaged to P5 and then seeded in culture dishes for experiment.

extract_protocol:
Trizol
TruSeq™ RNA Sample Prep

treatment_protocol: Halofuginone were added to culture media to reach final concentration of 200 nM for 24 hours.

value: heart


title: Halofuginone 2


title: siFFL rep1

description: rRNA-depleted total RNA


title: Halofuginone 1


title: Vehicle 3


title: Hsf1-/- control heat shock rep1


title: Vehicle 1


title: Vehicle 2


title: Meis1 ChIP-seq P19, RA 48hrs

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

institute: University Rennes 1

data_processing:
Reads were mapped to the reference genome (mouse mm8) by Bowtie (Langmead et al. Genome Biol. 2009) using parameters -l 28 -n 1 -m 1 --best --strata.
The .sam files were converted to .bam files using SAMtools and the bam files were then processed to generate .wig files using MACS 1.4.0. Note that the provided .wig files are not normalized.
Genome_build: mm8
Supplementary_files_format_and_content: wig files

source_name: RA-treated P19 EC cells, Meis1 ChIP

growth_protocol: P19 EC cells were routinely grown in DMEM complemented with 10% fetal calf serum. P19 EC cells were treated with 10-6 M retinoic acid for 0, 6, 12, 18, 24 or 48 hrs. Cells were either collected without crosslinking for genomic DNA extraction or fixed with 1.5% formaldehyde for chromatin immunoprecipitation.

extract_protocol:
For MeDIP and hMeDIP, cells were scraped in phosphate buffered saline and were pelleted at 100 g before genomic DNA extraction using a DNeasy Blood and Tissue kit (Qiagen, France). For ChIP, P19.6 cells were cross-linked with 1.5% formaldehyde for 10 min at room temperature. The cells were rinsed with cold PBS, harvested and lysed with 1% SDS, 10 mM EDTA, and 50 mM Tris-HCl (pH 8.1) containing a protease inhibitor cocktail (Roche). Chromatin fragmentation was subsequently obtained by sonicating samples for 14 min (30 sec on/off cycles) using a Bioruptor (Diagenode) set up at the highest intensity. The soluble chromatin was diluted 10 times in a buffer containing 1% Triton, 2 mM EDTA, 150 mM NaCl, and 20 mM Tris-HCl (pH 8.1), and incubated overnight with antibodies. Sepharose beads (Amersham Pharmacia Biosciences) were then added to the samples together with yeast tRNA as non-specific competitors. After 4 h, beads were serially washed using 1mL of washing buffer I (2mM EDTA, 20mM Tris-HCl (pH8.1), 0.1% SDS, 1% Triton X-100, 150mM NaCl), washing buffer II (2mM EDTA, 20mM Tris-HCl (pH 8.1), 0.1% SDS, 1% Triton X-100, 500 mM NaCl), washing buffer III (1mM EDTA, 10mM Tris-HCl (pH8.1), 1% NP-40, 1% deoxycholate, 0.25M LiCl) and then twice with 1mM EDTA, 10mM Tris-HCl (pH8.1), and immune complexes were eluted using 100 mL of 1% SDS and 0.1 M NaHCO3. Samples were incubated overnight at 65C to reverse cross-linking. DNA was finally purified using the NucleoSpin Extract II kit (Macherey-Nagel). Each ChIP was performed 10 times.
The (h)MeDIP, ChIP, FAIRE and input libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina, ref. IP-202-1012). Libraries were sequenced by Illumina HiSeq following the manufacturer’s protocol.

tag: cell-type

value: P19 embryonal carcinoma (EC) cells treated 48 hrs with RA

tag: antibody

value: anti-Meis1, Abcam, ab19867

tag: antibody lot number


title: patient 1 [SLX-8966.N701_N503]

description: processed data file: patient1.txt

value: hameatopoietic stemand progenitor cells


title: Input-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells


title: Input-seq P19, RA 12hrs

value: P19 Embryonal carcinoma (EC) cells treated 12 hrs with RA


title: Input-seq P19, RA 6hrs

value: P19 embryonal carcinoma (EC) cells treated 6 hrs with RA


title: Meis1 ChIP-seq P19, RA 12hrs


title: Meis1 ChIP-seq P19, RA 18hrs

value: P19 embryonal carcinoma (EC) cells treated 18 hrs with RA


title: Pbx1 ChIP-seq, P19, RA 48 hrs

source_name: RA-treated P19 EC cells, Pbx1 ChIP

value: anti-Pbx1, Abnova, H00005087-M01


title: Input-seq P19, RA 18hrs


title: Tet2 ChIP-seq, P19, RA 48 hrs

source_name: RA-treated P19 EC cells, Tet2 ChIP

value: anti-Tet2, ProteinTech, 21207-1-AP


title: H3K27ac ChIP-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells, H3K27ac ChIP

value: anti-H3K27ac, Abcam, ab4729


title: Input-seq P19, RA 24hrs

value: P19 embryonal carcinoma (EC) cells treated 24 hrs with RA


title: H3K27ac ChIP-seq P19, RA 18hrs


title: Meis1 ChIP-seq P19, RA 6hrs


title: Meis1 ChIP-seq P19, veh

source_name: untreated P19 EC cells, Meis1 ChIP

value: P19 embryonal carcinoma (EC) cells


title: H3K27ac ChIP-seq P19, RA 24hrs


title: H3K27ac ChIP-seq P19, veh

source_name: untreated P19 EC cells, H3K27ac ChIP


title: H3K27ac ChIP-seq P19, RA 6hrs


title: H3K27ac ChIP-seq P19, RA 12hrs


title: MeDIP-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells, MeDIP

value: anti-5mC, Diagenode, Mab-081-500


title: Mesi1 ChIP-seq P19, RA 24hrs


title: FoxA1 ChIP-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells, FoxA1 ChIP

value: anti-FoxA1, Abcam, ab5089


title: MeDIP-seq P19, RA 24hrs


title: FoxA1 ChIP-seq P19, veh

source_name: untreated P19 EC cells, FoxA1 ChIP


title: MeDIP-seq P19, RA 12hrs


title: MeDIP-seq P19, RA 18hrs


title: FAIRE-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells, FAIRE


title: FAIRE-seq P19, RA 24hrs


title: HSC_Q12

city: San Francisco

first: Emmanuelle

last: Passegue

address: 35 Medical Center Way, RMB-1017, Box 0667

department: Department of Medicine, Hem/Onc Division

institute: The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Adapter sequences were filtered out using the FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/)
Reads were aligned to the mm10 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool.
Genome_build: mm10
Supplementary_files_format_and_content: The myCpG.txt is a tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT.

growth_protocol: Activated HSC were grown in culture for 20hr

extract_protocol:
DNA was isolated from HSCs using the Qiagen Allprep kit
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012) with modified size selection to accomadate the low amount of input DNA (see materials and methods).

treatment_protocol: FACS was used to isolate HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD48-/CD150+)  from mouse bone marrow

value: WT

value: bone marrow

value: Hematopoietic stem cell (HSC)

tag: cycling status

value: Quiescent


title: Input-seq P19, veh

source_name: untreated P19 EC cells


title: MeDIP-seq P19, RA 6hrs


title: HSC_A11

tag: tissue

value: Activated


title: HSC_A9

tag: strain background


title: FAIRE-seq P19, RA 6hrs


title: HSC_Q8


title: FAIRE-seq P19, RA 12hrs


title: HSC_Q10


title: FAIRE-seq P19, RA 18hrs


title: H3K4me1 ChIP-seq P19, RA 48hrs

source_name: RA-treated P19 EC cells, H3K4me1 ChIP

value: P19 embryonal carcinoma (EC) cells treated 48 hrs with RA

value: anti-H3K4me1, Abcam, ab8895


title: hMeDIP-seq P19, RA 12hrs

source_name: RA-treated P19 EC cells, hMeDIP

value: P19 Embryonal carcinoma (EC) cells treated 12 hrs with RA

value: anti-5hmC, Diagenode, CS-HMC-100


title: hMeDIP-seq P19, RA 18hrs

value: P19 embryonal carcinoma (EC) cells treated 18 hrs with RA


title: MeDIP-seq P19, veh

source_name: untreated P19 EC cells, MeDIP


title: FAIRE-seq P19, veh

source_name: untreated P19 EC cells, FAIRE


title: hMeDIP-seq P19, RA 48hrs


title: hMeDIP-seq P19, RA 24hrs


title: HSC_A7


title: hMeDIP-seq P19, RA 6hrs

value: P19 embryonal carcinoma (EC) cells treated 6 hrs with RA


title: HSC_Q2


title: H3K4me1 ChIP-seq P19, RA 24hrs


title: H3K4me1 ChIP-seq P19, RA 18hrs


title: hMeDIP-seq P19, veh

source_name: untreated P19 EC cells, hMeDIP


title: H3K4me1 ChIP-seq P19, RA 12hrs


title: HSC_A1


title: HSC_A3


title: H3K4me1 ChIP-seq P19, RA 6hrs


title: Cnt37

source_name: Hematopoietic stem cell (HSC)

growth_protocol: Primary, uncultured cells

tag: genotype

value: HSC

tag: cell markers


title: Cnt34

tag: strain


title: Cnt36


title: H3K4me1 ChIP-seq P19, veh

source_name: untreated P19 EC cells, H3K4me1 ChIP


title: HSC_Q6


title: cKO46


title: cKO25


title: XL28_IPTG_rep2

city: Groningen

first: Jelle

last: Slager

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

description: total RNA, rRNA depleted

data_processing:
Illumina Casava 1.8 software was used for basecalling.
S. pneumoniae reads were mapped with Rockhopper version 2.0.3, using default parameters, on the D39 genome, modified with the genetic adaptations described in the genotype column of strain XL28.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. This was done internally by Rockhopper version 2.03 after aligning reads. Upper-quartile normalization (to be able to compare expression between samples) was performed with Rockhopper version 2.03, using default parameters.
Genome_build: Streptococcus pneumoniae D39 (accession NC_008533, assembly GCF_000014365.1), adapted as described in data-processing step 2.
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

organism: Streptococcus pneumoniae

source_name: IPTG-induced S. pneumoniae cells

growth_protocol: S. pneumoniae strain XL28 and XL29 were grown to OD600=0.4 in 5 ml tubes at 37ºC, and then diluted 1:100 in 20 ml fresh C+Y medium with (XL28 and XL29) or without (only XL28) 1 mM IPTG (two replicates per condition). The cultures were incubated at 37ºC for 2.5 hours.

extract_protocol:
After 2.5 hours of incubation at 37º, growth was stopped on ice and cells collected by centrifugation at 4ºC, 8000 rcf, 10 min. The pellets were washed with cold TE buffer (10 mM Tris-Cl, pH 7.5. 1 mM EDTA), quickly frozen in liquid nitrogen and then stored at -80ºC. For isolation of RNA, cells were thawed and lysed by bead beating in TE buffer. RNA was purified using phenol-chloroform extractions and ethanol precipitations. DNA was removed from the sample with RNase-free DNase I (Fermentas) treatment for 45 min. Ribolock (Fermentas) was added to avoid RNA degradation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bgaA::Plac-dCas9sp (TcR); prsA::F6-lacI (GmR); SPD_0423_P3-luc_SPD_0422 (KmR); CEP::P3-sgRNAluc1 (SpcR)

tag: treated with

value: 1 mM IPTG


title: ATACseq_animal2_70hpf

city: PASADENA

first: Robert

middle: Andrew

last: Cameron

address: Caltech 1200 EAST CALIFORNIA BOULEVARD

department: Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
Quality of each read sample at each time point were analyzed. ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.2.5 with maximum fragment length of 2000 (-X 2000); other parameters used were default. Filter aligned reads with MAPQ score < 30
duplicate fragments were then removed using Picard.
MACS2 (Zhang et al., 2008) was used for peak calling with the parameters –g dm –nomodel –nolambda –extsize 239 –keep-dup all.
Jbrowse is used for visulization of predicted ATACseq peaks (http://www.echinobase.org/Echinobase/jbrowse/index.html?data=data_atac_sp)
Genome_build: assembly Spur_3.1; https://www.ncbi.nlm.nih.gov/assembly/GCF_000002235.3
Supplementary_files_format_and_content: BED6+4 format file which contains the peak locations together with peak summit, pvalue and  qvalue.

organism: Strongylocentrotus purpuratus

source_name: S. purpuratus embryos_70 hpf

growth_protocol: Grown at 15C in 0.45 micron filtered sea water

extract_protocol:
Embryos were dissociated to individual cells and nuclei prepared.   500,000 cells were used in the transposition reaction following which the transposed genomic DNA was extracted and purified.
To amplify transposed DNA, the following reaction was prepared: 10 ul Transposed DNA, 15 ul of PCR master mix (Illumina, Nextera DNA 24 sample prep kit), 5 ul of PCR primer cocktail, 5 ul of each Index primer to be used (Illumina, Nextera 96 sample Index kit).

tag: aminal id

value: animal 2

tag: developmental stage

value: Embryo

tag: age

value: 70 hpf


title: cKO28

tag: cell type


title: XL28_IPTG_rep1

description: total RNA, rRNA depleted


title: XL29_IPTG_rep1

description: total RNA, rRNA depleted

value: bgaA::Plac-dCas9sp (TcR); prsA::F6-lacI (GmR); SPD_0423_P3-luc_SPD_0422 (KmR); CEP::(empty vector) (SpcR)


title: XL29_IPTG_rep2

description: total RNA, rRNA depleted


title: ATACseq_animal1_60hpf

source_name: S. purpuratus embryos_60 hpf

value: animal 1

value: 60 hpf


title: XL28_cont_rep2

description: total RNA, rRNA depleted

source_name: Untreated S. pneumoniae cells

value: none (untreated)


title: ATACseq_animal2_60hpf


title: cKO45

value: bone marrow


title: ATACseq_animal3_50hpf

source_name: S. purpuratus embryos_50 hpf

value: animal 3

value: 50 hpf


title: ATACseq_animal3_60hpf


title: ATACseq_animal1_39hpf

source_name: S. purpuratus embryos_39 hpf

value: 39 hpf


title: ATACseq_animal1_50hpf


title: ATACseq_animal2_50hpf


title: ATACseq_animal2_30hpf

source_name: S. purpuratus embryos_30 hpf

value: 30 hpf


title: ATACseq_animal3_30hpf


title: ATACseq_animal2_39hpf


title: ATACseq_animal1_70hpf


title: ATACseq_animal1_30hpf


title: ATACseq_animal3_39hpf


title: Cnt1

value: WT


title: ATACseq_animal1_24hpf

source_name: S. purpuratus embryos_24 hpf

value: 24 hpf


title: ATACseq_animal2_24hpf


title: ATACseq_animal3_18hpf

source_name: S. purpuratus embryos_18 hpf

value: 18 hpf


title: ATACseq_animal3_24hpf


title: ATACseq_animal3_70hpf


title: ATACseq_animal2_18hpf


title: ATACseq_animal1_18hpf


title: SAM19398131 E11.5

status: Public on Mar 02 2017

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Cells with  <2 million reads/cell, ≥5% mitochondrial reads, or <10% of annotated genes (~3,700) detected were discarded (and not part of this GEO series). Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from Medial Ganglionic Eminence

extract_protocol: MGE tissues from mouse CD1 embryonic brains were dissected out from various embryonic ages. A single-cell suspension was prepared and then analyzed with C1 Single Cell Autoprep System per manufacturers’ recommended protocols (Fluidigm).

value: Medial Ganglionic Eminence

tag: extendedphenotype

value: maturing

tag: subtype

tag: nonneuralcelltype

tag: date


title: SAM19055863 E15.5


title: SAM19055848 E15.5


title: SAM17928788 E17.5


title: SAM19398171 E11.5

value: proliferating

value: Epend


title: SAM19055877 E15.5


title: SAM19369705 E11.5


title: SAM19369742 E11.5


title: SAM17928675 E13.5

value: microglia


title: SAM19398138 E11.5


title: SAM19369720 E11.5


title: SAM17928792 E17.5


title: SAM19055858 E15.5


title: SAM19055891 E15.5


title: SAM19398122 E11.5


title: SAM19398123 E11.5


title: SAM19398152 E11.5


title: SAM17928671 E13.5


title: SAM19055886 E15.5


title: SAM19055899 E15.5


title: SAM19055844 E15.5


title: SAM19369739 E11.5


title: XL28_cont_rep1

description: total RNA, rRNA depleted

tag: genotype/variation

value: bgaA::Plac-dCas9sp (TcR); prsA::F6-lacI (GmR); SPD_0423_P3-luc_SPD_0422 (KmR); CEP::P3-sgRNAluc1 (SpcR)


title: SAM19055909 E13.5


title: SAM19369748 E11.5


title: SAM19055914 E13.5


title: SAM19055888 E15.5


title: XM201_Transcriptome

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Streptomyces hygroscopicus XM201 genome assembly using bowtie2（version: 2-2.0.5）.
Gene abundance measurements were generationed and normalized  using BEDTools (version:2.16.1) ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Genome_build: Streptomyces hygroscopicus XM201 (CP018627, not released yet)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Streptomyces hygroscopicus

source_name: bacteria

growth_protocol: For fermentation, S. hygroscopicus XM201 was grown in seed medium (10g/L tryptone, 10g/L glucose and 5g/L yeast extract) for 36 hours, then 15% inoculum was transferred into the fermentation medium containing (per litter) 40g soybean powder, 30g corn starch, 70g glucose, 3g (NH4)2SO4, 10g CaCO3, 0.01g CoCl2 and 1.0g soybean oil. All cultivations of Streptomyces were carried out at 30°C.

extract_protocol:
Cells of S. hygroscopicus XM201 were harvest and the total RNA was extracted using trizol according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4-day old

value: wildtype


title: SAM19398121 E11.5


title: SAM17865195 E15.5


title: SAM19055875 E15.5


title: SAM17928833 E17.5


title: SAM19369732 E11.5


title: SAM19055842 E15.5


title: SAM17928799 E17.5


title: SAM17865173 E15.5


title: SAM19398143 E11.5


title: SAM19055929 E13.5


title: SAM19369735 E11.5


title: SAM19398160 E11.5


title: SAM19369701 E11.5


title: SAM19398155 E11.5


title: SAM19398144 E11.5


title: SAM17928687 E13.5


title: SAM19055853 E15.5


title: SAM19369718 E11.5


title: SAM19369733 E11.5


title: SAM19369743 E11.5


title: SAM19055943 E13.5


title: SAM17928832 E17.5


title: SAM17928790 E17.5


title: SAM19055849 E15.5


title: SAM19055935 E13.5

value: endothelial


title: SAM19369719 E11.5


title: SAM19398165 E11.5


title: SAM17928759 E17.5


title: SAM19369725 E11.5


title: SAM17928692 E13.5


title: SAM17865180 E15.5


title: SAM19398135 E11.5


title: SAM19055874 E15.5


title: SAM19055865 E15.5


title: SAM19055878 E15.5


title: SAM19055913 E13.5


title: SAM17928797 E17.5


title: SAM19369751 E11.5


title: SAM19398166 E11.5


title: SAM17928767 E17.5


title: SAM19055846 E15.5


title: SAM19398156 E11.5


title: SAM19055864 E15.5


title: SAM19398129 E11.5


title: SAM19369728 E11.5


title: SAM17928730 E13.5


title: SAM19369744 E11.5


title: SAM19398173 E11.5


title: SAM19398127 E11.5


title: SAM19055919 E13.5


title: SAM19055947 E13.5


title: SAM19369746 E11.5


title: SAM19369711 E11.5


title: SAM19398172 E11.5


title: SAM19055851 E15.5


title: SAM19369726 E11.5


title: SAM19055884 E15.5


title: SAM17928710 E13.5


title: SAM19398125 E11.5


title: SAM19369749 E11.5


title: SAM19055882 E15.5


title: SAM19055955 E13.5


title: SAM19055951 E13.5


title: SAM19055873 E15.5


title: SAM19369723 E11.5


title: SAM19055869 E15.5


title: SAM19055881 E15.5


title: SAM19398139 E11.5


title: SAM19398133 E11.5


title: SAM19369702 E11.5


title: SAM19369734 E11.5


title: SAM19055906 E13.5


title: SAM17865179 E15.5


title: SAM19369704 E11.5


title: SAM19055895 E15.5


title: SAM19369708 E11.5


title: SAM19369707 E11.5


title: SAM19398130 E11.5


title: SAM19398137 E11.5


title: SAM19398158 E11.5


title: SAM19055894 E15.5


title: SAM19369745 E11.5


title: SAM17865192 E15.5


title: SAM19055856 E15.5


title: SAM19369738 E11.5


title: SAM19055854 E15.5


title: SAM19055930 E13.5


title: SAM17928837 E17.5


title: SAM19398161 E11.5


title: SAM19398128 E11.5


title: SAM19055859 E15.5


title: SAM17928830 E17.5


title: SAM19398162 E11.5


title: SAM19055911 E13.5


title: SAM19398154 E11.5


title: SAM19369717 E11.5


title: SAM19398126 E11.5


title: SAM19055855 E15.5


title: SAM19398141 E11.5


title: SAM19055845 E15.5


title: SAM19055883 E15.5

value: astrocytes Epend


title: SAM17865198 E15.5


title: SAM17928695 E13.5


title: SAM19369727 E11.5


title: SAM17928666 E13.5


title: SAM19055870 E15.5

value: Vsmc


title: SAM19369740 E11.5


title: SAM19055896 E15.5


title: SAM17928803 E17.5


title: SAM19055890 E15.5

value: astrocytes


title: SAM19055945 E13.5


title: SAM19055857 E15.5


title: SAM19398170 E11.5


title: SAM17928667 E13.5


title: SAM19398157 E11.5


title: SAM19055872 E15.5


title: SAM19055954 E13.5


title: SAM17928814 E17.5


title: SAM19369737 E11.5


title: SAM19055887 E15.5


title: SAM19398153 E11.5


title: SAM17865196 E15.5


title: SAM19055932 E13.5


title: SAM19055939 E13.5


title: SAM19055852 E15.5


title: SAM19055880 E15.5


title: SAM17865199 E15.5


title: SAM17928691 E13.5


title: SAM19369753 E11.5


title: SAM19055925 E13.5


title: SAM17928682 E13.5


title: SAM19369703 E11.5


title: SAM19055922 E13.5


title: SAM19369712 E11.5


title: SAM19055923 E13.5


title: SAM19055905 E13.5


title: SAM17928663 E13.5


title: SAM19055862 E15.5


title: SAM19369730 E11.5


title: SAM19055841 E15.5


title: SAM19055871 E15.5


title: SAM17928795 E17.5


title: SAM17928780 E17.5


title: SAM19055926 E13.5


title: SAM19055850 E15.5


title: SAM19369706 E11.5


title: SAM19055861 E15.5


title: SAM19369729 E11.5


title: SAM19398167 E11.5


title: SAM17865188 E15.5


title: SAM19055860 E15.5


title: SAM17928718 E13.5


title: SAM17928732 E13.5


title: SAM19369756 E11.5


title: SAM19055879 E15.5


title: SAM19398134 E11.5


title: SAM19369758 E11.5


title: SAM19369715 E11.5


title: SAM19055957 E13.5


title: SAM19369714 E11.5


title: SAM17928707 E13.5


title: SAM19369713 E11.5


title: SAM19369752 E11.5


title: SAM19398159 E11.5


title: SAM19398150 E11.5


title: SAM19055904 E13.5


title: SAM19055843 E15.5


title: SAM19055934 E13.5


title: SAM19398169 E11.5


title: SAM17865193 E15.5


title: SAM19055902 E13.5


title: SAM19398145 E11.5


title: SAM19398120 E11.5


title: SAM17928835 E17.5


title: SAM17928836 E17.5


title: SAM19369731 E11.5


title: SAM17928784 E17.5


title: SAM19369709 E11.5


title: SAM19055912 E13.5


title: SAM17928689 E13.5


title: SAM19055908 E13.5


title: SAM19369710 E11.5


title: SAM19055917 E13.5


title: SAM19055927 E13.5


title: SAM19055876 E15.5


title: SAM19398142 E11.5


title: SAM19055949 E13.5


title: SAM19398151 E11.5


title: SAM19369741 E11.5


title: SAM19398168 E11.5


title: SAM19055892 E15.5


title: SAM19369747 E11.5


title: SAM19398148 E11.5


title: SAM19369721 E11.5


title: SAM19055885 E15.5


title: SAM19096163 GFP+

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Cells with  <2 million reads/cell, ≥5% mitochondrial reads, or <10% of annotated genes (~3,700) detected were discarded (and not part of this GEO series). Supplementary files use Entrez Gene IDs, counts and nRPKM statistics. Reads not aligning to mouse genome were then aligned to the EGFP coding sequence and nRPKM values were
calculated (using the size factors determined from the genome). These values are attached as a sample characteristic.

source_name: RNA from ES Cells or Differentiated ES Cells

extract_protocol: Mouse ES J14 cells (Lhx6-GFP) were maintained in culture or differented. Single cells were analyzed with C1 Single Cell Autoprep System per manufacturers’ recommended protocols (Fluidigm).

tag: group

value: GFP+ differentiated cells

tag: egfp nrpkm

tag: cell line


title: SAM19286200 GFP+


title: SAM19286128 Unsorted

value: differentiated cells (unsorted, of which less than 10% are GFP+)


title: SAM19030232 ES

value: ES (undifferentiated)


title: SAM19286097 Unsorted


title: SAM19096135 GFP+


title: SAM19096155 GFP+


title: SAM17928693 E13.5

tag: tissue


title: SAM19096153 GFP+


title: SAM19096157 GFP+


title: SAM19096167 GFP+


title: SAM19030230 ES


title: SAM19055889 E15.5


title: SAM19369755 E11.5


title: SAM19056142 Unsorted


title: SAM19055868 E15.5


title: SAM19056183 Unsorted


title: SAM19096158 GFP+


title: SAM19286120 Unsorted


title: SAM19286094 Unsorted


title: SAM19030225 ES


title: SAM19096169 GFP+


title: SAM19096159 GFP+


title: SAM19096161 GFP+


title: SAM19286103 Unsorted


title: SAM19286125 Unsorted


title: SAM19030222 ES


title: SAM19286156 GFP+


title: SAM19056193 Unsorted


title: SAM19286135 Unsorted


title: SAM19096174 GFP+


title: SAM19056201 Unsorted


title: SAM19056149 Unsorted


title: SAM19030247 ES


title: SAM19096143 GFP+


title: SAM19286124 Unsorted


title: SAM19096124 GFP+


title: SAM19286101 Unsorted


title: SAM19096140 GFP+


title: SAM19286098 Unsorted


title: SAM19056112 GFP+


title: SAM19056188 Unsorted


title: SAM19030234 ES


title: SAM19286174 GFP+


title: SAM19030224 ES


title: SAM19030241 ES


title: SAM19286136 Unsorted


title: SAM19056094 GFP+


title: SAM19030246 ES


title: SAM19096166 GFP+


title: SAM19286142 Unsorted


title: SAM19030235 ES


title: SAM19096165 GFP+


title: SAM19096171 GFP+


title: SAM19030240 ES


title: SAM19286095 Unsorted


title: SAM19096128 GFP+


title: SAM19286210 GFP+


title: SAM19286166 GFP+


title: SAM19030242 ES


title: SAM19030249 ES


title: SAM19056136 Unsorted


title: SAM19056177 Unsorted


title: SAM19096125 GFP+


title: SAM19096179 GFP+


title: SAM19286208 GFP+


title: SAM18604736 Unsorted


title: SAM19096129 GFP+


title: SAM19286108 Unsorted


title: SAM19030238 ES


title: SAM19286126 Unsorted


title: SAM19286150 Unsorted


title: SAM19286141 Unsorted


title: SAM19096178 GFP+


title: SAM19286099 Unsorted


title: SAM19286090 Unsorted


title: SAM19030223 ES


title: SAM19030233 ES


title: SAM19286183 GFP+


title: SAM19286112 Unsorted


title: SAM18604786 Unsorted


title: SAM19286216 GFP+


title: SAM18604733 Unsorted


title: SAM19286119 Unsorted


title: SAM19286203 GFP+


title: SAM19286213 GFP+


title: SAM19286204 GFP+


title: SAM19286219 GFP+


title: SAM19030239 ES


title: SAM19286091 Unsorted


title: SAM19286206 GFP+


title: SAM19056122 GFP+


title: SAM19286123 Unsorted


title: SAM19030243 ES


title: SAM19096126 GFP+


title: SAM19056185 Unsorted


title: SAM19286093 Unsorted


title: SAM19030316 ES


title: SAM19030231 ES


title: SAM19286102 Unsorted


title: SAM19096130 GFP+


title: SAM19286151 Unsorted


title: SAM19286114 Unsorted


title: SAM19096172 GFP+


title: SAM19286218 GFP+


title: SAM19096170 GFP+


title: SAM19286175 GFP+


title: SAM19096120 GFP+


title: SAM19286146 Unsorted


title: SAM19096148 GFP+


title: SAM19096144 GFP+


title: SAM19096147 GFP+


title: SAM19096156 GFP+


title: SAM19286143 Unsorted


title: SAM19096123 GFP+


title: SAM19286139 Unsorted


title: SAM19096122 GFP+


title: SAM18604748 Unsorted


title: SAM19286132 Unsorted


title: SAM19286180 GFP+


title: SAM18604752 Unsorted


title: SAM19030248 ES


title: SAM19286164 GFP+


title: SAM19096160 GFP+


title: SAM19286133 Unsorted


title: SAM19286130 Unsorted


title: SAM19286149 Unsorted


title: SAM19056134 Unsorted


title: SAM19096142 GFP+


title: SAM19030229 ES


title: SAM19096150 GFP+


title: SAM19056143 Unsorted


title: SAM19096154 GFP+


title: SAM19096133 GFP+


title: SAM19096132 GFP+


title: SAM19030245 ES


title: PA573_c

city: Gent

first: Jonas

last: Van Belleghem

state: Oost-Vlaanderen

address: De Pintelaan 185

department: Dept. Clinical Chemistry, Microbiology and Immunology (GE06)

country: Belgium

institute: Ghent University

data_processing:
Illumina Casava1.7 software used for basecalling. As performed by BGI
Clean reads were respectively aligned to the reference genome and transcriptome using SOAP2
The gene expression level was measured by the number of uniquely mapped reads per kilobase of exon region per million mappable reads (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: PBMC

growth_protocol: PMBCs were incubated together with their respective stimuli for 20 h

extract_protocol:
PBMCs were isolated from whole blood and stored in Fetal calf serum with 10 % DSMO at -80 °C until used for stimulation. After stimulation cells were lysed with 1 ml Qiazol and 16 h storage at -80 °C
RNA libraries were prepared for sequencing using standard Illumina protocols, as performed by BGI

value: Whole Blood

value: PBMC

tag: treatment

value: P. aeruginosa strain 753 stimulated


title: SAM19096164 GFP+


title: SAM19056106 GFP+


title: SAM19286145 Unsorted


title: SAM18604751 Unsorted


title: PA573_b


title: SAM19286154 GFP+


title: LBR19_c

value: phage PNM lysate stimulated


title: LBR19_a


title: PA573_a


title: SAM19096162 GFP+


title: LBR19_b


title: Control_b

value: non-stimulated control


title: Control_a


title: RNA-seq of ceramide treated HSC rep2

city: Boston

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

data_processing:
Raw RNA-seq data were mapped into human reference genome (hg19) with bowtie2 (v2.1.0). Furthermore, HTSeq (v0.6.1) was used to quantify expression of coding genes  in HSCs under different conditions. The mapped reads in bam format were converted into BigWig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: Hepatic stellate cells (HSC) with ceramide treatment

growth_protocol: HSC myofibroblasts were cultured ex vivo in DMEM with 10% FCS.

extract_protocol:
Total RNA was extracted with TRIzol reagent, treated with DNAse I and cleaned using an acid-phenol:chloroform extraction. RNA quality was checked using an Agilent TapeStation 2200. All samples had a RIN score greater than 9.
RNA-seq libraries were prepared from 600 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA Kit and barcoded for sequencing.

treatment_protocol: HSC myofibroblasts were treated with either ethanol vehicle or nortriptyline (27 uM), or ethanol vehicle or ceramide (25 uM) for 48 hours prior to RNA extraction. Prior to TGF-beta stimulation, HSCs were serum starved in media containing DMEM with 0.2% bovine serum albumin (BSA) for 48 hours.  Cells were then treated with TGF-β (2.5ng/ml) and either ethanol vehicle or nortriptyline (27 uM) for 16 hours prior to harvest.

value: adult HSC myofibroblasts

tag: passage

value: passage 7-8

value: with ceramide (25 uM) for 48 hours


title: RNA-seq of ceramide treated HSC rep1


title: RNA-seq of Vehicle treated HSC rep2 - ceramide control

source_name: Hepatic stellate cells (HSC) with vehicle treatment

value: with ethanol vehicle for 48 hours


title: SAM19096136 GFP+


title: RNA-seq of Vehicle treated HSC rep1- ceramide control


title: SAM19286122 Unsorted


title: Rep3-TSA-RNA-seq

first: Kevin

last: White

address: 900 E 57th Street

department: Institute for Genomics and Systems Biology

institute: University of Chicago

description:
total RNA
Replicate 3 of TSA treated
processed data file: 150923_TSA_edgeR_gene_table.txt

data_processing:
Reads from Illumina Hiseq2000 were mapped to the human genome hg19 by Tophat (Trapnell et al. 2012). Reads were intersected with gene annotations from Refseq and RPKM values were calculated as estimates of gene expression levels.  We first counted reads for each gene under each condition and then used EdgeR (Robinson et al. 2010) (GLM tagwise dispersion used, q-value < 0.05) to identify genes that were differentially regulated comparing TSA to vehicle.
genome build: hg19
processed data files format and content: BED files of peak calls, and for RNA-seq differential expression, a gene list with associated log(fold change), log(CPM), and p-values fore each gene
processed data files format and content: 150923_TSA_edgeR_gene_table.txt: LNCaP differential gene expression by TSA treatment

source_name: human prostate adenocarcinoma cells

growth_protocol: 1.0X105 cells per well were seeded in 6-well plates in phenol red free RPMI 1640 medium (ThermoFisher Scientific) supplemented with 10% charcoal:dextran stripped FBS (Gemini) and 1% antibiotic-antimycotic (ThermoFisher Scientific) for 72 hours before treatment.

extract_protocol:
Total RNA was extracted from TSA/DMSO treated cells using PerfectPure RNA Cultured Cell Kit (5PRIME).
RNA-seq library preparation was conducted using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s protocol (1ug total RNA was used as initial material).

treatment_protocol: Cells were treated with either 100 ng/ml TSA (Sigma Aldrich) or DMSO for 24 hours before harvest to achieve three biological replicates.

value: LNCaP

value: TSA 24h @ 100 ng/ml


title: Rep1-DMSO-RNA-seq

description:
total RNA
Replicate 1 of DMSO treated
processed data file: 150923_TSA_edgeR_gene_table.txt

value: DMSO 24h


title: Rep2-DMSO-RNA-seq

description:
total RNA
Replicate 2 of DMSO treated
processed data file: 150923_TSA_edgeR_gene_table.txt


title: Rep3-DMSO-RNA-seq

description:
total RNA
Replicate 3 of DMSO treated
processed data file: 150923_TSA_edgeR_gene_table.txt


title: Rep2-TSA-RNA-seq

description:
total RNA
Replicate 2 of TSA treated
processed data file: 150923_TSA_edgeR_gene_table.txt


title: Rep3-untreated-RNA-seq

description:
total RNA
Replicate 3 of untreated
processed data file: 150923_TSA_edgeR_gene_table.txt

value: control


title: Rep1-TSA-RNA-seq

description:
total RNA
Replicate 1 of TSA treated
processed data file: 150923_TSA_edgeR_gene_table.txt

value: TSA  24h @ 100 ng/ml


title: Control_c


title: Rep1-DMSO-ATAC-seq

description:
genomic DNA
Replicate 1 of DMSO treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2252-2253-2254_bff_100_fseq_35bp_map_pool.sorted.top38813.bed

data_processing:
Library strategy: ATAC-seq
Cutadapt was used to trim adapter sequeces from paired ends. We used Bowtie and Bowtie2(Langmead and Salzberg 2012) for each library to do a two-round alignment to the hg19 human genome. In the first round, Bowtie was used and only uniquely mappable reads were kept and unmappable reads were gathered as the input for the second round.  We removed potential PCR duplicates by running Picard.  All uniquely mappable reads aligning to the plus strand were offset by +4-bp, and those aligning to the minus strand were offset −5-bp. used Fseq (Boyle et al. 2008) at default parameters (http://fureylab.web.unc.edu/software/fseq/) to call peaks in both vehicle condition and TSA treatment. We then merged peaks across conditions and counted the ATAC-seq reads number for each peak in each condition. Genomic regions showing differential accessibility after TSA treatment were called by EdgeR (we treated each region as if it was a gene, GLM tagwise dispersion used, q-value < 0.05).
genome build: hg19
processed data files format and content: BED files of peak calls, and for RNA-seq differential expression, a gene list with associated log(fold change), log(CPM), and p-values fore each gene
processed data files format and content: 160505_TSA_diff_ATAC_Seq.txt: LNCaP differential ATAC-Seq sites by TSA treatment. 2015-2252-2253-2254_bff_100_fseq_35bp_map_pool.sorted.top38813.bed : LNCaP Veh 24hr ATAC-Seq sites.

extract_protocol:
Nuclei from 50,000 TSA/DMSO treated cells were freshly extracted and incubated with Tn5 transposase (Illmina).
ATAC-seq was performed as previously described (Buenrostro JD et al., 2013). Transposed DNA was extracted from nuclei, and PCR amplified using NEBNext High-Fidelity DNA polymerase (NEB) and customized Nextera PCR primers.


title: Rep2-DMSO-ATAC-seq

description:
genomic DNA
Replicate 2 of DMSO treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2252-2253-2254_bff_100_fseq_35bp_map_pool.sorted.top38813.bed


title: Rep1-untreated-RNA-seq

description:
total RNA
Replicate 1 of untreated
processed data file: 150923_TSA_edgeR_gene_table.txt


title: Rep3-DMSO-ATAC-seq

description:
genomic DNA
Replicate 3 of DMSO treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2252-2253-2254_bff_100_fseq_35bp_map_pool.sorted.top38813.bed


title: Rep2-untreated-RNA-seq

description:
total RNA
Replicate 2 of untreated
processed data file: 150923_TSA_edgeR_gene_table.txt