title: A549_MEP50kd_1

description:
biological replicate 1
total RNA, rRNA depleted


title: A549_PRMT5kd_2

status: Public on Jun 09 2016

type: SRA

city: Bronx

first: David

last: Shechter

state: New York

address: 1300 Morris Park Ave

department: Biochemistry

country: USA

institute: Albert Einstein College of Medicine

description:
biological replicate 2
total RNA, rRNA depleted

library_source: transcriptomic

data_processing:
Trim Galore for removal of AGATCGGAAGAGC TruSeq Indexed Adapters
Mapping to hg19 with STAR aligner
gene counts determined with htseq-count
DESeq2 and edgeR differential expression analysis
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: A549 lung adenocarcinoma PRMT5 shRNA knockdown

growth_protocol: RPMI and 10% FBS

extract_protocol:
Total RNA extraction with Rneasy kit (Qiagen)
Stranded ribrary construction after depletion of rRNA with riboerase

treatment_protocol: Stable depletion with shRNA under selection with 1ug/ml puromycin

tag: knockdown

value: PRMT5 knockdown

tag: cell line

value: A549 lung adenocarcinoma


title: A549_PRMT5kd_3

description:
biological replicate 3
total RNA, rRNA depleted


title: PARP-1KD_VEH_HDAg-S_NELFE_2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

library_source: genomic

data_processing:
The ChIP-seq reads were aligned to the mm9 or hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bed” files for all analyses
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

source_name: PARP-1 Knockdown, vehicle, HDAg-S_NELFE

growth_protocol: MCF-7 cells were grown in culture as previously described (Hah et al. Cell 2011). PARP-1 knockout MEFs expressing analog-senstive PARP-1 were cultured in DMEM supplemented with 10% fetal bovine serum, penicillin, and streptomycin containing 1 µg/mL puromycin.

extract_protocol:
PARP-1 ChIP-seq:  Following mock ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.  Click-ChIP-seq:  Following 8-Bu(3-yne)T-ADP-ribosylation in intact nuclei from MEFs as described above, the nuclei were crosslinked with 0.5% formaldehyde and clicked to biotin. Nuclei were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and bound to streptavidin-conjugated magnetic beads.  Following extensive washing, the beads were collected in a magnetic field and de-crosslinked overnight at 65°C.  DNA was to be sequenced was recovered by magnetic separation from the beads and purified by PCIAA extraction and ethanol precipitation. All Other ChIP-seq:  Cells were sonicated in a water bath sonicator to a DNA fragment size distribution of 200 to 500 bp and chromatin was used for chromatin immunoprecipitation.
After purification, 50 ng of ChIP’d DNA for each condition was used to generate libraries for sequencing, as previously described  {Robertson, 2007 #41}, with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated with Ilumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250 ± 25 bp) was size-selected by agarose gel electrophoresis and extraction, amplified by PCR, and purified using AmPure beads (Beckman Coulter).  The final libraries were subjected to QC (size, purity, adapter contamination) and sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: MCF-7 Cells were grown in (1) MEM supplemented 1 µg/mL doxycycline for four all four days, (2) MEM with charcoal stripped calf serum for three days, and (3) vehicle (DMSO) or DRB (100 µM) containing medium (1:1000 dilution of DMSO) for 1 hour prior to their crosslinking with 1% formaldehyde in PBS. Crosslinking was quenched with 0.1 M Glycine after 10 minutes at room temperature, and cells were harvested with cold PBS for sonication (200-500 bp) and chromatin immunoprecipitation.  MEFs were harvested in cold PBS and collected by centrifugation.  The cells were swollen in Nuclei Isolation Buffer (10 mM HEPES, pH 8.0, 2 mM MgCl2, 3 mM CaCl2, 300 mM sucrose, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) and the nuclei were released by the addition of 0.65% NP-40 with moderate vortexing.  Following collection by centrifugation, the nuclei were resuspended in PARP Reaction Buffer (30 mM Tris•HCl, pH 7.5, 10 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 0.01% NP-40, 0.05 mM EDTA, 20% glycerol, with freshly added 1 mM DTT, protease inhibitors, and phosphatase inhibitors) containing 250 μM 8-Bu(3-yne)T-NAD+ for 30 minutes at 25°C with occasional gentle mixing to allow ADP-ribosylation to occur in the isolated nuclei.

tag: cell type

value: human breast cancer cells

tag: chip antibody

value: NELFE


title: PARP-1KD_VEH_GFP_NELFE_2

source_name: PARP-1 Knockdown, vehicle, GFP, NELFE


title: A549_GFPkd_2

source_name: A549 lung adenocarcinoma control (GFP) knockdown

value: GFP (control knockdown)


title: PARP-1KD_VEH_GFP_PolII_1

source_name: PARP-1 Knockdown, vehicle, GFP, PolII

value: PolII


title: A549_GFPkd_3


title: PARP-1KD_VEH_GFP_NELFE_1


title: PARP-1KD_VEH_HDAg-S_IgG_2

source_name: PARP-1 Knockdown, vehicle, HDAg-S, IgG

value: IgG


title: sgf11 rep2

city: WEST LAFAYETTE

first: Vikki

last: Weake

state: INDIANA

address: 175 S. University St.

department: Biochemisty

institute: Purdue University

data_processing:
bcl2fastq(aka, CASAVA v1.8.4) software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and further trimmed for quality sequence less than 30 and result in reads less than 50 using Trimmomatic v0.32.
Quality trimmed reads were mapped against the bowtie-2 v2.2.4  indexed D. melanogaster genome (Drosophila_melanogaster.BDGP5.78) using Tophat v2.0.13 .
The raw counts for each sample were generated by Htseq-count v0.6.1.
comparision was made between nonstop and wild type, sgf11 and wild type respectively using edgeR analysis. Differentially expressed genes were called based on false discovery rate (FDR)< 0.01.
Genome_build: Drosophila_melanogaster.BDGP5.78
Supplementary_files_format_and_content: edgeR output of csv files of differential analysis of  nonstop vs. wild type and sgf11 vs. wild type.

organism: Drosophila melanogaster

source_name: glial nuclei

growth_protocol: Flies were maintained at 25°C on standard media and wondering third instar larvae were used for experiments

extract_protocol:
Total RNA was extracted from labeled glial nuclei isolated from the central nervous system and eye antennal disc of Drosophila melanogaster third instar larvae and dsDNA was generated using the Ovation RNA-Seq System V2 (Nugen techonologies).
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: wandering third instar larvae

value: glia

tag: genotype


title: A549_GFPkd_1


title: LucKD_DRB_HDAg-S_PolII_2

source_name: Luciferase Knockdown, DRB, HDAg-S, PolII


title: A549_PRMT5kd_1


title: PARP-1KD_VEH_HDAg-S_IgG_1


title: PARP-1KD_VEH_GFP_IgG_2

source_name: PARP-1 Knockdown, vehicle, GFP, IgG


title: sgf11 rep4


title: nonstop rep4

value: nonstop -/-


title: NELF-EKD_VEH_flagNELF-Ewildtype_FLAG_2

source_name: NELF-E Knockdown, vehicle, flagNELF-Ewildtype, FLAG

value: FLAG


title: sgf11 rep3


title: LucKD_DRB_HDAg-S_PolII_1


title: PARP-1KD_VEH_HDAg-S_NELFE_1


title: sgf11 rep1


title: nonstop rep3


title: LucKD_DRB_GFP_PolII_1

source_name: Luciferase Knockdown, DRB, GFP, PolII


title: nonstop rep2


title: PARP-1KD_VEH_GFP_IgG_1


title: wild type rep4

value: wild type


title: LucKD_DRB_HDAg-S_NELFE_1

source_name: Luciferase Knockdown, DRB, HDAg-S_NELFE


title: PARP-1KD_VEH_GFP_PolII_2


title: LucKD_DRB_HDAg-S_NELFE_2


title: LucKD_DRB_GFP_NELFE_2

source_name: Luciferase Knockdown, DRB, GFP, NELFE


title: LucKD_DRB_GFP_NELFE_1


title: LucKD_DRB_GFP_PolII_2


title: wild type rep1


title: LucKD_VEH_GFP_FLAG_2

source_name: Luciferase Knockdown, vehicle, GFP, FLAG


title: LucKD_DRB_GFP_IgG_2

source_name: Luciferase Knockdown, DRB, GFP, IgG


title: LucKD_DRB_GFP_IgG_1


title: nonstop rep1


title: LucKD_VEH_GFP_FLAG_1


title: LucKD_VEH_HDAg-S_PolII_2

source_name: Luciferase Knockdown, vehicle, HDAg-S, PolII


title: LucKD_VEH_HDAg-S_PolII_1


title: LucKD_DRB_HDAg-S_IgG_1

source_name: Luciferase Knockdown, DRB, HDAg-S, IgG


title: LucKD_VEH_GFP_PolII_2

source_name: Luciferase Knockdown, vehicle, GFP, PolII


title: LucKD_VEH_GFP_PolII_1


title: LucKD_VEH_HDAg-S_NELFE_2

source_name: Luciferase Knockdown, vehicle, HDAg-S_NELFE


title: LucKD_VEH_GFP_NELFE_2

source_name: Luciferase Knockdown, vehicle, GFP, NELFE


title: LucKD_VEH_GFP_NELFE_1


title: LucKD_VEH_HDAg-S_NELFE_1


title: LucKD_DRB_HDAg-S_IgG_2


title: wild type rep3


title: LucKD_VEH_HDAg-S_IgG_2

source_name: Luciferase Knockdown, vehicle, HDAg-S, IgG


title: Comp. Fur Mutant Iron-Replete (Replicate 2)

city: Boston

first: Caroline

middle: Attardo

last: Genco

state: MA

address: 136 Harrison Ave

institute: Tufts University

data_processing:
fastq files were examined with the Rockhopper program.  This program performs alignment, gene counts, normalization and outputs expression levels for each gene in each samples.  Adjusted q values are also assigned to each pair-wise comparison between all samples.  Fastq files were aligned to the genome of Neisseria gonorrheoae FA1090
Genome_build: Neisseria gonorrheoae FA1090
Supplementary_files_format_and_content: Text files with normalized expression values for each gene

organism: Neisseria gonorrhoeae

source_name: Planktonic cells

extract_protocol:
RNA was extracted via TRIzol, treated with DNAse and ribosome depleted  (Agilents  MicrobeExpress kit)
Libraries were prepared with BioChain   s High Yield Directional mRNA Sample Prep Kit

treatment_protocol: N. gonorrhoeae* F62 wild-type, fur mutant and fur complement were grown in chemically defined media (CDM) with or without iron for 1 hour prior to RNA harvest.

tag: strain

tag: genotype/variation

value: complemented fur mutant

tag: treatment

value: high (100 uM iron)


title: wild type rep2


title: LucKD_VEH_GFP_IgG_1

source_name: Luciferase Knockdown, vehicle, GFP, IgG


title: LucKD_VEH_GFP_IgG_2


title: Fur mutant Iron-Deplete (Replicate 2)

value: fur mutant

value: low (100 uM desferal)


title: Nutlin-3a_3

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
The raw reads were mapped and the genes were counted using STAR with default parameters and UCSC hg19 reference genome
Cufflinks was used to generate FPKM values at gene level and transcript level
DESeq2 was used with default settings to calculate differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include mean FPKM values, log2 fold changes and p-values for each Sample

source_name: HCT116 p21-/- cells

extract_protocol:
RNA was extracted using the RNeasy Plus Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 p21-/- cells were treated with 10 µM Nutlin-3a, 0.2 µM doxorubicin, or the solvent DMSO for 24 h


title: Comp. Fur Mutant Iron-Replete (Replicate 1)


title: Nutlin-3a_4


title: Wild-type Iron-Deplete (Replicate 2)


title: Fur mutant Iron-Replete (Replicate 1)


title: Nutlin-3a_1


title: Comp. Fur Mutant Iron-Deplete (Replicate 1)


title: doxorubicin_3


title: doxorubicin_4


title: doxorubicin_1


title: Nutlin-3a_2


title: DMSO_4


title: LucKD_VEH_HDAg-S_IgG_1


title: Fur mutant Iron-Deplete (Replicate 1)


title: DMSO_3


title: DMSO_2


title: Wild-type Iron-Deplete (Replicate 1)


title: DMSO_1


title: Air2-HTP_2

status: Public on Jun 08 2016

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description: Sample 19

data_processing:
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using fastx-clipper (http://hannonlab.cshl.edu/fastx_toolkit/) to remove the 3’-linker sequence and quality filtered using using fastq_quality_trimmer and fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00.
Collapsing reads: To remove PCR duplicates, reads mapped to the same start position in the genome and sharing the same 3-nucleotide random barcode sequence were collapsed.
Genome_build: sacCer3
Supplementary_files_format_and_content: Genomic coordinates of mapped reads in gff format.  All gff files have been analyzed using the same script.

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged protein were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with the protein of interest were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while Rpb1-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilized by in-vivo UV crosslinking.

tag: expressing

value: HTP-tagged Air2

tag: barcode

value: NNNTGGAGC


title: Wild-type Iron-Replete (Replicate 2)


title: doxorubicin_2


title: Wild-type Iron-Replete (Replicate 1)


title: Air2-HTP_1

description: Sample 18

value: NNNGCGCAGC


title: Trf4-HTP_1

description: Sample 17

value: HTP-tagged Trf4

value: NNNCACTAGC


title: Rrp44-HTP_1

description: Sample 13

value: HTP-tagged Rrp44


title: Rrp6-HTP_1

description: Sample 15

value: HTP-tagged Rrp6

value: NNNTAAGC


title: Rpo21-2_S7IP

description: Sample 12

source_name: BY4741 Rpo21-HTP

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged Rpb1 were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with Rpb1 were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while Rpb1-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: antibody

value: NNNACTCAGC


title: Rpo21-2_Y1IP

description: Sample 4

value: NNNCGCTTAGC


title: Rpo21-3_S2IP

description: Sample 6


title: Rpo21-4_S5IP

description: Sample 10


title: Rpo21_Y1IP

description: Sample 3


title: Rpo21-2_nabFT

description: Sample 2

value: nabFT

value: NNNGACTTAGC


title: Rpo21_S5IP

description: Sample 9


title: Rrp44-HTP_2

description: Sample 14

value: NNNTCTCTAGC


title: Rpo21-2_T4IP

description: Sample 8


title: Rpo21_S7IP

description: Sample 11


title: Rpo21-2_S2IP

description: Sample 5

value: NNNCTAGC


title: KO rep 3

city: Chicago

first: Cara

middle: J

last: Gottardi

address: 240 East Huron St., McGaw Pavilion, M-323

department: Departments of Medicine

institute: Northwestern University

description:
replicate 3
KO_R3

data_processing:
The raw data of FASTQ format were processed to remove as much technical artifacts as possible. Low quality ends (phred score <20) were trimmed using the FASTX tool kit (http://hannonlab.cshl.edu/fastx_toolkit). Adapter trimming was performed with cutadapt 1.2.1. Reads shorter than 15 bp after adapter trimming were removed. Quality filtering was done using FastX 0.0.13 and ShortRead 1.16.3. PolyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed. The remaining clean reads were aligned against the reference genome of Mus musculus (mus_musculus_GRCm38.73), using the TopHat v2.0.8b software. As parameter options we used: --library-type fr-unstranded –min-intron-length 50 --max-intron-length 500000 –no-coverage-search --no-mixed --read-realign-edit-dist 3. Quality filtering (removal of reads that are non-primary mappings or have a mapping quality < 20), sorting and indexing of the resulting bam-files were done with samtools 0.1.19.
Gene expressions of the transcripts were calculated by counting the number of reads in the alignments that overlap with the gene features, using htseq-count 0.5.4p3. As parameters we took: -m union --stranded=reverse -a 0 -t exon -i gene id. Subsequently, the edgeR 3.12.0 tool was utilized to detect the differentially expressed genes between the alphaT-cat WT and KO samples. The modeling of the variance for each gene was done using both the common dispersion model (the same dispersion value is used for each gene) and the moderated tagwise dispersion model (a distinct, individual dispersion is estimated and used for each gene). EdgeR used with the moderated tagwise dispersion model tends to rank more highly as DE genes that are more consistent in their counts within groups. Finally, genes with a p-value ≤ 0.01, corresponding to a false discovery rate (FDR) value ≤ 0.3, were considered as differentially expressed (DE).
Genome_build: mus_musculus_GRCm38.73
Supplementary_files_format_and_content: tab-delimited text file including raw counts (output HTSeqCount) for each sample. Excel file contains statistical analysis.

organism: Mus musculus

extract_protocol:
After dissection of the brain, cerebellar tissue (n=3) was used for RNA extraction using TRIzol/chloroform during homogenation of the fatty brain tissue. Subsequently, the Aurum Total RNA mini Kit (Bio-rad) was used according to the manufacturer’s protocol.
Library construction protocol not provided.

tag: age

value: 7-8 weeks

tag: background strain

value: alphaT-catenin KO

tag: tissue

value: cerebellum


title: KO rep 1

description:
replicate 1
KO_R1


title: KO rep 2

description:
replicate 2
KO_R2


title: WT rep 1

description:
replicate 1
WT_R1

value: wildtype


title: WT rep 2

description:
replicate 2
WT_R2


title: WT rep 3

description:
replicate 3
WT_R3


title: Rrp6-HTP_2

description: Sample 16


title: Rpo21_T4IP

description: Sample 7


title: Rpo21_nabFT

description: Sample 1


title: Mus musculus WT-Th1 RA Med1

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

data_processing:
Basecalls performed using CASAVA
Polony  identification, base  calling  and  QC  statistics were performed using GOAT and Bustard module
Reads (in fastq files) were filtered to remove adapters using fastq-mcf and for quality using seqkt and aligned to the human (hg19) or mouse genome (mm9) with Bowtie2 (default settings). Bigwig files for visualization in the UCSC genome browser were generated using a custom pipeline; duplicate reads were first removed, coverage calculated with genomeCoverageBed and tag density calculated in 10bp windows. unionBedGraphs was then used to subtract input (or total histone H3 for histone ChIPs) signals and bigwig files generated using bedGraphToBigWig. Regions of significant enrichment were identified using MACS version 1.4 (Zhang et al., 2008) using input or total histone H3 as background, with the setting --keep-dup=1. A p-value threshold of 10-7 was used, unless stated otherwise.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: peaks.bed

source_name: In vitro differentiated Th1 cells, wild-type

growth_protocol: Naïve human CD4+ T-cells (CD4+CD45RA+CD45RO-CD25-CCR7+) were isolated by negative immunomagnetic selection (Miltenyi Biotec) followed by sorting using a FACSAria II (BD Bioscience). Cells were activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 µg/ml, BD Pharmingen) and were then cultured for 10 days with rhIL-2 (Biolegend, 10ng/ml). Conditions for T cell polarization were: rhIL-12 (10 ng/ml, Biolegend) and anti-IL-4 (10 µg/ml, R&D) for Th1, rhIL-4 (10 ng/ml, Biolegend) and anti-IFN-γ (10 µg/ml, R&D) for Th2.    For H3K4me3 ChIP-seq, CD4+ naive T-cells were differentiated into either Th1 or Th2 cells in vitro for 28 days.    Naïve murine CD4+ T-cells (CD4+CD25-CD62LhighCD44low) were purified from pooled spleen and lymph node cell suspensions of WT and T-bet -/- mice by immunomagnetic selection (Miltenyi Biotec) followed by sorting. Cells were activated for 72 hours with plate-bound anti-CD3 and anti-CD28 monoclonal antibodies (both 2 µg/ml) and then cultured for 5 days in the presence of 20 ng/ml IL-2 (Biolegend). Conditions for T cell polarization were: 20 ng/ml IL-12 (eBioscience) and 5 µg/ml anti-IL-4 (BioXCell) for Th1 or 20 ng/ml IL-4 (eBioscience) and 10 µg/ml anti-IFN-γ (BioXCell) for Th2.    CCR5+ memory Th1 cells were enriched with CD4 microbeads (Miltenyi Biotech) and CCR5+ Th1 (anti-CCR5, BD Biosciences) effector memory cells isolated by flow cytometry, activated with plate-bound anti-CD3 and anti-CD28 for 4  days, and expanded in media containing IL-2.

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent. For RNA pol II ChIP, an alternative set of lysis and wash buffers were used (Rahl et al., 2010). Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 10 µg of purified antibody or, for the case of T-bet, 10 µl of purified serum (see Table S6). Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNase A, proteinase K and phenol:chloroform extraction followed by ethanol precipitation.    H3K4me3 ChIP was performed on native chromatin. Chromatin was prepared by using the protocol of Feil and colleagues (http://www.epigenome-noe.net/researchtools/protocol.php?protid=2) with some minor modifications. Mono and dinucleosomal chromatin was recovered from nuclei treated with micrococcal nuclease (10U/µl for 7 mins) and chromatin quality assessed by agarose gel elecrophoresis and semi-quantitated using a nanodrop. ChIP for H3K4me3 and total H3 was performed with Protein G beads (Active Motif). DNA was purified by phenol/chloroform phase separation, ethanol precipitation, followed by clean up with Qiagen PCR purification columns.
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 35 or 50 bp single-end read sequencing with an Illumina GAIIx or HiSeq 2500 sequencer.

treatment_protocol: Human T cells were formaldehyde crosslinked on day 13 either before (unstimulated) or after (restimulated) treatment with PMA and ionomycin. For experiments testing the role of NF-κB, cells were restimulated for 5 hours with PMA/ionomycin in the presence of 20 µM BAY 11-7082 (Calbiochem) or DMSO before fixation.    Human T cells for H3K4me3 ChIP-seq, cells were activated for 4 hrs with 5 ng/ml PMA (Sigma) and 500 ng/ml ionomycin (CN Biosciences)     EL4 cells were formaldehyde crosslinked before and after stimulation with PMA (50 ng/ml) and ionomycin (1 µM) for 5 hours.

value: Bethyl Laboratories (A300-793A)

tag: treatment/agent

value: PMA/ionomycin


title: Mus musculus T-bet-KO-Th1 RA Brd4

source_name: In vitro differentiated Th1 cells, T-bet-/-

value: Bethyl Laboratories (A301-985A100)


title: Mus musculus WT-Th1 RA Brd4


title: Mus musculus T-bet-KO-Th1 RA Aff4

value: Bethyl Laboratories (A302-539A)


title: Mus musculus EL4-T-bet RA Aff4

source_name: EL4-T-bet cell line, stimulated


title: Mus musculus T-bet-KO-Th1 RA Med1


title: Mus musculus EL4-GFP RA Aff4

source_name: EL4-GFP cell line, stimulated


title: Mus musculus WT-Th1 RA RelA

value: Santa Cruz C-20 (sc-372)


title: Mus musculus EL4-T-bet RA Med1


title: Mus musculus EL4-T-bet RA Brd4


title: Mus musculus EL4-GFP RA Brd4


title: Mus musculus EL4-GFP RA Med1


title: Mus musculus EL4-Gata3 GFP FLAG-T-bet

source_name: EL4-Gata3 GFP cell line, stimulated

value: EL4-Gata3 GFP

value: Sigma M2


title: Mus musculus WT-Th1 RA Aff4


title: Mus musculus EL4-T-bet Plum FLAG-T-bet

source_name: EL4-T-bet mPlum cell line, stimulated

value: EL4-T-bet mPlum


title: Mus musculus Th1 RA H3

value: Abcam ab46540


title: Mus musculus T-bet-KO-Th1 RA H3


title: Mus musculus T-bet-KO-Th1 RA RelA


title: Limb bud Input DNA

city: Los Angeles

first: Kevin

last: Peterson

state: CA

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

data_processing:
Base pair calling was performed according to Illumina pipeline
sequence reads were mapped to mm9 using bwa-0.7.3a
sam files were generated with bwa-0.7.3a samse with n = 1
bam files containing reads from chr13:63,112,841-64,166,828 were created with samtools-0.1.19
bedgraph files were generated with bedtools v2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: Limb bud

extract_protocol:
Samples were crosslinked for 30' in 1% formaldehyde, lysed in (140mM NaCl, 0.5% NP40, 0.25% Triton-X 100, 10% glycerol, 1mM EDTA, 50mM HEPES-KOH, pH7.5) and cleared by sonication
Libraries were prepared according to Illumina protocols

tag: developmental stage


title: Mus musculus Th1 RA H3K4me3

value: Abcam ab8580


title: Cerebellum Input DNA

source_name: Cerebellum


title: Trunk Gli2 ChIP-seq

source_name: Trunk

value: Gli2 (R&D Systems, AF3635)


title: Limb bud Gli2 ChIP-seq


title: Mus musculus EL4-GFP RA RelA


title: Head Gli2 ChIP-seq

source_name: Head


title: Mus musculus EL4-T-bet RA RelA


title: Mus musculus T-bet-KO-Th1 RA H3K4me3


title: 22d-iN_iN4_39

city: Stanford CA

first: Barbara

last: Treutlein

address: 318 Campus Drive

department: Bioengineering

institute: Stanford University

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: sorted.genes.fpkm_tracking file (Cufflinks output) including FPKM values for each single cell.

source_name: induced neuronal (iN) cells

growth_protocol: Tau-Egfp reporter MEFs were isolated, infected with dox-inducible lentiviral constructs of  Ascl1,Brn2 and Myt1l and reprogrammed into iN cells as previously described in (Vierbuchen et al., Nature 2010). Cells were plated onto glia 7 days post dox-induction, and harvested 22 days post dox-induction.

extract_protocol:
Homozygous TauEGFP knock-in mice21 were purchased from the Jackson Laboratories and bred with C57BL/6 mice (Taconic) to generate TauEGFP heterozygous embryos. MEFs were isolated from E14.5 embryos using a dissection microscope (Leica). Tail tips were sliced into small pieces, trypsinized and plated to derive fibroblast cultures. All fibroblasts were expanded for three passages before being used for experiments. Complementary DNAs for candidate genes were cloned into doxycycline-inducible lentiviral vectors,
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000 (and 1:4,000 in case of 5d experiment).
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Cultured cells were trypsinized to generate a single cell suspension, FAC-sorted for Tau-Egfp+ cells and loaded onto a medium Fluidigm C1 chip at a concentration of 350,000 cells/ml.

value: iN cells derived from MEFs 22 days upon induction of Ascl1, Brn2 and Myt1l

value: Tau-EGFP +/-


title: 22d-iN_iN4_42


title: 22d-iN_iN4_43


title: 22d-iN_iN4_44


title: 22d-iN_iN4_40


title: Cerebellum Gli2 ChIP-seq


title: 22d-iN_iN4_41


title: 22d-iN_iN4_37


title: 22d-iN_iN4_46


title: 22d-iN_iN4_32


title: 22d-iN_iN4_36


title: 22d-iN_iN4_31


title: 22d-iN_iN4_34


title: 22d-iN_iN4_35


title: 22d-iN_iN4_33


title: 22d-iN_iN4_28


title: 22d-iN_iN4_27


title: 22d-iN_iN4_29


title: 22d-iN_iN4_30


title: 22d-iN_iN4_23


title: 22d-iN_iN4_21


title: 22d-iN_iN4_24


title: 22d-iN_iN4_22


title: 22d-iN_iN4_25


title: 22d-iN_iN4_38


title: 22d-iN_iN4_19


title: 22d-iN_iN4_18


title: 22d-iN_iN4_20


title: 22d-iN_iN4_17


title: 22d-iN_iN4_15


title: 22d-iN_iN4_6


title: 22d-iN_iN4_10


title: 22d-iN_iN4_8


title: 22d-iN_iN4_11


title: 22d-iN_iN4_16


title: 22d-iN_iN4_13


title: 22d-iN_iN4_9


title: 22d-iN_iN4_1


title: 22d-iN_iN4_7


title: 22d-iN_iN4_4


title: 22d-iN_iN4_5


title: 22d-iN_iN4_12


title: 22d-iN_iN4_3


title: 5d-iN_iN3_53

growth_protocol: Tau-Egfp reporter MEFs were isolated, infected with dox-inducible Ascl1 lentiviral constructs, reprogrammed into iN cells as previously described in (Chanda et al.,Stem Cell Reports 2014) and harvested 5 days after dox-induction.

treatment_protocol: Cultured cells were trypsinized to generate a single cell suspension, FAC-sorted for Tau-Egfp+ and Tau-Egfp- cells and the two cell populations were mixed again in a 1:1 ratio. Then they were loaded onto a medium Fluidigm C1 chip at a concentration of 350,000 cells/ml.

value: iN cells derived from MEFs 5 days upon Ascl1 induction


title: 5d-iN_iN3_54


title: 5d-iN_iN3_50


title: 5d-iN_iN3_48


title: 5d-iN_iN3_49


title: 5d-iN_iN3_51


title: 5d-iN_iN3_47


title: 5d-iN_iN3_55


title: 5d-iN_iN3_42


title: 5d-iN_iN3_43


title: 5d-iN_iN3_46


title: 5d-iN_iN3_45


title: 5d-iN_iN3_44


title: 22d-iN_iN4_2


title: 5d-iN_iN3_41


title: 5d-iN_iN3_40


title: 5d-iN_iN3_37


title: 5d-iN_iN3_33


title: 5d-iN_iN3_52


title: 5d-iN_iN3_35


title: 5d-iN_iN3_31


title: 5d-iN_iN3_29


title: 5d-iN_iN3_36


title: 5d-iN_iN3_39


title: 5d-iN_iN3_26


title: 5d-iN_iN3_34


title: 5d-iN_iN3_32


title: 5d-iN_iN3_28


title: 5d-iN_iN3_24


title: 5d-iN_iN3_23


title: 5d-iN_iN3_25


title: 5d-iN_iN3_22


title: 5d-iN_iN3_21


title: 5d-iN_iN3_20


title: 5d-iN_iN3_17


title: 5d-iN_iN3_15


title: 5d-iN_iN3_19


title: 5d-iN_iN3_18


title: 5d-iN_iN3_16


title: 5d-iN_iN3_38


title: 5d-iN_iN3_14


title: 5d-iN_iN3_30


title: 5d-iN_iN3_11


title: 5d-iN_iN3_13


title: 5d-iN_iN3_27


title: 5d-iN_iN3_12


title: 5d-iN_iN3_9


title: 5d-iN_iN3_8


title: 5d-iN_iN3_7


title: 5d-iN_iN3_5


title: 5d-iN_iN3_1


title: 5d-iN_iN3_6


title: 5d-iN_iN3_3


title: 5d-iN_iN3_4


title: 2d-iN_iN1_81

growth_protocol: Tau-Egfp reporter MEFs were isolated, infected with dox-inducible Ascl1 lentiviral constructs, reprogrammed into iN cells as previously described in (Chanda et al.,Stem Cell Reports 2014) and harvested 2 days after dox-induction.

treatment_protocol: Cultured cells were trypsinized to generate a single cell suspension and loaded onto a medium Fluidigm C1 chip at a concentration of 350,000 cells/ml.

value: iN cells derived from MEFs 2 days upon Ascl1 induction


title: 2d-iN_iN1_79


title: 2d-iN_iN1_77


title: 2d-iN_iN1_78


title: 5d-iN_iN3_2


title: 2d-iN_iN1_74


title: 2d-iN_iN1_76


title: 2d-iN_iN1_75


title: 2d-iN_iN1_72


title: 2d-iN_iN1_73


title: 2d-iN_iN1_71


title: 2d-iN_iN1_69


title: 5d-iN_iN3_10


title: 2d-iN_iN1_70


title: 2d-iN_iN1_66


title: 2d-iN_iN1_67


title: 2d-iN_iN1_68


title: 2d-iN_iN1_65


title: 2d-iN_iN1_63


title: 2d-iN_iN1_62


title: 2d-iN_iN1_80


title: 2d-iN_iN1_61


title: 2d-iN_iN1_64


title: 2d-iN_iN1_57


title: 2d-iN_iN1_58


title: 2d-iN_iN1_60


title: 2d-iN_iN1_56


title: 2d-iN_iN1_55


title: 2d-iN_iN1_54


title: 2d-iN_iN1_49


title: 2d-iN_iN1_51


title: 2d-iN_iN1_47


title: 2d-iN_iN1_48


title: 2d-iN_iN1_52


title: 2d-iN_iN1_45


title: 2d-iN_iN1_46


title: 2d-iN_iN1_43


title: 2d-iN_iN1_44


title: 2d-iN_iN1_42


title: 2d-iN_iN1_41


title: 2d-iN_iN1_59


title: 2d-iN_iN1_40


title: 2d-iN_iN1_39


title: 2d-iN_iN1_38


title: 2d-iN_iN1_37


title: 2d-iN_iN1_53


title: 2d-iN_iN1_34


title: 2d-iN_iN1_36


title: 2d-iN_iN1_35


title: 2d-iN_iN1_32


title: 2d-iN_iN1_33


title: 2d-iN_iN1_30


title: 2d-iN_iN1_29


title: 2d-iN_iN1_27


title: 2d-iN_iN1_25


title: 2d-iN_iN1_28


title: 2d-iN_iN1_23


title: 2d-iN_iN1_18


title: 2d-iN_iN1_19


title: 2d-iN_iN1_17


title: 2d-iN_iN1_20


title: 2d-iN_iN1_26


title: 2d-iN_iN1_22


title: 2d-iN_iN1_21


title: 2d-iN_iN1_16


title: 2d-iN_iN1_50


title: 2d-iN_iN1_14


title: 2d-iN_iN1_15


title: 2d-iN_iN1_13


title: 2d-iN_iN1_10


title: 2d-iN_iN1_9


title: 2d-iN_iN1_12


title: 2d-iN_iN1_31


title: 2d-iN_iN1_11


title: 2d-iN_iN1_6


title: 2d-iN_iN1_7


title: 2d-iN_iN1_8


title: 2d-iN_iN1_5


title: 2d-iN_iN1_24


title: 2d-iN_iN1_3


title: 2d-iN_iN1_2


title: 2d-iN_iN1_1


title: 0d-MEFs_iN2_73

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were isolated as described in (Vierbuchen et al., Nature 2010) from E14.5 embryos of TauEGFP heterozygous mice using a dissection microscope (Leica). Briefly, tail tips of embryonic mice were sliced into small pieces, trypsinized and plated to derive fibroblast cultures.

value: Fibroblast culture from embryonic (E14.5) mouse tail tips


title: 0d-MEFs_iN2_72


title: 0d-MEFs_iN2_71


title: 0d-MEFs_iN2_70


title: 0d-MEFs_iN2_69


title: 0d-MEFs_iN2_68


title: 0d-MEFs_iN2_66


title: 0d-MEFs_iN2_67


title: 0d-MEFs_iN2_63


title: 0d-MEFs_iN2_62


title: 0d-MEFs_iN2_64


title: 0d-MEFs_iN2_61


title: 0d-MEFs_iN2_60


title: 0d-MEFs_iN2_59


title: 0d-MEFs_iN2_58


title: 2d-iN_iN1_4


title: 0d-MEFs_iN2_56


title: 0d-MEFs_iN2_55


title: 0d-MEFs_iN2_57


title: 0d-MEFs_iN2_54


title: 0d-MEFs_iN2_53


title: 0d-MEFs_iN2_50


title: 0d-MEFs_iN2_49


title: 0d-MEFs_iN2_47


title: 0d-MEFs_iN2_48


title: 0d-MEFs_iN2_46


title: 0d-MEFs_iN2_44


title: 0d-MEFs_iN2_45


title: 0d-MEFs_iN2_51


title: 0d-MEFs_iN2_41


title: 0d-MEFs_iN2_40


title: 0d-MEFs_iN2_42


title: 0d-MEFs_iN2_38


title: 0d-MEFs_iN2_37


title: 0d-MEFs_iN2_36


title: 0d-MEFs_iN2_35


title: 0d-MEFs_iN2_34


title: 0d-MEFs_iN2_33


title: 0d-MEFs_iN2_30


title: 0d-MEFs_iN2_52


title: 0d-MEFs_iN2_26


title: 0d-MEFs_iN2_28


title: 0d-MEFs_iN2_27


title: 0d-MEFs_iN2_29


title: 0d-MEFs_iN2_65


title: 0d-MEFs_iN2_24


title: 0d-MEFs_iN2_21


title: 0d-MEFs_iN2_20


title: 0d-MEFs_iN2_22


title: 0d-MEFs_iN2_25


title: 0d-MEFs_iN2_43


title: 0d-MEFs_iN2_19


title: 0d-MEFs_iN2_39


title: 0d-MEFs_iN2_18


title: 0d-MEFs_iN2_23


title: 0d-MEFs_iN2_16


title: 0d-MEFs_iN2_15


title: 0d-MEFs_iN2_17


title: 0d-MEFs_iN2_13


title: 0d-MEFs_iN2_14


title: 0d-MEFs_iN2_32


title: 0d-MEFs_iN2_12


title: 0d-MEFs_iN2_31


title: codY LBMM 2

city: Tel Aviv

first: Lior

last: Lobel

state: Israel

address: Ramat Aviv

department: Molecular Microbiology

country: Israel

institute: Tel Aviv University

description: rRNA depleted total RNA

data_processing:
Quality control using the SeqMonk software
Trimming if needed using the FASTX tool kit
Alignment using Rockhopper software V1.3
Differential expression analysis using Rockhopper software V1.3
Genome_build: Listeria monocytogenes 10430S genome (the Broad Institute)
Supplementary_files_format_and_content: RPKM values with DE analysis

organism: Listeria monocytogenes 10403S

source_name: codY LBMM

growth_protocol: L. monocytogenes were grown to mid exponenital growth phase (OD 600nm = 0.3) in BHI or low BCAAs minimal medium (LBMM) and then harvested for RNA exctraction

extract_protocol:
Total RNA was extracted using the RNAsnap method followed by rRNA depletion using Epicentre RiboZero kit.
RNA-Seq libraries were prepared using the TruSeq RNA sample Prep kit™ (Illumina®)

value: codY (LMRG_00730) deletion mutant

tag: medium

value: Minimal (low BCAAs minimal medium)


title: 0d-MEFs_iN2_11


title: WT LBMM 2

description: rRNA depleted total RNA

source_name: WT LBMM

value: wild-type


title: WT LBMM 3

description: rRNA depleted total RNA


title: WT LBMM 1

description: rRNA depleted total RNA


title: 0d-MEFs_iN2_10


title: codY BHI 3

description: rRNA depleted total RNA

source_name: codY BHI

value: Rich (BHI)


title: 0d-MEFs_iN2_9


title: codY BHI 2

description: rRNA depleted total RNA


title: WT BHI 3

description: rRNA depleted total RNA

source_name: WT BHI


title: codY BHI 1

description: rRNA depleted total RNA


title: 0d-MEFs_iN2_8


title: WT BHI 2

description: rRNA depleted total RNA


title: WT BHI 1

description: rRNA depleted total RNA


title: 0d-MEFs_iN2_7


title: 0d-MEFs_iN2_4


title: 0d-MEFs_iN2_5


title: 0d-MEFs_iN2_2


title: 0d-MEFs_iN2_6


title: 0d-MEFs_iN2_3


title: codY LBMM 1

description: rRNA depleted total RNA


title: 0d-MEFs_iN2_1


title: Mus musculus EL4-GFP US Input

data_processing:
Basecalls performed using CASAVA
Polony  identification, base  calling  and  QC  statistics were performed using GOAT and Bustard module
Genome_build: hg19/mm9

source_name: EL4-GFP cell line, unstimulated

extract_protocol:
Human Th1 and Th2 cells, pooled from multiple donors, were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detegerent. Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been preincubated with 10 ug of purified antibody or, for the case of T-bet, 10 ul of purified serum. Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl.  Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNAseA, proteinase K and phenol:chloroform extraction followed by ethanol precipitation. H3K4me3 ChIP was performed on native chromatin derived from ex vivo differentiated human Th1 and Th2 cells. Chromatin was prepared broadly using the protocol of Feil and colleagues with some minor modifications (http://www.epigenome-noe.net/researchtools/protocol.php?protid=2). Mono and dinucleosomal chromatin was recovered from nuclei treated with micrococcal nuclease (10U/µl for 7 mins). Chromatin quality was assessed by agarose gel elecrophoresis and semi-quantitated using a nanodrop. A second chromatin prep was also prepared from Th1 and Th2 cells, these cells were exposed  to fomaldehyde in order to cross link protein to DNA. Nuclei from these cells were treated with MNase followed by sonication (6x20 second bursts at 40% amplitude using a Sonics VibraCell probe sonicator). ChIP for H3K4me3 and total H3 was performed with Protein G beads (Active Motif). DNA was purified by phenol/chloroform phase separation, ethanol precipitation, followed by Qiagen clean up.
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification.

treatment_protocol: Naïve human CD4+ T-cells (CD4+CD45RA+CD45RO-CD25-CCD7+) were isolated from healthy donors by negative immunomagnetic selection (Miltenyi Biotec) and activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 µg/ml, R&D) and then cultured for 10 days with rhIL-2 (Biolegend, 10 ng/ml). Conditions for T ell polarisation were: rhIL-12 (10 ng/ml, Biolegend) and anti-IL-4 (10 μg/ml, R&D) for Th1, rhIL-4 (10 ng/ml, Biolegend) and anti-IFN-γ (10 μg/ml, R&D) for Th2. For ChIP, cells were formaldehyde crosslinked on day 13 either before (unstimulated) or after (restimulated) treatment with anti-CD3 and anti-CD28 antibodies (2 μg/ml). For H3K4me3 ChIP-Seq, CD4+ naive T-cells were differentiated into either Th1 or Th2 cells in vitro for 28 days, following an established protocol. Cells were activated for 4 hrs with 5 ng/ml PMA (Sigma) and 500 ng/ml ionomycin (CN Biosciences) and assessed for intracellular cytokine staining. Naïve murine CD4+ T-cells (CD4+CD25-CD62LhighCD44low) were purified by immunomagnetic selection (Miltenyi Biotec) from murine spleen and lymph nodes from WT and T-bet-/- mice (BALB/c background) or from WT and Gata3fl/fl x Tnfrsf4-Cre mice (C57BL/6 background). Cells were activated for 72 hours with plate-bound anti-CD3 and anti-CD28 monoclonal antibodies (both 2 μg/ml) and then cultured for 5 days in the presence of 20 ng/ml IL-2 (Biolegend). Conditions for T ell polarisation were: 20 ng/ml IL-12 (eBioscience) and 10 μg/ml anti-IL-4 (BioXCell) for Th1 or 20 ng/ml IL-4 (eBioscience) and 10 μg/ml anti-IFN-γ (BioXCell) for Th2. Cells were crosslinked on day 13 either before (unstimulaed) or after (restimulated) treatment with PMA (50 ng/ml) and ionomycin (1 μM) for 4 hours. EL4-GFP and EL4-T-bet cells were formaldehyde crosslinked before and after stimulation with PMA (50 ng/ml) and ionomycin (1 μM) for 4 hours.

value: unstimulated


title: Mus musculus EL4-T-bet US PTEF-b

source_name: EL4-T-bet cell line, unstimulated


title: Mus musculus EL4-T-bet US Input


title: Mus musculus EL4-GFP US PTEF-b


title: 2dAscl1clonal-iN_iN5_47

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing log2(FPKM) values for all 437 single cells (rows) and all genes (columns). In addition, the first 5 columns contain the following metadata: cell_name (unique identifier of each single cell that is linked to the name of the raw data file), assignment (identity of cell based on analysis in corresponding paper), log_tauGFP_intensity (log of the EGFP fluorescence intensity of each single cell as measured prior to cell lysis on the C1 microfluidic device), experiment (unique identifier of the experiment, iN1-iN8), time_point (time point in days post induction of Ascl1 or BAM via dox-treatment).

growth_protocol: Clonal Ascl1-inducible MEFs were isolated, reprogramming into iN cells was initiated by dox-treatment as previously described in (Chanda et al.,Stem Cell Reports 2014) and cells were harvested 2 days after dox-induction.

extract_protocol:
Homozygous TauEGFP knock-in mice21 were purchased from the Jackson Laboratories and bred with C57BL/6 mice (Taconic) to generate TauEGFP heterozygous embryos. MEFs were isolated from E14.5 embryos using a dissection microscope (Leica). Tail tips were sliced into small pieces, trypsinized and plated to derive fibroblast cultures. All fibroblasts were expanded for three passages before being used for experiments. Complementary DNAs for candidate genes were cloned into doxycycline-inducible lentiviral vectors. Clonal Ascl1-inducible MEFs were derived as described by Wapinski et al., Cell 2013.
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions at a dilution of 1:40,000 (and 1:4,000 in case of 5d experiment).
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

value: iN cells derived from clonal Ascl1-inducible MEFs 2 days upon Ascl1 induction


title: 2dAscl1clonal-iN_iN5_46


title: Mus musculus WT-Th2 NA pTefb

source_name: In vitro differentiated Th2 cells, wild-type


title: Mus musculus T-betKO-Th1 NA pTefb

source_name: In vitro differentiated Th1 cells, T-bet-/-


title: 2dAscl1clonal-iN_iN5_44


title: 2dAscl1clonal-iN_iN5_41


title: 2dAscl1clonal-iN_iN5_43


title: Mus musculus WT-Th1 NA pTefb

source_name: In vitro differentiated Th1 cells, wild-type


title: 2dAscl1clonal-iN_iN5_40


title: Mus musculus WT-Th2 NA Input


title: 2dAscl1clonal-iN_iN5_39


title: 2dAscl1clonal-iN_iN5_38


title: 2dAscl1clonal-iN_iN5_36


title: 2dAscl1clonal-iN_iN5_34


title: 2dAscl1clonal-iN_iN5_42


title: 2dAscl1clonal-iN_iN5_33


title: Mus musculus T-betKO-Th1 NA Input


title: Mus musculus EL4 GFP plusPI Input

source_name: EL4-GFP cell line, stimulated

value: PMA/ionomycin


title: Mus musculus EL4 GFP plusPI pTEF-b


title: 2dAscl1clonal-iN_iN5_31


title: 2dAscl1clonal-iN_iN5_45


title: 2dAscl1clonal-iN_iN5_29


title: 2dAscl1clonal-iN_iN5_28


title: 2dAscl1clonal-iN_iN5_27


title: 2dAscl1clonal-iN_iN5_24


title: 2dAscl1clonal-iN_iN5_22


title: 2dAscl1clonal-iN_iN5_25


title: 2dAscl1clonal-iN_iN5_23


title: 2dAscl1clonal-iN_iN5_21


title: Mus musculus WT-Th1 NA Input


title: Mus musculus EL4 T-bet plusPI pTEF-b

source_name: EL4-T-bet cell line, stimulated


title: 2dAscl1clonal-iN_iN5_19


title: 2dAscl1clonal-iN_iN5_35


title: 2dAscl1clonal-iN_iN5_37


title: 2dAscl1clonal-iN_iN5_15


title: 2dAscl1clonal-iN_iN5_16


title: 2dAscl1clonal-iN_iN5_14


title: 2dAscl1clonal-iN_iN5_11


title: 2dAscl1clonal-iN_iN5_30


title: Mus musculus EL4 T-bet plusPI Input


title: 2dAscl1clonal-iN_iN5_26


title: 2dAscl1clonal-iN_iN5_12


title: 2dAscl1clonal-iN_iN5_32


title: 2dAscl1clonal-iN_iN5_9


title: 2dAscl1clonal-iN_iN5_10


title: 2dAscl1clonal-iN_iN5_7


title: 2dAscl1clonal-iN_iN5_4


title: 2dAscl1clonal-iN_iN5_8


title: 2dAscl1clonal-iN_iN5_6


title: 2dAscl1clonal-iN_iN5_5


title: 2dAscl1clonal-iN_iN5_17


title: 2dAscl1clonal-iN_iN5_2


title: 2dAscl1clonal-iN_iN5_1


title: 22dAscl1-iN_iN8_53

growth_protocol: Tau-Egfp reporter MEFs were isolated, infected with dox-inducible Ascl1 lentiviral constructs, reprogrammed into iN cells as previously described in (Chanda et al.,Stem Cell Reports 2014). Cells were plated onto glia 7 days post dox-induction, and harvested 22 days post dox-induction.

value: iN cells derived from MEFs 22 days upon Ascl1 induction


title: 22dAscl1-iN_iN8_48


title: 22dAscl1-iN_iN8_55


title: 22dAscl1-iN_iN8_47


title: 22dAscl1-iN_iN8_50


title: 2dAscl1clonal-iN_iN5_13


title: 2dAscl1clonal-iN_iN5_3


title: 22dAscl1-iN_iN8_54


title: 22dAscl1-iN_iN8_39


title: 22dAscl1-iN_iN8_45


title: 22dAscl1-iN_iN8_38


title: 22dAscl1-iN_iN8_37


title: hh-luci-EA2

status: Public on Jun 10 2016

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

country: France

institute: CRCM

description:
day5
hh-luci-EA2_S19

data_processing:
cleaning (fastq-mcf)
mapping to D. melanogaster genome r_5.45 using TopHat2 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
Genome_build: Drosophila melanogaster dm3

source_name: eye-antennal imaginal disc

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
RNA was extracted using RNAeasy mini spin kit (Qiagen).
Quality control, library preparation and sequencing were performed by VIB Nucleomics Core Facility (Leuven, BE)

treatment_protocol: Wandering third instar larvae were collected and eye-antennal, leg, and wing imaginal discs were isolated by dissection for each genotype on the day indicated. Dissection tools and surfaces were prepared with RNA-Zap(Sigma). Discs were dissected from 35-50 larvae and transferred into RNAse-free 1xPBS on ice. In each genotype replicate 1 and replicate 2 represent independent dissections.

tag: developmental time point

value: third instar wandering larvae

value: Hand dissection

value: hh-Gal4, UAS-GFP/UAS-luc-RNAi


title: 22dAscl1-iN_iN8_40

tag: cell type


title: 22dAscl1-iN_iN8_36


title: 22dAscl1-iN_iN8_35


title: 22dAscl1-iN_iN8_42


title: 22dAscl1-iN_iN8_46


title: 22dAscl1-iN_iN8_41


title: 22dAscl1-iN_iN8_29


title: 22dAscl1-iN_iN8_27


title: 22dAscl1-iN_iN8_26


title: 22dAscl1-iN_iN8_23


title: 22dAscl1-iN_iN8_22


title: 22dAscl1-iN_iN8_21


title: 22dAscl1-iN_iN8_20


title: 22dAscl1-iN_iN8_24


title: 22dAscl1-iN_iN8_15


title: 22dAscl1-iN_iN8_18


title: 22dAscl1-iN_iN8_13


title: 22dAscl1-iN_iN8_11


title: 22dAscl1-iN_iN8_10


title: 22dAscl1-iN_iN8_9


title: 22dAscl1-iN_iN8_14


title: 22dAscl1-iN_iN8_2


title: 22dAscl1-iN_iN8_3


title: 22dAscl1-iN_iN8_4


title: 22dAscl1-iN_iN8_25


title: 22dAscl1-iN_iN8_6


title: 22dAscl1-iN_iN8_5


title: 22dAscl1-iN_iN7_34


title: 22dAscl1-iN_iN7_35


title: 22dAscl1-iN_iN8_1


title: 22dAscl1-iN_iN7_29


title: 22dAscl1-iN_iN7_32


title: 22dAscl1-iN_iN7_27


title: 22dAscl1-iN_iN7_26


title: 22dAscl1-iN_iN7_31


title: 22dAscl1-iN_iN7_22


title: 22dAscl1-iN_iN8_12


title: 22dAscl1-iN_iN7_24


title: 22dAscl1-iN_iN7_16


title: 22dAscl1-iN_iN7_18


title: 22dAscl1-iN_iN7_21


title: 22dAscl1-iN_iN7_15


title: 22dAscl1-iN_iN7_20


title: 22dAscl1-iN_iN7_14


title: 22dAscl1-iN_iN7_17


title: 22dAscl1-iN_iN7_19


title: 22dAscl1-iN_iN7_28


title: 22dAscl1-iN_iN7_10


title: 22dAscl1-iN_iN7_11


title: 22dAscl1-iN_iN7_5


title: 22dAscl1-iN_iN7_30


title: 22dAscl1-iN_iN7_8


title: 22dAscl1-iN_iN7_12


title: 22dAscl1-iN_iN7_4


title: 22dAscl1-iN_iN7_6


title: 22dAscl1-iN_iN7_13


title: 22dAscl1-iN_iN7_23


title: 22dAscl1-iN_iN7_3


title: 20dAscl1-iN_iN6_46

growth_protocol: Tau-Egfp reporter MEFs were isolated, infected with dox-inducible Ascl1 lentiviral constructs, reprogrammed into iN cells as previously described in (Chanda et al.,Stem Cell Reports 2014). Cells were plated onto glia 7 days post dox-induction, and harvested 20 days post dox-induction.

value: iN cells derived from MEFs 20 days upon Ascl1 induction


title: 20dAscl1-iN_iN6_45


title: 20dAscl1-iN_iN6_43


title: 22dAscl1-iN_iN7_9


title: 20dAscl1-iN_iN6_42


title: 22dAscl1-iN_iN7_1


title: 20dAscl1-iN_iN6_39


title: 20dAscl1-iN_iN6_37


title: 20dAscl1-iN_iN6_29


title: 20dAscl1-iN_iN6_33


title: 20dAscl1-iN_iN6_28


title: 20dAscl1-iN_iN6_27


title: 20dAscl1-iN_iN6_25


title: 20dAscl1-iN_iN6_26


title: 20dAscl1-iN_iN6_22


title: 22dAscl1-iN_iN7_2


title: 20dAscl1-iN_iN6_21


title: 22dAscl1-iN_iN7_25


title: 20dAscl1-iN_iN6_18


title: 20dAscl1-iN_iN6_13


title: 20dAscl1-iN_iN6_16


title: 20dAscl1-iN_iN6_12


title: 20dAscl1-iN_iN6_17


title: 20dAscl1-iN_iN6_11


title: 20dAscl1-iN_iN6_9


title: 20dAscl1-iN_iN6_8


title: 20dAscl1-iN_iN6_5


title: 20dAscl1-iN_iN6_6


title: 20dAscl1-iN_iN6_4


title: 20dAscl1-iN_iN6_1


title: Neural progenitors t0 H3K27me3 ChIP-seq

description: Embryoid bodies were formed by two days of suspension culture

source_name: Neural progenitors t0

value: ES cell derived embryoid bodies

value: H3K27me3 (Millipore, 07-449)


title: Neural progenitors t72 + SAG H3K27me3 ChIP-seq

description: Embryoid bodies were formed by two days of suspension culture followed by induction with all-trans retinoic acid (RA, 500nM) plus Smo agonist. Samples were collected 72h post-induction.

source_name: Neural progenitors t72 + SAG


title: Sym ChIP Uninduced cells

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description:
RTA protein is under tet-inducible promoter
H4R3sym ChIP DNA

data_processing:
The libraries were run on Illumina Hi-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the KSHV genome databaseto determine the DNA bound by H4R3sym histone H4
ChIP peaks were calculated using CLC workbench ChiP-peak tool using input as reference
Genome_build: NCBI genome build of KSHV sequence accession# NC_009333
Supplementary_files_format_and_content: ChIp peaks on the viral genomes are in wig file (CLC workbench)

source_name: TRExBCBL1-RTA cells

growth_protocol: TRExBCBL1-Rta  cells were grown in RPMI medium with 10% FBS.

extract_protocol:
lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
Chromatins were immunoprecipitated using anti-H4R3symmtreic antibody by following standard ChIP protocol

treatment_protocol: Cells were induced for lytic reactivation by Doxycycline for 24h.

value: KSHV infected Body Cavity Based Lymphoma Cells

tag: antibody manufacturer

value: Active Motif

tag: antibody catalog #

tag: antibody lot #


title: 20dAscl1-iN_iN6_23

source_name: induced neuronal (iN) cells

tag: strain

tag: genotype

value: Tau-EGFP +/-


title: Input for Uninduced cells

description:
RTA protein is under tet-inducible promoter
DNA extracted from the sonicated chromatin

value: none, Input DNA


title: 20dAscl1-iN_iN6_7


title: Sym ChIP Induced cells


title: SR106-11

first: Susan

last: Realegeno

address: 615 Charles E Young Dr. South

department: Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

description: PBMC

data_processing:
Alignment was done using Bowtie2 and Tophat
HT-SEQ was used to assign uniquely mapped reads to exons and genes using annotation file for build hg19 from Ensembl in order to generate raw count data
Normalized counts determined by DESeq, followed by differential expression
Genome_build: hg19
Supplementary_files_format_and_content: .csv file contains normalized counts as a matrix of ENSEMBL ID per sample, values repoted are normalized counts determined by DESEQ

molecule: polyA RNA

source_name: Donor 5, IFN-g, 24hrs

growth_protocol: Human CD14+ monocytes isolated from PBMC were differentiated in M-CSF for 4 days into monocyte-derived macrophages

extract_protocol:
RNA was isolated with Qiagen RNAeasy Micro Kit
Libraries were prepared using standard protocols with Illumina Truseq kit

treatment_protocol: media control, TLR2/1 ligand, or interferon-gamma

value: monocyte-dervied macrophages

tag: stimulation length

value: 24 hours

tag: stimulation

value: interferon gamma


title: 20dAscl1-iN_iN6_24


title: Input for Induced cells


title: 20dAscl1-iN_iN6_14


title: SR106-10

description: PBMC

source_name: Donor 5, TLR2/1L, 24hrs

value: TLR2/1 ligand


title: SR106-05

description: PBMC

source_name: Donor 5, Media, 6hrs

value: 6 hours

value: media alone


title: SR106-02

description: PBMC

source_name: Donor 5, TLR2/1L, 2hrs

value: 2 hours


title: SR106-09

description: PBMC

source_name: Donor 5, Media, 24hrs


title: SR106-06

description: PBMC

source_name: Donor 5, TLR2/1L, 6hrs


title: SR106-01

description: PBMC

source_name: Donor 5, Media, 2hrs


title: SR100-11

description: PBMC

source_name: Donor 4, IFN-g, 24hrs


title: 20dAscl1-iN_iN6_31


title: SR100-10

description: PBMC

source_name: Donor 4, TLR2/1L, 24hrs


title: SR100-07

description: PBMC

source_name: Donor 4, IFN-g, 6hrs


title: 2dAscl1clonal-iN_iN5_18

value: iN cells derived from clonal Ascl1-inducible MEFs 2 days upon Ascl1 induction


title: SR100-03

description: PBMC

source_name: Donor 4, IFN-g, 2hrs


title: SR100-05

description: PBMC

source_name: Donor 4, Media, 6hrs


title: SR100-02

description: PBMC

source_name: Donor 4, TLR2/1L, 2hrs


title: 22dAscl1-iN_iN7_7

value: iN cells derived from MEFs 22 days upon Ascl1 induction


title: SR100-06

description: PBMC

source_name: Donor 4, TLR2/1L, 6hrs


title: SR097-11

description: PBMC

source_name: Donor 3, IFN-g, 24hrs


title: SR097-09

description: PBMC

source_name: Donor 3, Media, 24hrs


title: SR097-06

description: PBMC

source_name: Donor 3, TLR2/1L, 6hrs


title: SR097-10

description: PBMC

source_name: Donor 3, TLR2/1L, 24hrs


title: SR097-05

description: PBMC

source_name: Donor 3, Media, 6hrs


title: SR097-02

description: PBMC

source_name: Donor 3, TLR2/1L, 2hrs


title: SR106-03

description: PBMC

source_name: Donor 5, IFN-g, 2hrs


title: SR106-07

description: PBMC

source_name: Donor 5, IFN-g, 6hrs


title: 2dAscl1clonal-iN_iN5_20

source_name: induced neuronal (iN) cells


title: SR097-01

description: PBMC

source_name: Donor 3, Media, 2hrs


title: SR100-01

description: PBMC

source_name: Donor 4, Media, 2hrs


title: SR097-03

description: PBMC

source_name: Donor 3, IFN-g, 2hrs


title: SR095-11

description: PBMC

source_name: Donor 2, IFN-g, 24hrs


title: SR100-09

description: PBMC

source_name: Donor 4, Media, 24hrs


title: SR095-10

description: PBMC

source_name: Donor 2, TLR2/1L, 24hrs


title: SR095-09

description: PBMC

source_name: Donor 2, Media, 24hrs


title: SR095-07

description: PBMC

source_name: Donor 2, IFN-g, 6hrs


title: SR095-06

description: PBMC

source_name: Donor 2, TLR2/1L, 6hrs


title: SR095-02

description: PBMC

source_name: Donor 2, TLR2/1L, 2hrs


title: SR095-01

description: PBMC

source_name: Donor 2, Media, 2hrs


title: SR097-07

description: PBMC

source_name: Donor 3, IFN-g, 6hrs


title: SR095-05

description: PBMC

source_name: Donor 2, Media, 6hrs


title: SR094-10

description: PBMC

source_name: Donor 1, TLR2/1L, 24hrs


title: BS siFOXA1 rep2

city: Beijing

first: Yu

last: Zhang

address: Xueyuan Road

country: China

institute: Peking University Health Science Center

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. For Bisulfite-seq, after filtering, the clean data was mapped to the reference genome by BSMAP, and we then removed the duplication reads and merged the mapping results according to each library. The methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the 5mCG content at each CpG site.

source_name: MCF-7 cells

extract_protocol:
For Bisulfite-seq, the genomic DNA was extracted and purified by phenol–chloroform.
For normal Bisulfite-seq library constructing, the DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of approximately 250 bp, followed by the blunt-ending, dA addition to 3'-end, finally, adaptor ligation (in this case of methylated adaptors to protect from bisulfite conversion), essentially according to the manufacturer’s instructions. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size fragments were excised from the same lane of a 2% TAE agarose gel. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. At last, Sequencing was performed using the HighSeq4000.

value: MCF-7 cells (siFOXA1- transfected)

tag: method

value: bisulfite conversion


title: BS siNS rep2

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format.
For Bisulfite-seq, after filtering, the clean data was mapped to the reference genome by BSMAP, and we then removed the duplication reads and merged the mapping results according to each library. The methylation level was determined by dividing the number of reads covering each mC by the total reads covering that cytosine, which was also equal the mC/C ratio at each reference cytosine.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the 5mCG content at each CpG site.

value: MCF-7 cells (siNS- transfected)


title: SR094-09

description: PBMC

source_name: Donor 1, Media, 24hrs


title: SR094-07

description: PBMC

source_name: Donor 1, IFN-g, 6hrs


title: BS siNS rep1


title: SR094-06

description: PBMC

source_name: Donor 1, TLR2/1L, 6hrs


title: POLB/siFOXA1 ChIP-seq

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the reads coverage for ChIP-seq.

extract_protocol: For ChIP-seq, the FOXA1-complex components and their associated DNA were extracted from the sonicated nuclei and isolated with antibody. 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer’s instructions.

value: MCF-7 cells (FOXA1- knockdown)

value: enriched with POLB antibody


title: SR094-05

description: PBMC

source_name: Donor 1, Media, 6hrs


title: SR094-03

description: PBMC

source_name: Donor 1, IFN-g, 2hrs


title: qsp1∆ Saturated Experiment 1 RNA-Seq replicate 2

city: San Francisco

first: Christina

middle: M.

last: Homer

department: Biochemistry & Biophysics

institute: UCSF

data_processing:
RNA-Seq data were aligned using Tophat. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wild-type and knockout mutant samples.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM lists and ratios for each gene for RNA-seq samples.

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: 50 ODs of cells from overnight YPAD cultures were washed once in water and resuspended in 20 mLs DMEM, transferred to 150mm tissue culture dishes, and incubated for 24 hours at 37ºC, 5% CO2

extract_protocol:
mRNA was isolated using trizol to isolate total RNA and oligotex mRNA mini kit to isolate mRNA. ChIP DNA was isolated from antibody incubation by SDS/proteinase K followed by purification using MN Nucleospin Gel Cleanup columns
cDNA libraries were prepared from DNase-treated mRNA using NEBNext Ultra Directional RNA Library Prep Kit. ChIP DNA libraries were prepared using End-It DNA End Repair Kit followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp

value: Kn99alpha(wild-type) with qsp1(del)

tag: media

value: YPAD

tag: cell density

value: Saturated


title: qsp1∆ Saturated Experiment 1 RNA-Seq replicate 3


title: Kn99alpha WT Saturated Experiment 1 RNA-Seq replicate 1


title: Kn99alpha WT Saturated Experiment 1 RNA-Seq replicate 2


title: qsp1∆ Saturated Experiment 1 RNA-Seq replicate 1


title: BS siFOXA1 rep1


title: SR094-02

description: PBMC

source_name: Donor 1, TLR2/1L, 2hrs

value: monocyte-dervied macrophages


title: IgG ChIP-seq

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads was removed.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record the reads coverage for ChIP-seq.

value: MCF-7 cells

value: enriched with normal IgG


title: SR095-03

description: PBMC

source_name: Donor 2, IFN-g, 2hrs

value: interferon gamma


title: qsp1∆ Log phase RNA-Seq replicate 3


title: POLB ChIP-seq

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were analyzed by BGI programs. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were removed . The peak positions were determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files record reads coverage for ChIP-seq.


title: qsp1∆ Log phase RNA-Seq replicate 2


title: SR094-01

description: PBMC (peripheral blood mononuclear cell)

source_name: Donor 1, Media, 2hrs


title: FOXA1 ChIP-seq

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. Low-quality reads include two types, and the reads meeting any one of the two conditions will be removed: 1) Unknown bases are more than 10%; 2) The ratio of bases whose quality was less than 20 was over 10%. After filtering, the remaining reads are called "clean reads" and stored as FASTQ format. The clean data was mapped to the reference genome by BOWTIE, and the duplication reads were further removed. The peak positions were then determined by MACS using aligned bam file as input.
Genome_build: hg19
Supplementary_files_format_and_content: FOXA1.bedGraph: bedgraph file records reads coverage for FOXA1 ChIP-seq.

value: enriched with FOXA1 antibody


title: qsp1∆ Log phase RNA-Seq replicate 1


title: Kn99alpha WT Log phase RNA-Seq replicate 2


title: Homo sapiens Th1 DMSO P-TEFb

source_name: In vitro differentiated Th1 cells

tag: antibody

value: PMA/ionomycin, DMSO


title: Homo sapiens Th1 BAY Med1

value: Bethyl Laboratories (A300-793A)

value: PMA/ionomycin, BAY 11-7082


title: Kn99alpha WT Log phase RNA-Seq replicate 1


title: SR094-11

description: PBMC

source_name: Donor 1, IFN-g, 24hrs

value: 24 hours


title: Homo sapiens Th1 BAY Brd4

value: Bethyl Laboratories (A301-985A100)


title: Homo sapiens Th1 RA Med1


title: Homo sapiens Th1 RA Brd4


title: Homo sapiens Th1 BAY p65 SC

value: Santa Cruz C-20 (sc-372)


title: liv3∆ RNA-Seq replicate 2

data_processing:
RNA-Seq data were aligned using Tophat. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wild-type and knockout mutant samples.
paired with wild-type replicates 1 and 2
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.

value: CM18(wild-type) with liv3(del)


title: Kn99alpha WT RNA-Seq replicate 1

data_processing:
RNA-Seq data were aligned using Tophat. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wild-type and knockout mutant samples.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.


title: Homo sapiens Th1 RA p65 SC

data_processing:
Basecalls performed using CASAVA
Polony  identification, base  calling  and  QC  statistics were performed using GOAT and Bustard module
Reads (in fastq files) were filtered to remove adapters using fastq-mcf and for quality using seqkt and aligned to the human (hg19) or mouse genome (mm9) with Bowtie2 (default settings). Bigwig files for visualization in the UCSC genome browser were generated using a custom pipeline; duplicate reads were first removed, coverage calculated with genomeCoverageBed and tag density calculated in 10bp windows. unionBedGraphs was then used to subtract input (or total histone H3 for histone ChIPs) signals and bigwig files generated using bedGraphToBigWig. Regions of significant enrichment were identified using MACS version 1.4 (Zhang et al., 2008) using input or total histone H3 as background, with the setting --keep-dup=1. A p-value threshold of 10-7 was used, unless stated otherwise.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: peaks.bed


title: Homo sapiens CCR5-Th1 RA H3K4me3

source_name: CCR5+ memory Th1 cells

value: Abcam ab8580

value: PMA/ionomycin


title: Homo sapiens Th1 RA Aff4

value: Bethyl Laboratories (A302-539A)


title: Homo sapiens Th1 BAY P-TEFb


title: liv3∆ RNA-Seq replicate 1


title: Homo sapiens Th1 BAY Aff4


title: gat204∆ RNA-Seq replicate 2

value: CM18(wild-type) with gat204(del)


title: gat204∆ RNA-Seq replicate 1


title: gat201∆ RNA-Seq replicate 2

value: CM18(wild-type) with gat201(del)


title: gat201∆ RNA-Seq replicate 1


title: Kn99alpha WT RNA-Seq replicate 2


title: CM18 WT RNA-Seq replicate 2


title: CM18 WT RNA-Seq replicate 1


title: Kn99alpha WT Log phase RNA-Seq replicate 3

value: YPAD


title: Th1 d13 reactivated total RNA rep2

description: total genomic RNA

data_processing:
Basecalls performed using CASAVA
paired-end fastq files quality filtered using fastq-mcf -S -t 0.0001 -l 20
qc paired-end fastq files mapped using tophat v2.0.9 using tophat2 --b2-very-sensitive -g 2 -p 4 --library-type fr-secondstrand
mapped data run in cufflinks v2.1.1 with default settings (masking for rRNA, snRNA, Mt_rRNA, snoRNA and miRNA listed in Gencode v19 gene annotation)
Genome_build: hs19
Supplementary_files_format_and_content: Transfrags predicted by Cufflinks, out put in GTF format

extract_protocol:
Total RNA naïve CD4+ cells and day 13 resting and restimulated Th1 and Th2 cells was obtained from samples previously used for microarray analysis.
Poly-adenylated RNA was purified from 1 mg of total RNA using the Qiagen Oliogtex kit and ribosomal RNA was depleted from total RNA using Ribo-Zero Gold (EpiCentre), as per manufacturers instructions. 5’ cap structures were removed with tobacco acid pyrophosphatase (TAP, Life Technologies) and RNA fragmented with potassium acetate (100mM) and magnesium acetate (30mM) at 94oC for 3 mins. RNA was then repaired with Antartic phosphatase and PNK, according to the instructions in the Illumina Directional mRNA-Seq Sample Prep Guide. Libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina kit, with 14 cycles of PCR amplification, and products between 130bp and 350bp gel purified. Libraries were quantified by qPCR (Library Quantification Kit, Kapa Biosystems) and average fragment size determined on an Agilent 2100 Bioanalyzer using DNA HS assays to pool libraries at equimolar concentrations.

treatment_protocol: Naïve human CD4+ T-cells (CD4+CD45RA+CD45RO-CD25-CCD7+) were isolated from healthy donors by negative immunomagnetic selection (Miltenyi Biotec) and activated for 72 hours by plate bound anti-CD3 and anti-CD28 antibodies (2 µg/ml, R&D) and then cultured for 10 days with rhIL-2 (Biolegend, 10 ng/ml). Conditions for T ell polarisation were: rhIL-12 (10 ng/ml, Biolegend) and anti-IL-4 (10 μg/ml, R&D) for Th1, rhIL-4 (10 ng/ml, Biolegend) and anti-IFN-γ (10 μg/ml, R&D) for Th2. For ChIP, cells were formaldehyde crosslinked on day 13 either before (unstimulated) or after (restimulated) treatment with anti-CD3 and anti-CD28 antibodies (2 μg/ml). For H3K4me3 ChIP-Seq, CD4+ naive T-cells were differentiated into either Th1 or Th2 cells in vitro for 28 days, following an established protocol. Cells were activated for 4 hrs with 5 ng/ml PMA (Sigma) and 500 ng/ml ionomycin (CN Biosciences) and assessed for intracellular cytokine staining.

tag: passages

value: 13 days


title: Th2 d13 unstimulated total RNA rep2

description: total genomic RNA


title: Input ChIP-Seq Replicate 4

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.


title: Input ChIP-Seq Replicate 3


title: 20dAscl1-iN_iN6_34

source_name: induced neuronal (iN) cells

value: iN cells derived from MEFs 20 days upon Ascl1 induction

value: Tau-EGFP +/-


title: Homo sapiens CCR5-Th1 RA H3

value: Abcam ab46540

tag: treatment/agent


title: MI_day 13_27C_sample 7

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

country: Australia

institute: University of New South Wales

description: processed data file: day13_MI_RSEM_genes.counts.matrix

data_processing:
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity > 90%) were removed from the assembled transcriptomes using cd-hit-est
Genome_build: the assembeled transcriptome
Supplementary_files_format_and_content: tab-delimited text files include expression count matrices for each sample at each time point

organism: Cladocopium sp. C1

source_name: MI_day 13_27C

growth_protocol: Symbiodinium populations were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). For temperature experiments, 5x10^7 cells (1.5x10^6 cells/ml) of each population were added to eight replicate culture flasks per population. Light was provided at an intensity of 30 µmol quanta m-2 s-1 with a 12 h light-dark cycle.

extract_protocol:
Precisely after six hours of light exposure, 2-4 x 10^6 cells per population were immediately snap frozen in liquid nitrogen within 10 s of removal from experimental incubators and stored at -80°C. Snap frozen cells were thawed at room temperature and pelleted at 4°C (3,000 x g, 5 min). Media was removed, and pellets were lysed in buffer RLT (RNeasy plant mini kit, Qiagen) containing β-mercaptoethanol by bead beating with 0.3 g of 710-1,180 µm acid-washed glass beads (Sigma) using a TissueLyser II (Qiagen) for 90 s at 30 Hz. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) with an added on-column DNase I treatment (Qiagen).
Total RNA (150-500 ng) of each sample was sent to the Australian Genome Research Facility for confirmation of high quality RNA on an Agilent 2100 bioanalyzer, polyA-purification, Illumina TruSeq stranded library preparation, and sequencing on an Illumina HiSeq2500 (single end 100 bp, ~107 reads per sample)

treatment_protocol: Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C for two weeks. Two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C.

tag: population

value: Magnetic Island (MI)

tag: population source

value: Magnetic Island, Great Barrier Reef

tag: thermal tolerance phenotype

value: tolerant

tag: sampling time point

value: day 13

tag: temperature treatment

tag: incubator

value: incubator 4

tag: sample type

value: cell culture

value: filtered sea water + IMK nutrient supplement

tag: coral host from which it was isolated

value: Acropora tenuis


title: MI_day 13_27C_sample 8

tag: medium


title: Th1 d13 unstimulated total RNA rep2

description: total genomic RNA

tag: cell type


title: Input ChIP-Seq Replicate 2

tag: strain


title: Th2 d13 reactivated mRNA rep2

description: mRNA


title: MI_day 13_32C_sample 6

source_name: MI_day 13_32C

value: incubator 3


title: Th2 d13 reactivated total RNA rep2

description: total genomic RNA


title: Th2 d13 unstimulated mRNA rep2

description: mRNA


title: MI_day 13_27C_sample 3

value: incubator 2


title: Liv3-FLAG ChIP-Seq Replicate 2

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
paired with input replicate 2
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.

value: CM18(wild-type) with Liv3-CBP-FLAG


title: Liv3-FLAG ChIP-Seq Replicate 3

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
paired with input replicate 4
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.


title: Th1 d13 reactivated mRNA rep2

description: mRNA


title: Th1 d13 unstimulated mRNA rep2

description: mRNA


title: MI_day 13_27C_sample 4


title: CD4 naïve mRNA rep2

description: mRNA

source_name: Naive CD4+ cells

value: Naive CD4+ cells

value: 0 days


title: Liv3-FLAG ChIP-Seq Replicate 1

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
paired with input replicate 1
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.


title: Th2 d13 reactivated total RNA rep1

description: total genomic RNA

value: 13 days


title: Gat204-FLAG ChIP-Seq Replicate 3

value: CM18(wild-type) with Gat204-CBP-FLAG


title: MI_day 9_27C_sample 8

description: processed data file: day9_MI_RSEM_genes.counts.matrix

source_name: MI_day 9_27C

value: day 9


title: Gat204-FLAG ChIP-Seq Replicate 2


title: Th2 d13 unstimulated total RNA rep1

description: total genomic RNA


title: Input ChIP-Seq Replicate 1


title: MI_day 13_32C_sample 5


title: MI_day 13_32C_sample 1

value: incubator 1


title: MI_day 13_32C_sample 2

value: Magnetic Island (MI)


title: Gat204-FLAG ChIP-Seq Replicate 1


title: MI_day 9_27C_sample 7

value: Magnetic Island, Great Barrier Reef


title: Th1 d13 reactivated total RNA rep1

description: total genomic RNA


title: Gat201-FLAG ChIP-Seq Replicate 3

value: CM18(wild-type) with Gat201-CBP-FLAG


title: Gat201-FLAG ChIP-Seq Replicate 2

data_processing:
ChIP-Seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence. Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDTools.
Peaks in ChIP-Seq data were called using MACS with a manually set shift-size calculated using the spp package.
Motif calling was performed using Gimsan with default settings.
paired with input replicate 3
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM tables for RNA-seq samples.


title: MI_day 9_32C_sample 6

source_name: MI_day 9_32C

value: tolerant


title: MI_day 9_27C_sample 4


title: Th1 d13 reactivated mRNA rep1

description: mRNA


title: Th1 d13 unstimulated total RNA rep1

description: total genomic RNA


title: Th1 d13 unstimulated mRNA rep1

description: mRNA


title: MI_day 9_32C_sample 2


title: Th2 d13 reactivated mRNA rep1

description: mRNA


title: MI_day 9_32C_sample 1


title: Th2 d13 unstimulated mRNA rep1

description: mRNA


title: MI_day 9_32C_sample 5


title: MI_day 9_27C_sample 3


title: 20dAscl1-iN_iN6_40

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing log2(FPKM) values for all 437 single cells (rows) and all genes (columns). In addition, the first 5 columns contain the following metadata: cell_name (unique identifier of each single cell that is linked to the name of the raw data file), assignment (identity of cell based on analysis in corresponding paper), log_tauGFP_intensity (log of the EGFP fluorescence intensity of each single cell as measured prior to cell lysis on the C1 microfluidic device), experiment (unique identifier of the experiment, iN1-iN8), time_point (time point in days post induction of Ascl1 or BAM via dox-treatment).

value: iN cells derived from MEFs 20 days upon Ascl1 induction

tag: genotype

value: Tau-EGFP +/-


title: Input on DMSO-treated cells

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05 bigwig file converted from bedGraph pileup from MACS 2.0 output
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file converted from bedGraph pileup from MACS 2.0 output

source_name: A375 melanoma cell line

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
After chromatin immunoprecipitation, cross-link reversal is carried out and precipitated DNA is purified by phenol:chloform:isoamyl alcohol extraction.
The End-It DNA End-Repair Kit (Epicentre) was used to turn DNA overhangs into phosphorylated blunt ends and the Agencourt AMPure XP PCR Purification Kit (Beckman Coulter) was used to purify the resulting samples using a 1.8X ratio of beads to sample. Next, a single A in the 3’ end was added to samples using the Klenow Fragment enzyme (NEB) to allow for directional ligation and the AMPure Kit was again used to purify samples. Illumina adaptor oligos (1:10 dilution) were added to samples using the Quick Ligation Kit (NEB) and NEBNext Multiplex Oligos for Illumina Kit (NEB), and samples were purified with the AMPure Kit. Samples were then size-selected with the AMPure beads with a 0.9X bead to sample ratio. Multiplexing primers from the NEBNext Multiplex Oligos Kit were added during the 18-cycle PCR enrichment step, which utilized the Phusion High-Fidelity PCR Master Mix (NEB), to generate indexed libraries. Indexed libraries were separated on a 2% agarose gel. Products between 150-350 base pairs were excised and gel purified using the QIAquick Gel Extraction Kit (Qiagen). The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One hundred million A375 cells per condition were treated with DMSO or 25 μM A771726.  After a 48 hr treatment, cells were fixed in 11% formaldehyde and subjected to chromatin immunoprecipitation with HEXIM1 antibody (Abcam) or Cdk9 (C-20) antibody (Santa Cruz).

tag: cell line


title: H3k27ac ChIP on DMSO-treated cells


title: Gat201-FLAG ChIP-Seq Replicate 1

tag: cell density


title: Homo sapiens Th2 RA IgG

data_processing:
Basecalls performed using CASAVA
Polony  identification, base  calling  and  QC  statistics were performed using GOAT and Bustard module
Genome_build: hg19/mm9

source_name: In vitro differentiated Th2 cells

tag: antibody

value: Abcam 46540

value: PMA/ionomycin


title: MI_day -1_27C_sample 7

description: processed data file: day-1_MI_RSEM_genes.counts.matrix

source_name: MI_day -1_27C

value: day -1

value: incubator 4

value: cell culture

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis


title: Homo sapiens Th1 RA IgG


title: Small RNAs from testis of spnE/spnE

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

source_name: testis

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

tag: tissue

value: testis


title: MI_day -1_27C_sample 5

value: incubator 3


title: MI_day -1_27C_sample 4

value: incubator 2


title: Homo sapiens Th2 US Input

source_name: In vitro differentiatedTh2 cells

tag: treatment/agent

value: unstimulated


title: Homo sapiens Th2 RA PolII-N20

value: Santa-Cruz N-20 (sc-899)


title: Homo sapiens Th2 US PTEF-b


title: CD4 naïve mRNA rep1

description: mRNA

value: Naive CD4+ cells

tag: passages

value: 0 days


title: Homo sapiens Th1 RA PolII-N20


title: Homo sapiens Th1 reactivated Input rep2


title: Homo sapiens Th1 US PolII-N20


title: Small RNAs from testis of spnE/+


title: Homo sapiens Th1 US PTEF-b


title: Homo sapiens Th2 reactivated Input  rep2


title: SM_day 13_27C_sample 8

description: processed data file: day13_SM_RSEM_genes.counts.matrix

source_name: SM_day 13_27C

tag: population

value: South Molle (SM)

tag: population source

value: South Molle Island, Great Barrier Reef

value: sensitive

value: day 13


title: SM_day 13_32C_sample 5

source_name: SM_day 13_32C

tag: thermal tolerance phenotype

tag: sampling time point


title: SM_day 13_32C_sample 6

tag: temperature treatment

tag: incubator


title: SM_day 13_27C_sample 7

tag: sample type

tag: coral host from which it was isolated


title: Homo sapiens Th2 reactivated Input  rep1

tag: cell type

value: PMA/ionomycin


title: Homo sapiens Th1 reactivated Input rep1


title: MI_day -1_27C_sample 8

value: Magnetic Island (MI)

value: Magnetic Island, Great Barrier Reef

value: tolerant

value: day -1

tag: medium


title: Homo sapiens Th2 reactivated PolII-N20


title: Homo sapiens Th1 US Input


title: SM_day 13_32C_sample 2

value: incubator 1

value: cell culture

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis


title: SM_day 13_27C_sample 3

value: incubator 2


title: Homo sapiens Th2 unstimulated PolII-N20

value: Santa-Cruz N-20 (sc-899)

value: unstimulated


title: SM_day 9_27C_sample 8

description: processed data file: day9_SM_RSEM_genes.counts.matrix

source_name: SM_day 9_27C

value: day 9

value: incubator 4


title: Homo sapiens Th1 unstimulated PolII-N20

source_name: In vitro differentiated Th1 cells


title: Homo sapiens Th2 US PolII-N20


title: SM_day 13_27C_sample 4

value: South Molle (SM)

value: South Molle Island, Great Barrier Reef


title: SM_day 9_27C_sample 7

value: sensitive


title: SM_day 9_32C_sample 6

source_name: SM_day 9_32C

value: incubator 3


title: MI_day -1_27C_sample 6

value: Magnetic Island (MI)


title: SM_day 9_32C_sample 5


title: Homo sapiens Th1 reactivated pTEFb

value: PMA/ionomycin


title: Homo sapiens WT Th2 H3 for K27ac

value: Abcam ab4729


title: Homo sapiens WT Th1 H3 for K27ac


title: Homo sapiens WT Th1 Input


title: Homo sapiens Th2 reactivated pTEFb


title: SM_day 9_27C_sample 4


title: SM_day 13_32C_sample 1

value: day 13


title: Homo sapiens WT Th1 T-bet

value: SY4530 (custom)


title: Homo sapiens Th2 PI K27ac


title: SM_day 9_32C_sample 1

value: incubator 1

value: cell culture


title: SM_day 9_27C_sample 3

value: filtered sea water + IMK nutrient supplement

value: Acropora tenuis


title: SM_day -1_27C_sample 8

description: processed data file: day-1_SM_RSEM_genes.counts.matrix

source_name: SM_day -1_27C

value: day -1


title: Homo sapiens Th1 reactivated PolII-N20

value: Santa-Cruz N-20 (sc-899)


title: SM_day 9_32C_sample 2

value: day 9


title: Homo sapiens Th1 PI K27ac


title: SM_day -1_27C_sample 4

value: incubator 2


title: SM_day -1_27C_sample 6

value: South Molle (SM)


title: Homo sapiens Th2 Native H3

value: Abcam ab46540


title: SM_day -1_27C_sample 7

value: South Molle Island, Great Barrier Reef

value: sensitive

value: incubator 4


title: SM_day -1_27C_sample 3


title: Homo sapiens Th1 Native H3K4me3

value: Abcam ab8580

value: PMA/ionomycin


title: Homo sapiens Th2 Native H3K4me3


title: SM_day -1_27C_sample 2


title: Homo sapiens Th1 Native H3


title: Small RNA long-time

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

institute: Chinese Academy of Agricultural Sciences

description: small RNA

data_processing:
Raw sequencing reads were processed into clean full-length reads by the BGI small RNA pipeline. After the raw sequence reads were obtained, adapter sequences, low quality tags, contaminants and sequences beyond 15 nt to 30 nt were filtered.
The remaining sequences were aligned to Rfam (http://www.sanger.ac.uk/resources/databases/rfam.html) and Genbank database to annotate rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails.
To identify conserved miRNAs,cleandata  were align to the mature miRNAs of all plants in miRBase (http://www.mirbase.org/) allowing two mismatches and free gaps
The cleandata was further align to the above temporary miRNA database and the expression of miRNA is generated by summing the count of tags which can align to the temporary miRNA database.
The identification of novel miRNAs were analyzed by MFOLD software (http://mfold.rna.albany.edu/) on the RNA secondary structure of the miRNA::miRNA* and pre-miRNA hairpin energy.
Genome_build: miRNA Registry Database, miRBase database
Supplementary_files_format_and_content: match_mirbase.txt  This file contains small RNAs whose sequences are similar with miRNAs deposited at miRBase

organism: Gossypium hirsutum

source_name: Cotton leaves

growth_protocol: The upland cotton cultivar SN-011 was used in this study. Seeds were sterilized and germinated in vermiculite. Growth conditions were 30/22 day/night temperature, 55–70% relative humidity, and a 14 h/10 h light/dark cycle under 450 μmol m−2⋅s−1 light intensity. At the two-leaf stage, healthy seedlings were grown in pots containing aerated nutrient solution. Plants were cultured under non-saline conditions for 10 d to ensure full establishment before starting the salinity treatments. The pH was maintained close to 6.9 by adding H2SO4 or KOH as required.

extract_protocol:
Total RNA was isolated using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany).Then,total RNA was separated by 15% denaturing polyacrylamide gel electrophoresis (PAGE) to recover the population of small RNAs.
The extracted small RNAs then was dephosphorylated using alkaline phosphatase and ligated to 5'- and 3'-RNA adaptors by T4 RNA ligase. The adaptor-ligated sRNAs were subsequently transcribed to single-stranded cDNA using SuperScript II Reverse Transcriptase. After polymerase chain reaction (PCR) amplification, PCR products were purified and subjected to SBS sequencing with a Solaxa genome analyzer II at the BGI (Beijing Genomics Institute, Shenzhen, China).

treatment_protocol: For short-term salt treatment samples, seedlings were treated with 150 mM solution of NaCl. After exposing the seedlings to salt stress for 4 h, cotton leaves of the short-term salt treatment samples were harvested. For long-term salt treatment samples, seedlings were exposed to salinity by adding NaCl to the growth medium in 50 mM increments every 12 h, until a final concentration of 150 mM was reached. After exposing the seedlings to salt stress for 5 d, leaves were harvested directly into liquid nitrogen and stored at −80 °C for subsequent use.

value: leaves

tag: treatment

value: seedlings were treated with 150 mM solution of NaCl for 5 days

tag: cultivar


title: SM_day -1_27C_sample 1

data_processing:
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity > 90%) were removed from the assembled transcriptomes using cd-hit-est
Genome_build: the assembeled transcriptome
Genome_build: the assembeled transcriptome
Supplementary_files_format_and_content: tab-delimited text files include expression count matrices for each sample at each time point

value: incubator 1