title: ES line RB4

source_name: Embryonic stem (ES) cells

growth_protocol: Passage 9 cells (line RB4), growing on Matrigel for four days (to deplete the MEF feeders) in N2B27 medium supplemented with 3 μM CHIR99021, 1 μM PD0325901, and 1000 U/mL LIF.

value: ES line RB4


title: ES line RB3

status: Public on Nov 13 2014

type: SRA

city: Madison

first: David

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

country: USA

institute: Morgridge Institute for Research

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
TPMs renormalized to transcripts per million non-mitochondrial transcripts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

molecule: total RNA

organism: Mus musculus

growth_protocol: Passage 9 cells (line RB3), growing on Matrigel for four days (to deplete the MEF feeders) in N2B27 medium supplemented with 3 μM CHIR99021, 1 μM PD0325901, and 1000 U/mL LIF.

extract_protocol:
Cells were lysed in Trizol (Life Technology), and total RNA was purified from the lysates using RNeasy columns (Qiagen) with on-column DNAse treatment.
Total RNAs were converted to cDNAs and otherwise prepared for sequencing using the Tru-seq RNA Sample Prep Kit v2 (Illumina), as described by the manufacturer.

tag: facs purification

tag: cell line

value: ES line RB3


title: ES line RB2

growth_protocol: Passage 9 cells (line RB2), growing on Matrigel for four days (to deplete the MEF feeders) in N2B27 medium supplemented with 3 μM CHIR99021, 1 μM PD0325901, and 1000 U/mL LIF.

value: ES line RB2


title: ago6_mock_FLAG-IP_Replicate_A

status: Public on Nov 14 2014

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: mock control: FLAG-IP without the FLAG antigen

data_processing:
Illumina software was used for basecalling. Sequenced reads de-multiplexed and were trimmed for adaptor sequence. Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, tRNA and rRNA-matching reads were removed, and only small RNAs that perfectly match the genome are reported (UEA small RNA tool v 2.5.0 used).
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced

organism: Arabidopsis thaliana

growth_protocol: Plants were grown on soil in 18 hour long days at 23C.

extract_protocol:
For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. For the IP libraries, mock and IPs were performed as in MuCue et al (in preparation). Small RNAs were extracted from proteins using Trizol LS.
Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit

tag: ecotype background

tag: genotype/variation

value: ago6 mutant

tag: tissue

value: unopened flower buds

tag: ip antibody

value: FLAG Antibody

tag: ip antibody vendor

value: Sigma

tag: molecule subtype

value: Immunoprecipitated small RNA


title: N98_48hpi_TB

city: Dunsany

first: Peter

last: Vegh

state: Meath

address: Grange, Batterjohn Crossroads

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

description: miRNA

data_processing:
Basecalls performed using CASAVA
FastQC (version 0.10.0) was used for quality control
Cutadapt (version 1.2.1) was used for adapter removal
Fastq quality filter (version 0.0.13.2)
Novoalign (version 2.08.03) in 'mirna' mode was used for alignment to bovine genome
HTSeq-count (part of the HTSeq framework, version 0.5.3p3) in 'union' mode was used to count aligned reads, using miRBase version 20
Genome_build: bosTau6
Supplementary_files_format_and_content: Tab-delimited text containing the raw miRNA gene counts for all 88 samples

organism: Bos taurus

source_name: Lung lavage

growth_protocol: Alveolar macrophages were obtained by pulmonary lavage of lungs post mortem. Macrophages were cultured in 24 well cell culture plates, in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 µg/ml ampicillin and 25 µg/ml gentamycin.

extract_protocol:
Small RNA fractions were prepared by the Qiagen RNeasy Plus Mini kit, using the manufacturer's protocol (appendix E).
Libraries were prepared according to the manufacturer's protocol of the Illumina Truseq Small RNA Sample Preparation Kit, using 5 uL small RNA as input material.

tag: cell type

value: Alveolar macrophage

tag: animal

tag: timepoint

tag: treatment

value: M. bovis infected


title: N98_24hpi_CN

description: miRNA

value: control


title: N1864_24hpi_TB

description: miRNA


title: N98_2hpi_CN

description: miRNA


title: N1859_2hpi_TB

description: miRNA


title: N1870_24hpi_CN

description: miRNA


title: N1861_2hpi_CN

description: miRNA


title: N98_0hpi_CN

description: miRNA


title: N138_24hpi_TB

description: miRNA


title: N1855_48hpi_TB

description: miRNA


title: N138_0hpi_CN

description: miRNA


title: N1855_2hpi_CN

description: miRNA


title: N98_2hpi_TB

description: miRNA


title: Day 3 endothelial cells derived from RB3.6.5

source_name: Endothelial progeny of eHB cells

growth_protocol: Derived from eHB cells (line RB3.6.5). Differentiated three days on Matrigel in N2B27 medium supplemented with 20 ng/mL murine VEGF, 0.25 mM 8-Bromoadenosine 3′,5′-cyclic monophosphate sodium salt, 4 μM SB431542, 20 ng/mL human BMP4, and 12.5 ng/mL human FGF2.


title: N158_24hpi_CN

description: miRNA


title: N98_6hpi_CN

description: miRNA


title: N1864_2hpi_CN

description: miRNA


title: N1864_6hpi_CN

description: miRNA


title: N1870_6hpi_CN

description: miRNA


title: N1861_6hpi_TB

description: miRNA


title: N1870_6hpi_TB

description: miRNA


title: N1861_6hpi_CN

description: miRNA


title: N1870_2hpi_CN

description: miRNA


title: N98_48hpi_CN

description: miRNA


title: N1859_48hpi_CN

description: miRNA


title: N1855_24hpi_TB

description: miRNA


title: N1855_2hpi_TB

description: miRNA


title: N158_2hpi_TB

description: miRNA


title: N121_48hpi_TB

description: miRNA


title: N138_6hpi_CN

description: miRNA


title: N1178_2hpi_TB

description: miRNA


title: N1178_0hpi_CN

description: miRNA


title: N98_24hpi_TB

description: miRNA


title: N1178_48hpi_TB

description: miRNA


title: N1859_24hpi_TB

description: miRNA


title: N1864_48hpi_TB

description: miRNA


title: N1855_48hpi_CN

description: miRNA


title: N1864_6hpi_TB

description: miRNA


title: N1855_0hpi_CN

description: miRNA


title: N1861_24hpi_TB

description: miRNA


title: N1859_48hpi_TB

description: miRNA


title: N158_6hpi_TB

description: miRNA


title: N158_24hpi_TB

description: miRNA


title: N1859_2hpi_CN

description: miRNA


title: N158_0hpi_CN

description: miRNA


title: N1178_2hpi_CN

description: miRNA


title: N138_2hpi_TB

description: miRNA


title: 15_28d_Dnmt3a3b

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description: rRNA depleted total RNA

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Sequence reads were mapped to the mouse genome (GRCm38/mm10) with Tophat v2.0.9 41 using the following parameters: -r 90 --solexa-quals --library-type fr-firststrand. To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAMtools.
The paired end reads were treated as separate single-end runs. The bigWig files were normalized to display uniquely mapped reads per 50 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: in vitro differentiated ES cells

growth_protocol: ES cell lines were cultured on a feeder layer of mitomycin C-treated primary MEFs in an ES medium containing Glasgow Minimum Essential Medium (G-MEM, Wako, Osaka, Japan) supplemented with 15% fetal bovine serum (FBS, Hyclone, South Logan, UT), 0.1 mM MEM nonessential amino acids (Nacalai Tesque, Kyoto, Japan), 0.1 mM 2-mercaptoethanol (Sigma, St. Louis, U.S.A.), 1,000 units/mL of leukemia inhibitory factor (LIF) and 100 units/mL of penicillin–streptomycin (Nacalai Tesque).

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (QIAGEN), according to the manufacturer’s instructions.
0.5 µg of total RNA was depleted of ribosomal RNAs using Ribo-Zero Gold (Illumina). Sequencing libraries were constructed using TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s instruction (Illumina).

treatment_protocol: In vitro differentiation of ESCs was performed as described recently (Umemura et al. 2013). Briefly, after ESCs were trypsinized and feeder cells were removed, embryoid bodies (EBs) were generated by harvesting 2,000 cells and seeding them onto low-attachment 96-well plates (Lipidure Coat, NOF, Tokyo, Japan) in a differentiating medium without LIF supplementation (EFM), which was comprised of a high-glucose DMEM (Nacalai Tesque) containing 10% FBS, 1 mM sodium pyruvate (Nacalai Tesque), 0.1 mM nonessential amino acids, GlutaMaxTM-I (Invitrogen), 100 µM β-mercaptoethanol and 100 units/mL penicillin-streptomycin. Two day later, EBs were plated onto gelatin-coated tissue culture 24-well plates and grown for several additional weeks. EFM was changed every 1–2 day.

tag: genotype

value: Dnmt3a -/-, Dnmt3b -/-

tag: days after differentiation

value: Double KO


title: N158_6hpi_CN

description: miRNA


title: N1178_24hpi_CN

description: miRNA


title: 14_28d_Dnmt3b

description: rRNA depleted total RNA

value: Dnmt3b -/-


title: N98_6hpi_TB

description: miRNA


title: 12_28d_TKO

description: rRNA depleted total RNA

value: Dnmt1 -/-, Dnmt3a -/-, Dnmt3b -/-

value: Triple KO


title: 13_28d_Dnmt3a

description: rRNA depleted total RNA

value: Dnmt3a -/-


title: N121_2hpi_TB

description: miRNA


title: N1178_6hpi_CN

description: miRNA


title: N1864_24hpi_CN

description: miRNA


title: 11_7d_TKO

description: rRNA depleted total RNA


title: N1870_2hpi_TB

description: miRNA


title: N1870_0hpi_CN

description: miRNA


title: N1870_48hpi_TB

description: miRNA


title: 09_28d_Dnmt1

description: rRNA depleted total RNA

value: Dnmt1 -/-


title: N1861_24hpi_CN

description: miRNA


title: 08_7d_Dnmt1

description: rRNA depleted total RNA


title: N1859_6hpi_CN

description: miRNA


title: 07_ESC_Dnmt1

description: rRNA depleted total RNA

source_name: ES cells


title: N1864_2hpi_TB

description: miRNA


title: conv2

city: New York

first: Elisabeth

last: Kernbauer

state: NY

address: 540 First Avenue

institute: New York University School of Medicine, Skirball Institute

description: uni-vs-conv.de.genes

data_processing:
basecalling with Illumina Casava1.8.2
Alignment to the mouse mm9 reference genome with Illumina Casava1.8.2
Differential gene expression calculated with BioConductor package edgeR
Genome_build: mm9
Supplementary_files_format_and_content: BAM files contain aligned reads from each sample, xls files summarize gene expression values and differential gene expression fold change and p-values

source_name: small intestinal tissue (ileum)

extract_protocol:
2 cm of small intestine was removed and immediately snap frozen in liquid nitrogen. RNA extraction was performed using Trizol reagent according to standard protocols. TruSeq RNA sample kit v2 (RS-122-2001) from Illumina was used to prepare the library for sequencing. 1µg of RNA was used.
RNA libraries were prepared for sequencing using standard Illumina protocols from TruSeq RNA sample Prep v2 guide.

value: conventionalization day 10

tag: strain

value: WT


title: 05_7d_Per2Luc

description: rRNA depleted total RNA

value: wild-type


title: 06_28d_Per2Luc

description: rRNA depleted total RNA


title: conv3

description: uni-vs-conv.de.genes


title: N1859_0hpi_CN

description: miRNA


title: conv1

description: uni-vs-conv.de.genes


title: MNV3

description: uni-vs-MNV.de.genes

value: murine norovirus infection day 10


title: 04_ESC_Per2Luc

description: rRNA depleted total RNA


title: MNV1

description: uni-vs-MNV.de.genes


title: 03_28d_KY

description: rRNA depleted total RNA


title: uni2

description:
uni-vs-conv.de.genes
uni-vs-MNV.de.genes

value: uninfected


title: uni1


title: uni3


title: 10_ESC_TKO

description: rRNA depleted total RNA


title: N138_48hpi_TB

description: miRNA


title: 02_7d_KY

description: rRNA depleted total RNA


title: 01_ESC_KY

description: rRNA depleted total RNA


title: N138_48hpi_CN

description: miRNA


title: N1855_24hpi_CN

description: miRNA


title: Cre-infected cKO MEFs 10%TI histone ChIPseq biological replicate 3

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

library_source: genomic

data_processing:
RNAseq: The reads were mapped using Tophat (v2.0.3) calling Bowtie (v2.0.0.6) and using samtools (v0.1.18.0) to the NCBIM37 genome annotation. Cufflinks (v2.0.1) was then run with the -G option to the annotated NCBIM37 genes and a mask file containing rRNA, Mt_rRNA, and Mt_tRNA sequences. The assemblies were compiled using Cuffmerge with the -g option to annotated genes and -s to the NCBIM37 genome. Cuffdiff was then run using the mask file, the --frag-bias-correct option, and performing upper quartile normilization (--upper-quartile-norm) to more accuratley call low expressed genes.
RB ChIPseq: The reads were mapped to the NCBIM37 genome using BWA. Aligned reads were converted to bed files using Samtools (v0.1.18) and bedTools (v2.16.2). Bed files were converted to aln files using CisGenome (v2.0) and then the "Two Sample Peak Calling" was run with both biological replicates and their respective 10% Total Input samples with the following parameters modified (E=450, B=25, W=2, and without the standardization of win statistics). Output bar files were converted to wig.
Histone ChIPseq: The reads were mapped to the NCBIM37 genome using BWA and peaks called using MACS (v1.4.1) without model building (--nomodel) and the band width set to the average library length calculated using a bioanalyzer.

molecule: genomic DNA

source_name: conditional KO Rb MEF

growth_protocol: Cells were grown at 37oC in 5% CO2 in standard media (DMEM, 10% serum, glutamine, penn/strep)

extract_protocol: Purified RNA was isolated using Trizol and a Qiagen RNEasy Kit. After assessing RNA quality using an Agilent 2100 Bioanalyzer , cDNA was made using an Ovation® RNA-Seq System V2 (NuGEN) and sonicated using a Covaris S2 Sonicator. Sequencing libraries were generated using the NEBNext® DNA Sample Prep Master Mix Set (New England Biolabs) and purified using Agencourt® Ampure® XP beads (Bechman Coulter).

treatment_protocol: To conditionally delete Rb cells were infected with titered Adeno-Cre or Adeno-GFP as a control, 1x10^6 cells at a time. In the RNAseq or Rb ChIPseq samples, the cells were then infected with a puro-selectable 4F construct or an empty pSicoR-Puro. Puro was added the following day and selection was maintained until the third day when the cells were harvested for sample processing. For the histone ChIPseq, the MEFs were infected with Adeno_GFP or Adeno-Cre and then expanded no more than 3 passages to opbtain enough cells.

value: MEFs

value: mixed B6;129 background

tag: gfp/cre-infected

value: Cre

value: no 4F

tag: chip antibody

value: Input


title: Cre-infected cKO MEFs H3K9me3 ChIPseq biological replicate 3

tag: chip vendor/catalog#

value: Millipore #07-442


title: Cre-infected cKO MEFs H3K27me3 ChIPseq biological replicate 3

value: Millipore #07-449


title: Cre-infected cKO MEFs H3Ac ChIPseq biological replicate 3

value: Millipore #06-599


title: Cre-infected cKO MEFs H3K4me3 ChIPseq biological replicate 3

value: Abcam #ab8580


title: N138_24hpi_CN

description: miRNA

value: Alveolar macrophage

value: control


title: ChIP:H3K27ac_ab4729_Jurkat3_091914 [lab: Look-DFCI]

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline.
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

organism: Homo sapiens

source_name: T-ALL

growth_protocol: Cells were grown according to ATCC guidelines

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

treatment_protocol: Untreated

value: Jurkat

tag: antibody manu.

value: Abcam

tag: antibody catalog

tag: system

value: Blood

tag: tal1 enhancer status


title: ChIP:MYB_ab45150_Jurkat3_091914 [lab: Look-DFCI]

value: MYB


title: N121_2hpi_CN

description: miRNA


title: GFP-infected cKO MEFs H3K27me3 ChIPseq biological replicate 3

value: GFP


title: MNV2

description: uni-vs-MNV.de.genes

value: murine norovirus infection day 10

value: WT


title: N1855_6hpi_TB

description: miRNA

value: M. bovis infected


title: GFP-infected cKO MEFs H3K9me3 ChIPseq biological replicate 3

value: MEFs

value: mixed B6;129 background


title: Input for ChIP:Jurkat3_091914 [lab: Look-DFCI]


title: GFP-infected cKO MEFs H3K4me3 ChIPseq biological replicate 3

value: no 4F


title: GFP-infected cKO MEFs H3Ac ChIPseq biological replicate 3


title: N121_48hpi_CN

description: miRNA


title: GFP-infected cKO MEFs 10%TI histone ChIPseq biological replicate 1

value: Input


title: ChIP:MYB_ab45150_Jurkat4_091914 [lab: Look-DFCI]


title: N158_2hpi_CN

description: miRNA


title: GFP-infected cKO MEFs RB ChIPseq

description: biological rep1 & 2


title: N121_0hpi_CN

description: miRNA


title: Input for ChIP:Jurkat1_091914 [lab: Look-DFCI]

value: WT/Jurkat


title: ChIP:H3K27ac_ab4729_Jurkat1_091914 [lab: Look-DFCI]


title: GFP-infected with 4F cKO MEFs RB ChIPseq

description: biological rep1 & 2

value: with 4F


title: GFP-infected with 4F cKO MEFs 10%TI ChIPseq

description: biological rep1 & 2


title: N138_6hpi_TB

description: miRNA


title: N1178_6hpi_TB

description: miRNA


title: GFP-infected cKO MEFs 10%TI ChIPseq

description: biological rep1 & 2


title: ChIP:MYB_ab45150_Jurkat1_091914 [lab: Look-DFCI]


title: N1870_48hpi_CN

description: miRNA


title: N1870_24hpi_TB

description: miRNA


title: Cre-infected with 4F cKO MEFs RNAseq

description: biological rep1 & 2

molecule: polyA RNA

value: Cre


title: GFP-infected with 4F cKO MEFs RNAseq

description: biological rep1 & 2


title: Input for ChIP:Jurkat4_091914 [lab: Look-DFCI]


title: Wildtype Replicate 2

city: Boston

first: Michael

middle: E.

last: Talkowski

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Massachusetts General Hospital

data_processing:
Basecalls performed using CASAVA version 1.5
Alignment was performed with Gsnap v2012-07-20 using default parameters and the zv9 genome/transcriptome from Ensembl
Accurate dose response was verified with custom analysis tools and the included ERCC RNA spike-ins
Aligned reads were quantified with Cufflinks v2.1.0 using default parameters and the zv9 transcriptome from Ensembl
Genome_build: zv9
Supplementary_files_format_and_content: Cufflinks v2.1.0 genes.fpkm_tracking

organism: Danio rerio

source_name: whole head

growth_protocol: Zebrafish embryos from natural matings were maintained at 28C in 6 or 10cm dishes. 5 days post fertilization, the heads of 80-100 embryos per replicate were obtained for RNA extraction.

extract_protocol:
TRIzol (Invitrogen) extraction per manufactor's instructions
Strand-specific, polyA selected RNA-Seq libraries were constructed using a custom dUTP method similar to the standard Illumina protocols, with the addition of 1ul of a 1:10 dilution of ERCC RNA spike-ins prior to polyA selection.

tag: develolpmental stage

value: 5 days post fertilization embryo

tag: tissue

value: whole head


title: GFP-infected cKO MEFs RNAseq

description: biological rep1 & 2


title: Wildtype Replicate 3


title: ChIP:H3K27ac_ab4729_Jurkat4_091914 [lab: Look-DFCI]

value: Jurkat


title: N1864_0hpi_CN

description: miRNA

value: Alveolar macrophage

value: control


title: N1861_2hpi_TB

description: miRNA


title: N1861_0hpi_CN

description: miRNA


title: N1864_48hpi_CN

description: miRNA


title: Cre-infected cKO MEFs RNAseq biological replicate 2


title: Wildtype Replicate 1


title: N1855_6hpi_CN

description: miRNA


title: N158_48hpi_CN

description: miRNA


title: N1859_6hpi_TB

description: miRNA


title: N1859_24hpi_CN

description: miRNA


title: N138_2hpi_CN

description: miRNA


title: N1178_48hpi_CN

description: miRNA


title: N1178_24hpi_TB

description: miRNA


title: N158_48hpi_TB

description: miRNA


title: N121_24hpi_CN

description: miRNA


title: N121_24hpi_TB

description: miRNA


title: N121_6hpi_TB

description: miRNA


title: N121_6hpi_CN

description: miRNA


title: ChIP:TAL1_sc12984_MOLT3_062714

value: Santa Cruz

value: Blood

value: WT/MOLT3 WT


title: Input for ChIP:MOLT3_062714


title: Input for ChIP:MYB_Jurkat_040314 04182014_C4JDGACXX_6.CAGATC

description: Input for ChIP:MYB_Jurkat_040314

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples, reads were aligned with bowtie 0.12.9 to the mm9 genome.  Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.

source_name: T-ALL cell line

growth_protocol: Human Jurkat cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA was prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: antibody catalog number

value: None WCE

tag: cell line

tag: barcode (already removed)

value: CAGATC


title: ChIP:MYB_ab45150_Jurkat_040314 04182014_C4JDGACXX_6.ACAGTG

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: MYB

value: Abcam AB45150

value: ACAGTG


title: ChIP:H3K27ac_ab4729_MOLT3_062714

tag: cell type

value: Abcam


title: ChIP:vMYB_ab45150_MOLT3_062714


title: Med1_ChipSeq 11252013_C2GUGACXX_3.TTAGGC

description: Chromatin IP against Med1

value: Bethyl A300-793A

value: TTAGGC


title: ChIP:MYB_05-175_Jurkat_040314 04182014_C4JDGACXX_6.GCCAAT

value: Millipore 05-175

value: GCCAAT


title: RNA-Seq_Caco-2_TET1

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

data_processing:
Basecalls performed using CASAVA version 1.8
Reads for RNA-Seq were mapped on hg18 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
genome_build: hg18
supplementary_files_format_and_content: wig files were generated using WIGGLES v1.2.0

growth_protocol: RPMI + 10% FCS

extract_protocol:
total RNA was extracted using Trizol following the manufacturing protocol
library was performed using TruSeq RNA Sample Prep kit v2

treatment_protocol: Caco-2 cell line stably expressing ectopic inducible TET1 was treated for 96h with Doxycyclin 1ug/ml to express TET1

value: colon cancer line


title: NL4-3_GagCLIP_virions

status: Public on Nov 12 2014

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

address: Washington University School of Medicine

description:
Viral (HIV-1) and cellular RNA
CLIP-seq

data_processing:
The FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) was used to process the reads from libraries before mapping. Briefly, reads that contained ambiguous nucleotides, did not contain the 3′ adapter sequence or were shorter than 15nt were discarded. The remaining reads were then separated based on their 5’ barcode sequences and collapsed to generate a set of unique sequences.
Reads were then aligned to the human genome (hg19) or to the HIV-1 genome(NL4-3 and NDK), with up to 2 mismatches allowed using the Bowtie algorithm. In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2 --best --strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
BEDTools was used to convert the mapped reads to unique CLIP tags.
Genome_build: hg19, NL4-3 and NDK genomes
Supplementary_files_format_and_content: BED files with unique CLIP tags.

source_name: 293T cells transfected

growth_protocol: HEK293T cells grown in 10-cm dishes were transfected with 10 μg of the indicated proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
UV-crosslinked cells and virions were lysed, Gag-RNA complexes were immunoprecipitated and RNA was further extracted for library construction.
Libraries were prepared with sequential ligation of the following primers: 3' adapter: 5'adenylated/TCG TAT GCC GTC TTC TGC TTG-3'dideoxyC / 5' adapters containing the barcodes are as follows: rGUU CAG AGU UCU ACA GUC CGA CGA UC AGUGC  rGUU CAG AGU UCU ACA GUC CGA CGA UC GAUGC  rGUU CAG AGU UCU ACA GUC CGA CGA UC GUGGC  rGUU CAG AGU UCU ACA GUC CGA CGA UC ACGGC  rGUU CAG AGU UCU ACA GUC CGA CGA UC UAGGC  rGUU CAG AGU UCU ACA GUC CGA CGA UC AUCGC

treatment_protocol: For PAR-CLIP, one day following transfection and 14 hours before harvesting cells and virions, 100 μM 4-thiouridine (4SU) or 6-thioguanosine (6SG) was added to the cell culture medium.

value: 293T cells transfected

tag: clip antibody

value: mouse anti-HA


title: NL4-3_GagCLIP_cells

institute: Washington University School of Medicine

description:
Viral (HIV-1) and cellular RNA
CLIP-seq


title: H3K4me2 ChIP (Nutlin-3a)

city: Philadelphia

first: Morgan

last: Sammons

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: ChIP of H3K4me2 from Nutlin-treated IMR90.

data_processing:
Raw fastq files were aligned to hg19/ncbi37 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -k1 -N1
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <ChIP_Bowtie_output.map> -n <Condition_Input.map> -s 50 -f SAM -g 3107677273
Only peaks with an F.D.R < 1% were used in the analysis.
HOMER was used to generate BedGraph files for visualization. First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
BedGraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto', and bigWigs were generated using bedGraph2bigWig.pl
TSS, Enhancers, and Protoenhancer BED files were processed using H3K4me1 and H3K4me3 overlap with p53_Nutlin_Peaks_hg19_FDR1.txt.
Genome_build: ncbi37/hg19
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BigWig files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNA-seq data in tab-delimited text format.

source_name: IMR90 fetal lung fibroblasts

growth_protocol: IMR90 fibroblasts were grown in DMEM with 10% FBS at 3% oxygen.

extract_protocol:
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor.
For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.

treatment_protocol: Proliferating IMR90 fibroblasts were treated with either DMSO or nutlin3a (5uM final) for 6hrs before harvesting.

tag: treatment

value: Nutlin-3a (5uM final, 6hrs)

tag: passages

tag: antibody

value: H3K4me2 (Millipore)


title: H3K4me2 ChIP (DMSO)

description: ChIP of H3K4me2 from DMSO-treated IMR90.

value: DMSO (6hrs)


title: ATAC-seq (DMSO)

description: library stategy: ATAC-seq

data_processing:
Processed data files were generated for both genome builds hg18 and hg19.

hg18 (file names do not include "hg18"):
Raw fastq files were aligned to hg18/ncbi36 using Bowtie, allowing for only uniquely aligned reads to be reported.
bowtie --chunkmbs 512 -m 1 --best <hg18_index> -q <file.fastq> <file.map>
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <ChIP_Bowtie_output.map> -n <Condition_Input.map> -s 50 -f BOWTIE -g 3107677273
Only peaks with an F.D.R < 1% were used in the analysis.
HOMER was used to generate BedGraph files for visualization. First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Genome_build: ncbi36/hg18
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BedGraph files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNAseq data in tab-delimited text format

hg19 (file names include "hg19"):
Raw fastq files were aligned to hg19/ncbi37 using Bowtie2, allowing for only uniquely aligned reads to be reported.
bowtie2 -k1 -N1
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <ChIP_Bowtie_output.map> -n <Condition_Input.map> -s 50 -f SAM -g 3107677273
Only peaks with an F.D.R < 1% were used in the analysis.
HOMER was used to generate BedGraph files for visualization. First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
BedGraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto', and bigWigs were generated using bedGraph2bigWig.pl
TSS, Enhancers, and Protoenhancer BED files were processed using H3K4me1 and H3K4me3 overlap with p53_Nutlin_Peaks_hg19_FDR1.txt.
Genome_build: ncbi37/hg19
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BigWig files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNA-seq data in tab-delimited text format.

extract_protocol:
For ChIP-seq, cells were crosslinked with formaldehyde (1% final) for 10min at room temperature, and harvested for sonication. Nuclei were extracted and chromatin was sheared to an average size of 200bp using a Diagenode Bioruptor.
For RNA-seq, cells were harvested and PolyA+ RNA was isolated using the NEBNext Ultra RNA-seq Isolation Module.
For ATAC-seq, cells were harvested, nuclei were prepped,and transposase was added for 30 minutes at 30C.
Sequencing libraries for ChIP-seq were constructed using the NEBNext Ultra kit as per manufacturer's recommended instructions.
Sequencing libraries for ATAC-seq were constructed using custom Nextera-compatible primers, from Nextera-adapted DNA fragments


title: C8_FTD3_6

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Sequenced reads were trimmed for quality (Q > 20, fastx toolkit), adaptor sequence (cutadapt), and filtered for low-quality sequence, low-complexity and illumina internal control phiX. Then mapped to the human GRCh37.73 whole genome (downloaded from ensembl) using Tophat v2.0.8b with parameters --library-type fr-unstranded --min-intron-length 50 --max-intron-length 500000 --no-coverage-search --no-mixed --read-realign-edit-dist 3. With samtools 0.1.19-44428cd we removed reads from the alignment that are non-primary mappings or have a mapping quality <20.
The number of reads mapping to each Ensembl gene was counted with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count; parameters: union and reverse stranded).
Genome_build: GRCh37.73
Supplementary_files_format_and_content: ProcessedData.xlsx contains non-normalized read counts assigned to genes.

source_name: Neuronal progeny differentiated from FTD3#6-iPSC

growth_protocol: hESC and iPSC lines were differentiated toward neural-specific progeny into 5 cm dishes (150288, NUNC) pre-coated with Matrigel (734-1440, VWR) diluted in DMEM:F-12 for 1 h at 37 °C, in a 21% O2 – 5.8% CO2 – 37°C incubator. Cells were expanded in mTeSR medium (Stem Cell Technologies, 05850) for two days in presence of ROCK inhibitor (Y-27632; 10 mM Calbiochem, 688000). To induce neural differentiation, medium was switched to a Defined Default Medium (DDM) (Gaspard et al., 2008) with B27 without Vitamin A (Gibco, 12587-010), supplemented with recombinant human Noggin (6057-NG, R&D Systems) for 16 days. All culture media and supplements were from Invitrogen unless otherwise stated.  The neural progenitor cells on d24 were manually dissociated and transferred on laminin/poly-D-Lysine coated glass coverslips and allowed to differentiate without medium change until d40.

extract_protocol:
Sigma Kit for RNA extraction
RNA libraries were prepared for sequencing using Illumina Truseq Stranded mRNA library prep.

value: Neuronal Progeny

tag: genotype

value: Differentiated from FTD3#6-iPSC

tag: experiment

value: Experiment number 8


title: RNA-Seq_Caco-2_control

treatment_protocol: Caco-2 cell line stably expressing ectopic inducible TET1 not treated


title: ATAC-seq (Nutlin-3a)

description: library stategy: ATAC-seq


title: C3_H9

source_name: Neuronal progeny differentiated from H9-hESC

value: Differentiated from H9-hESC

value: Experiment number 3


title: C5_NF8_9

source_name: Neuronal progeny differentiated from FTD3#6-PGRN

value: Differentiated from FTD3#6-PGRN

value: Experiment number 5


title: C1_H9bis

value: Experiment number 1


title: C10_FTD3_6

value: Experiment number 10


title: PolyA+ RNAseq (Nutlin-3a)


title: Input (Nutlin-3a)

data_processing:
Raw fastq files were aligned to hg18/ncbi36 using Bowtie, allowing for only uniquely aligned reads to be reported.
bowtie --chunkmbs 512 -m 1 --best <hg18_index> -q <file.fastq> <file.map>
Significant Peaks were called using macs (v1.4) with input controls and default mfold
macs -t <ChIP_Bowtie_output.map> -n <Condition_Input.map> -s 50 -f BOWTIE -g 3107677273
Only peaks with an F.D.R < 1% were used in the analysis.
HOMER was used to generate BedGraph files for visualization. First, HOMER-specifc TagDirectories were generated from bowtie output files (file.map) using the command 'makeTagDirectory <ChIP_TagDirectory> <ChIP_Bowtie_output.map> '
Bedgraphs were then generated using the command 'makeUCSCfile <ChIP_TagDirectory> -o auto'
Genome_build: ncbi36/hg18
Supplementary_files_format_and_content: Peak BED files (3 column, from MACS)
Supplementary_files_format_and_content: BedGraph files (from HOMER, for visualization in UCSC)
Supplementary_files_format_and_content: FPKM values of gene expression from RNAseq data in tab-delimited text format


title: Input (DMSO)


title: PolyA+ RNAseq (DMSO)


title: p53 ChIP (Nutlin-3a)

value: p53 (EMD Millipore (DO1))


title: p53 ChIP (DMSO)


title: RNAPII ChIP (DMSO)

value: RNAPII (Abcam (8wG16))


title: RNAPII ChIP (Nutlin-3a)


title: H4K16ac ChIP (Nutlin-3a)

value: H4K16ac (Millipore)


title: H3K27ac ChIP (DMSO)

value: H3K27ac (Active Motif)


title: H4K16ac ChIP (DMSO)


title: 03C7-2 rep2

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Pyricularia oryzae

source_name: Mycelium

growth_protocol: The strains were cultured in liquid CM medium at 25 °C with shaking at 180 rpm for 2 d

extract_protocol:
Total RNA was extracted from ground mycelia in liquid nitrogen with RNeasy Plant mini kit (QIAGEN). Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB)with standard Illumina protocols

treatment_protocol: The mycelia were collected and incubated in H2O at 25 °C for 4 h

tag: strain

value: Mycelia under starvation


title: H3K4me1 ChIP (DMSO)

value: H3K4me1 (Abcam)


title: H3K4me3 ChIP (Nutlin-3a)

value: Nutlin-3a (5uM final, 6hrs)

value: H3K4me3 (Abcam)


title: 01F1-1 rep2


title: C3_NF8_9

value: Neuronal Progeny


title: H3K4me3 ChIP (DMSO)

value: DMSO (6hrs)


title: 01F1-1 rep3


title: H3 ChIP (Nutlin-3a)

value: H3 (Abcam)


title: 03C7-2 rep1


title: 01F1-1 rep1


title: WT rep3

value: wild type


title: H3 ChIP (DMSO)


title: WT rep1


title: WT rep2


title: KO_8-3

city: Logan

first: Ralph

middle: G

last: Meyer

state: UT

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

data_processing:
Basecalls performed with Illumina base calling software [Illumina Real time analysis(RTA) 1.13.48]
Reads were mapped to the mm9 genome using RUM (version 2.0.3) (GR Grant et al.)
Differential expression analysis was performed using DESeq version 1.10.0
Genome_build: mm9
Supplementary_files_format_and_content: Text file containing the number of reads mapped to each transcript.

source_name: Parg(110)-/-_father 8_2-cell embryo

extract_protocol:
RNA from individual embryos was isolated and amplified using the WT-Ovation One-Direct RNA Amplification kit (NuGen Technologies)
RNA-seq libraries were constructed from individual 2-cell embryos using amplified double stranded cDNA as the substrate in the Illumina bar-coded DNA-sequencing library preparation protocol (Illumina, San Diego, CA).

tag: strain background

tag: genotype/variation

tag: father id

value: 2-cell embryo


title: KO_7-2

source_name: Parg(110)-/-_father 7_2-cell embryo


title: KO_8-2


title: KO_8-1


title: KO_6-2

source_name: Parg(110)-/-_father 6_2-cell embryo


title: KO_7-3


title: KO_7-1


title: KO_6-3


title: H3K27ac ChIP (Nutlin-3a)


title: 03C7-2 rep3


title: KO_6-1


title: WT_3-3

source_name: WT_father 3_2-cell embryo

value: WT


title: H3K4me1 ChIP (Nutlin-3a)


title: WT_2-1

source_name: WT_father 2_2-cell embryo


title: WT_2-3


title: WT_2-2


title: WT_1-3

source_name: WT_father 1_2-cell embryo


title: WT_3-1


title: H3K4me1 ChIP-seq

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2.1.0 with default parameters.
Reads of control experiment were normalized using total reads of the experiment (read per million reads per kilobase genome) and those of treated cells were normalized using internal control (5 positions from Rpl13a).
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated using our in-house program and converted to TDF files using IGVTools version 2.2.1.

source_name: 11 dpc embryonic forebrain_H3K4me1 ChIP-seq

extract_protocol:
Lysates were clarified from sonicated nuclei and HISTONE-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB's instructions accompanying the DNA Sample Kit (NEB# E6240L). 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.

tag: age

value: 11 dpc embryo

value: forebrain

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: H3K27me3

status: Public on Nov 11 2014

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: processed data file: primaryTumor_H3K27me3_peaks.bed.gz

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters
Peak calling was done by MACS v1.4 with default parameters, using input samples as control
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing MACS-called peaks

source_name: T cell acute lymphocytic leukemia

growth_protocol: Primary murine T-ALL cells were obtained from mice that received KrasG12D bone marrow transduced with the Notch1 L1601P mutant [PMID: 18677410]; GFP positive CD4+CD8+ T cells were then sorted from spleen.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific 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.

tag: tissue

value: spleen

value: Primary murine T-ALL cells

tag: cell subtype

value: GFP,CD4, CD8  positive cells

value: Millipore


title: WT_1-2


title: H3K4me3

description: processed data file: primaryTumor_H3K4me3_peaks.bed.gz

treatment_protocol: GFP positive CD4+CD8+ T cells were then sorted from spleen.

tag: cell type


title: CSL_2

description: processed data file: primaryTumor_RBPJ_D10A4E12_1_and_2_peaks.bed.gz

value: CSL(RBPSUH)

value: Cell signaling


title: H3K4me1

value: abcam


title: WT_1-1


title: CSL_1


title: Notch1_2

description: processed data file: primaryTumor_Notch1_JA1_and_2_peaks.bed.gz

value: Notch1 (antisera made in lab)


title: Notch1_1


title: input_2


title: Ago1-associated miRNA Seq

city: Shanghai

first: Zhao

last: Jing

address: 1239 Siping Road

institute: Tongji university

description: Protocol: HITS-CLIP

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequence tags from Soxla sequencing will go through the data cleaning analysis to get credible clean tags. We will get rid of some contaminant reads from the fq file and get the final clean reads. The data is processed by the following steps:1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table)2) Getting rid of reads with 5' primer contaminants3) Getting rid of reads without 3' primer4) Getting rid of reads without the insert tag5) Getting rid of reads with poly A6) Getting rid of reads shorter than 18nt7) Summarize the length distribution of the clean reads.
Tags map to genome by SOAP or bowtie to analyze their expression and distribution on the genome.
Then the standard analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and seed edit of potential known miRNA.After getting miRNAresult,target prediction target genes will be analysed. Tags align to miRBase database using blast or bowtie，indentify known miRNA.Known miRNAs also use to subsequent analysis. We developed a prediction software mireap(animal/plant) or mirdeep(animal) to predict novel
Differential expression analysis of miRNA with Known miRNA and Novel miRNA. ExpDiff method is used which compare the known or novel miRNA expression between two samples to find out the differentially expressed miRNA with logR>1 and pvalue <0.05.
The target predition is used RNA hybrid software
Genome_build: ASM15177v1
Supplementary_files_format_and_content: miRNA-Known.fa  The miRNAs whose sequences are similar with miRNAs deposited at miRBase,fasta format. mir-novel.fa The mature novel miRNA data,fasta format. tag_CLIP1_known.txt The Known miRNAs and its predicted targets by our sequence program, txt format.

organism: Schistosoma japonicum

source_name: 28d worm

growth_protocol: In order to collect S.japonicum worms(28d)）,  New Zealand white rabbits were infected percutaneously with cercariae of S. japonicum (400worms/rabbit) which shed from naturally infected snails.

extract_protocol:
We isolated and identified the small RNAs associated with the S. japonicum Argonaute protein, SjAgo1, by HITS-CLIP
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: The worms were collected at desired time point from the mesenteric veins and liver of infected rabbit, respectively.

tag: geographic origin of sample

value: Anhui province of China

tag: host

value: New Zealand white rabbit

tag: gender

value: male and female

value: anti-SjAgo1; non-commercial antibody


title: input_1


title: clasy1 smRNAseq rep1

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

description: smRNAseq

data_processing:
For dsRNAseq, RNAseq, RNAseq-DSN, PolyA+ RNAseq, PolyA- RNAseq, the reads were mapped back twice. Firstly, the nonredundant reads without adapter trimming  were mapped perfectly using BWA without mismatches. Secondly, the unmapped reads  trimmed off adapter were mapped perfectly using BWA without mismatches again. The reads were joined together. For smRNAseq, the reads  trimmed off adapters were mapped perfectly using BWA without mismatches. For the reads that mapped to multiple position, they are counted only at one randomly position.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million). Please note that some wig files contain  both positive and negative values associated with a given chromosome position since the libraries contain strand information, and file s are viewable in popular genome browsers (IGV browser).

source_name: clasy1 smRNAseq

growth_protocol: Plants were grown with 16hr of light

extract_protocol:
The total RNA was extracted with trizol, and treated with Dnase I to clean up the genomic DNA contamination
All the libraries were built using True-seq small RNA preparation kits(Illumina) using different RNA input. dsRNA, the Rnase One(Promega) treated rRNA-depleted RNA. RNAseq and RNAseq-DSN , total rRNA-depleted RNA. RNAseq-DSN,the RNAseq libraries were normalized with DSN kit (Evrogen) before sequencing. PolyA+ RNAseq, polyA+ RNA. PolyA- RNAseq, rRNA-depleted polyA- RNA. smRNA, small RNA of size 15-40nt.

value: unopened flower buds

tag: molecule subtype

value: RNA from 15-40nt


title: WT_3-2

value: WT

value: 2-cell embryo


title: dcl234 nrpd1 smRNAseq rep1

description: smRNAseq

source_name: dcl234 nrpd1 smRNAseq

value: dcl 234 nrpd1


title: dcl234 nrpd1 smRNAseq rep2

description: smRNAseq


title: dcl234 smRNAseq rep2

description: smRNAseq

source_name: dcl234 smRNAseq


title: dcl3 smRNAseq rep1

description: smRNAseq

source_name: dcl3 smRNAseq


title: nrpd1 smRNAseq rep2

description: smRNAseq

source_name: nrpd1 smRNAseq


title: dcl3 smRNAseq rep2

description: smRNAseq


title: rdr2 smRNAseq rep1

description: smRNAseq

source_name: rdr2 smRNAseq


title: dcl234 smRNAseq rep1

description: smRNAseq


title: nrpd1 smRNAseq rep1

description: smRNAseq


title: H3K27ac ChIP-seq

source_name: 11 dpc embryonic forebrain_H3K27ac ChIP-seq

value: 11 dpc embryo

value: forebrain

value: Active Motif


title: WT smRNAseq rep2

description: smRNAseq

source_name: WT smRNAseq


title: dcl 234 nrpd1 PolyA- RNAseq rep2

description: PolyA- RNAseq

source_name: dcl 234 nrpd1 PolyA- RNAseq

value: rRNA-depleted Poly A- RNA


title: dcl 234 nrpd1 PolyA- RNAseq rep1

description: PolyA- RNAseq


title: rdr2 smRNAseq rep2

description: smRNAseq


title: dcl 234 nrpd1 PolyA+ RNAseq rep1

description: PolyA+ RNAseq

source_name: dcl 234 nrpd1 PolyA+ RNAseq

value: Poly A+ RNA


title: dcl234 PolyA- RNAseq rep2

description: PolyA- RNAseq

source_name: dcl234 PolyA- RNAseq


title: dcl234 PolyA+ RNAseq rep2

description: PolyA+ RNAseq

source_name: dcl234 PolyA+ RNAseq


title: dcl234 PolyA+ RNAseq rep1

description: PolyA+ RNAseq


title: dcl 234 nrpd1 PolyA+ RNAseq rep2

description: PolyA+ RNAseq


title: dcl 234 RNAseq-DSN

description:
DSN normalization was applied on the RNAseq libraries
RNAseq-DSN

source_name: dcl 234 RNAseq-DSN

value: dcl 234

value: total rRNA-depleted RNA


title: dcl 234 rdr2 RNAseq-DSN

source_name: dcl 234 rdr2 RNAseq-DSN


title: dcl 234 nrpd1 RNAseq-DSN

source_name: dcl 234 nrpd1 RNAseq-DSN


title: dcl 234 nrpd1 RNAseq rep2

description: RNAseq

source_name: dcl 234 nrpd1 RNAseq


title: dcl 234 nrpd1 RNAseq rep1

description: RNAseq


title: dcl234 RNAseq rep3

description: RNAseq

source_name: dcl234 RNAseq


title: dcl234 RNAseq rep2

description: RNAseq


title: dcl234 RNAseq rep1

description: RNAseq


title: dcl 234 nrpd1 dsRNAseq rep1

description: dsRNAseq

source_name: dcl 234 nrpd1 dsRNAseq

value: double-stranded RNA


title: dcl234 dsRNAseq rep3

description: dsRNAseq

source_name: dcl234 dsRNAseq


title: WT smRNAseq rep1

description: smRNAseq


title: 1 hr FGF Rep3

city: San Francisco

first: Harish

last: Vasudevan

address: 555 Mission Bay Blvd South, Room 452H

department: Radiation Oncology

institute: University of California San Francisco

description: 50 ng/mL FGF1 + 1 μg/mL heparin

data_processing:
Library construction and sequencing were performed at MSSM Genomics Core.  Illumina CASAVA software was used for basecalling.
Sequence reads were trimmed and Tophat was used to align FastQ files to reference genome. The resulting alignments were used to perform abundance estimates and differential exprsesion analysis using CuffDiff
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file including FPKM values for each sample

source_name: E13.5 Palate Cells (MEPM)

growth_protocol: Cells were grown in DMEM  + 10%FBS and serum starved overnight in 0.1% FBS

extract_protocol:
RNA was isolated from cells using the Qiagen RNeasy kit and polyA selected (MSSM Genomics Core)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Palate

value: mouse embryonic palatal mesenchyme cells


title: 1 hr FGF Rep2

description: 50 ng/mL FGF1 + 1 μg/mL heparin


title: 1 hr PDGF Rep4

description: 30 ng/mL PDGFA


title: dcl234 dsRNAseq rep1

description: dsRNAseq


title: dcl234 dsRNAseq rep2

description: dsRNAseq


title: dcl234 PolyA- RNAseq rep1

description: PolyA- RNAseq


title: 1 hr PDGF Rep3

description: 30 ng/mL PDGFA


title: Serum starved Rep4

description: 0.1% FBS O/N


title: dcl 234 nrpd1 RNAseq rep3

description: RNAseq


title: Serum starved Rep3

description: 0.1% FBS O/N


title: Meis1_4OHT_Rep1

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaloesvej 5

department: Finsen Centre

country: Denmark

institute: Rigshospitalet

description: Sample 7

data_processing:
All data was mapped with bowtie v. 0.12.7, using standard parameters
All data was converted into BigWig format and vizualized in the UCSC genome browser
Peaks were called with MACS, v. 1.4 with an IgG mock sample as control and following settings: Band width = 300, model fold = 10,30 p-value cutoff < 10-9.
Genome_build: mm9
Supplementary_files_format_and_content: Raw data files in fastq and processed files as bigwig and txt

source_name: c-kit+ bone marrow cells

growth_protocol: c-kit+ bone marrow cells were transformed using the fusion oncogene MLL-AF9. The MLL-AF9 cells were further transduced with an inducible pMIG-TGIF1-ER construct.

extract_protocol:
Cell lystaes were sonicated to an avarge fragment length of 300bp
Precipitated DNA was mixed with E. Coli DNA up to 2ng and libraries were prepared using the NEB Next ChIP-seq library prep master mix for Illumina according to manufacturer's instructions.

treatment_protocol: For induction of TGIF1-ER, the cells were treated with 4-OHT for 20 hrs

value: MLL-AF9 transformed cells

tag: feature

value: Transduced with pMIG-TGIF1-ER

tag: treatment

value: Meis (Abcam, catalog# ab19867, lot# GR76623-1)


title: Meis1_EtOH_Rep1

description: Sample 5

tag: strain

value: EtOH


title: Meis1_4OHT_Rep2

description: Sample 8


title: Meis1_EtOH_Rep2

description: Sample 6


title: 1 hr PDGF Rep1

description: 30 ng/mL PDGFA


title: dcl 234 nrpd1 dsRNAseq rep3

description: dsRNAseq

tag: genotype/variation

value: unopened flower buds


title: TGIF1_4OHT_Rep1

description: Sample 3

value: TGIF (H-172) (Santa Cruz Biotechnology, catalog# sc-9084, lot# K2608)


title: IgG

description: Sample 9

value: IgG (Sigma, catalog# I8140, lot# 115k7551)


title: TGIF1_4OHT_Rep2

description: Sample 4


title: Serum starved Rep1

description: 0.1% FBS O/N


title: 1 hr FGF Rep1

description: 50 ng/mL FGF1 + 1 μg/mL heparin


title: dcl 234 nrpd1 dsRNAseq rep2

description: dsRNAseq

value: dcl 234 nrpd1


title: 0S

city: Wuhan

first: Jianfang

last: Gui

address: No.7 Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

tag: disease state

value: un-infected


title: 24S

value: 24h post-SVCV infection


title: TGIF1_EtOH_Rep1

description: Sample 1


title: 6S

value: 6h post-SVCV infection


title: 24K

source_name: head kidney

value: head kidney


title: 1 hr PDGF Rep2

description: 30 ng/mL PDGFA

tag: age


title: 0K


title: C. elegans JGG1 nsun-5 mutant

status: Public on Nov 10 2014

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
All reads were sorted by their bar codes and bar codes were subsequently removed (self-made Perl script).
Reads were aligned to the reference sequences using the Needleman-Wunsch algorithm. Before each alignment, the respective longer sequence (either the query- or the reference-sequence) was trimmed. Each sequence position was scored by following parameters: match = 10, cytosine to thymine conversion = 9, mismatch = 4, gap = 3, opening a new gap = 1
Aligned reads were filtered for sequences having less than 15% insertions or 15% deletions, or less than 20% insertions plus deletions. Sequences not fulfilling these requirements were removed (self-made Perl script).
In the remaining sequences the number of individual nucleotides was counted (self-made Perl script).
Genome_build: S. cerevisiae 25S rRNA [J01355.1] and C. elegans 28S rRNA [NR_000055.1]
Supplementary_files_format_and_content: base counts per sequence position as matrix

organism: Caenorhabditis elegans

source_name: whole young adult hermaphrodites

growth_protocol: S. cerevisiae: Wild-type and rcm1 knockout yeast were grown overnight in 3 mL SC medium at 28°C with shaking. On the next day, 100 ml SD were inoculated with the overnight culture to an OD600 of 0.003 and grown at 28°C with shaking until the OD600 reached 0.5 - 0.6. C. elegans: Worms were synchronized by bleaching and cultivated until day 3 of adulthood.

extract_protocol:
RNA isolated from yeast polysome or monosome fractions was purified using Trizol (Life Technologies), DNAse I (Thermo Scientific) digested for 1 h, phenol-chloroform extracted, isopropanol precipitated and dissolved in 20 µl water. For C. elegans ~200 whole young adult hermaphrodites were washed 3x in PBS and lysed directly in Trizol by 30 cycles of sonication (30 s on, 30 s off) in a Bioruptor (Diagenode).
The EZ RNA Methylation Kit (Zymo Research) was used for bisulfite treatment and purification of converted RNA according to the instructions provided by the manufacturer. 400 ng RNA were reverse-transcribed using Super Script III reverse transcriptase (Life Technologies) and gene-specific reverse primers (see below) for 50 min following the manufacturer’s instructions. 5 µl cDNA was subjected to the following touchdown-PCR program in a 25 µl reaction with KAPA2G Robust Polymerase and Buffer A (Kapa Biosystems):  95°C  3 min  95°C  30 s*  55-45°C 30s*  *20 cycles, -0.5°C annealing per cycle   72°C  1 min*  95°C  30 s**  45°C  30 s**  **35 cycles  72°C  1 min**  72°C  5 min  PCR products were gel-purified using PCR- and Gel Extraction Kit (Favorgen) and eluded in 30 µl. 5 µl were subjected to a second round of PCR as above using barcoded primers and only 30 cycles in the second cycling step (**). Up to 24 barcoded samples were pooled to equal molarity and subjected to IonTorrent sequencing using a 314 Torrent Sequencing Chip Kit (Life Technologies).    Primer sequences (without barcode):  SC-25S-rRNA_bisulfite_sense: TGGTTAGAAAGTGATGTT  SC-25S-rRNA_bisulfite_as: TCTCATTAATCCATTCA  CE-28S-rRNA_bisulfite_sense: TGAATGTTAAATTGTAGTAATT  CE-28S-rRNA_bisulfite_as: TCTCGTTAATCCATTCA    For barcode sequences see "barcode" field in the SAMPLES section

treatment_protocol: S. cerevisiae: 0.4 mM H2O2 (only for stress conditions) and after 15 or 75 min, 125 µg/ml cycloheximide (Sigma) were added and the cells were incubated at the same temperature with shaking for further 15 min.

tag: genotype

value: JGG1 (nsun-5 mutant)

tag: h2o2 stress

tag: barcode

value: ACGCTCGACA


title: Serum starved Rep2

description: 0.1% FBS O/N

value: Palate


title: 6K


title: C. elegans N2 wild-type

value: N2 (wild-type)

value: ACGAGTGCGT


title: C_albicans_R2_without_iron

city: Buffalo

last: Buck

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

description: Candida albicans no iron Replicate 2

data_processing:
Sequencing reads were aligned to the most recent genome build for (C_albicans_SC5314_version_A21-s02-m01-r25) using the Bowtie algorithm and allowing up to 1 mismatch
Data processing is limited to alignments to reference genomes because downstream data processing for MNase-seq experiments is still in its infancy.  For this publication all analysis was performed directly on the BAM files using ArchTEx (http://sourceforge.net/projects/archtex/). Chromatin data was visualized and extracted from aligned BAM files with the ArchTEx NGS data analysis platform with a 120 bp tag extension at 10 bp resolution (Lai et al., 2012). Data were either converted into normalized log2 space or standardized tag count space (standardized to 10 million sequenced tags).
Genome_build: ASM18296v1

organism: Candida albicans

source_name: Log phase culture without iron

growth_protocol: C. albicans cultures were grown in 1.7g/l YNB media without iron (4027-112; MP Biomedicals), 5g/l NH4SO4, 2% glucose, 0.79g/l amino acid supplement (Complete Supplement Mix: 4500-012, MP Biomedicals), with 2.5 µm CuSO4.

extract_protocol:
Briefly, in vivo chromatin structure was fixed through treatment with formaldehyde, isolated using mechanical digestion via bead-beating, and mono-nucleosomal DNA was isolated for sequencing using a combination of MNase digestion followed by phenol:chloroform-based DNA precipitation. MNase digestions were closely matched to enrich for a near 100% mono-nucleosomal DNA population to limit the influence that DNA fragment size-selection has on downstream signal comparisons between distinct MNase-seq datasets
MNase-seq libraries were generated using standard Illumina ChIP-seq procedures

treatment_protocol: Samples were crosslinked with 1% formaldehyde (final volume) for 30 min followed by a 5 minute 125mM glycine quenching reaction.


title: C_albicans_R2_with_iron

description: Candida albicans with iron Replicate 2

source_name: Log phase culture with iron

growth_protocol: C. albicans cultures were grown in 1.7g/l YNB media without iron (4027-112; MP Biomedicals), 5g/l NH4SO4, 2% glucose, 0.79g/l amino acid supplement (Complete Supplement Mix: 4500-012, MP Biomedicals), with 2.5 µm CuSO4 and 100 µm FeCl3*6H2O


title: C_albicans_R1_with_iron

description: Candida albicans with iron Replicate 2


title: 96P

city: Wenatchee

first: Yanmin

last: Zhu

state: WA

address: 1104 N. Western Ave

institute: USDA-ARS

description: total RNA by CTAB method

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Malus domestica v1.0 using using CLC Genomics Workbench (CLC GW) v5.5.1 (CLCBio, Cambridge, Massachusetts)
Genome_build: Malus domestica v1.0
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample

organism: Malus domestica

source_name: Root tissues

growth_protocol: Seedlings were grown at 23ºC, 95% humidity, under 12/12 hours light/dark conditions for 3 week

extract_protocol:
Total RNA was isolated following the modified method as described by Gasic et al.,2004.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Pathogen inoculation is done by dipping one quarter to one third of the root system into the inoculum for 5 seconds and then planting treated seedlings

value: root

tag: time (hpi)

value: Infected by P. ultimum

value: 6-week old seedlings

tag: sample size

value: pooled root tissues of 20 plant


title: C_albicans_R1_without_iron

description: Candida albicans no iron Replicate 1


title: TGIF1_EtOH_Rep2

description: Sample 2

value: MLL-AF9 transformed cells

value: Transduced with pMIG-TGIF1-ER

value: EtOH

tag: chip antibody

value: TGIF (H-172) (Santa Cruz Biotechnology, catalog# sc-9084, lot# K2608)


title: 72P

description: total RNA by CTAB method

tag: tissue


title: 24P

description: total RNA by CTAB method


title: 48P

description: total RNA by CTAB method


title: 4P

description: total RNA by CTAB method


title: 8P

description: total RNA by CTAB method


title: 96M

description: total RNA by CTAB method

value: Mock-inoculation


title: 48M

description: total RNA by CTAB method


title: 24M

description: total RNA by CTAB method


title: 72M

description: total RNA by CTAB method


title: 8M

description: total RNA by CTAB method


title: 1M

description: total RNA by CTAB method


title: 4M

description: total RNA by CTAB method


title: 0T

description: total RNA by CTAB method

value: non-treatment or non-inoculation


title: clr4Δ replicate 1

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

description: paired with WT replicates 3 and 4

data_processing:
ChIP-seq data were aligned using Bowtie1, allowing up to two mismatches within the seed sequence and, if a read could align equally well to multiple loci, a locus was chosen at random
Indexed, sorted bam files were created for each dataset using SAMtools and bedgraph files were created using BEDtools
A sliding window of 1000-bp size was used to smooth the bedgraphs for each ChIP-Seq dataset and then subtelomere regions were called using those smoothed bedgraphs.
RNA-seq data were aligned using Tophat, allowing reads to align to up to 50 loci in the genome. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wildtype samples and knockout mutant samples.
Genome_build: Sequence and feature files for C. neoformans var. grubii H99 were obtained from the Broad Institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Bedgraph files with 1000-bp sliding window called on them for ChIP-Seq samples and RPKM tables for RNA-seq table.

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: 100ml cultures of cells in YPAD were grown at 30˚C to an OD600 of 1.0

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

value: clr4 knockout

tag: media

value: YPAD media

tag: cell density


title: WT replicate 4

value: CM18 (wild-type)


title: WT replicate 3


title: clr4Δ replicate 2

description: paired with WT replicates 3 and 4


title: ccc1-w52a replicate 2

description: paired with WT replicates 1 and 2

value: ccc1-w52a mutant


title: msl1Δ replicate 1

description: paired with WT replicates 1 and 2

value: msl1 knockout


title: msl1Δ replicate 2

description: paired with WT replicates 1 and 2


title: ccc1-w52a replicate 1

description: paired with WT replicates 1 and 2


title: ccc1Δ replicate 1

description: paired with WT replicates 1 and 2

value: ccc1 knockout


title: ezh2Δ replicate 2

description: paired with WT replicates 1 and 2

value: ezh2 knockout


title: ezh2Δ replicate 1

description: paired with WT replicates 1 and 2


title: ccc1Δ replicate 2

description: paired with WT replicates 1 and 2


title: WT replicate 2


title: WT replicate 1


title: 1P

description: total RNA by CTAB method

value: root


title: WCE replicate 1


title: H3K9me2 ccc1-w52a replicate 1


title: H3K9me2 clr4Δ replicate 1


title: H3K27me3 ccc1-w52a clr4Δ replicate 1

value: clr4 knockout, ccc1-w52a mutant


title: H3K27me3 clr4Δ replicate 1


title: H3K27me3 ccc1-w52a replicate 3


title: H3K9me2 ezh2Δ replicate 1


title: H3K27me3 ccc1Δ replicate 2


title: H3K27me3 ccc1-w52a replicate 1


title: H3K27me3 ccc1Δ replicate 1


title: H3K27me3 msl1Δ replicate 2


title: H3K27me3 msl1Δ replicate 1


title: H3K27me3 WT replicate 2


title: H3K27me3 WT replicate 3


title: TT-Ago2_Untagged_ES_iCLIP

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

description: iCLIP

data_processing:
Sequenced reads were trimmed for adapter sequence and mapped to the UCSC mouse genome build mm9 using Bowtie1. Reads mapping to >1 location or with >2 mismatches were discarded.  Reads were collapsed  based on identical 5’ and 3’ end mapped coordinates. To include reads mapping across exon-exon junctions, we extracted splice junction coordinates from the isoforms produced by Tophat from RNA-seq data and used custom python scripts to generate a fasta file of the sequences +/- 45 nt of these splice junctions. We then mapped any previously unmapped iCLIP reads to these exon-exon junction sequences and added any splice junction mapping reads to the total mapped dataset. After initially calling putative Ago2 bound regions by identifying clusters of more overlapping reads than a null poisson distribution model with cut-off p value < 0.001, we filtered out any clusters that had the same mismatched nucleotide in >70% of its reads.  Finally, the remaining clusters were required to have significantly more tagged reads than untagged reads (binomial, p<0.05) after median-based normalization of the read counts in both libraries, using background regions found in both tagged and untagged datasets.  Annotation of genomic regions was taken from Ensembl NCBIM37 build annotation. Single nucleotide 5P end files that largely reflect crosslink sites are included as BigWig files for visualization.
Genome_build: mm9

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential  Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo  Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential  amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-  mercaptoethanol

extract_protocol:
Crosslinked cell pellets were resuspended in lysis buffer, partially digested with RNase I, and serially immunoprecipitated with FLAG and HA antibodies. Protein-RNA complexes were resolved on SDS-PAGE gels and transferred to nitrocellulose. Regions corresponding to crosslinked Ago2 complexes were extracted from nitrocellulose with proteinase K digestion and RNA isolated by phenol extraction.
Dephosphorylated RNA was ligated to a 3’ linker and reverse transcribed. The resulting cDNA was purified on a denaturing polyacrylamide gel, circularized, and PCR amplified using Illumina-compatible barcoded primers. PCR product was gel purified on a denaturing polyacrylamide gel. Samples were pooled and sequenced on the Illumina HiSeq platform.

treatment_protocol: TT-FHAgo2 and TT-Ago2 clonal cell lines were propagated in 0.1  μg/mL doxycycline (Sigma). Cell lines were induced to 2.5 μg/mL for 24 hours for wildtype Ago2 levels.

tag: cell type

value: mouse embryonic stem cells

tag: cell line

value: 2.5 μg/mL  Dox


title: H3K27me3 WT replicate 1


title: TT-FHAgo2_nodox96h_rep2

description: UTP prepared RNAseq library

data_processing:
Reads were mapped to the Ensembl NCBIM37 build with Tophat v2.0.9. Isoform estimates were generated with Cufflinks v2.1.1. For spike-in experiments, reads were trimmed to 40nt length before mapping.
Supplementary_files_format_and_content: NCBIM37

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β- mercaptoethanol. MSCs were cultured in α-MEM supplemented with 10% FBS, 100 Units Penicillin, and 100 ug Streptomycin.

extract_protocol:
For ESC, strand-specific mRNA sequencing libraries were prepared using either the UTP method or Truseq sample preparation kit from Illumina. Muliplexing barcode sequences were incorporated during the PCR amplification. For MSC, libraries from polyA RNA were generated with the Illumina TruSeq kit. To estimate copies per cells, a separate RNA-seq biological replicate was performed for ES and MSCs with spike-in standard RNAs. Cells were counted before extracting total RNA.
1.5ng External RNA Controls Consortium ERCC (Life Technologies) mix 1 RNA spike-ins of known concentrations were added to the cellular RNA post oligo dT purification step, corresponding to ~1-5% of total poly A RNA input into Illumina sequencing prep. FPKM expression values were converted based on regression fit for the known concentration of standards, and this was related to cell counts by total RNA input into prep.

treatment_protocol: TT-FHAgo2 clonal cell lines were propagated in 0.1μg/mL doxycycline (Sigma)  and induced to 2.5 μg/mL for wildtype Ago2 levels or removed from doxycycline for 96h.

tag: cell line name

value: No Dox


title: MSC_spikeIn

description: TruSeq prepared RNAseq library

data_processing:
Reads were mapped to the Ensembl NCBIM37 build with Tophat v2.0.9. Isoform estimates were generated with Cufflinks v2.1.1. For spike-in experiments, reads were trimmed to 40nt length before mapping.
Genome_build: NCBIM37

source_name: Mesenchymal stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential  Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo  Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential  amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β-  mercaptoethanol. MSCs were cultured in α-MEM supplemented with 10% FBS, 100 Units Penicillin, and 100 ug Streptomycin.

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies)
For ESC, strand-specific mRNA sequencing libraries were prepared using either the UTP method or Truseq sample preparation kit from Illumina.  Muliplexing barcode sequences were incorporated during the PCR amplification. For MSC, libraries from polyA RNA were generated with the Illumina TruSeq kit. To estimate copies per cells, a separate RNA-seq biological replicate was performed for ES and MSCs with spike-in standard RNAs. Cells were counted before extracting total RNA.  1.5ng External RNA Controls Consortium ERCC (Life Technologies) mix 1 RNA spike-ins of known concentrations were added to the cellular RNA post oligo dT purification step, corresponding to ~1-5% of total poly A RNA input into Illumina sequencing prep. FPKM expression values were converted based on regression fit for the known concentration of standards, and this was related to cell counts by total RNA input into prep.

treatment_protocol: TT-FHAgo2 clonal cell lines were propagated in 0.1μg/mL doxycycline (Sigma) and induced to 2.5 μg/mL for wildtype Ago2 levels or removed from doxycycline for 96h.

value: Mesenchymal stem cells


title: TT-FHAgo2_Tagged_ES_iCLIP

description: iCLIP

tag: treatment


title: TT-FHAgo2_nodox96h_rep1

description: UTP prepared RNAseq library


title: TT-FHAgo2_+dox48h_spikeIn

description: TruSeq prepared RNAseq library


title: RIP_shBRD4_YFP-BRD4short 2

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

data_processing:
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 and the 5’ 29 bases were identified as giving the maximum number of genomic matches. The 29 base reads were thus used throughout this study. Reads aligned to ribosomal DNA were first removed. The ribo-free reads were then mapped to the mouse genome mm9 with bowtie 0.12.8 (uniquely mapped only, allowing 2 mismatches).
peaks, RNA-seq: Strand specific bed files and bigWig files were made with BEDtools, the UCSC genome browser tool bedGraphToBigWig, and in house developed python scripts. Partek Genomic Suite 6.6 was used to calculate exon-mapped-reads-only RPKMs and all-reads (intron-mapped reads also included) RPKMs.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph for peak files, bigWig for viewing strand specific  nuclear RNA data with the UCSC genome browser

molecule: nuclear RNA

source_name: NIH3T3 fibroblasts

growth_protocol: NIH3T3 cells were serum-starved in the presence of 0.5% serum for 48 hr, preincubated with JQ1 (500 nM) or vehicle (DMSO) for 30 min; and stimulated with 15% serum for 30 min or left unstimulated in the continued presence of JQ1 or vehicle. Control cells and cells expressing YFP-tagged constructs were cultured in the continuous presence of 10% serum.

extract_protocol:
RIP-seq: Nuclei were isolated, and incubated at 30°C for 5 min in Nuclear Run-On Master Mix without Sarkosyl (5 mM TrisHCl pH8.0, 150 mM KCl, 2.5 mM MgCl2, 0.5 mM DTT, 0.25 mM ATP, 0.25 mM GTP, 0.0012 mM CTP, 0.25 mM Br-UTP). The run-on nuclei were digested with DNase I. Insoluble materials were removed by centrifugation, and the supernatant was pre-cleared with Dynabeads Protein A, and then  incubated with the Dynabeads Protein A coupled with anti-YFP antibody. The beads were washed five times with RIP Wash Buffer, and RNA was extracted with Trizol.
RIP-seq: The precipitated RNA was ligated with a pre-adenylated RNA 3’ adapter (TruSeq Small RNA Sample Preparation kit, Illumina), using T4 RNA ligase 2. The RNA was fragmented by base hydrolysis in 0.2 M NaOH, neutralized and immunoprecipitated with anti-BrdU agarose beads. The 5’ cap structure was removed with Tobacco Acid Pyrophosphatase. The 5'-ends of the hydrolyzed RNA fragments were phosphorylated with T4 Polynucleotide Kinase. Ligation of RNA 5'-adapter (Illumina), reverse transcription and PCR with multi-index primers were performed according to the Illumina protocol.

treatment_protocol:
1. NIH3T3 cells were serum-starved in the presence of 0.5% serum for 48 hr, preincubated with JQ1 (500 nM) or vehicle (DMSO) for 30 min; and stimulated with 15% serum for 30 min or left unstimulated in the continued presence of JQ1 or vehicle. Control cells were cultured in the continuous presence of 10% serum.
2. NIH3T3 cells were sequentially infected with shRNA retrovirus (pSRneo-shBRD4) and YFP or YFP-BRD4 expressing retrovirus (pMSCVpuro-YFP, pMSCVpuro-YFP-BRD4, pMSCVpuro-YFP-BRD4short or pMSCVpuro-YFP-BRD4short-mBD) in the presence of polybrene. The transduced cells were selected with G418 and puromycin.

tag: culture condition

value: continuous culture

tag: transfection

value: shBRD4 and YFP-BRD4short


title: CD103+ DC2 rep 3

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

description: Rare dendritic cell population with robust T cell stimulatory capacity

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed of the first 11 bp for quality reasons, then mapped to mm10 whole genome using tophat v2.0.11 with parameters -q -p 10 --no-coverage-search --segment-length 20
Raw reads were aggregated across all isoforms on a per-gene basis, using only reads mapping to exons, using htseq-count. S Anders, T P Pyl, W Huber: HTSeq — A Python framework to work with high-throughput sequencing data. bioRxiv 2014. doi: 10.1101/002824.
Raw reads were normalized using DESeq: Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw per-gene values for each sample

source_name: B78chOVA tumor infiltrating dendritic cells (CD103+)

growth_protocol: B78chOVA tumor cells are injected subcutaneously in the flank of male C57BL/6 mice and allowed to develop for 14 days. Tumors are then harvested and digested and cell populations are sorted for RNA.

extract_protocol:
Cells were sorted directly into trizol. RNA was then extracted using the Arcturus Picopure RNA isolation kit, followed by bioanalyzation.
RNA libraries were prepared for sequencing using standard protocols with the Nugen Ovation library kit

tag: stain

value: ectopic melanoma tumor

tag: surface makers


title: H3K9me2 WT replicate 1

tag: strain


title: H3K27me3 ccc1-w52a replicate 2


title: CD103+ DC2 rep 2


title: CD103+ DC2 rep 1


title: RIP_shBRD4_YFP-BRD4short 1


title: CD11b+ DC1 rep 2

description: Rare dendritic cell population with limited T cell stimulatory capacity

source_name: B78chOVA tumor infiltrating dendritic cells (CD11b+)


title: Dox2.5_2_130611

description: 5'-phosphate dependent cloning

data_processing:
Custom software was used to process raw reads and are summarized by sequence identity (observations). Details of processing are described in the manuscript.
Genome_build: mm9
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was extracted with Trizol (Life Technologies). RNA between 18-75 nt was size selected via 15% denaturing polyacrylamide gels.
5’-phosphate dependent cloning was performed using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs). (3' adapter sequence: AGATCGGAAGAGCGGTTCAGCAGGAATGCCGA)

treatment_protocol: TT-FHAgo2 clonal cell lines were propagated in 0.1  μg/mL doxycycline (Sigma). Induced to 2.5 μg/mL for wildtype Ago2 levels.


title: TT-FHAgo2_+dox48h_rep2

description: UTP prepared RNAseq library


title: H3K27me3 ezh2Δ replicate 1


title: RIP_shBRD4_YFP-BRD4

value: shBRD4 and YFP-BRD4


title: TT-FHAgo2_+dox48h_rep1

description: UTP prepared RNAseq library


title: CD11b+ DC1 rep 1


title: RNA_starved_JQ1 2

extract_protocol:
RNA-seq: Cells were scraped in Swelling Buffer (10 mM TrisHCl, pH 7.5; 2 mM MgCl2; 3 mM CaCl2), and  lysed in Sucrose Lysis Buffer (5 mM TrisHCl, pH 7.5; 1 mM MgCl2; 3 mM CaCl2; 0.5% NP-40, 0.25 M sucrose). The nuclear pellet was resuspended in Chromatin Wash Buffer (10 mM TrisHCl, pH 7.5; 150 mM NaCl; 7.5 mM MgCl2; 0.1 mM EDTA; 0.5 M urea; 0.5% NP-40; 0.5 mM DTT). The nucleoplasmic supernatant was removed and the chromatin pellet was lysed with Trizol. Chromatin-associated RNA was extracted according to the Trizol protocol, treated with DNase I, and re-extracted with acid phenol chloroform and chloroform/isoamyl alcohol.
RNA-seq: The chromatin-associated RNA was depleted of rRNA, and treated with RNA 5' Polyphosphatase and Terminator 5'-phosphate-dependent exonuclease. The 3' hydroxyl group of the nascent RNA was ligated with a pre-adenylated RNA 3' Adapter (TruSeq Small RNA Sample Preparation kit, Illumina) using T4 RNA ligase 2. The RNA was fragmented in 200 mM NaOH (most fragments <200 nt). The cap structure was removed with Tobacco Acid Pyrophosphatase. The 5'-ends of the hydrolyzed RNA fragments were phosphorylated with T4 Polynucleotide Kinase, 3' Phosphatase Minus, in the presence of ATP. Ligation of RNA 5'-adapter (TruSeq Small RNA Sample Preparation kit, Illumina), reverse transcription and PCR with multi-index primers were performed according to the Illumina protocol. Library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq 2000 following the manufacturer's protocols.

value: serum starved

tag: chemicals


title: RNA_serum_DMSO 2

value: serum starved and re-fed

value: DMSO


title: H3K27me3 ezh2Δ replicate 2

value: YPAD media


title: TAM2 rep 3

description: Phagocytic macriphage population with no T cell stimulaotry capacity

source_name: B78chOVA tumor infiltrating macrophage (CD11c+)

value: CD45+, Ly6C-, MHCII+, F480+ CD11blo CD11c+


title: TAM2 rep 2


title: TAM2 rep 1


title: CD11b+ DC1 rep 3


title: TAM1 rep 2

source_name: B78chOVA tumor infiltrating macrophage (CD11b+)


title: sec63mVenusBirA_sec65-1_30min37C_+CHX_2minBiotin_input

first: Jonathan

last: Weissman

address: 1700 4th Street

institute: UCSF

description: ribosome protected mRNA fragment

data_processing:
Library strategy: ribosome profiling
base calls were called with Illumina CASAVA software (1.6-1.8)
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3 for yeast) or to UCSC known gene cDNA sequences (hg19)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3 and hg19
Supplementary_files_format_and_content: tab delimited file containing gene annotations, count and rpkm data

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.  Mammalian cells were grown in DMEM + 10% charcoal/dextran filtered FBS biotin depleted with streptactin sepharose.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.  Mammalian cells were lysed directly in plates with scraping.
Footprinting was performed with RNase I (yeast) or MNase (293 cells), monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads.  RNA was extracted with trizol and protected fragments gel purified.  Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Where indicated, cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction for the times shown.  Yeast cells were induced with 10 nM biotin.  Mammalian cells were treated with 50 µM biotin

tag: genotype

value: sec65::sec65-1::KAN sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1

tag: lentivirally transduced transgenes


title: sec63mVenusBirA_sec65-1_30min37C_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment


title: RNA_serum_JQ1 2


title: RNA_starved_DMSO 1


title: RNA_starved_JQ1 1


title: RNA_serum_JQ1 1


title: RNA_starved_DMSO 2


title: TAM1 rep 1

tag: gender

value: male


title: RNA_serum_DMSO 1


title: RNA_shBRD4_YFP-BRD4short 2


title: sec63mVenusBirA_sec65-1_25C_+CHX_2minBiotin_input

description: ribosome protected mRNA fragment


title: suv420H1/suv420H2 double heterozygote

first: Stavros

last: Lomvardas

institute: Univ of California - SF

description:
rna-seq data
suv420_gene_exp.xlsx

data_processing:
map fastq with tophat to generate .bam
Quantify expression with cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff – rpkm values per genotype

source_name: olfactory epithelium from PND21 mouse

growth_protocol: mice with mixed genetic background

extract_protocol:
trizol followed by polyA purification with polydT magnetic beads
scriptseq V2 (illumina/epicentre)

value: mixed background originating chiefly from C57/B6

value: suv420H1/suv420H2 double heterozygote

value: olfactory epithelium from PND21 mouse


title: sec63mVenusBirA_+CHX_7minBiotin_replicate_pulldown

description: ribosome protected mRNA fragment

value: sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3delta0 met15delta0 his3delta1


title: sec63mVenusBirA_+CHX_7minBiotin_replicate_input

description: ribosome protected mRNA fragment


title: TAM1 rep 3


title: sec63mVenusBirA_+CHX_7minBiotin_pulldown

description: ribosome protected mRNA fragment


title: suv420H1/suv420H2 double knockout

description:
rna-seq data
suv420_gene_exp.xlsx

value: suv420H1/suv420H2 double knockout


title: RNA -shBRD4_YFP-BRD4short-mBD 2

value: shBRD4 and YFP-BRD4short-mBD


title: sec63mVenusBirA_-CHX_7minBiotin_pulldown

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_sec65-1_25C_+CHX_2minBiotin_pulldown

description: ribosome protected mRNA fragment


title: WCE_serum_JQ1

data_processing:
alignment, ChIP-seq: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp (SICER).
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph for peak files, bigWig for viewing strand specific  nuclear RNA data with the UCSC genome browser

extract_protocol:
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase 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 HiSeq 2000 or 2500 following the manufacturer's protocols.


title: WCE_noStarv

value: continuous culture


title: RNA_shBRD4_YFP 2

value: shBRD4 and YFP


title: RNA_shBRD4_YFP 1


title: RNA -shBRD4_YFP-BRD4short-mBD 1


title: RNA_shBRD4_YFP-BRD4short 1

value: shBRD4 and YFP-BRD4short


title: sec63mVenusBirA_+CHX_7minBiotin_input

description: ribosome protected mRNA fragment


title: WCE_serum_DMSO


title: sec63mVenusBirA_-CHX_7minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_-CHX_5minBiotin_pulldown

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_-CHX_3minBiotin_pulldown

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_-CHX_3minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_-CHX_5minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_-CHX_1minBiotin_pulldown

description: ribosome protected mRNA fragment


title: H4-Ac_serum_JQ1

tag: chip antibody

value: H4 Ac (Millipore, 06-866 )


title: sec63mVenusBirA_-CHX_1minBiotin_input

description: ribosome protected mRNA fragment


title: H4-Ac_serum_DMSO


title: H4-Ac_starved_DMSO

value: serum starved


title: yeast rcm1 knockout, 90 min H2O2, monosomes

description: RNA monosome fraction

source_name: whole exponentially growing cells

tag: h2o2 stress

value: 90 min 0.4 mM

tag: barcode

value: CGAGAGATA