title: CP190 Ibf2/cg9740-KO

city: Barcelona

first: M Lluisa

last: Espinas

address: Baldiri Reixac 10

institute: IBMB-CSIC

description: genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie 0.12.5 version. Reads were aligned to a unique location in the genome, allowing up to 2 mismatches in the first 28 bases and no gapped alignments
Data were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
First, we used the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini–Yekutieli adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e. putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 100 reads.
After peak calling, we used the mergeRegions function from htSeqTools to merge adjacent peaks closer than 300bp.
Genome_build: dm3
Supplementary_files_format_and_content: BED files include chromosome, start and end of the identified peaks in the dm3 Drosophila melanogaster  genome.

source_name: Third instar larvae

growth_protocol: Flies were kept on standard fly food at 25 degrees. Third instar wandering larvae were used for ChIP.

extract_protocol:
Lysates were clarified from crosslinked and sonicated larval tissues and chromatin complexes were isolated with rabbit aCP190 polyclonal antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 18 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

tag: genotype/variation

value: IP


title: Sample 3

status: Public on Apr 18 2014

type: SRA

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

country: United Kingdom

institute: Imperial College

library_source: transcriptomic

data_processing:
Sequences were mapped to gga3 using Tophat v1.4.0 with default settings
Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to calculate RPKM
Genome_build: gga3
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values of individual samples

molecule: total RNA

organism: Gallus gallus

source_name: Basal papilla

extract_protocol:
Chicken cochleae were dissected from E6.5 embryos.  Cochlea were divided into three approximately equal sized pieces to produce proximal, middle, and distal pieces.  Pieces from each region were pooled together and immediately transferred into three 1.5 mL eppendorf tubes containining 0.5 mL Tri Reagent RT (Molecular Research Center, Inc.).  Samples were then stored at -20C until further processing.  Samples from each section of the cochlea were then processed using Illumina mRNA-seq or TrueSeq preparation kits.  Separate biological replicates were also prepared and similarly analyzed.  mRNA was selected by oligo-dT magnetic beads and fragmented.  First-strand cDNA was then generated using random primers.  Second-strand synthesis, end repair and addition of a single A base and adaptor ligation were then performed.  Each RNA-seq library was DNA-sequenced the Illumina HiSeq 2000.
libraries were made using Illumina mRNA-seq or TrueSeq preparation kits.

tag: tissue

value: cochlea

tag: cochlear region

tag: age

value: embryonic day 6.5


title: Input Ibf2/cg9740-KO

country: Spain

description: genomic DNA

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

tag: sample type

value: Input

tag: chip antibody


title: CP190 wt

description: genomic DNA

value: wild type


title: mES_WT_1

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

country: USA

institute: Johns Hopkins University

description: RNA-Seq of polyA-selected RNA from wild type male mouse embryonic stem cells

data_processing:
Basecalls were performed using CASAVA 1.8
Reads were aligned using Tophat2 with default options
Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.
Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.
Genome_build: mm9

molecule: polyA RNA

organism: Mus musculus

source_name: mouse Embryonic Stem Cells (male)

growth_protocol: HeLa cells were grown in DMEM + 10% FBS + 1% Pen-strep + 1% L-glutamine at 37ºC at 5% CO2; Mouse ES cells were grown in previously gelatinized (0.2%) dishes with media containing 125 mL DMEM/F12 (Invitrogen), 83.5 μL BSA fraction V (50 μg/ml relative to DMEM) (Invitrogen, 15260-037, 75mg/ml), 125 mL Neurobasal medium (Invitrogen, 21103-049), 625 μL of the Ndiff Neuro2 (200X, relative to Neurobasal medium) (Millipore, SCM012), 2.5 mL B27 minus vitamin A (50X, relative to Neurobasal medium) (Invitrogen, 12587-010), 2 μL beta-mercaptoethanol (for 250 mL medium), 1 μM PD0325901 (Stemgent, 04-0006), 3 μM CHIR99021 (Stemgent 04-0004), 25 μL LIF ESGRO (stock is 107 units LIF/mL from Chemicon, ESG1106), 1% pen-strep (Invitrogen, 15140-163), 1% Non-Essential Amino Acids (Invitrogen, 11140-076), 1% L-glutamine (Invitrogen, 25030-164). The plating density of mES cells was chosen to be 30,000-50,000/cm2.

extract_protocol:
1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.
Illumina TruSeq RNA

treatment_protocol: siRNAs were transfected using Lipofectamine RNAiMax (5 μl/well) at a final oligo concentration of 75nM; Gapmer oligos were designed with 2-O methyoxyethyl and transfected with Lipofectamine 2000 at a final concentration of 75nM.

tag: knockdown chemistry

value: Wild type

tag: knockdown target

tag: cell type

value: embryonic stem cells


title: Sample 1

value: Proximal-BP


title: Sample 2

value: Mid-BP


title: mES_KO_1

description: RNA-Seq of polyA-selected RNA from Firre knockout male mouse embryonic stem cells

value: Knockout

value: Firre


title: mES_WT_2


title: Input wt

description: genomic DNA


title: suhw-rb-a

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description:
suhw-rb-a
processed data file: suhw.bed

data_processing:
Trim adapters with Trimmomatic v0.20 (Su(Hw), Mod(mdg4)2.2) or cutadapt v1.1 (Rump, CP190)
Align to UCSC dm3, excluding chrUextra, with bowtie v0.12.8 parameters -p8 --best --strata --sam -m1 -n2 --tryhard -k1
Remove reads mapping to annotated RepMask repetitive regions (BEDTools v2.17.0)
Remove duplicate reads (Picard v1.77 MarkDuplicates)
Call peaks with spp v1.11, FDR=0.01 (CP190, Su(Hw)) or IDR (https://sites.google.com/site/anshulkundaje/projects/idr) using SPP (Rump, Mod(mdg4)2.2, Shep); see manuscript for details
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BED files (called peaks), bigWig files (scaled signal; units are “reads per million mapped reads”)

growth_protocol: Kc167 cells were grown in CCM3 media (HyClone).  Cells were maintained in monolayer at 25°C.

extract_protocol:
ChIP was performed as in Matzat LH, Dale RK, Moshkovich N, Lei EP (2012) Tissue-specific regulation of chromatin insulator function. PLoS Genet 8: e1003069
ChIP was performed as in Matzat LH, Dale RK, Moshkovich N, Lei EP (2012) Tissue-specific regulation of chromatin insulator function. PLoS Genet 8: e1003069.  “a” or “b” in filenames indicates which of 2 chromatin preps was used

tag: cell line

value: Su(Hw) rabbit

tag: chip antibody reference

tag: input used

value: input-a


title: rump-10c3-a

description:
rump-10c3-a
processed data file: rump.bed

value: Rump 10c3


title: mES_WT_3


title: mouse_e11.5_limb_H3K4me1

status: Public on Apr 19 2014

city: Berkeley

first: Matthew

middle: James

last: Blow

state: CA

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue pooled from ~150 embryos Chromatin IP against H3K4me1

data_processing:
Bam: Sequence reads were mapped to the mouse (mm9) genome using bwa with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Unique BWA-aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection in FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: macs14 -t chip.bam –control=input.bam –name=chip_output  –format=BAM –gsize=mm –tsize=36 –bw=300 –mfold=10,30 –nolambda –nomodel –shiftsize=150 -p 0.00001. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9
Supplementary_files_format_and_content: bed and wig

source_name: Mouse embryonic day 11.5 (e11.5) limb

extract_protocol: Embryonic heart and hindbrain was isolated from CD1 mouse embryos at e11.5  .Tissue samples were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation.  ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters.   ChIP and input DNA between 300 and 500bp was sequenced on the  Illumina HiSeq 2000 to generate 50 or 36bp reads.

tag: developmental stage

value: limb

tag: strain

tag: Sex

value: pooled male and female


title: rump-5g4-a

description:
rump-5g4-a
processed data file: rump.bed

value: Rump 5g4


title: modmdg4-gp-a

description:
modmdg4-gp-a
processed data file: modmdg4.bed

value: Mod(mdg4)2.2 guinea pig


title: modmdg4-rb-a

description:
modmdg4-rb-a
processed data file: modmdg4.bed

value: Mod(mdg4)2.2 rabbit


title: CG8436

description: genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the dm3 genome assembly using Eland version 2. Reads were aligned to a unique location in the genome, allowing up to 2 mismatches in the first 32 bases and no gapped alignment
Data were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
First, we used the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini–Yekutieli adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e. putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 100 reads.
After peak calling, we used the mergeRegions function from htSeqTools to merge adjacent peaks closer than 300bp.
Genome_build: dm3
Supplementary_files_format_and_content: BED files include chromosome, start and end of the identified peaks in the dm3 Drosophila melanogaster  genome.

source_name: S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml strptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with rat αIbf-1 and αIbf-2 and rabbit aCP190 polyclonal antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 18 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

value: IP


title: input-a

description: input-a

value: input


title: CG9740

description: genomic DNA


title: input-b

description: input-b


title: shep-gp-a

description:
shep-gp-a
processed data file: shep.bed

value: Shep guinea pig


title: TAC_1wk_FVB_F_9wk_smallRNA_4

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

data_processing:
Illumina Casava1.6 software was used for basecalling; 42 nt reads with phred64 quality scores.
Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the mouse genome and quantitate mapped reads.  Mouse noncoding RNA and miR-3p/5p annotation was current as of 3/7/14.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: GRCm37 / mm9
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.

source_name: Heart

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq small RNA preparation kits (version C) were used for all library construction.  3' and 5' adapters capable of recognizing non-mRNA species were sequentially ligated to 1 microgram of total cardiac RNA, followed by reverse transcription, limited PCR amplification to add indexes, and size-selection.

value: FVB/NJ

value: Whole-heart tissue

tag: age (weeks)

value: F


title: cp190-rb-b

description:
cp190-rb-b
processed data file: cp190.bed

value: CP190 rabbit

value: input-b


title: TAC_1wk_FVB_F_9wk_smallRNA_3


title: TAC_1wk_FVB_F_9wk_smallRNA_5


title: shep-rb-a

description:
shep-rb-a
processed data file: shep.bed

value: Shep rabbit


title: mES_KO_2

value: Knockout

value: Firre

value: embryonic stem cells


title: TAC_1wk_FVB_F_9wk_smallRNA_2


title: TAC_1wk_FVB_F_9wk_mRNA_2

data_processing:
Illumina Casava1.6 software was used for basecalling; 42 nt reads with phred64 quality scores.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm9 genome and associated bowtie index provided by Illumina iGenomes, using tophat v1.3.0 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene

extract_protocol:
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.


title: TAC_1wk_FVB_F_9wk_mRNA_3


title: TAC_1wk_FVB_F_9wk_mRNA_1


title: TAC_1wk_FVB_F_9wk_mRNA_5


title: Rectum_C4_Nec_R1

status: Public on Apr 17 2014

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

data_processing:
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2
zipped using gzip
For mRNAseq: Reads were mapped against rhesus genome with Bowtie and Tophat .
HTSeq was used to generate gene counts
Genome_build: GTF for Rhesus version Mmul_1 (Ensembl) from igenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.ilmn)
Supplementary_files_format_and_content: tab-delimited text files include: 1 scaled gene counts for each sample of mRNAseq

organism: Macaca mulatta

source_name: Rectum

extract_protocol:
Qiagen miRNeasy Isolation Kit from Trizol homogenates
Illumina TruSeq mRNA

treatment_protocol: intrarectally challenged, baseline controls, and uninfected controls

value: rectal mucosa

tag: treatment

value: SIVmac251 infected

tag: hrs post treatment

value: Day 3

tag: group


title: TAC_1wk_FVB_F_9wk_smallRNA_1

tag: tissue


title: Rectum_E4_Nec_50_R1

value: Day 12


title: Rectum_C4_BL_R1

value: Baseline controls

value: Day -14


title: Rectum_E4_Nec_R1


title: Rectum_E4_BL_50_R1


title: Rectum_C4_Nec_50_R1


title: Input

description: genomic DNA

value: Input


title: Rectum_C4_BL_50_R1


title: C2_Basal_50_R1


title: E3_Nec_50_R1


title: E1_Nec_50_R1


title: E3_Basal_50_R1


title: CP190

description: genomic DNA

value: IP


title: C3_Basal_50_R1


title: 10164_Basal_50_R1

value: uninfected controls


title: E1_Basal_50_R1


title: E2_Nec_50_R1


title: C1_Nec_50_R1


title: C3_Nec_50_R1


title: R09076_Basal_50_R1


title: TAC_1wk_FVB_F_9wk_mRNA_4

value: FVB/NJ

value: Whole-heart tissue


title: E2_Basal_50_R1


title: Rectum_E4_BL_R1


title: BF39_Basal_50_R1


title: C.elegans(N2) female rep2 RNAseq

city: New York

first: Sarah

middle: Elizabeth

last: Albritton

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: New York University

data_processing:
DNA seq reads were aligned to genome version WS228 with Bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
DNA seq bam files were sorted and used to generate bedgraph files (bedtools version 2.15.0)
RNA seq reads were aligned to genome version WS228 with tophat version 2.0.0
Using RNAseq bam files, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.0.2 using default parameters supplying gene annotations for WS228.
Genome_build: WS228

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Worms were synchronized by bleaching gravid adults grown on plates at 20C temperature. Embryos were hatched overnight and starved as L1s. L1s were plated and grown to indicated stage at 20C temperature.

extract_protocol:
staging protocol: worms were synchronized by bleaching gravid adults from male-heavy plates. At least 750 young adult worms were hand picked for each replicate.
rna isolation protocol: RNA was extracted by freeze cracking embryos by freezein gin liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA RNA was cleaned up through Qiagen RNeasy column.
cdna synthesis protocol: mRNA was purified from 5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212
400uL of Worm Lysis Buffer (0.1M TrisHCl; 0.1M NaCl; 50mM EDTA; 1.25%SDS) was added before sonicating to obtain chromatin fragments of majority size of between 200 and 800 bp.
Isolate DNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Worms were hand picked into 1X M9. Worms were washed 3 times by settling with TE. Worms were suspended in 100uL TE and stored at -80C until DNA isolation.

value: L4 / young adult


title: C.elegans(N2) female rep4 RNAseq


title: C.elegans(N2) female rep3 RNAseq


title: C1_Basal_50_R1


title: C.elegans(N2) male rep3 RNAseq


title: C.elegans(N2) male rep1 RNAseq


title: C2_Nec_50_R1


title: C.elegans(N2) male rep2 RNAseq


title: Th17 cells treated with GSK805 (0.5uM) [RNA2-2]

first: Nir

last: Yosef

address: Berkeley

department: EECS

institute: UC Berkeley

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009). The resulting alignments were processed by Scripture (Guttman et al., 2010) to evaluate the expression of transcripts from RefSeq (Pruitt et al., 2007).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files output by the scripture software (Guttman et al. 2010);  columns: (1--3) genomic location (4) gene name (5) RPKM

source_name: Th17 cells

growth_protocol: Naïve CD4+ T cells were cultured under Th17 cell polarizing conditions with or without RORgt inhibitors for 4 days.

extract_protocol:
RNA was extracted with RNeasy Plus kits (Qiagen)
RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3′ ligation of an RNA adaptor using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed using AffinityScript Multiple Temperature Reverse Transcriptase (Agilent), and the cDNA was subjected to a 3′ ligation with a second adaptor using T4 ligase. The single-stranded cDNA product was then amplified for 9-14 cycles in a PCR reaction.

treatment_protocol: Naive CD4+ cells were activated with plate-bound anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) in 96-well or 24-well plates. For Th17 cell differentiation, cultures were supplemented with IL-6 (20 ng/ml) plus TGF-β1 (1 ng/ml), and IL-23 (10 ng/ml) was added after 48 h. For iTreg cell conversion, TGF-β1 (5 ng/ml) was added into the cultures. RORγt inhibitors (TMP778, 2.5 μM; TMP920, 10 μM; Digoxin, 10 μM; GSK805, 0.5μM) or vehicle control DMSO was also included in the cultures, or as indicated in figure legends. After 96 h, cells were collected for further experiments.

value: Th17 cells

tag: agent

tag: age

value: 6-8 weeks


title: Rorc knockout cells treated with DMSO under Th17 polarizing conditions [RNA2-2]

description: Rorc knockout + DMSO

value: Rorc knockout cells

value: DMSO under Th17 polarizing conditions


title: Th17 cells treated with Digoxin (10uM) [RNA2-2]

description: Digoxin

value: Digoxin (10uM)


title: Th17 cells treated with Digoxin (10uM) [RNA2-1]

description: Digoxin


title: Th17 cells treated with TMP920 (10uM) [RNA2-2]


title: Th17 cells treated with DMSO [RNA2-2]

description: DMSO

value: DMSO


title: Th17 cells treated with DMSO [RNA2-1]

description: DMSO


title: Th17 cells treated with TMP778 (2.5uM) [RNA2-1]


title: Tko_1

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

description: Strategy: hMeDIP, Barcode: CGAAAC

data_processing:
Library strategy: hMeDIP-Seq
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
Mapping: bowtie 2.0
computation of coverage values: wiggles
Genome_build: mm9
Supplementary_files_format_and_content: Format: bedgraph, Content: genomic coverage

source_name: embryoid bodies

extract_protocol:
Homogenized mouse tissues were incubated overnight in 100mM Tris-HCl pH 8 containing 5mM EDTA, 0.2% SDS, 200 mM NaCl and 400 µg/ml proteinase K, and DNA was then isolated using a standard protocol with phenol:chloroform:isoamyl alcohol and Phase Lock Gel™ separation tubes. Genomic DNA was finally treated with RNAse A (20 µg/ml) for 30 minutes at 37°C.
Five µg of genomic DNA for each sample was sonicated to 300bp fragments using a Covaris S220 (Covaris). Sheared DNA was ethanol precipitated, washed with 70% ethanol, and dissolved in TE buffer (pH8.0). Illumina adapters were ligated using the End-It DNA End-repair kit (Epicentre). DNA was purified with the QiaQuick PCR purification kit (Qiagen) and diluted to 122.5µl with ddH2O. After the addition of 15µl NEB buffer 2, 3.5µl of 10mM ATP and 9µl of 5U/µl Klenow exo- (NEB), reactions were incubated at 37°C for 50min. DNA was subsequently purified with the QiaQuick PCR purification kit, diluted to 24µl with ddH2O, and mixed with 50µl of 2x NEB quick ligation buffer, 20 µl of barcoded Illumina adapter and 6µl of quick T4 DNA ligase (NEB). After 20 minutes incubation at room temperature, DNA was purified again with QiaQuick PCR purification kit. Ligation efficiency was analyzed by PCR on 10ng of final ligated DNA with Illumina sequencing primers. Finally, five µg of adapter ligated DNA was used for the immunoprecipitation, as described above. Immunoprecipitated DNA was resolved in 20µl of water and all (h)MeDIP samples were pooled to create the MeDIP and hMeDIP libraries, respectively. Both libraries were purified on e-Gel (Invitrogen) and the 300bp bands (containing roughly 200bp fragments of adapter-ligated immunopurified DNA) were extracted. Libraries were amplified using Illumina-Enrichment Primers for 12 cycles and purified using Agencourt AMPure XP beads (Beckman Coulter). DNA concentrations were measured using a Agilent High Sensitivity DNA Assay (Agilent Technologies) and 7 pmol were used for cluster PCR and substantial 100bp paired-end sequencing on a HiSeq2000 (Illumina).

value: embryoid bodies

value: mixed 129|C57BL/6

tag: tet1/tet2 treatment

value: TET1, TET2 and TET3 knocked out


title: Th17 cells treated with TMP778 (2.5uM) [RNA2-2]


title: Tko_3

description: Strategy: hMeDIP, Barcode: GTATAG


title: Tko_2

description: Strategy: hMeDIP, Barcode: GCCTAA


title: Wt_2

description: Strategy: hMeDIP, Barcode: AGCGCT

value: WT


title: Wt_1

description: Strategy: hMeDIP, Barcode: AAGTGC


title: C.elegans(N2) male rep4 RNAseq


title: C.elegans(N2) female rep1 RNAseq


title: anti-Foxp3-EL4 (control)

description: anti-Foxp3-EL4 (control)

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using Bowtie (Langmead et al., 2009). Duplicated reads were filtered (allowing no more than 2 reads at the same location).
Two programs were used to infer enriched binding regions (peaks): QuEST (Valouev et al., 2008) and MACS (Zhang et al., 2008). As negative control for defining background binding to the Rorγt analysis, we used an antibody for the isotype control immunoglobulin (IgG), and anti-RORγt antibody in a RORγt-deficient population. As a negative control for the Foxp3 analysis we used the Foxp3 antibody in EL4 cells (with no exogenous Rorc). As negative control for the EL4 peaks we used cells with no exogenous Rorc.  The output of the two programs is a list of enriched binding regions (peaks) together with an estimate of statistical significance. For QuEST we retain all the peaks with p-value<10-8; for MACS we used a p-value cutoff of 10-8 or estimated FDR below 5%. We then applied a post-processing step, consolidating all the peaks that for a given algorithm (QuEST or MACS) was detected (up to a distance of 50bp) with all of the controls. We report this unified set of peaks. Associated p-values are minimum over QuEST or MACS.
Genome_build: mm9
Supplementary_files_format_and_content: TDF format; generated with igvtools count program
Supplementary_files_format_and_content: BED files - output of peak callers

source_name: EL4 cells

extract_protocol:
~50-100 x 106 cells for each ChIP were crosslinked with formaldehyde, lysed, and fragmented with a Misonix Sonicator 3000. Following immunoprecipitation with  antibody or  IgG control,  the protein-DNA crosslinks were reversed and DNA was purified and used for the preparation of Illumina sequencing libraries
Purified ChIP DNA was used to prepare ChIP-seq libraries using the Illumina TruSeq DNA Sample Preparation v2 kit

treatment_protocol: Naive CD4+ cells were activated with plate-bound anti-CD3 (2 μg/ml) and anti-CD28 (2 μg/ml) in 96-well or 24-well plates. For Th17 cell differentiation, cultures were supplemented with IL-6 (20 ng/ml) plus TGF-β1 (1 ng/ml), and IL-23 (10 ng/ml) was added after 48 h. For iTreg cell conversion, TGF-β1 (5 ng/ml) was added into the cultures. RORγt inhibitors (TMP778, 2.5 μM; TMP920, 10 μM; Digoxin, 10 μM) or vehicle control DMSO was also included in the cultures, or as indicated in figure legends. After 96 h, cells were collected for further experiments.

value: EL-4 cells

tag: antibody

value: Rabbit Anti-Foxp3( Nature. 2007;445:936-40.


title: Flag-Rorc EL4 with exogeneous Rorc

description: Flag-Rorc EL4 with exogeneous Rorc

value: Flag-tagged RORγt-expressing EL-4 cells

value: Anti-Flag, Sigma, F3165


title: Flag-Rorc EL4 no exogeneous Rorc (control)

description: EL4 no exogeneous Rorc (control)


title: Rorc knockout + DMSO (control)

description: Rorc knockout + DMSO (control)

tag: genotype/variation

value: DMSO and Th17 polarizing conditions

value: Anti-RORgamma(t),  eBioscience, AFKJS-9, 14-6988, E11084-325


title: Digoxin

description: Digoxin

tag: cell type

value: wildtype


title: Rorc knockout (control)

description: Rorc knockout (control)

value: Th17 cells

value: Th17 polarizing conditions


title: Th17 cells treated with GSK805 (0.5uM) [RNA2-1]

value: 6-8 weeks


title: DMSO

description: DMSO


title: TMP778


title: Rorc knockout cells treated with DMSO under Th17 polarizing conditions [RNA2-1]

description: Rorc knockout + DMSO

value: Rorc knockout cells

value: DMSO under Th17 polarizing conditions


title: Th17 cells treated with TMP920 (10uM) [RNA2-1]


title: Untreated

description: Untreated


title: IgG antibody (control)

description: IgG antibody (control)

value: rat IgG2a,  eBioscience, 14-6988,


title: Rorc knockout cells treated with DMSO under Th17 polarizing conditions, 2

description: Rorc knockout + DMSO

extract_protocol:
RNA was extracted with RNeasy Plus kits (Qiagen)
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit.


title: Th17 cells treated with TMP920 (10uM)


title: Th17 cells treated with DMSO, 2

description: DMSO

value: DMSO


title: Rorc knockout cells treated with DMSO under Th17 polarizing conditions, 1

description: Rorc knockout + DMSO


title: anti-Foxp3-iTreg

source_name: iTreg cells

value: iTreg cells


title: Th17 cells treated with Digoxin (10uM)

description: Digoxin

value: Digoxin (10uM)


title: Th17 cells treated with DMSO, 1

description: DMSO


title: Th17 cells treated with TMP778 (2.5uM)


title: 4sU_RNA-seq exp3, 3T3-L1 4h

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Quality of all libraries were assessed using FastQC (Babraham Bioinformatics). Reads were trimmed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
ChIP-seq reads were aligned to the genome (mm9) using Bowtie (Langmead B, et al., Genome Biol. 10:R25) with the following parameters: –best –strata -m 3, with all other parameters set at default. Only one read was kept at locations  where multiple reads align to the exact same position. 4sU-RNA-seq reads were aligned to the mm9 genome and to a pseudo genome containing all possible exon-exon junctions for all genes using Bowtie with the following parameters: --best --strata –m 1. Mapped tags were subsequently combined.
Regions enriched for transcription factor binding were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589). Peaks were called for each transcription factor if they were four times enriched relative to the local background (20 kb around the peak), four times enriched relative to a 3T3-L1 input control sample (Siersbæk et al., 2011, EMBO J, 30, 1459-1472), and significant at a false discovery rate of 0.01%. A master set of peaks containing all the identified peaks for all transcription factors (if the center of two or more peaks were within 200 bp, the peaks were merged) was defined. All peaks from this master set containing at least 20 tags per 10M tags in a 250 bp window around the center of each peak for a given transcription factor were called as high-confidence transcription factor binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were created using HOMER for visualization of binding profiles and expression data in the UCSC genome browser.

source_name: 3T3-L1 pre-adipocytes (4h)

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM supplemented with 10% calf serum. Two days post confluency (day 0), the cells were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS).

extract_protocol:
4sU-RNA-seq was performed essentially as described previously (Rabani et al., 2011, Nature biotechnology 29, 436-442). Briefly, cells were incubated with 400 μM 4-thiouridine (4sU) for 30 min and then harvested in TRIzol (Invitrogen). RNA was then purified according to the manufacturer’s instructions. Purified RNA was biotinylated and pulled down using streptavidin beads. Enriched RNA was then purified and subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions.
ChIP-seq: Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). Chromatin used for ChIP-seq of p300 and MED1 was also cross-linked in 2 mM disuccinimidyl glutarate (DSG) for 45 minutes at RT prior to cross-linking by formaldehyde.
RNA-seq: RNA was purified using TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: 3T3-L1 pre-adipocytes (day 0) were induced to differentiate using a cocktail of adipogenic inducers (1 μM dexamethasone, 0.5 mM 3-isobutyl-1-methylxantine, 1 μg/mL insulin, 10% FCS). Cells were harvested four hours after induction.

tag: cell line

value: pre-adipocytes (4hr after induction)


title: MED1 ChIP-seq, 3T3-L1 4h

extract_protocol:
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).
ChIP-seq: Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). Chromatin used for ChIP-seq of p300 and MED1 was also cross-linked in 2 mM disuccinimidyl glutarate (DSG) for 45 minutes at RT prior to cross-linking by formaldehyde.
RNA-seq: RNA was purified using TRIzol (Invitrogen) according to the manufacturer’s instructions.

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: 4sU_RNA-seq exp2, 3T3-L1 D0

source_name: 3T3-L1 pre-adipocytes (D0)

value: pre-adipocytes (Day 0)


title: 4sU_RNA-seq exp2, 3T3-L1 4h


title: 4sU_RNA-seq exp3, 3T3-L1 D0


title: BRG1 ChIP-seq, 3T3-L1 4h

value: Epitomics


title: RXR ChIP-seq, 3T3-L1 4h


title: TMP920

tag: strain


title: VDR ChIP-seq, 3T3-L1 4h


title: STAT1 ChIP-seq, 3T3-L1 4h


title: p300 ChIP-seq, 3T3-L1 4h


title: PBX1 ChIP-seq, 3T3-L1 4h

value: Cell signaling


title: KLF4 ChIP-seq, 3T3-L1 4h


title: JunB ChIP-seq, 3T3-L1 4h


title: FOSL2 ChIP-seq, 3T3-L1 4h


title: cJun ChIP-seq, 3T3-L1 4h

value: cJun (H79)


title: ATF7 ChIP-seq, 3T3-L1 4h


title: ATF2 ChIP-seq, 3T3-L1 4h


title: KLF5 ChIP-seq, 3T3-L1 4h

tag: chip antibody provider

value: kind gift from Dr. Huck-Hui Ng


title: NoDice(4-25) kshv-miR-K12-11 Transfected RISC-Associated Small RNA

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

description:
Ago2 PAR-CLIP
Processed alignments of total small RNA reads to miRbase v20 mature microRNAhirpins
425w155ripseq

data_processing:
Initial reads were quality filtered with cassava 1.8.2.
3' adapter sequences were clipped and reads >15 nt in length quality filtered using the FASTX-toolkit v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Bowtie v.0.12.7 (Langmead et al. 2009) was used to map reads to miRbase version 20 and the human genome
For the PAR-CLIP libraries, PARalyzer v1.1 (Corcoran et al. 2011) was used for cluster generation.  Overlapping background clusters, with a minimum read depth of 5, identified in the non-transfected NoDice(4-25) cell line, or NoDice(4-25) cells transfected with the miR-92a duplex described above, were then subtracted from the >50 read depth cluster sets obtained from the miR-155 and miR-K11 transfected NoDice(4-25) cells. Then, both of these high stringency data sets were used to subtract the overlap of the miR-K11 (miR-155 set) or miR-155 (miR-K11 set) to obtain RISC-binding clusters specific for each set. Specifically, the miR-K11 or miR-155 ≥10 read depth cluster set was subtracted from the high stringency ≥50 read depth sets described above.
Genome_build: Hg19, miRbase v.20
Supplementary_files_format_and_content: Tab-separated normalized reads per total library reads (*.tsv): contains a small RNA sequence, the particular microRNA matching the sequence, sense strand to which the sequence aligns, read start coordinate with respect to the miRNA, read end coordinate with respect to the miRNA, and normalized read depth per total small RNA reads
Supplementary_files_format_and_content: Comma-separated microRNA targets (*.csv):  Chromosome, strand, start coordinate, end coordinate of microRNA target, seed sequence of targeting microRNA, seed type, target ID, sequence of microRNA target, targeting microRNAs, and filter type

organism: Homo sapiens

source_name: 293T Cell Line

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium containing 10% Fetal Bovine Serum and Gentamicin

extract_protocol:
Immunoprecipitation of RISC  with Abcam anti-Ago2 antibody (AB57113) followed by mirVana miRNA isolation as previously described (Flores et al, 2013 [PMID 23536669])
Illumina TruSeq Small RNA Sample Preparation Kit.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix

tag: transfection reagent

value: Lipofectamine 2000

tag: transfected rna duplex

value: kshv-miR-K12-11 RNA duplex

tag: days post-transfection at time of harvest

value: anti-Ago2 antibody

tag: antibody vendor

value: Abcam

tag: antibody cat. #

tag: illumina 3' index number

tag: molecule subtype

value: RISC-associated small RNA


title: NoDice(4-25) hsa-miR-155 Transfected RISC-Associated Small RNA

description:
Ago2 RIP-Seq
Processed alignments of total small RNA reads to miRbase v20 mature microRNAhirpins
425wK11ripseq

value: hsa-miR-155 RNA duplex


title: NoDice(4-25) hsa-miR-92a Transfected RISC-Associated Crosslinked RNA

description:
Ago2 PAR-CLIP
MicroRNA targets as determined by PAR-CLIP
425w92aparclip

extract_protocol: Illumina TruSeq Small RNA Sample Preparation Kit.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix

value: hsa-miR-92a RNA duplex

value: RISC-associated Crosslinked RNA


title: NoDice(4-25) RISC-Associated Small RNA

description:
Ago2 RIP-Seq
Processed alignments of total small RNA reads to miRbase v20 microRNA hairpins
425ripseq


title: 293T RISC-Associated Small RNA

description:
Ago2 RIP-Seq
Processed alignments of total small RNA reads to miRbase v20 microRNA hairpins
293Tripseq

value: Wild Type


title: NoDice(4-25) hsa-miR-155 Transfected RISC-Associated Crosslinked RNA

description:
Ago2 PAR-CLIP
MicroRNA targets as determined by PAR-CLIP
425wK11parclip


title: NoDice(4-25) RISC-Associated Crosslinked RNA

description:
Ago2 PAR-CLIP
MicroRNA targets as determined by PAR-CLIP
425parclip


title: NoDice(4-25) kshv-miR-K12-11 Transfected RISC-Associated Crosslinked RNA

description:
Ago2 PAR-CLIP
MicroRNA targets as determined by PAR-CLIP
425w155parclip


title: NoDice(4-25) Drosophila Dicer1 and Loqs-PB Rescue Total Small RNA

description:
Processed alignments of total small RNA reads to miRbase v20 microRNA hairpins
425dmeD1B

extract_protocol:
TRIzol total RNA isolation followed by the mirVana miRNA  isolation kit
Illumina TruSeq Small RNA Sample Preparation Kit.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix

tag: plasmid transfected

value: pcDNA-FLAG-Loqs-PB

value: total small RNA


title: NoDice(2-20) Total Small RNA

description:
Processed alignments of total small RNA reads ranging from 19-25nt to miRbase v20 microRNA hairpins
NoDice220

extract_protocol:
TRIzol total RNA isolation followed by electrophoresis on a 15% polyacrylamide TBE-urea gel.  Small RNAs ~15-40nt in length were identified using radiolabeled markers and electroeluted from the gel slice
Constructed with a protocol analogous to the illumina TruSeq small RNA.  RNA adapters identical to the illuman adapters were ligated overnight with 3' adapter-ligated small RNAs purified by gel electrophoresis on a 10% TBE-urea acrylamide gel and electroeluted in lieu of the “stop” solution.  Reverse transcription was performed with Invitrogen SuperScript III and PCR amplification using Promega's GoTaq Green Master Mix


title: S39-E2F1-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r2

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

data_processing:
Single-end 36 bp reads generated by the Illumina HiSeq 2000 were aligned against the Human Reference Genome (assemby GRCh37, NCBI Build 37) using BWA version 0.5.9. Reads were filtered by removing those with a BWA alignment quality score less than 15 as well as duplicate reads.
Enriched regions of the genome were identified by comparing ChIP samples to input samples using MACS Version 1.4.2
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS peaks in .bed file format

growth_protocol: RPMI & 10% Foetal Bovine Serum & Puromycin

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Bicalutamide 1µM or Vehicle (Ethanol)

tag: factor

tag: condition

value: BICALUTAMIDE

tag: antibody


title: NoDice(4-25) Human Dicer Rescue Total Small RNA

description:
Processed alignments of total small RNA reads to miRbase v20 microRNA hairpins
425huDicer

tag: cell line

tag: genotype/variation


title: NoDice(4-25) Total Small RNA

description:
Processed alignments of total small RNA reads ranging from 19-25nt to miRbase v20 microRNA hairpins
NoDice425


title: S40-E2F1-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r4


title: S37-AR-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r3

value: AR


title: S36-E2F1-CHIP-LNCAP-LM-EV-VEHICLE_r4

value: Vehicle


title: sinonasal sarcoma RNA-Seq

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

data_processing:
Illumina's Genome Analyzer system software programs for base-calling
the 50bp paired end reads were aligned using BWA 0.6.2
the fusion transcripts were identified using SnowShoes-FTD version 2.0
Genome_build: hg19
Supplementary_files_format_and_content: the input files were the fastq files of the two ends, and the out put files were the SnowShoes-FTD called fusion transcripts

source_name: connective tissue

extract_protocol:
RNA was extracted by Qiagen Mini RNeasy Kit (Qiagen)
TruSeq RNA sample preparation kit (Illumina)

tag: tissue

value: sinonasal sarcoma


title: S34-AR-CHIP-LNCAP-LM-EV-VEHICLE_r4


title: S33-AR-CHIP-LNCAP-LM-EV-VEHICLE_r3


title: S32-E2F1-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r4


title: S30-AR-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r4


title: S35-E2F1-CHIP-LNCAP-LM-EV-VEHICLE_r2


title: S29-AR-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r3


title: S31-E2F1-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r2


title: S27-E2F1-CHIP-LNCAP-LM-HES6-VEHICLE_r2


title: NoDice(4-25) Mock Total Small RNA

description:
Processed alignments of total small RNA reads to miRbase v20 microRNA hairpins
425mock


title: S26-AR-CHIP-LNCAP-LM-HES6-VEHICLE_r4


title: C.remanei female rep 2 DNAseq

organism: Caenorhabditis remanei

extract_protocol:
staging protocol: 50 -100 young adults were hand picked from mixed stage plates.
400uL of Worm Lysis Buffer (0.1M TrisHCl; 0.1M NaCl; 50mM EDTA; 1.25%SDS) was added before sonicating to obtain chromatin fragments of majority size of between 200 and 800 bp.
Isolate DNA was ligated to Illumina adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

tag: developmental stage

value: young adult


title: C.remanei male rep 2 DNAseq

tag: strain


title: S24-E2F1-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r3


title: C.remanei female rep 1 DNAseq


title: C.remanei male rep 1 DNAseq


title: 293T Total Small RNA

description:
Processed alignments of total small RNA reads ranging from 19-25nt to miRbase v20 microRNA hairpins
293T


title: C.briggsae female rep 2 DNAseq

organism: Caenorhabditis briggsae


title: S25-AR-CHIP-LNCAP-LM-HES6-VEHICLE_r3


title: C.briggsae female rep 1 DNAseq


title: S22-AR-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r2


title: S19-E2F1-CHIP-LNCAP-LM-EV-VEHICLE_r1


title: S20-E2F1-CHIP-LNCAP-LM-EV-VEHICLE_r3


title: S18-AR-CHIP-LNCAP-LM-EV-VEHICLE_r2


title: C.briggsae male rep 2 DNAseq


title: S17-AR-CHIP-LNCAP-LM-EV-VEHICLE_r1


title: S21-AR-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r1


title: S16-E2F1-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r3


title: S28-E2F1-CHIP-LNCAP-LM-HES6-VEHICLE_r4


title: S14-AR-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r2


title: C.brenneri female rep 2 DNAseq

organism: Caenorhabditis brenneri


title: S13-AR-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r1


title: S12-E2F1-CHIP-LNCAP-LM-HES6-VEHICLE_r3


title: C.brenneri female rep 1 DNAseq


title: ASGV-infected

city: Beijing

first: Ting

last: Ye

address: No. 2, Yuanmingyuan West Road, Haidian District

department: Plant Pathology

country: China

institute: China Agricultural University

description:
Sample 1
Malus × domestica Borkh cv. Fuji

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequences were cleaned by removal of adaptor sequences, N-containing reads with more than 10% of unknown bases, low-quality sequences containing 50% bases of quality value  5, and adaptor-alone sequences. The clean reads were mapped to reference sequences in Malus x domestica Whole Genome v1.0 (http://www.rosaceae.org/species/malus/malus_x_domestica/genome_v1.0) using SOAPaligner/soap2 (Li et al., Bioinformatics, 2009) allowing no more than 2 nucleotide mismatches.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008.
Genome_build: Malus x domestica Whole Genome v1.0
Supplementary_files_format_and_content: Tab-delimited text files include matched unique reads number, gene length, coverage, RPKM values, GO annotation and BLAST nr for each sample.

organism: Malus domestica

source_name: in vitro-grown apple plantlets

growth_protocol: In vitro-grown plantlets of Malus × domestica Borkh cv. Fuji were cultured on a medium (pH5.8) composed of Murashige and Skoog medium (MS) containing 3% sucrose, 1mg L-1 6-Benzylaminopurine (6-BA) and 0.02 mg L-1 1-naphthlcetic acid (NAA) solidified with 0.8% agar powder. Stock cultures were maintained at a temperature of 25±1oC under a 16-h light/8-h dark photoperiod with a light intensity of 3600Lx by cool-white fluorescent tubes. Subculture was performed every 4 weeks.

extract_protocol:
Two RNA pools were obtained, separately, from 10 ASGV-infected plantlets and 10 virus-free plantlets cultured under the same growth conditions. Total RNA was extracted from mixed samples according to the method described by Gambino et al., Phytochemical Analysis, 2008. After treatment with DNase I and extraction with phenol/chloroform and precipitation, RNA pellets were dissolved in 30 μL of RNase-free water and visualized in a 1.0% agarose gel and quantified using a NanoDrop ND-2000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: well-developed single shoots (>2cm in length) were excised from ASGV-infected stock cultures and cultured in 150 mL triangular flasks. After 7 days, the flasks were transferred to a heat chamber programmed for a cycle of 16-h light at 37 °C followed by an 8-h darkness at 34 °C for 38 days. After thermotherapy, meristems of 1 mm were excised under a microscope and cultured for 7 days on solid MS medium containing 3% sucrose and supplemented with 1 mg L-1 6-BA, 0.2 mg L-1 NAA and 0.5 mg L-1 gibberellin A3 at a temperature of 25oC in the dark for survival and plant regeneration. RT-PCR and Northern blotting were performed to detect ASGV, ACLSV, ASPV, Apple skin scar viroid (ASSVd) and Apple dimple fruit viroid (ADFVd) in the regenerated shoots with specific primers.

tag: host

value: in vitro-grown apple plantlets

tag: infection

value: ASGV-infected


title: Virus-free

description:
Sample 2
Malus × domestica Borkh cv. Fuji

value: ASGV-eliminated, and virus-free


title: S23-E2F1-CHIP-LNCAP-LM-EV-BICALUTAMIDE_r1


title: S11-E2F1-CHIP-LNCAP-LM-HES6-VEHICLE_r1


title: S10-AR-CHIP-LNCAP-LM-HES6-VEHICLE_r2


title: H3K4me2 ChIP-seq exp2, 3T3-L1 4h

tag: cell type

value: pre-adipocytes (4hr after induction)

tag: chip antibody

tag: chip antibody vendor

value: Cell Signaling

tag: chip antibody cat. #


title: C.brenneri male rep 3 DNAseq


title: S09-AR-CHIP-LNCAP-LM-HES6-VEHICLE_r1


title: C.briggsae male rep 1 DNAseq


title: H3K4me1 ChIP-seq exp1, 3T3-L1 4h

value: Abcam


title: C.brenneri male rep 2 DNAseq


title: IL-LNCAP-LM-EV-BICALUTAMIDE-INPUT-D7_r1

source_name: LNCAP cell line

value: Input


title: S15-E2F1-CHIP-LNCAP-LM-HES6-BICALUTAMIDE_r1


title: C.brenneri male rep 1 DNAseq


title: P.pacificus female rep3 RNAseq

organism: Pristionchus pacificus

value: J4 / young adult


title: H3K27ac ChIP-seq exp2, 3T3-L1 4h


title: H3K27ac ChIP-seq exp1, 3T3-L1 4h


title: IK-LNCAP-LM-EV-VEHICLE-INPUT-D7_r1


title: II-LNCAP-LM-HES6-VEHICLE-INPUT-D7_r1


title: H3K4me1 ChIP-seq exp2, 3T3-L1 4h


title: P.pacificus female rep1 RNAseq


title: P.pacificus female rep2 RNAseq


title: MED1 ChIP-seq, 3T3-L1 4h, NoDex_4h_exp2_MED1

value: Santa Cruz


title: P.pacificus male rep3 RNAseq


title: IG-LNCAP-LM-EV-VEHICLE-INPUT-D2_r1


title: P.pacificus male rep2 RNAseq


title: MED1 ChIP-seq, 3T3-L1 4h, DMI_4h_exp2_MED1


title: H3K4me2 ChIP-seq exp1, 3T3-L1 4h


title: IF-LNCAP-LM-HES6-BICALUTAMIDE-INPUT-D2_r1


title: P.pacificus male rep1 RNAseq


title: MED1 ChIP-seq, 3T3-L1 4h, NoDex_4h_exp1_MED1


title: ID-LNCAP-LM-HES6-BICALUTAMIDE-INPUT-D26_r1


title: P.pacificus female rep 2 DNAseq


title: MED1 ChIP-seq, 3T3-L1 4h, DMI_4h_exp1_MED1


title: P.pacificus female rep 1 DNAseq


title: P.pacificus male rep 2 DNAseq


title: MED1 ChIP-seq, 3T3-L1 4h, Scr_4h_exp2_MED1

tag: transfected with

value: Scr. Lentivirus expressing shRNA against a scrambled sequence


title: MED1 ChIP-seq, 3T3-L1 4h, Scr_4h_exp1_MED1


title: IH-LNCAP-LM-EV-BICALUTAMIDE-INPUT-D2_r1


title: MED1 ChIP-seq, 3T3-L1 4h, CEBPb_4h_exp1_MED1

value: Lentivirus expressing shRNA against C/EBPβ (C/EBPβ knockdown)


title: P.pacificus male rep 1 DNAseq


title: Rps6_mock

status: Public on Apr 16 2014

city: West Lafayette

first: Meixia

last: Zhao

address: 915 W State Steet

department: Agronomy

institute: Purdue University

data_processing:
base-calling
Sequenced reads were trimmed for adaptor sequences, and masked for low-quality and < 101 bp sequences, then mapped to Glycine max reference genome (v1.0) using Tophat 2.0.4, with the parameters -r 0 -g 1 -i 25 -I 100000 -p 8 --read-mismatches 1.
The raw count of each gene was calculated by HTSeq (http://www-huber.embl.de/users/anders/HTSeq) with the “intersection_nonempty” mode, and preceded to edgeR package (Robinson et al. 2009) in the R-Bioconductor tools.
Counts of gene per million reads (CPM)  were caculated using cpm function in edgeR.
Genome_build: V1.0
Supplementary_files_format_and_content: Soybean_RNA-Seq_Normalized_read_counts.txt (linked as a supplementary file on the Series record) is a tab-delimited text file reporting CPM values for each Sample.

organism: Glycine max

source_name: Rps6_mock, Soybean hypocotyl

growth_protocol: greenhouse

extract_protocol:
Qiagen RNeasy Plant Mini Kit, Cat. No. 74904
RNA libraries were prepared for sequencing using TrueSeq RNA Sample Preparation Kit, Cat. No. FC-122-1002 with standard Illumina protocols

treatment_protocol: Standard hypocotyl inoculation with Phytophthora Sojae

tag: line

value: hypocotyl (stem)

tag: inoculation

value: mock-inoculated


title: rrp6l1-2_mRNA_Seq

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

description: mRNA

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China). Basecalling were done by  Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China).
For mRNA-Seq: Reads were mapped to TAIR10 by TopHat2 with preset option --b2-very-sensitive.
For MethylC-Seq: Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
For sRNA-Seq: Briefly, after adapter sequences were trimmed, clean reads of size 18-32 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 100. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
mRNA-Seq:Total RNAs were isolated from 14-d-old seedlings by Trizol reagent (Invitrogen), and were treated with DNase I (Ambion) to remove DNA. mRNAs were enriched with Oligo (dT)-conjugated magnetic beads and were then sent to Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China) for library preparation and Illumina sequencing
Genomic DNA was extracted from 14-d-old seedlings.  RNA extracted using Trizol.

tag: genotype

value: rrp6l1-2 mutant

value: seedling


title: Rps4_mock

source_name: Rps4_mock, Soybean hypocotyl


title: rrp6l1-2_sRNA-Seq

description: small RNA

extract_protocol:
sRNA-Seq:Total RNAs were isolated from 14-d-old seedlings by Trizol reagent (Invitrogen). Small RNAs were precipitated by  PEG 8000 solution (20% PEG, 1 M NaCl) and were then sent to Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China) for library preparation and Illumina sequencing.
Genomic DNA was extracted from 14-d-old seedlings.  RNA extracted using Trizol.


title: WT_mRNA-Seq (rrp6l1-2 control)

description: mRNA

value: WT


title: GmDof4

first: Jin

last: Xu

state: Chaoyang District

address: No.7 Beitucheng West Road

institute: Beijing Institute of Genomics

data_processing:
We first merged all of the short reads from the two libraries as the input data for de novo assembling. We yielded 13,566 contigs with lengths of at least 300bp using SOAPdenovo with parameters "-K 31 –d 3 –R" .
The 13,566 contigs were used as reference genes sequence. To detect the different expression genes, we mapped the short reads to the reference genes using the BWA program with default parameters for each library separately. The number of reads mapping to each contig  was counted as the expression level of each contig.
Supplementary_files_format_and_content: Tab-delimited text files include contig names, raw counts and RPKM values.

organism: Pseudochlorella pringsheimii

source_name: GmDof4 transgenic strain Dof4-1

growth_protocol: C. ellipsoidea strain IGDB-1 was used in this study. Cells were grown in Endo medium for mixotrophic culture in a rotary shaker (120 g) at 25°C under illumination (100 μmol photons m-2 s-1) for 120 h.

extract_protocol: Cells at a concentration of approximately 1×10^7 cells/mL were collected for library construction and sequencing. RNA was harvested using Trizol reagent. The Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 μg of total RNA for the construction of sequencing libraries.

treatment_protocol: The cells were transformed with a Baekon 2000 (Baekon Co., CA, USA) electroporation device using 6 kV of 0.001-0.02 s pulse duration, 210 pulse frequency, and 2 mm pulse distance for 100 cycles. The transformed cells were screened using selection medium SE agar medium containing 30 mg/L G418.

tag: strain/background

value: cultured Chlorella ellipsoidea cells

value: GmDof4 transgenic


title: WT_sRNA-Seq

description: small RNA


title: Rps5_mock

source_name: Rps5_mock, Soybean hypocotyl


title: Rps3-b_mock

source_name: Rps3-b_mock, Soybean hypocotyl


title: CK

source_name: pCK transgenic line CK-1

value: pCK transgenic

tag: sample type

value: control


title: Rps3-c_mock

source_name: Rps3-c_mock, Soybean hypocotyl


title: Rps1-k_mock

source_name: Rps1-k_mock, Soybean hypocotyl


title: Rps1-c_mock

source_name: Rps1-c_mock, Soybean hypocotyl


title: MED1 ChIP-seq, 3T3-L1 4h, CEBPb_4h_exp2_MED1

tag: cell line

value: pre-adipocytes (4hr after induction)


title: Rps1-a_mock

source_name: Rps1-a_mock, Soybean hypocotyl


title: Rps6_Inoc

source_name: Rps6_Inoc, Soybean hypocotyl

value: P. sojae inoculated


title: Williams_mock

source_name: Williams_mock, Soybean hypocotyl

value: Williams


title: Rps4_Inoc

source_name: Rps4_Inoc, Soybean hypocotyl


title: Rps3-a_mock

source_name: Rps3-a_mock, Soybean hypocotyl


title: Rps3-b_Inoc

source_name: Rps3-b_Inoc, Soybean hypocotyl


title: Rps1-b_mock

source_name: Rps1-b_mock, Soybean hypocotyl


title: RNA-seq cardiomyocytes PN1

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

description:
Cardiomyocytes neonatal
CG33474

data_processing:
TopHat 2.0.5 is used to align reads to reference genome. The tophat parameters are: -g 1 -r 80 --mate-std-dev 180, others are default. For strand-specific data, use --library-type fr-secondstrand
Fragments Per Kilobase per Megabase of library size (FPKM) were calculated using Cufflinks 2.1.1 with customer parameter -N
The isoform quantification is performed against the mouse Ensemble Gene Model (Downloaded from UCSC Table October 2012)
Genome_build: mm9
Supplementary_files_format_and_content: isoform FPKM

source_name: Cardiomyocytes neonatal

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
RNeasy fibrous tissue mini kit was used for ventricles and cardiomyocytes, and micro RNeasy kit for cardiac fibroblasts (all from Qiagen)
Illumina TruSeq RNA protocols were used for cardiomyocytes and cardiac fibroblast. For developmental ventricle analysis, RNA was rRNA depleted with the Ribo-Zero Magnetic Gold Kit and libraries were prepared using ScriptSeq v2 RNA-seq library preparation kits (Epicentre).

treatment_protocol: In all the cases atria were removed. Cardiomyocytes from adult and PN30 animals were isolated by Langendorff perfusion method. Cardiac  fibroblasts of all the stages were isolated by preplating method with a previous step of enzymatic digestion. Neonatal cardiomyocytes were obtained by preplating method using Cellutron kit.

value: FvB

tag: genotype/variation

value: wild type

tag: age

value: Cardiomyocytes


title: RNA-seq cardiomyocytes PN1-2

description:
Cardiomyocytes neonatal
CG31667

tag: tissue


title: RNA-seq cardiomyocytes PN30

description:
Cardiomyocytes PN30
CG33548

source_name: Cardiomyocytes

tag: strain


title: Rps3-c_Inoc

source_name: Rps3-c_Inoc, Soybean hypocotyl


title: RNA-seq cardiac fibroblasts PN1-2

description:
Cardiac fibroblasts neonatal
CG31428

source_name: Cardiac fibroblasts neonatal

value: Cardiac fibroblasts


title: RNA-seq cardiac fibroblasts PN1-3

description:
Cardiac fibroblasts neonatal
CG31061


title: Rps1-c_Inoc

source_name: Rps1-c_Inoc, Soybean hypocotyl


title: RNA-seq cardiac fibroblasts PN60 (adult)

description:
Cardiac fibroblasts PN60
CG30979

source_name: Cardiac fibroblasts

value: PN60 (adult)


title: Rps5_Inoc

source_name: Rps5_Inoc, Soybean hypocotyl

value: hypocotyl (stem)


title: RNA-seq ventricle E17

description:
Ventricle E17
CG31965

source_name: ventricle

value: ventricle


title: RNA-seq ventricle PN1

description:
Ventricle PN1
CG31926


title: RNA-seq ventricle PN10

description:
Ventricle PN10
CG31960


title: RNA-seq ventricle PN28

description:
Ventricle PN28
CG31963


title: Rps1-b_Inoc

source_name: Rps1-b_Inoc, Soybean hypocotyl


title: Williams_Inoc

source_name: Williams_Inoc, Soybean hypocotyl


title: Rps3-a_Inoc

source_name: Rps3-a_Inoc, Soybean hypocotyl


title: rrp6l1-2_MethylC-Seq

description:
genomic DNA
treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China). Basecalling were done by  Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China).
For mRNA-Seq: Reads were mapped to TAIR10 by TopHat2 with preset option --b2-very-sensitive.
For MethylC-Seq: Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
For sRNA-Seq: Briefly, after adapter sequences were trimmed, clean reads of size 18-32 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 100. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

source_name: Seedlings

extract_protocol:
MethylC-Seq:Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols
Genomic DNA was extracted from 14-d-old seedlings.  RNA extracted using Trizol.

value: rrp6l1-2 mutant


title: RNA-seq ventricle PN90 (adult)

description:
Ventricle PN90
CG31920

value: PN90 (adult)


title: mouse_e11.5_face_smarcc2-flag_control

description: Tissue pooled from ~300 embryos Chromatin IP against Smarcc2/FLAG - input control

data_processing:
Bam: Sequence reads were mapped to the mouse (mm9) genome using bwa with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Unique BWA-aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection in FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: gsize=2260035739 --tsize=50 or 36 --bw=300 --pvalue=1e-5 --mfold=10,30 --llocal=20000 --shiftsize=100. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9

source_name: Mouse embryonic day 11.5 (e11.5) face

extract_protocol:
Chromatin IP: Chromatin Immuno precipitation performed using Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. (Lot #: 088K6018)
ANTI-FLAG bound chromatin is treated with proteinase K and RNAse followed by clean up using QIAGEN QIAquick PCR Purification Kit (28104)
Embryonic tissues were isolated from 129/C57BL/6 (FLAG knock-in) mouse embryos at e11.5. ESCs from the same line were cultured as per standard protocols. Tissue samples and ESCs were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-FLAG antibody.  ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the  Illumina HiSeq 2000 to generate 50 or 36 bp reads

value: face

value: SMARCA4/FLAG knock-in

tag: Sex

value: pooled male and female

tag: developmental stage


title: mouse_e11.5_midbrain_smarca4-flag_control

description: Tissue pooled from ~300 embryos Chromatin IP against Smarca4/FLAG - input control

source_name: Mouse embryonic day 11.5 (e11.5) midbrain

value: midbrain


title: mouse_e11.5_midbrain_smarca4-flag

description: Tissue pooled from ~300 embryos Chromatin IP against Smarca4/FLAG


title: mouse_e11.5_hindbrain_smarcc2-flag

description: Tissue pooled from ~300 embryos Chromatin IP against Smarcc2/FLAG

source_name: Mouse embryonic day 11.5 (e11.5) hindbrain

value: hindbrain


title: mouse_e11.5_hindbrain_smarcc2-flag_control


title: mouse_e11.5_hindbrain_ncoa2-flag_control

description: Tissue pooled from ~300 embryos Chromatin IP against Ncoa2/FLAG - input control


title: RNA-seq cardiomyocytes PN67 (adult)

description:
Cardiomyocytes PN67
CG33549

value: PN67 (adult)


title: mouse_e11.5_hindbrain_ncoa2-flag

description: Tissue pooled from ~300 embryos Chromatin IP against Ncoa2/FLAG


title: mouse_ESC_ep300-flag

description: Mouse ESC chromatin IP against Ep300/FLAG

source_name: Mouse embryonic stem cells

value: ES cells


title: mouse_e11.5_hindbrain_ncoa1-flag_control

description: Tissue pooled from ~300 embryos Chromatin IP against Ncoa1/FLAG - input control


title: mouse_e11.5_hindbrain_ncoa1-flag

description: Tissue pooled from ~300 embryos Chromatin IP against Ncoa1/FLAG


title: mouse_e11.5_face_ep300-flag_control

description: Tissue pooled from ~300 embryos Chromatin IP against Ep300/FLAG - input control


title: mouse_e11.5_face_ep300-flag

description: Tissue pooled from ~300 embryos Chromatin IP against Ep300/FLAG


title: RNA-seq cardiac fibroblasts PN28

description:
Cardiac fibroblasts PN28
CG32461


title: Rps1-a_Inoc

source_name: Rps1-a_Inoc, Soybean hypocotyl

value: P. sojae inoculated


title: mouse_e11.5_heart_control

data_processing:
Bed: Sequence reads were mapped to the mouse (mm9) genome using bwa with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: Peak detection in SMARCA4-FLAG ChIP samples was performed using MACS1.4 with the appropriate matched control sample where present. Parameters were: gsize=2260035739 --tsize=50 or 36 --bw=300 --pvalue=1e-5 --mfold=10,30 --llocal=20000 --shiftsize=100. Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.
Genome_build: mm9

extract_protocol: Embryonic heart and hindbrain was isolated from 129/C57BL/6 (smarca4/FLAG knock-in) mouse embryos at e11.5. ESCs from the same line were cultured as per standard protocols. Tissue samples and ESCs were cross linked and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-FLAG antibody [Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018].  ANTI-FLAG bound chromatin is treated with proteinase K and RNAse followed by clean up using QIAGEN QIAquick PCR Purification Kit (28104). ChIP DNA was sheared by sonication, end-repaired, ligated to illumina sequencing adapters.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the  Illumina HiSeq 2000 to generate 50 or 36 bp reads

value: Mouse embryonic day 11.5 (e11.5) heart


title: mouse_e11.5_hindbrain_smarca4-flag

description: Tissue pooled from ~150 embryos Chromatin IP against SAMRCA4/FLAG

value: Mouse embryonic day 11.5 (e11.5) forebrain


title: mouse_e11.5_heart_smarca4-flag

description: Tissue pooled from ~300 embryos Chromatin IP against SAMRCA4/FLAG


title: mouse_e11.5_limb_smarca4-flag

description:
Limb
Tissue pooled from ~150 embryos. Chromatin IP against SMARCA4/FLAG.

data_processing:
Sequence reads were mapped to the mouse (mm9) genome using the Burrows-Wheeler Aligner (BWA) with default parameters. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites, were discarded.

Wig files: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.

Peaks.bed files: Peak detection in SMARCA4-FLAG ChIP samples was performed using CCAT with the appropriate matched control sample. Parameters were: fragment size = 200, slidingWinSize=500, movingStep=50 isStrandSensitiveMode=0, minCount=4, outputNum=100000, randomSeed=123456, minScore=2.0, bootstrapPass=50. Peaks overlapping repeats, or duplicated regions of the genome, were removed as likely mapping artifacts.

Genome_build: mm9

source_name: Mouse embryonic day 11.5 (e11.5) limb, FLAG-ChIP

extract_protocol: Embryonic face, forebrain, limb and neural tube tissue were isolated from 129/C57BL/6 (smarca4/FLAG knock-in) mouse embryos at e11.5.  Tissue samples were cross-linked, and cells were dissociated and subject to chromatin isolation, sonication and immunoprecipitation using an anti-FLAG antibody [Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #: 088K6018].  ANTI-FLAG bound chromatin is treated with proteinase K and RNAse followed by clean up using QIAGEN QIAquick PCR Purification Kit (28104). ChIP DNA was sheared by sonication, end-repaired, and ligated to illumina sequencing adapters.  Gel-purified amplified ChIP DNA between 300 and 500bp was sequenced on the  Illumina  HiSeq 2000 to generate 50 bp reads.

value: embryonic day 11.5 (e11.5)

value: limb

value: anti-FLAG [Sigma- F1804 [ 1mg/ml ]-Monoclonal ANTI-FLAG M2 antibody produced in mouse. Lot #:088K6018]


title: mouse_e11.5_neural-tube_smarca4-flag

description:
Neural tube
Tissue pooled from ~150 embryos. Chromatin IP against SMARCA4/FLAG.

source_name: Mouse embryonic day 11.5 (e11.5) neural tube, FLAG-ChIP

value: tube


title: mouse_e11.5_limb_control

description:
Limb control
Tissue pooled from ~150 embryos.

source_name: Mouse embryonic day 11.5 (e11.5) limb, control


title: mouse_e11.5_neural-tube_control

description:
Neural tube control
Tissue pooled from ~150 embryos.

source_name: Mouse embryonic day 11.5 (e11.5) neural tube, control


title: mouse_e11.5_forebrain_control

description:
Forebrain control
Tissue pooled from ~150 embryos.

source_name: Mouse embryonic day 11.5 (e11.5) forebrain, control

value: forebrain


title: mouse_e11.5_face_smarca4-flag

description:
Face
Tissue pooled from ~150 embryos. Chromatin IP against SMARCA4/FLAG.

source_name: Mouse embryonic day 11.5 (e11.5) face, FLAG-ChIP


title: mouse_ESC_smarca4-flag

value: Mouse embryonic stem cells


title: mouse_e11.5_face_smarcc2-flag


title: wt_MEFs_Ser2_ChIP_(20130118_7_6)

status: Public on Apr 15 2014

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: RNA Polymerase II Ser2 phosphorylated chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing wildtype Chd1.

data_processing: 1. We used Bowtie-0.12.8 to map paired-end 25bp reads to release MM9 of the Mus musculus genomic sequence obtained from U.C.Santa Cruz. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: wildtype-Chd1 MEFs Ser2 ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing wildtype transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (Ser2) against the Serine-2 phosphorylated form of RNA Polymerase II. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.

tag: cell type

value: embryonic fibroblasts

tag: transgene

tag: antibody

value: Ser2 (Abcam anti-RNA polymerase II CTD (phospho Serine-2) catalog #ab5095)


title: wt_MEFs_N20_ChIP_(20120817_5_4)

description: RNA Polymerase II chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing wildtype Chd1.

data_processing: 1. We used Bowtie-0.12.7 to map paired-end 25bp reads to release MM9 of the Mus musculus genomic sequence obtained from U.C.Santa Cruz. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: wildtype-Chd1 MEFs N20 ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing wildtype transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (N20) against the N-terminus of the largest subunit of RNA Polymerase II. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.

value: N20 (Santa Cruz catalog #sc-899)


title: mouse_e11.5_forebrain_smarca4-flag

description:
Forebrain
Tissue pooled from ~150 embryos. Chromatin IP against SMARCA4/FLAG.

source_name: Mouse embryonic day 11.5 (e11.5) forebrain, FLAG-ChIP

value: SMARCA4/FLAG knock-in

value: pooled male and female

tag: chip antibody


title: wt_MEFs_MNase_(20120817_4_6)

description: Mouse embryonic fibroblasts expressing wildtype Chd1 were crosslinked and the chromatin digested with micrococcal nuclease, followed by sequencing of the extracted DNA.

source_name: wildtype-Chd1 MNase digested chromatin

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing wildtype transgenic Chd1 were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing.


title: wt_MEFs_FLAG_ChIP_(20120817_6_4)

description: FLAG-tagged Chd1 chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing wildtype Chd1.

source_name: wildtype-Chd1 MEFs FLAG ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing wildtype transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (FLAG) against the N-terminus of the transgenic Chd1. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.

value: FLAG (Sigma anti-FLAG M2 agarose beads catalog #A2220)


title: K510R_MEFs_MNase_(20120817_4_12)

description: Mouse embryonic fibroblasts expressing K510R Chd1 were crosslinked and the chromatin digested with  micrococcal nuclease, followed by sequencing of the extracted DNA.

source_name: K510R-Chd1 MNase digested chromatin

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing K510R transgenic Chd1 were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing.


title: K510R_MEFs_FLAG_ChIP_(20120817_6_12)

description: FLAG-tagged Chd1 chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing K510R Chd1.

source_name: K510R-Chd1 MEFs FLAG ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing K510R transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (FLAG) against the N-terminus of the transgenic Chd1. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.


title: K510R_MEFs_N20_ChIP_(20120817_5_6)

description: RNA Polymerase II chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing K510R Chd1.

source_name: K510R-Chd1 MEFs N20 ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing K510R transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (N20) against the N-terminus of the largest subunit of RNA Polymerase II. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.


title: K510R_MEFs_Ser2_ChIP_(20130118_7_12)

description: RNA Polymerase II Ser2 phosphorylated chromatin immunoprecipitation followed by sequencing from mouse embryonic fibroblasts (MEFs) expressing K510R Chd1.

source_name: K510R-Chd1 MEFs Ser2 ChIP_seq

extract_protocol: Mouse embryonic fibroblasts (MEFs) expressing K510R transgenic Chd1 were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody (Ser2) against the Serine-2 phosphorylated form of RNA Polymerase II. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.


title: Rps1-k_Inoc

source_name: Rps1-k_Inoc, Soybean hypocotyl

extract_protocol:
Qiagen RNeasy Plant Mini Kit, Cat. No. 74904
RNA libraries were prepared for sequencing using TrueSeq RNA Sample Preparation Kit, Cat. No. FC-122-1002 with standard Illumina protocols

value: hypocotyl (stem)


title: gtaCKO 5h developing; replicate 2

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 0.12.7. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_raw.tab" contain raw expression values while files ending with "_nor.tab" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: gtaCKO 5h developing

growth_protocol: Wild-type and gene deletion cell lines were cultured axenically in HL5 supplemented with antibiotics.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries. We prepared 15 (or 20) individual libraries separately (one from each sample) and added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II using the manufacturer's recommended pipeline (versions 1.2 and 1.3, read length = 50 bases)

treatment_protocol: For development on non-nutrient agar, cells were washed with developmental buffer (DB) and plated on solidified DB agar at a density of 5.2^105 cells/cm2

value: gtaC

tag: replicate

tag: developmental time

value: 5 h


title: gtaCKO 1h developing; replicate 1

source_name: gtaCKO 1h developing

value: 1 h


title: gtaCKO 0h developing; replicate 1

source_name: gtaCKO 0h developing

value: 0 h


title: gtaCKO 1h developing; replicate 2


title: gtaCKO 5h developing; replicate 1


title: gtaCKO 2h developing; replicate 1

source_name: gtaCKO 2h developing

value: 2 h


title: NLS 5h developing; replicate 2

source_name: NLS 5h developing

value: NLSex-GFP-GtaC/gtaC


title: gtaCKO 0h developing; replicate 2


title: gtaCKO 2h developing; replicate 2


title: NLS 2h developing; replicate 2

source_name: NLS 2h developing


title: NLS 2h developing; replicate 1


title: NLS 0h developing; replicate 2

source_name: NLS 0h developing


title: NLS 0h developing; replicate 1


title: NLS 1h developing; replicate 1

source_name: NLS 1h developing


title: GtaCGFP 2h developing; replicate 2

source_name: GtaCGFP 2h developing

value: GFP-GtaC/gtaC


title: GtaCGFP 5h developing; replicate 2

source_name: GtaCGFP 5h developing


title: NLS 1h developing; replicate 2


title: GtaCGFP 5h developing; replicate 1


title: GtaCGFP 1h developing; replicate 1

source_name: GtaCGFP 1h developing


title: GtaCGFP 0h developing; replicate 2

source_name: GtaCGFP 0h developing


title: GtaCGFP 2h developing; replicate 1


title: GtaCGFP 0h developing; replicate 1


title: GtaCGFP 1h developing; replicate 2


title: AX2 5h developing; replicate 2

source_name: AX2 5h developing

value: wildtype


title: AX2 2h developing; replicate 2

source_name: AX2 2h developing


title: AX2 5h developing; replicate 1


title: AX2 2h developing; replicate 1


title: NLS 5h developing; replicate 1


title: NPC_Time_2_rep2

first: Loyal

last: Goff

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

data_processing:
Reads were aligned to the human (hg19) reference genome assemblies using Tophat2 with default options.
Aligned fragments were used as input for Cuffdiff2 to determine expression levels (FPKM) and differential expression between conditions using the default options.
CummeRbund v2.1 (http://compbio.mit.edu/cummeRbund/) was used to process, index, and visualize the output of the Cuffdiff2 analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CummeRbund diffTable output. Contains log ratios and differential significance test results.
Supplementary_files_format_and_content: see diffTable output for locations on the genome

source_name: H1-derived neural progenitor cells

growth_protocol: H1 human neural stem cells were prepared as described previously (Arnold et al., 2008; Goff et al., 2009) and grown at 37°C, 5% CO2 on 1:4 diluted Matrigel-coated wells in neural proliferation medium (NPM; 50% DMEM/F12 Glutamax, 50% Neurobasal medium, 0.5X N2, 0.5X B27 without vitamin A, 20 ng/ml FGF [Life Technologies]). For differentiation, cells were plated at a density of 106 cells per well in a 6-well plate and allowed to proliferate for one day in the NPM medium. Neural induction was then initiated by withdrawal of FGF and addition of BDNF by switching the medium to neural differentiation medium (NDM; 100% Neurobasal medium, 1X B27 without vitamin A [Life Technologies], 10 ng/ml BDNF [Peprotech, Rocky Hill, NJ].) Differentiating cultures were maintained by refreshing NDM every other day until collection. Samples of these cultures were collected at days 0, 1, 2, and 4. Remaining cells (those designated for collection at days 5, 11, and 18) were replated at day 4 at a density 106 cells per well of a Poly-D-lysine/laminin-coated 6-well plate.

extract_protocol:
Cells were harvested with Accutase (Stem Cell Technologies, Vancouver, Canada). Total RNA was isolated using TRIzol (Life Technology, Carlsbad, CA)/chloroform extraction followed by spin-column purification (RNeasy mini kit, Qiagen, Venlo, Netherlands) according to the manufacturer instructions. RNA concentration and purity were determined using a Nanodrop (Thermo Fisher, Waltham, MA). RNA integrity was assessed on a Bioanalyzer (Agilent, Santa Clara, CA) using the RNA 6000 RNA chip. High-quality RNA samples (RNA Integrity Number ≥8) were used for library preparation.
200ng total RNA was used as input for the TruSeq RNA-Seq kit (Illumina) for each of the samples described. Prior to sequencing, libraries were run on a Bioanalyzer DNA7500 chip to assess purity, fragment size, and concentration. Libraries free of adapter dimers and with a peak region area (220–500 bp) ≥80% of the total area were sequenced. Individually barcoded samples were pooled and sequenced on the Illumina HiSeq 2000 platform.

value: ES-derived neural progenitor cells

tag: time

value: Day 2


title: KD_MEFs_MNase_(20130520_1,2_12)

description: Mouse embryonic fibroblasts expressing a short hairpin RNA against Chd1 were crosslinked and the chromatin digested with  micrococcal nuclease, followed by sequencing of the extracted DNA.

source_name: control-Chd1 MNase digested chromatin

extract_protocol: Mouse embryonic fibroblasts (MEFs) transduced with lentivirus expressing a short hairpin RNA to knockdown expression of Chd1. Cells were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.

value: embryonic fibroblasts

tag: rna

value: short hairpin Chd1i1 RNAi


title: AX2 1h developing; replicate 2

source_name: AX2 1h developing

tag: genotype


title: AX2 0h developing; replicate 2

source_name: AX2 0h developing


title: AX2 0h developing; replicate 1


title: LYP9 5hmC

first: Shuhui

last: Song

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: chemical labeling

data_processing:
The deep sequencing reads were stripped of the adaptor sequences with the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that were less than 25 nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the TIGR rice genome  Oryza sativa subsp. japornica (ver6.1), with up to two mismatches allowed, by the BWA 0.5.8 algorithm (Li and Durbin 2009). All non-redundant uniquely mapped reads were used for peaks calling using MACS (P-value<10-5) (Zhang et al. 2008). The location that peaks relative to a known transcript was determined based on the TIGR v6.1 database (Yuan et al. 2003; Ouyang et al. 2007).
Genome_build: TIGR  ver6.1

organism: Oryza sativa

source_name: Panicle

growth_protocol: Panicle materials in 3-4mm length were simultaneously collected from the super-hybrid rice group cultivars in a test field of China National Hybrid Rice R&D Center in Hunan Province, and DNA were extracted for Dot-blots assay.

extract_protocol: Genomic DNAs from panicle were denatured 95℃ for 10min and immediately chilled on ice for 5min. The Dot blot was performed on a bio-Dot Apparatus (#170-6545, Bio-Rad). The completely dried charged nylon-based membrane was baked for 2h at 80℃, after that 254 UV crosslink 10min and then blot Briefly with 5% non-fat milk at 1.5h room temperature. The primary rabbit anti-5-hydroxymethylytosine antibody (1:10k, #39769, Ative Motif) was applied to the membrane and incubated 1h at RT or overnight at 4℃, followed by peroxidase-conjugated anti-rabbit IgG secondary antibody. The signal was visualized by using ECL-Plus (Amersham Pharmacia Biotech).Purified genomic DNA should be sonicated into short fragments (200~300 bp) by Covaris DNA shearing with microTUBEs according to manufacturer’s instructions. Then 5hmC labeling reaction were performed in 75-ul solution containing 50mM HEPES buffer(PH7.9), 250 mM MgCl2, 100 µM UDP-6-N3-Glu, and 80 U βGT. The reactions were incubated for 2h at 37℃. After the reaction, The DNA substrates were purified and exchange buffer in H20 via Bio-rad micro bio spin according to the manufacturer’s instructions. The click chemistry was performed with the addition of 150µM biotin into the DNA solution and incubated 2h at 37℃.The DNA samples were then purified by Invitrogen DynabeadsMyOneTM Streptavidin C1 according to manufacturer’s instructions.

tag: tissue type

value: panicle

tag: passages

value: anti-5-hydroxymethylytosine #39769, Active Motif


title: PA64s 5hmC

description: chemical labeling


title: control_MEFs_MNase_(20130520_1,2_6)

description: Mouse embryonic fibroblasts (MEFs) expressing a control short hairpin RNA were crosslinked and the chromatin digested with  micrococcal nuclease, followed by sequencing of the extracted DNA.

extract_protocol: Mouse embryonic fibroblasts (MEFs) transduced with lentivirus expressing a control short hairpin RNA were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Illumina (Solexa) sequencing.

value: short hairpin control


title: 93-11 5hmC

description: chemical labeling


title: NPC_Time_4_rep0

tag: cell line

value: Day 4


title: NPC_Time_18_rep2

value: Day 18


title: NPC_Time_18_rep1


title: NPC_Time_2_rep0


title: NPC_Time_18_rep0


title: NPC_Time_11_rep2

value: Day 11


title: NPC_Time_1_rep2

value: Day 1


title: NPC_Time_11_rep0


title: NPC_Time_1_rep1


title: NPC_Time_0_rep2

value: Day 0


title: NPC_Time_0_rep1


title: NPC_Time_1_rep0


title: AX2 1h developing; replicate 1

value: 1 h


title: spl7_MS

city: Charlottesville

first: xin

last: zhao

state: VA

address: Department of Biology, 229 Gilmer Hall

institute: University of Virginia

data_processing:
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava 1.8.2
RNA-seq reads were aligned to the TAIR10 genome assembly using Tophat, allowing for up to two mismatching nucleotides, max intron length 2000bp, min isoform fraction 0 and no gaps. Only uniquely mapped reads were retained for further analysis.
Cufflinks software was used to identify differentially expressed genes. Parameters were set as following: FDR 0.01; minimum alignment count 50; Quartile normolization True.
genome build: TAIR10
processed data files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: Seeds were cold-treated at 4°C for 4 day, sowed on standard MS medium or MS medium with 5µM CuSO4, transferred to growth chamber, and allowed to growth at 22°C for 7 day under continuous white light.

extract_protocol:
Whole seedlings were harvested, ground to powder in liquid nitrogen, and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA treated with DNase I for the construction of sequencing libraries.
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit'.

value: whole seedlings

value: spl7 mutant

tag: age

value: post germination day 7


title: spl7_cu+

tag: tissue