title: marco morphant_infected (rep4)

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

data_processing:
Image analysis and base calling was done by the Illumina HCS version 1.15.1; One sequencing run for sample 1 was performed while the raw data from 3 sequencing runs (samples 2, 9 and 10) were combined to generate one fastq file and one tsv file each. The generated fastq files were used to calculate average insert sizes and standard deviations for paired end experiments.
Sequence reads were quality trimmed using the quality_trim module in the CLCbio Assembly Cell v4.0.6. Filtered reads were mapped to Ensembl transcripts (Danio_rerio.Zv9.67.dna.toplevel / Danio_rerio.Zv9.67.cdna.all.fa (http://www.ensembl.org/info/data/ftp/index.html)) using the ref_assemle_short module in the CLCbio Assembly Cell v4.0.6.
Accumulation of transcripts to Ensembl genes was done by first converting the mapping files to a table with the assembly_table module in the CLCbio Assembly Cell v4.0.6. Secondly, a custom script was used that sums all reads belonging to the same gene. Non-uniquely mapped reads were divided between genes according to their ratio of uniquely mapped reads. Finally, read counts of transcripts belonging to the same gene were summed to obtain count data at Ensembl gene level.
Fold-change and differential expression significance values were calculated from gene level read counts using the DESeq package (version 1.8.3) available in Bioconductor (version 2.10).
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Danio rerio

source_name: zebrafish embryo injected with marco morpholino, M. marinum infected, 4 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts) containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich)

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA-Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 2 x 50 nucleotides.

treatment_protocol: Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro-injected into the caudal vein with 200 CFU of M. marinum Mma20 bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. At 5 days post fertilization (4 days post infection) pools of 30 embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using QIAZOL reagent.

tag: morpholino injection at 1-cell stage

value: marco morpholino 0.02 mM

tag: blood island injection at 28 hpf

value: M. marinum, Mma20 strain 200 cfu

tag: developmental stage (rna isolation)

value: 4 dpi


title: SDY4_sim_MP2

status: Public on Aug 06 2014

type: SRA

city: Irvine

first: Shu-Dan

last: Yeh

state: CA

address: 321 Steinhaus Hall

department: Ecology and Evolutionary Biology

country: USA

institute: University of California, Irvine

description:
SDY3_sim_MP1 and SDY4_sim_MP2 are from the same total RNA sample but different library preparations
processed data file: Reads_summary.xls, alignments_Dme_mirBase.txt, alignments_Dsi_mirBase.txt, alignments_Dya_mirBase.txt

library_source: transcriptomic

data_processing:
Sequenced reads were sorted by index sequences, trimmed for adaptor and index sequences, masked for low-quality sequence, then mapped to known Dme, Dsi, and Dya miRNA hairpin sequences (miRBase release15)  using bowtie-0.12.5 with parameters -faS -n 0 -l 99
Read number of 5' and 3' of miRNA hairpin sequene were counted separately
Genome_build: The known miRNA miRNA hairpin sequence of D. melanogaster, D. simulans, and D. yakuba in miRBase release15
Supplementary_files_format_and_content: The read number of 5' and 3' of miRNA for each sample is listed in Reads_summary.xls (i.e. read counts of different miRNAs in small RNA libraries from larva and pupa specimens). The alignments of reads from all libraries to the known miRNA hairpin sequences from miRBase release15 are provided in alignments_Dme_mirBase.txt (aligned to D. melanogaster known miRNAs), alignments_Dsi_mirBase.txt (aligned to D. simulans known miRNAs), and alignments_Dya_mirBase.txt (aligned to D. yakuba known miRNAs).

molecule: total RNA

organism: Drosophila simulans

source_name: Whole body

growth_protocol: Flies were grown in standard corn meal medium, constant lighting conditions, and at 25⁰C. Larvae were raised under non-crowded conditions in medium with 0.05% bromophenol blue.  Wandering larvae exhibiting dark blue gut, which corresponds to 18 hours before puparium formation, were collected, rinsed with water, and separated by sex.  For the 0-1 hr white prepuparia, wandering larvae with light blue to white gut were separated by sex, placed in a Petri dish on damped light-wipe tissue until appropriate moment for collection. Samples were snap frozen in liquid nitrogen and stored at -80C until RNA isolation.

extract_protocol:
The total RNAs were extracted and the enriched small RNAs were purified by miRVana miRNA isolation kit (Ambion Inc.)
The four nucleotide indexes: SDY_mel_ML1, ACTG; SDY1_mel_FL1, CTGA; SDY1_mel_MP1, TGAC; SDY1_mel_FP1, GACT; SDY3_mel_ML2, ACTG; SDY3_mel_MP2, TGAC; SDY3_sim_MP1, GACT; SDY3_yak_MP1, CGAT; SDY4_sim_MP2, ACTG; SDY4_yak_MP2, TGAC; SDY4_sim_ML1, GACT; SDY4_yak_ML1, CGAT.  Adaptor-ligated cDNAs were prepared according to Illumina small RNA preparation protocol (Preparing Samples for Analysis of Small RNA Using the Oligo Only Kit, http://www.illumina.com).  Briefly, 16-28nt small RNAs were size selected from a denaturing polyacrylamide gels, 5’ adaptors with four nucleotide indexes at the 3' end and 3’ adaptors were ligated using T4 RNA ligase (Ambion 2140) and the resulting molecules were purified by size selection from denaturing polyacrylamide gels after each ligation reaction.  Four samples with different indexes were pooled for 3’ adaptor ligation and further preparation steps.  The ligated small RNAs were reversed transcribed using Superscript II reverse transcriptase (Invitrogen 18064), subsequently PCR amplified with a Phusion high fidelity PCR DNA polymerase (Finnzymes F-506) through 10 cycles, and purified from denaturing polyacrylamide gels. The 5' adaptor sequence is 5'-GUUCAGAGUUCUACAGUCCGACGAUC-4nt RNA index-3'.  The 3' adaptor sequence is 5'-P-UCGUAUGCCGUCUUCUGCUUGUidT-3'

tag: strain

tag: developmental stage

value: white prepupae

tag: Sex

value: male

tag: tissue

value: Whole body


title: marco morphant_uninfected (rep4)

source_name: zebrafish embryo injected with marco morpholino, not-infected


title: standard control_infected (rep1)

source_name: zebrafish embryo injected with control morpholino, M. marinum infected, 4 dpi

value: control morpholino 0.2 mM


title: standard control_uninfected (rep1)

source_name: zebrafish embryo injected with control morpholino, not-infected


title: SDY3_sim_MP1


title: input DNA

city: Bronx

first: Shira

last: Rockowitz

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

library_source: genomic

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome (hg19/GRCh37) using the Bowtie program. Unique reads mapped to a single genomic location (allowing three mismatches) were kept for peak identification using the spp algorithm.
Peak detection was performed with the spp algorithm. More details as described in Rockowitz et al., 2013
Genome_build: hg19
Supplementary_files_format_and_content: [narrowPeak file] includes spp-called peaks for the sample
Supplementary_files_format_and_content: [wig files] bam files were processed to wig using the 'count' function in igvtools. Reads were extended 200 bp using the -e option otherwise defaults were used.

molecule: genomic DNA

organism: Homo sapiens

source_name: CD4+ T cell

growth_protocol: CD4+ T cells were purified from human blood using human CD4+ T cell isolation kit II kits (Miltenyi).

extract_protocol:
20 million CD4+ T cells were used in total for the ChIP-seq experiments. Cells were cross-linked by the addition of 1% of formaldehyde for 10 minutes at room temperature.  Before ChIP, cells were lysed and sonicated. For sonication, lysates were treated with Triton X-100 to 1% and then subjected to 20 cycles of 20 seconds sonication followed by 60 second rest in a Bioruptor UCD-200 (Diagenode). The supernatant was incubated for 24 hrs at 4°C with 20 μl of Dynabead Protein G beads (Invitrogen) which had been conjugated with 10 μg of the REST antibody (Millipore 07-579). After ChIP, samples were washed with low salt, high salt, LiCl and Tris-EDTA buffer for 5 min. Bound complexes were eluted and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract DNA was also treated for crosslink reversal.
Purified immunoprecipitated DNA was prepared for sequencing following the guidelines of Illumina library preparation kit. In short, DNA was end-repaired using a (End-It DNA Repair Kit, Epicentre). A-tails were added to the blunt ends and Adaptor Oligo Mix (Illumina) was used in the ligation step using LigaFast Kit (Promega). Following adapter ligation, DNA was PCR amplified for 25 cycles and agarose gel extraction was used to isolate library fragments of 150-300 bp. The purified DNA was captured on an Illumina flow cell. Libraries were sequenced on an Illumina HiSeq 2000 following the manufacturer's protocols.

tag: cell type

value: CD4+ T cell

tag: chip antibody


title: REST_ChIPSeq

value: anti-REST Ab (Millipore 07-579)


title: SDY4_sim_ML1

description: processed data file: Reads_summary.xls, alignments_Dme_mirBase.txt, alignments_Dsi_mirBase.txt, alignments_Dya_mirBase.txt

value: late third instar larvae (≥18BPF)


title: JEKO-1

status: Public on Aug 07 2014

city: New York

first: Samir

last: Parekh

address: 1470 Madison Ave, 5th FL, Room 114

department: Hematology and Medical Oncology

institute: Icahn School of Medicine at Mount Sinai

description: parental cell

data_processing:
Sequence data generated from the sequencer were run through in house pipeline WASP - 3.0.60. FASTQ files are  generated from Illumina QSEQ files, include Sanger (Phred+33) encoded quality scores
Raw FASTQ files were trimmed for adapter sequences using quart.
Alignment to the reference genome was performed using gsnap.
htseq - v0.5.3p3  was used for read quantitation
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: Hg19
Supplementary_files_format_and_content: Excel file containing RPKM values and Gene symbols for each Sample.

source_name: MCL cell line

growth_protocol: The MCL cell lines Granta-519, JEKO-1 and Z138 were grown in a humidified incubator at 37°C and 5% CO2 with RPMI 1640 medium (Cellgro, Herndon, VA) supplemented with 10% fetal bovine serum (FBS; Gemini Bio-Products, Woodland, CA), 2 mM L-glutamine, 100 units/mL of penicillin G and 100 µg/mL of streptomycin (Cellgro, Herndon, VA).

extract_protocol:
Cell pellets were lysed in TRIzol (Life Technology, Cat.#  15596-026 ) and total RNA were extracted with PureLink RNA Mini kit (Life Technology, Cat.#  12183018A) following manufacturer's instructions.
RNA libraries were prepared for sequencing from 100 ng of total RNA using Illumina TruSeq RNA sample (Illumina, # FC-122-1001)preparation kit following manufacturer's instructions.

treatment_protocol: 7 million MCL cells were transfected with 100 uM of either SOX11 siRNA or non-targeting siRNA using the Amaxa system (Kit T, program G016).  Cells were collected 48 hours after trasfection and total RNA were extracted as discussed in the extract protocol.

tag: cell line

tag: treatment

value: control

tag: genotype

value: parental


title: SDY4_yak_MP2

description:
SDY3_yak_MP1 and SDY4_yak_MP2 are from the same total RNA sample but different library preparations
processed data file: Reads_summary.xls, alignments_Dme_mirBase.txt, alignments_Dsi_mirBase.txt, alignments_Dya_mirBase.txt

organism: Drosophila yakuba


title: SDY3_yak_MP1


title: BX005

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

data_processing:
RNA-Seq reads were aligned to the human genome (GRCh37/hg19) and transcriptome (hg19 RefSeq from Illumina iGenomes) using the software TopHat (version 2.0.9) and Cufflinks  (version 2.1.1.Linux_x86_64), respectively (43, 44). We counted the number of fragments mapped to each gene annotated in the UCSC hg19. Transcript abundances were measured in FPKM (fragments per kilobase of exon per million fragments mapped).
Illumina's CASAVA 1.8.2 was used for basecalling.
STAR aligner 2.3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney

extract_protocol:
Kidney samples were obtained from routine surgical nephrectomies and from leftover portions of diagnostic kidney biopsies. Only normal, non-neoplasmatic part of the tissue was used for further investigation.
RNA sequencing was carried out on microdissected kidney tubules. Total RNA was isolated using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNase1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilent 2100 Bioanalyzer. Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and an A260:A230 ratio above 2.2. Briefly, total RNA was converted to cDNA using oligodT, which was then used for Illumina sequencing library preparation. Single end 100 bp RNA-seq was carried on an Illumina HiSeq2500.

tag: disease state

value: normal

value: Kidney tubules


title: SDY4_yak_ML1


title: siSART1, replicate B

status: Public on Aug 05 2014

city: Copenhagen

first: Kristoffer

last: Vitting-Seerup

address: Ole maaloesvej 5

department: Department of Biology

country: Denmark

institute: University of Copenhangen, Denmark

description: cervix adenocarcinoma

data_processing:
For initial read mapping assessment, all reads were aligned to the human genomic sequence and quantified using the CLC Genomic Workbench Software (CLC Bio)
Reads were mapped with a minimum of 50 bases of consecutive matches, allowing for up to three mismatches.
Full-length transcripts were obtained via Cufflinks v2.1.1 using UCSC hg19 annotations (provided by Illumina though the iGenomes package) as reference transcriptome, setting min-isoform-fraction parameter to 0.03. All full-length transcripts from RefSeq and Gencode were downloaded from the UCSC genome browser on August 8, 2013.
The cufflinks output were analyzed using the R package spliceR
Genome_build: hg19

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium containing 10% fetal bovine serum

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer's protocol
Transcriptome libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer's instructions

treatment_protocol: Cells were transfected with siRNAs (20 nM) using RNAiMAX (Invitrogen) according to the manufacturer's instructions

value: HeLa

tag: sirna treatment


title: siUBL5#58, replicate B

description: cervix adenocarcinoma


title: siSART1, replicate A

description: cervix adenocarcinoma


title: siUBL5#57, replicate B

description: cervix adenocarcinoma


title: siUBL5#58, replicate A

description: cervix adenocarcinoma


title: siUBL5#82, replicate A

description: cervix adenocarcinoma


title: siCTRL, replicate B

description: cervix adenocarcinoma

value: CTRL


title: 10 mM glc rep 3

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd BRB II/III RM 632

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Calling and alignment with RUM RNA-Seq analysis package, see Grant et al Bioinformatics. 2011 Sep 15;27(18):2518-28. Epub 2011 Jul 19. PMID: 21775302
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample

source_name: Glioblastoma

growth_protocol: LN229 cells were grown to subconfluency (80%) in 6 well dishes

extract_protocol:
RNA was extracted using Invitrogen's Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated for 24 hours in RPMI medium containing 10% dialyzed FBS and 1 mM or 10 mM glucose +/- 5 mM acetate

value: glioblastoma


title: 10 mM glc rep 2


title: siUBL5#57, replicate A

description: cervix adenocarcinoma


title: K27m3_MCMV_d3.5

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

description: K27m3 ex vivo purified NK d3.5 MCMV

data_processing:
Alignment: 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: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
Genome_build: mm9
Supplementary_files_format_and_content: peak

organism: Mus musculus

source_name: primary NK cells from spleens purified by negative selection

growth_protocol: cells from spleens were isolated after positive cell depletion to negatively select for NK cell population

extract_protocol:
Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
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 following the manufacturer's protocols.

treatment_protocol: ex vivo isolated NK cells from MCMV infected mice

value: C57BL/6J (wild type)

value: NK cell

value: spleens pooled

tag: passages

value: purified by negative selection


title: 10 mM glc rep 4


title: BX019


title: 10 mM glc rep 1


title: K36m3_MCMV_d3.5

description: K36m3 ex vivo purified NK d3.5 MCMV


title: 1 mM glc + Acetate rep 4


title: K36m3_MCMV_d1.5

description: K36m3 ex vivo purified NK d1.5 MCMV


title: K27m3_MCMV_d1.5

description: K27m3 ex vivo purified NK d1.5 MCMV


title: 1 mM glc + Acetate rep 2


title: K27m3_MCMV_d0

description: K27m3 ex vivo purified NK d0 MCMV


title: 1 mM glc + Acetate rep 1


title: 1 mM glc rep 2


title: 1 mM glc rep 4


title: K36m3_MCMV_d0

description: K36m3 ex vivo purified NK d0 MCMV


title: K4m3_MCMV_d3.5

description: K4m3 ex vivo purified NK d3.5 MCMV

value: H3K4m3(Millipore #04-745)


title: K4m3_MCMV_d0

description: K4m3_ex vivo purified NK d0 MCMV


title: siCTRL, replicate A

description: cervix adenocarcinoma


title: 1 mM glc rep 1


title: DamID Runx1b::Dam 2

city: manchester

first: michael

last: lie-a-ling

address: The University of Manchester | Wilmslow Road

department: Stem Cell Biology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: FACS: cKIT+ TIE2+ CD41-

data_processing:
Sequencing reads were aligned to mm9 genome using SHRiMP2 with default settings. Reads aligning to multiple loci were discarded.
The BioConductor package BayesPeak was used to call peaks from the uniquely aligned reads for control and test samples seperrately, using the default settings. Peaks with a posterior probability > 0.9 were kept for further analysis.
Isolated peaks (that do not overlap with a peak in the control sample) were retained for subsequent analysis. We then identified all instances where one or more peaks from the test and control samples overlapped and extend the boundaries of these regions to contain all contiguous signal (irrespective of whether that came from control or test samples). We then calculated the RPKM (number of reads per kilo base per million reads) in the region from the test sample and the control sample respectively and ranked regions by the difference in RPKM between the test and control samples (i.e. ∆RPKM = RPKM_test - RPKM_control)
We selected the 10% of regions with the greatest difference and filtered further to discard loci where fold change of test to control, i.e. RPKM_test/RPKM_control, < 2. Peaks in the test sample overlapping with these remaining regions were added to the set of isolated peaks for further analysis.
We applied the Poisson model based scan statistic method (Kulldorff, M.Theory and Methods, 1997; 26:1481-1496) to this set of peaks to find peak-enriched regions in the genome. A 2000bp window was scanned along each chromosome at 400bp increments. At each position of the sliding window, we calculated the number of bases within the window corresponding to a peak. This value, together with length of the window, was used to compute the value of the scan statistic. Monte Carlo sampling was used to establish an approximate distribution of the scan statistic under the null hypothesis.
We selected those windows where the p-value of the scan statistic < 0.05 as peak-enriched windows (PEW) and merged contiguous PEWs to generate larger, peak-enriched regions (PERs), and trimmed the 5' and 3' boundaries of each region to remove nucleotides that do not overlap with any peak. Finally, we merged adjacent PERs closer than 300bp.
PERs were mapped to genome annotation using ENSEMBL (v66) via the BioConductor package annmap, and retaining PERs that overlapped, or within 30kb of a gene. Where multiple genes mapped to a single PER, the closest gene was selected in order to generate a PER_to_gene mapping for each test sample
Genome_build: mm9

source_name: Haemogenic Endothelium

growth_protocol: ES cell–derived haemogenic endothelium cells were routinely generated by isolating FLK1+ cells from d3.25 embryonic eody differentiations. FLK1+ cells where maintained on gelatin coated plates in liquid blast medium (IMDM supplemented with 10% FCS, P/S, 2mM L-Glutamine, 20μg/ml transferrin, 0.45mM MTG, 25μg/ml AA, 15% D4T conditioned medium, 5ng/ml VEGF and 10ng/ml IL6). After 2 days of liquid blast culture haemogenic endothelial cells where isolated either by sorting for FLK1+ or for the cKIT+ TIE2+ CD41- phenotype.

extract_protocol:
Genomic DNA was isolated from snap frozen samples using  the Wizard Genomic DNA Purification Kit  (Promega) according to manufacturers instructions and DamID samples where prepared as described (Vogel et al. Nat Protoc 2, 1467-1478, 2007)
For DamID-seq (ChIP-seq) standard barcoded fragment libraries were prepared as described in the Applied Biosystems SOLiD 4 Standard Library Preparation Manual (4445673)


title: DamID Runx1b::Dam 2 technical replicate

description: MACS:  FLK1+


title: DamID Runx1b::Dam 3

description: MACS:  FLK1+


title: 1 mM glc rep 3


title: DamID Runx1b::Dam 1 technical replicate 2

description: MACS:  FLK1+


title: DamID Runx1b::Dam 1 technical replicate 1

description: MACS:  FLK1+


title: DamID Dam control 3

description: MACS:  FLK1+

value: iDamko


title: DamID Dam control 2 technical replicate

description: MACS:  FLK1+


title: DamID Runx1b::Dam 1

description: FACS: cKIT+ TIE2+ CD41-


title: DamID Dam control 1 technical replicate 1

description: MACS:  FLK1+


title: 1 mM glc + Acetate rep 3


title: TS_WT

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
sRNA-seq
Genome-wide small RNA profiling
doubly homozygous T+S plant, which contains a target (T) locus containing a GFP reporter gene under the control of a minimal promoter and an upstream enhancer that drives GFP expression in shoot and root meristem regions, and a silencer ( S) locus that contains a Pol II-transcribed inverted DNA repeat of target enhancer sequences.

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: TAIR10
Supplementary_files_format_and_content: Tag count (.txt) file

organism: Arabidopsis thaliana

source_name: mix-stage inflorescence_TS_WT

extract_protocol:
Mix-stage inflorescence (contain majority of unopened flower buds) were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed from 1 microgram of  total RNA using Illumina Truseq small RNA sample preparation kit (RS-200-0012).

value: mixed-stage

tag: genotype/variation

value: positive control line for two-component transgene system, RdDM is triggered


title: DamID Dam control 1

description: FACS: cKIT+ TIE2+ CD41-


title: S_delta35S

description:
sRNA-seq
Genome-wide small RNA profiling
segregate plants from cis mutant TS_delta35S, contains silencer (S) locus with deleted 35S promoter but no T locus

source_name: mix-stage inflorescence_S_delta35S

value: inflorescence (contain majority of unopened flower buds)

value: mutant defected in RNA polymerase II-transcribed trigger for generating silencing siRNA for RdDM, without the Target (T) locus


title: TS_delta35S_nrpd1

description:
sRNA-seq
Genome-wide small RNA profiling
doubly homozygous mutant of TS_delta35S and nrpd1-7 mutant

value: mutant defected in RNA Polymerase II-transcribed trigger for generating silencing siRNA for RdDM, which is also defected in RNA Polymerase IV-dependent RdDM


title: T_WT

description:
sRNA-seq
Genome-wide small RNA profiling
homozygous plant contains a target (T) locus containing a GFP reporter gene under the control of a minimal promoter and an upstream enhancer that drives GFP expression in shoot and root meristem regions

source_name: mix-stage inflorescence_T_WT

value: control line for two component transgene system, containing only the Target (T) locus of RdDM


title: S_WT

description:
sRNA-seq
Genome-wide small RNA profiling
homozygous plant contains a silencer (S) locus that contains a Pol II-transcribed inverted DNA repeat of target enhancer sequences

source_name: mix-stage inflorescence_S_WT

value: control line for two component transgene system, containing only siRNA trigger Silencer(S) locus for generating silencing siRNA for RdDM


title: K4m3_MCMV_d1.5

description: K4m3 ex vivo purified NK d1.5 MCMV


title: TS_delta35S

description:
sRNA-seq
Genome-wide small RNA profiling
cis mutant from EMS mutant screen of TS_WT line,which contain the target (T) locus but the 35S promoter was deleted from the silencer (S) locus

source_name: mix-stage inflorescence_TS_delta35S

value: mutant defected in RNA polymerase II-transcribed trigger for generating silencing siRNA for RdDM, which still partially silences the Target (T) locus


title: Restricted Ovulatory rep5

city: Dunsany

first: Anthony

middle: Gerard

last: Doran

state: Co Meath

address: Grange

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned to Btau4.0 genome using Bowtie (settings:  -S -m 1 -n 2 --solexa1.3-quals), sorted and possible PCR duplicates were removed using Samtools.
Raw counts were enumerated using HTSEQ-count (settings: mode = union)
Genome_build: Btau_4.0
Supplementary_files_format_and_content: Tab delimited txt files
Supplementary_files_format_and_content: First row contains the ENSEMBL gene IDs and second row the raw number of reads that map to each gene

organism: Bos taurus

source_name: Hypothalmus

extract_protocol: Total RNA was extracted from hypothalamus tissue by homogenisation in Trizol. RNA was then DNAse treated and purified using Qiagen RNeasy spin columns. Standard Illumina single read mRNA-seq libraries were constructed from cDNA which was made from mRNA which had been purified from total RNA by two rounds of polyA tail selection using oligo dT beads.

treatment_protocol: A short term dietary restriction heifer model was developed which induced abrupt onset of anoestrus in some animals (Restricted Anovulatory; RA) while others maintained oestrous cyclicity (Restricted Ovulatory; RO). In addition a third control group (C) received a higher level of normal feeding. Heifers were slaughtered and hypothalamic tissue was collected after 18 days of differential feeding. mRNAseq was performed to examine differential gene expression profiles in hypothalamic tissue between groups.

tag: response

value: Restricted Ovulatory

value: Hypothalmus

tag: ovulation

value: Ovulation did occur

value: Restricted diet (0.4 Mn estimated energy requirement).


title: Restricted Ovulatory rep6


title: Restricted Ovulatory rep7


title: Control rep3

value: CONTROL

value: Higher level of feeding (1.2 Mn diet )


title: Restricted Ovulatory rep4


title: Restricted Ovulatory rep1


title: Control rep6


title: Control rep7


title: Control rep1


title: Restricted Anovulatory rep5

value: Restricted Anovulatory

value: Ovulation did not occur


title: Restricted Anovulatory rep7


title: Restricted Anovulatory rep6


title: DamID Dam control 1 technical replicate 2

description: MACS:  FLK1+

value: iDamko


title: Restricted Anovulatory rep4


title: Control rep2


title: Restricted Anovulatory rep3


title: Restricted Anovulatory rep1


title: Restricted Ovulatory rep2


title: Restricted Ovulatory rep3


title: siUBL5#82, replicate B

description: cervix adenocarcinoma

value: HeLa


title: Control rep5


title: Control rep4


title: DamID Dam control 2

description: FACS: cKIT+ TIE2+ CD41-


title: Restricted Anovulatory rep2


title: RNA-seq Runx1 ko 4

description: FACS: cKIT+ TIE2+ CD41-

data_processing:
Sequencing reads were aligned to mm9 genome using SHRiMP2 with default settings. Reads aligning to multiple loci were discarded.
Reads were aligned to ENSEMBL (v66) annotated genes using the annmap database and Bioconductor package and only exonic reads were selected.
The Bioconductor package edgeR (FDR < 0.05; exact test method) was used to call differentially expressed genes between Runx1ko  (iDamko, Ainv18ko ) and Runx1wt  Bry-GFP or Runx1wt  iDam HE samples
Common genes, which displayed same directional change, between the Runx1ko – Bry-GFP and Runx1ko – iDam comparisons were chosen for subsequent analysis
Genome_build: mm9

growth_protocol: ES cell–derived haemogenic endothelium cells were routinely generated by isolating FLK1+ cells from d3.25 embryonic eody differentiations. FLK1+ cells where maintained on gelatin coated plates in liquid blast medium (IMDM supplemented with 10% FCS, P/S, 2mM L-Glutamine, 20μg/ml transferrin, 0.45mM MTG, 25μg/ml AA, 15% D4T conditioned medium, 5ng/ml VEGF and 10ng/ml IL6). After 2 days of liquid blast culture haemogenic endothelial cells where isolated according to the cKIT+ TIE2+ CD41- phenotype.

extract_protocol:
RNA was isolated from snap frozen samples with the RNeasy Plus Mini Kit (Qiagen) and ribosomes depleted with the Ribozero Gold Kit (Epicentre) according to manufacturers instructions.
RNA-seq libraries were generated with the SOLiD Total RNA-Seq Kit (Life Technologies, 4445374).


title: RNA-seq Runx1 ko 2

description: FACS: cKIT+ TIE2+ CD41-


title: RNA-seq wt 4

description: FACS: cKIT+ TIE2+ CD41-

value: BryGFP


title: RNA-seq Runx1 ko 1

description: FACS: cKIT+ TIE2+ CD41-


title: RNA-seq wt 2

description: FACS: cKIT+ TIE2+ CD41-

value: iDam


title: RNA-seq wt 1

description: FACS: cKIT+ TIE2+ CD41-


title: RNAseq_single_embryo_replicate2

status: Public on Aug 04 2014

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

institute: Radboud University

data_processing:
Illumina BCL files were converted to FASTQ and demultiplexed using Illumina CASAVA 1.8.2.
Sequences were mapped to JGI 7.1 using gmap version 2012-04-21 with parameters -m 1 -B 4 -t 8 -N 1 -E 100 -w 100000 -n 1.
Transcript abundance and differential expression was calculated by quantifying the Reads Per Kilobase of transcript per Million reads mapped (RPKM value) using Cufflinks (version 2.1.1).
To compare the transcriptomes of the X. laevis eggs and embryos 10.5 the RNA-seq data were concatenated  for each developmental stage using the BamTools API, followed by the removal of random sequences with SAMtools v0.1.18 until the amount of mapped reads were similar. These files were analyze using Cufflinks version v2.1.1; results are in isoforms.fpkm_tracking.reduced.txt.
Genome_build: Xenopus leavis JGI 7.1 obtained from Xenbase (http://www.xenbase.org).
Supplementary_files_format_and_content: Isoforms.fpkm_tracking.individual.txt contains the Cuffdiff output for the egg and embryo replicates seperately. Isoforms.fpkm_tracking.reduced.txt contains the Cuffdiff output for the total egg and embryo reads.

organism: Xenopus laevis

source_name: embryo

growth_protocol: A single X.laevis  female was injected with 700u of human choriogonadotropin (Brevactid 1500 I.E., Ferring) and eggs were fertilized in vitro. Turned, uncleaved eggs were collected 60 minutes post fertilization, gastrulating embryos were staged according to Nieuwkoop and Faber and collected at stage 10.5.  Embryos were dejellied in 2% cysteine hydrochloride (Sigma) pH8 in 0.25X MMR. Each egg/embryo was collected in an independent tube, snap-frozen in liquid nitrogen and stored at -80°C until RNA isolation.

extract_protocol:
Total RNA was isolated using TRizol® Reagent (Ambion) and RNeasy Kit (Quiagen), and rRNA depleted with Ribo-Zero™ rRNA Removal Kits (Epicentre). rRNA-depleted RNA was then heat-fragmented in 40mMTris-acetate, 100mM potassium acetate and 30mM magnesium acetate (pH8.2) and used for cDNA synthesis. First cDNA strand was obtained from random examers primers using Superscript III (Invitrogen); second strand was made with E.coli DNA polymerase I (NEB), E.coli DNA ligase (NEB) and T4 DNA polymerase (Promega). Purified cDNA was used for strand-specific Illumina sample preparation.
Libraries were constructed according to standard Illumina protocols. Briefly cDNA was ligated with adapter sequences, size selected (300bp), and amplified by PCR. For the embryo samples purified cDNA was used for strand-specific Illumina sample preparation using Kapa Hyper Prep Kit, according to manufacturer protocol. To confer strand-specificity a USER enzyme (NEB) digestion step was performed prior to library amplification.

value: NF stage 10.5

value: whole embryo


title: RNAseq_embryo_technical_replicate2


title: RNAseq_single_embryo_replicate3


title: RNAseq_embryo_technical_replicate3


title: RNA-seq wt 3

description: FACS: cKIT+ TIE2+ CD41-


title: RNAseq_single_egg_replicate2

data_processing:
Illumina BCL files were converted to FASTQ and demultiplexed using Illumina CASAVA 1.8.2.
Sequences were mapped to JGI 7.1 using gmap version 2012-04-21 with parameters -m 1 -B 4 -t 8 -N 1 -E 100 -w 100000 -n 1.
Transcript abundance and differential expression was calculated by quantifying the Reads Per Kilobase of transcript per Million reads mapped (RPKM value) using Cufflinks (version 2.1.1).
To compare the transcriptomes of the X. laevis eggs and embryos 10.5 the RNA-seq data were concatenated  for each developmental stage using the BamTools API, followed by the removal of random sequences with SAMtools v0.1.18 until the amount of mapped reads were similar. These files were analyze using Cufflinks version v2.1.1; results are in isoforms.fpkm_tracking.reduced.txt.
Genome_build: Xenopus leavis JGI 7.1 obtained from Xenbase (http://www.xenbase.org).
Supplementary_files_format_and_content: isoforms.fpkm_tracking.single_eggs_embryos.txt contains the Cuffdiff output for the egg and embryo replicates seperately.
Supplementary_files_format_and_content: isoforms.fpkm_tracking.reduced.txt contains the Cuffdiff output for the total egg and embryo reads.

source_name: egg

growth_protocol: A single X.laevis female was injected with 700u of human choriogonadotropin (Brevactid 1500 I.E., Ferring) and eggs were fertilized in vitro. Turned, uncleaved eggs were collected 60 minutes post fertilization, gastrulating embryos were staged according to Nieuwkoop and Faber and collected at stage 10.5.  Embryos were dejellied in 2% cysteine hydrochloride (Sigma) pH8 in 0.25X MMR. Each egg/embryo was collected in an independent tube, snap-frozen in liquid nitrogen and stored at -80°C until RNA isolation.

extract_protocol:
Total RNA was isolated using TRizol® Reagent (Ambion) and RNeasy Kit (Quiagen), and rRNA depleted with Ribo-Zero™ rRNA Removal Kits (Epicentre). rRNA-depleted RNA was then heat-fragmented in 40mMTris-acetate, 100mM potassium acetate and 30mM magnesium acetate (pH8.2) and used for cDNA synthesis. First cDNA strand was obtained from random examers primers using Superscript III (Invitrogen); second strand was made with E.coli DNA polymerase I (NEB), E.coli DNA ligase (NEB) and T4 DNA polymerase (Promega). Purified cDNA was used for strand-specific Illumina sample preparation.
Libraries were constructed according to standard Illumina protocols. Briefly cDNA was ligated with adapter sequences, size selected (300bp), and amplified by PCR.

value: NF stage 1

value: whole egg


title: RNAseq_single_egg_replicate1


title: RNA-seq Runx1 ko 3

description: FACS: cKIT+ TIE2+ CD41-


title: RNAseq_single_egg_replicate4


title: RNAseq_single_egg_replicate5


title: RNAseq_embryo_technical_replicate1


title: VqsM-VSV-1

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial ChIP-seq reads were mapped to the P. auruginosa genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
Genome_build: P. aeruginosa PAO1

organism: Pseudomonas aeruginosa

source_name: liquid culture in LB

growth_protocol: LB medium with Amp

extract_protocol:
Wild type P. aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (OD=0.6), before was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 µl IP buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and sonicated the DNA to sizes of 100-300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 ul agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
Wild type P. aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (OD=0.6), before was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 µl IP buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and sonicated the DNA to sizes of 100-300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 ul agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol:
grow until mid-log phase
grow until mid-log phase

value: anti-VSV


title: VqsM-VSV-2


title: CK-1


title: v6.5 GLIB-Seq

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
The GLIB and input reads were mapped against mm9 in color-space using Bowtie.
The coverage tracks (RPM normalized) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The RPM normalized coverage tracks (bigWig)

source_name: V6.5 ES cells

growth_protocol: Mouse embryonic stem cells V6.5  were cultured in Knockout D-MEM with 15% ES-qualified FBS (Gemini Bio-products), 2 mM L-glutamine with 0.1 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids, 50 units/ml penicillin/streptomycin and 1000 U/ml ESGRO® (LIF; Chemicon)

extract_protocol: Genomic DNA was prepared by lysing ES or DP T cells, followed by treatment with RNase A (Qiagen) for 1 hour at 37 0C and then overnight treatment with proteinase K (Roche) at 550C with vigorous shaking. DNA was purified after sequential treatment with phenol, phenol/chlorophorm/isoamyl alcohol, chlorophorm/isoamyl alcohol (all obtained from Sigma) and then ethanol (Sigma) precipitation. DNA was resuspended in 10 mM Tris-Cl pH 8.0, 0.1mM EDTA .Biotin-glucosyl tagging and enrichment of 5hmC (Biotin-gmC, a variant of GLIB (Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011))): For specific biotinylation of 5hmC in DP T cells and ES cells, we used the Hydroxymethyl Collector kit  (Active Motif, Carlsbad, CA) to selectively label 5hmC bases with glucose and biotin moieties to form biotin-N3-5-gmC as previously described(Song C.-X. et al., Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine, Nature Biotechnology 29, 68–72 (2011)). To ensure efficient biotinylation, 2 µg of genomic DNA were biotinylated per reaction. In this case we used the 5500 SoliD fragment library preparation kit from Applied Biosystems in order to prepare the library and the 5500 SOLiD Library indexed adaptors 1-16 according to the manufacturer’s instructions. The samples were sequenced using the SOLiD 5500 platform.

value: embryonic stem cells


title: Pei3

first: Sylvia

middle: T

last: Nurnberg

address: 3400 Civic Center Blvd

department: Medicine

description: Sample 2

data_processing:
Alignment to reference genome;Bowtie 2 v2.0.0.6
file conversion from BAM to BIGWIG
samtools v 0.1.18
bedtools  v2.16.1
bedClip
bedGraphToBigWig
Quantification of FPKM and differential expression; TopHat v2.0.8b
Genome_build: hg19
Genome_build: mm10
Supplementary_files_format_and_content: BIGWIG; aligned reads
Supplementary_files_format_and_content: txt (diff, fpkm_tracking); differential transcript abundance

growth_protocol: SW13 cells were grown in DMEM medium supplemented with 10% FBS without antibiotics

extract_protocol:
Total RNA from cultured SW13 cells was extracted by direct lysis using the QIAGEN miRNeasy Mini Kit (Qiagen #217004) according to manufacturer’s instructions. Ribosome-associated RNA was obtained by using ARTseq™ Ribosome Profiling Kit (Epicenter, Illumina) and following manufacturer’s instructions.
Total RNA and ribosome-assoctiated RNA fragments were further converted into DNA libraries using ARTseq™ Ribosome Profiling Kit (Epicenter, Illumina).
Libraries were sequenced as 50bp paired-end reads on an Illumina MiSeq instrument.

treatment_protocol: 1 x 10^7 SW13 cells were transfected with 5ug of Add2-Mhrt779 and Add2-Hotair at 80% confluence using Lipofectamine 2000 (Invitrogen #11668) and reduced serum medium Opti-MEM (Gibco #31985). Cells were harvested 48 hours after transfection.

tag: procedure

value: human adrenal adenocarcinoma cells

value: Overexpression of murine non-coding RNAs


title: v6.5 Input BGT GLIB-Seq


title: Pei1

description: Sample 1


title: DP Input BGT GLIB-Seq

source_name: DP T cells

value: thymus

value: DP T cells


title: RNAseq_single_embryo_replicate1


title: CK-2


title: RNAseq_single_embryo_replicate4


title: CD4 naïve RNA-Seq

description: rRNA-depleted RNA

data_processing:
The sequencing reads given in color-space were mapped to the mm9 genome and exon-exon junctions using Tophat. The exon-exon junctions were derived from the RefSeq gene annotations downloaded on June 16, 2012.
The number of reads falling into each RefSeq gene was quantified using the HTSeq-count script. The CD4 and CD8 naïve RNA-seq libraries were constructed from total RNA, and thus the small nucleolar RNA transcripts were discarded from the analysis.
The RPKM values were calculated based on the read counts using a custom script.
Genome_build: mm9
Supplementary_files_format_and_content: The estimated gene expression values (RPKM, txt)

source_name: naïve CD4 cells

growth_protocol: Foxp3-GFP mice (in C57/BL6 background) were bred and maintained in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee.

extract_protocol:
RNA was isolated using Trizol (Invitrogen) and Qiagen RNAeasy column and ribosomal RNA was depleted by RiboZero (Epicentre)
According to the guideline of whole transcriptome library preparation for low input provided by SOLiD (Applied Biosystemss)

treatment_protocol: Naïve CD4 and CD8 cells (CD62Lhi, CD44lo, CD25-, Foxpgfp-) were FACS purified from spleen and lymph nodes

value: spleen and lymph nodes

value: naïve CD4 cells


title: CD8 naïve RNA-Seq

description: rRNA-depleted RNA

source_name: naïve CD8 cells

value: naïve CD8 cells


title: DP GLIB-Seq


title: MDA-MB-231 AGO HITS-CLIP Replicate 3

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

data_processing:
Library strategy: HITS-CLIP
Demultiplexed reads were aligned to the human genome (hg19) using Novoalign (Selangor, Malaysia). Adapter sequences were trimmed from the 3' end of read until mapped or until a read length of less than 16 bases.
Aligned reads were then filtered to exclude those with significant similarity to the 3’ adapter sequence.
Peaks were determined using MACS with nomodel, extsize=20, q=0.01, and keep-dup=all. Summits of peaks were determined by ascertaining the highest point of the peaks, and a peak footprint was determined by incorporating a 30 bp sequence up and downstream from the summit.
Consensus peaks were identified via peaktools-combine-replicates (https://github.com/jayhesselberth/peaktools) and were used for all further bioinformatics analysis. Peaks had to be present in at least 2 of 3 biological replicate samples to be included in analysis.
Genome_build: hg19
Supplementary_files_format_and_content: BED file containins consensus peak calls for each of the three cell lines.

source_name: MDA-MB-231, RNA from Argonaute IP

growth_protocol: MCF7 were maintained in MEM supplemented with 5% fetal bovine serum (FBS) and penicillin/streptomycin. BT474 and MDA-MB-231 were maintained in DMEM medium supplemented with 5% FBS and penicillin/streptomycin.

extract_protocol:
Extraction was performed as in Balakrishnan I, et al. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells Dayt Ohio. 2013.
Library construction was performed as in Balakrishnan I, et al. Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells. Stem Cells Dayt Ohio. 2013.

treatment_protocol: No treatment.

value: breast carcinoma

tag: subtype

value: triple negative


title: MDA-MB-231 AGO HITS-CLIP Replicate 2


title: BT474 AGO HITS-CLIP Replicate 3

source_name: BT474, RNA from Argonaute IP

value: Her2 amplified


title: BT474 AGO HITS-CLIP Replicate 2


title: MCF7 AGO HITS-CLIP Replicate 2

source_name: MCF7, RNA from Argonaute IP

value: estrogen receptor positive


title: MCF7 AGO HITS-CLIP Replicate 1


title: BT474 AGO HITS-CLIP Replicate 1


title: SOX2_iPSC

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

data_processing:
Basecalls performed using BCL2FASTQ version 1.8.3 for Of-S-M and O-Sf-M, and CASAVA version 1.8.1 for others.
For Of-S-K-M,O-Sf-K-M and O-S-Kf-M, the 81th bass were trimmed and filtered using Illumina's Quality Filtering by CASAVA version 1.8.1. For others, data were filtered using Illumina's Quality Filtering and last bases in reads were not used.
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.6.2-r126 with default parameters.
Peaks were detected using MACS version 1.4.2 with parameter --tsize=49 and other parameters were default without control samples.
Genome_build: hg19
Supplementary_files_format_and_content: bed files which contain peak information were generated using MACS version 1.4.2.

source_name: Induced pluripotent stem cells

extract_protocol:
Chromatins were fragmentated by sonication and immunoprecipitated with an anti-FLAG M2 antibody or antibodies against protein-of-interest. Immunoprecipitated DNA fragments were purified by QIAGEN's PCR purification Kit.
Ten ng of co-immunoprecipitated DNA fragments, exept for Of-S-M and O-Sf-M, were subjected to preparation of Illumina’s sequencing library using NEBNext ChIP-seq Library Prep Reagent (New England Biolabs), according manifacturer's instruction. After adapter ligation, DNA fragments were amplified by PCR with Illumina primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated by Caliper XT(Perkinelmer). For Of-S-M and O-Sf-M, Illumina’s sequencing libraries were generated by Ovation SP Iltralow Library System (NuGEN). The purified DNA was captured on an Illumina flow cell for cluster generation.

value: Induced pluripotent stem cells

value: anti SOX2 antibody


title: MCF7 AGO HITS-CLIP Replicate 3


title: IgG (before NME2 induced A549)

city: Delhi

first: Vinod

middle: Kumar

last: Yadav

state: Delhi

address: Mall Road

department: Bioinformatics

country: India

institute: IGIB

data_processing:
Basecalls performed using Genome Analyzer Pipeline v1.0
Reads were aligned (mapped) to the unmasked human reference genome (NCBI v36, hg18) using the MAQ (Mapping and Assembly with Qualities)
Sequence read distribution was processed with ChIP-Seq peak locator utility, CisGenome
Genome_build: hg18
Supplementary_files_format_and_content: Peaks list

source_name: A549 cells

growth_protocol: A549 cells were procured from ATCC. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma, USA) supplemented with 10% FBS and 5% CO2 at 37°C.

extract_protocol: ChIP assays were performed as per the protocol provided by Upstate Biotechnology with modifications as suggested in Fast ChIP protocol. Nearly 1x105 cells were plated to achieve a confluency of 80% and were transfected either myc-tagged pcDNA3-NME2 or myc-tagged pcDNA3as control. ChIP was performed after 48hrs of transfection using antibody against the Myc tag (From Sigma, monoclonal Anti-c-Myc-Cy3, Clone 9E10). Briefly, cells were fixed with 1% formaldehyde for 10 min and lysed. Chromatin was sheared to an average size of 500 bp using a Misonix 3000 sonicator. Twenty-five per cent of lysate was used to isolate input chromatin using phenol–chloroform and ethanol precipitation. Lysate was pre-cleared using protein-A sepharose beads, and ChIP was performed using 2 mg of the respective antibody incubated overnight at 4°C. Immune complexes were collected using herring sperm DNA-saturated protein-A Sepharose and washed extensively. MYC-tagged NME2 was quantified, and 10 ng from each sample was taken for end repair using Illumina sample preparation kit. Samples were purified using PCR purification kit (Qiagen, Germany).Thereafter ‘A’ base was added to the samples’ 3’end using Illumina sample prepration kit. Then flow-cell primer specific adapters were ligated to the ChIP DNA fragments and samples were further purified by MinElute columns. Size selection was done after adapter ligation using 2% agarose gel. Gel extraction columns (Qiagen) were used to purify DNA fragments ranging between 150 and 350 bases. These eluted samples were then purified using MinElute columns and were then amplified for 18 cycles to enrich adapter-ligated DNA fragments. After PCR purification and elution, the DNA was quantified using Picogreen method and then 3.5 picomoles of each sample was sequenced (36 cycles) on GAII (Illumina, USA) according to manufacturer’s protocol.

value: lung carcinoma

tag: sample type

value: IgG control (mouse)

tag: transfected


title: KLF4_iPSC

value: anti KLF4 antibody


title: OCT4_iPSC

value: anti OCT3 antibody


title: NME2 Chip-seq Replicate 2(after NME2 induced A549)

value: anti-c-Myc monoclonal, Clone 9E10

tag: chip vendor

value: Sigma

value: myc-tagged pcDNA3-NME2


title: NME2 Chip-seq Replicate 2(before NME2 induced A549)

tag: tissue

tag: chip vendor/catalog#

value: Santa Cruz Biotechnology Inc./sc-17587


title: NME2 Chip-seq Replicate 1(after NME2 induced A549)

tag: chip antibody


title: soxR-Day3a

city: Bryn Mawr

first: Joshua

middle: A

last: Shapiro

address: 101 N Merion Ave

department: Biology

institute: Bryn Mawr Collete

data_processing:
Base calling was performed using the CASAVA pipeline v.1.8
Reads were mapped using bwa aln version 05.9-r16 using default mapping parameters
Mapped reads were assigned to annotated transcripts using the count_overlaps tool v 0.1.0 in Galaxy (usegalaxy.org) without regard to strand
Genome_build: streCoel (Streptomyces coelicolor 07/01/1996 Assembly)
Supplementary_files_format_and_content: tab-delimited text files include total read counts for transcript; bedgraph files show-strand specific read coverage by position

organism: Streptomyces coelicolor

source_name: Bacterial culture

growth_protocol: About 100 million spores were grown on R2YE agar plates at 30C for either 24 h or 72 h.

extract_protocol:
Cells were lysed with lysozyme followed by sonication.  RNA was extracted using an Rneasy plant minikit (Qiagen).  Contaminating DNA was removed with DNaseI (Qiagen).  RNA was purified by extracting with phenol-chloroform.
Library was constructed and sequenced by Fasteris SA (Switzerland).  Ribosomal levels were reduced using MICROBExpress kit (Ambion).  RNA was fragmented using a buffered zinc solution.  First cDNA strand was synthesized using random primers in the presence of dUTPs.  After second strand synthesis and adaptor ligation, first cDNA strand was removed with uracil-DNA glycosylase.  Remaining fragments were PCR amplified and 150-200 bp amplicons were sequenced.

tag: strain

value: soxR null mutant

tag: age

value: 72 hour old hyphae


title: soxR-Day3b

tag: genotype


title: NME2 Chip-seq Replicate 1(before NME2 induced A549)

tag: cell line


title: MDA-MB-231 AGO HITS-CLIP Replicate 1

tag: cell type


title: soxR-Day1

value: 24 hour old hyphae


title: Th2 CMS-Seq Input BR2

data_processing:
The CMS-IP and input reads were mapped against mm9 and lambda phage DNA using the Bismark mapping tool.
The mapping was done using the Bowtie 2 backend in the paired-end mode with the following parameter values: -I 0 -X 600 -N 0.
Biological replicates were pooled for subsequent analysis.
The coverage tracks (RPM normalized) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The RPM normalized coverage tracks (bigWig)

source_name: Th2 cells

growth_protocol: 4-6 weeks old female C57/BL6 mice obtained from Jackson labs were used for cell isolation. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee.

extract_protocol: Genomic DNA was prepared by lysing T cells, followed by treatment with RNase A (Qiagen) for 1 hour at 37 0C and then overnight treatment with proteinase K (Roche) at 550C with vigorous shaking . DNA was purified after sequential treatment with phenol, phenol/chlorophorm/isoamyl alcohol, chlorophorm/isoamyl alcohol (all obtained from Sigma) and then ethanol (Sigma) precipitation. DNA was resuspended in 10 mM Tris-Cl pH 8.0, 0.1mM EDTA .In order to  prepare  Cytosine 5-methylenesulphonate immunoprecipitation (CMS-IP) sequencing libraries  genomic DNA was fragmented to an average size of 165 bp using  Covaris S2 (Covaris, Woburn, MA, USA). Genomic DNA was spiked with cl857 Sam7 Lambda DNA (Promega, Madison, WI) at a ratio of 200:1. The fragmented DNA was end repaired, 3’ adenylated, ligated to methylated Illumina adaptor oligonucleotides (Truseq), and bisulfite converted. Bisulfite conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) was followed by immunoprecipitation of genomic DNA fragments containing CMS with a specific antiserum to CMS. Briefly, bisulfite converted genomic DNA was  denatured for 10 minutes at 95°C (0.4 M NaOH, 10 mM EDTA), then neutralized by addition of cold 2 M Ammonium Acetate pH 7.0 and incubation on ice for 10 minutes. Subsequently, the DNA was incubated with anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100)  for 2h at  4°C , and then precipitated overnight at 4°C  with Protein A and G magnetic beads (Invitrogen). Precipitated DNA was washed 3 times with 1x IP buffer and eluted with Proteinase K, then purified with Phenol Chloroform. Following immunoprecipitation, sequencing libraries were amplified using the uracil insensitive Kapa HiFi HotStart Uracil+ (Kapa Biosystems).

treatment_protocol: Subsets of thymocytes were isolated by cell sorting  after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145-2C11), CD24 (M1/69).  DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo . Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions.  Briefly, for Th1 polarization naïve CD4 T cells were cultured in the presence of 10 ng/ml IL12, 10 µg/ml anti-IL-4, 1 µg/ml anti CD3 (clone 2C11) and 1 µg/ml anti-CD28 (clone 37.51) for 2 days. In the case of Th2 polarization naïve CD4 T cells were cultured in the presence of 1000 U/ ml IL-4, 5 µg/ml anti-IFN-γ, 3 µg/ml anti-IL-12, 1 µg/ml anti CD3 (clone 2C11) and 1 µg/ml anti-CD28 (clone 37.51) for 2 days. On day 3 of culture, cells were removed from TCR/ costimulation conditions and expanded in the presence of 20 U/mL IL-2 for the Th1 and 10 U/mL IL-2 for the Th2 polarization conditions IL-2 for 4 days.

value: spleen and lymph nodes

value: Th2 cells


title: MNase_Input_rep2

city: Charlottesville

first: Michael

middle: Joseph

last: Guertin

state: VA

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description:
MNase-ChIP-DNA
MNase_Input_rep2_PE1
MNase_Input_rep2_PE2

data_processing:
library-strategy: MNase-ChIP-Seq
We used bowtie to align to hg19, with default parametersand the addition arguments: "-v 2 -m 1". MNase sample were trimmed to 50bp prior to alignment using fastx tools: fastx_trimmer -l 50 -z .
We used MACS14 to call peaks on the merged replicate alignments, with the following arguments: "-g hs --keep-dup=all -B -S --call-subpeaks -m 20,300000".
We normalized the shirted tags from the MACS14 output to the total read depth of each library for the submitted bigWig files. The MNase ChIP-seq bigWigs files were generated by extending all positive strand concordant reads to the end of it's paired-read, then applying the bedtools tools "genomeCoverageBed" and the ucsc tool "wigToBigWig".
Mean insert size and standard deviation for this GEO submission was found by: awk '{ if ($9 > 0 && $9 < 500) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print "n="N", mean="M", stdev="sqrt ((S2-M*M*N)/(N-1))}' *.sam; note that anything with an insert size greater than 500 was excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Each bigWig file was derived from the -B option in MACS14. The shifted bedGraph files were normalized by total read depth in each library and converted to bigWig files using Jim Kent's wigToBigWig software.

growth_protocol: MCF-7 cells were grown in DMEM supplemented with fetal bovine serum to a final concentration of 10%. Cells were cultured in charcoal-dextran FBS for the three days prior to 100nM E2 stimulation.

extract_protocol:
To achieve high temporal resolution, ChIP crosslinking concentration of formaldehyde was 2% and crosslinking was quenched after 1 minute with 250mM glycine. The H3R26Cit antibody we used for IP was AbCam: ab19847. The H3K27ac antibody we used for IP was Millipore: 07-360.
The ends of the ChIP DNA were blunted and phosphorylated in 1X END Repair Buffer (Epicentre Biotechnologies, #ER0720), 250nM dNTPs, 1mM ATP, and 1X END-IT enzyme mix (Epicentre Biotechnologies, #ER0720) for 45 minutes. An A overhang was achieved in 1xNEB2 buffer, 200nM dATP (Invitrogen), 3units of Klenow (3¢-5¢ exo-) 5U/ml (from New England BioLabs), in 50ul volume for 30 minutes. 10nM of adapter was ligated to the DNA in 1X ligation buffer, 5ml (3000units) of UltraPure Ligase from enzymatics (Enzymatics T4 DNA Ligase #L603-HC-L) in a total volume of 50ul. Thirteen cycles of PCR with Phusion polymerase were performed to acquire the final library.

treatment_protocol: Cells were treated with 100nM estradiol for the indicated time points.

value: MCF-7 breast cancer cells

value: none (input)


title: WT-Day3b

value: wild type


title: WT-Day3a


title: Th2 CMS-Seq IP BR2


title: MNase_H3R26Cit_E2_10min_rep1

description:
MNase-ChIP-DNA
MNase_H3R26Cit_E2_10min_rep1_PE1
MNase_H3R26Cit_E2_10min_rep1_PE2

tag: agent

tag: time

value: H3R26Cit (AbCam, catalog# ab19847, lot# 135757)


title: WT-Day1


title: RNAseq_single_egg_replicate3

tag: developmental stage

value: NF stage 1

value: whole egg


title: MNase_H3K27ac_TSA_30min_rep2

description:
MNase-ChIP-DNA
MNase_H3K27ac_TSA_30min_rep2_PE1
MNase_H3K27ac_TSA_30min_rep2_PE2

value: TSA

value: H3K27ac (Millipore, catalog# 07-360, lot# GR104852)


title: Th1 CMS-Seq IP BR1

source_name: Th1 cells

value: Th1 cells


title: Th1 CMS-Seq Input BR1


title: RNAseq_single_embryo_replicate5

value: NF stage 10.5

value: whole embryo


title: MNase_H3K27ac_TSA_30min_rep1

description:
MNase-ChIP-DNA
MNase_H3K27ac_TSA_30min_rep1_PE1
MNase_H3K27ac_TSA_30min_rep1_PE2


title: MNase_H3K27ac_EtOH_rep2

description:
MNase-ChIP-DNA
MNase_H3K27ac_EtOH_rep2_PE1
MNase_H3K27ac_EtOH_rep2_PE2

value: EtOH


title: CD8 naïve CMS-Seq IP BR2

source_name: CD8 naïve T cells

value: CD8 naive T cells


title: IgG (after NME2 induced A549)

value: lung carcinoma

value: IgG control (goat)

value: myc-tagged pcDNA3-NME2


title: MNase_Input_rep1

description:
MNase-ChIP-DNA
MNase_Input_rep1_PE1
MNase_Input_rep1_PE2


title: MNase_H3K27ac_E2_10min_rep2

description:
MNase-ChIP-DNA
MNase_H3K27ac_E2_10min_rep2_PE1
MNase_H3K27ac_E2_10min_rep2_PE2


title: CD8 naïve CMS-Seq Input BR1

value: spleen and lymph nodes


title: MNase_H3K27ac_EtOH_rep1

description:
MNase-ChIP-DNA
MNase_H3K27ac_EtOH_rep1_PE1
MNase_H3K27ac_EtOH_rep1_PE2

value: MCF-7 breast cancer cells


title: CD8 naïve CMS-Seq IP BR1


title: MNase_H3R26Cit_E2_10min_rep2

description:
MNase-ChIP-DNA
MNase_H3R26Cit_E2_10min_rep2_PE1
MNase_H3R26Cit_E2_10min_rep2_PE2


title: CD4 naïve CMS-Seq Input BR2

source_name: CD4 naïve T cells

value: CD4 naive T cells


title: MNase_H3K27ac_E2_10min_rep1

description:
MNase-ChIP-DNA
MNase_H3K27ac_E2_10min_rep1_PE1
MNase_H3K27ac_E2_10min_rep1_PE2


title: CD4 naïve CMS-Seq IP BR2


title: CD4 naïve CMS-Seq Input BR1


title: Cit_40min

description:
ChIP-DNA
Cit ChIP-seq 40min E2 rep1
Cit ChIP-seq 40min E2 rep2

data_processing:
We used bowtie to align to hg19, with default parametersand the addition arguments: "-v 2 -m 1". MNase sample were trimmed to 50bp prior to alignment using fastx tools: fastx_trimmer -l 50 -z .
We used MACS14 to call peaks on the merged replicate alignments, with the following arguments: "-g hs --keep-dup=all -B -S --call-subpeaks -m 20,300000".
We normalized the shirted tags from the MACS14 output to the total read depth of each library for the submitted bigWig files. The MNase ChIP-seq bigWigs files were generated by extending all positive strand concordant reads to the end of it's paired-read, then applying the bedtools tools "genomeCoverageBed" and the ucsc tool "wigToBigWig".
Mean insert size and standard deviation for this GEO submission was found by: awk '{ if ($9 > 0 && $9 < 500) { N+=1; S+=$9; S2+=$9*$9 }} END { M=S/N; print "n="N", mean="M", stdev="sqrt ((S2-M*M*N)/(N-1))}' *.sam; note that anything with an insert size greater than 500 was excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Each bigWig file was derived from the -B option in MACS14. The shifted bedGraph files were normalized by total read depth in each library and converted to bigWig files using Jim Kent's wigToBigWig software.


title: CD4 naïve CMS-Seq IP BR1


title: Cit_10min

description:
ChIP-DNA
Cit ChIP-seq 10min E2 rep1
Cit ChIP-seq 10min E2 rep2


title: CD8 SP CMS-Seq Input BR2

source_name: CD8 SP T cells

value: thymus

value: CD8 SP T cells


title: CD8 SP CMS-Seq IP BR2


title: CD8 naïve CMS-Seq Input BR2


title: Cit_5min

description:
ChIP-DNA
Cit ChIP-seq 5min E2 rep1

value: H3R26Cit (AbCam, catalog# ab19847, lot# 135757)


title: 3 - macrophage + TNF

first: Laura

last: Donlin

department: Arthritis and Tissue Degeneration Program

institute: Hospital for Special Surgery

description: M + TNF

data_processing:
The TopHat program was used to align the reads to the UCSC Hg19 human reference genome.
The Cufflinks program was used to calculate measurements of transcript abundance (represented by Fragments Per Kilobase of exon model per Million mapped reads (FPKM)).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM

molecule: polyA RNA

source_name: primary macrophages

growth_protocol: Human CD14+ cells isolated from PBMCs were differentiated into macrophages for 1 day with MCSF (10ng/mL) in RPMI/10% FBS.  Transwell chambers with or without synovial fibroblasts were then placed above the macrophages. (Human synovial fibroblast cell lines were generated from synovial tissue extracted during knee arthroplasty, minced and collagenase digested.  Adherent cells at passage 4 or beyond were used for macrophage-fibroblast co-cultures.)

extract_protocol:
Macrophage RNA was isolated with RNAeasy mini kit (Qiagen) and polyA mRNA purified with the Truseq kit (Illumina).
Libraries were generated with the Truseq kit (Illumina).

treatment_protocol: Mono- or co-cultures were then treated with or without TNFa (20ng/mL) for 2 days.

value: primary macrophages

tag: treatment

value: TNF

tag: barcode

value: AGTCAA


title: 4 - macrophage + fibroblast & TNF

description: M (Fib) + TNF

value: TNF + co-culture with fibroblast

value: GTGAAA


title: CD8 SP CMS-Seq Input BR1


title: Cit_0min

description:
ChIP-DNA
Cit ChIP-seq 0min E2 rep1
Cit ChIP-seq 0min E2 rep2


title: 1 - macrophage

description: M -

value: CGATGT


title: CD8 SP CMS-Seq IP BR1


title: CD4 SP CMS-Seq Input BR2

source_name: CD4 SP T cells

value: CD4 SP T cells


title: TKCBV5-6-s1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.5 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) for LTR7,7A,7B,7C,7Y in RepeatMasker open-3.3.30-Repeat Libarary 20120124 were calcurated using Partek Genomic Suite version 6.6 with default parameter except changing "Require strict paired-end compatibility" option from "Yes" to "No".
Genome_build: hg19
Supplementary_files_format_and_content: Text files which contain RPKM for LTR7s were calcurated using Partek Genomic Suite version 6.6.

source_name: induced pluripotent stem cells

extract_protocol:
Total RNA was isolated using the Qiazol reagent (Qiagen) and a miRNeasy mini kit (Qiagen) according to the manufacturer's instruction.
One µg of total RNA was depleted of rRNA using Ribo-Zero gold kit (Epicentre), and then 100 ng of rRNA-depleted RNA fraction was subjected to Illumina’s sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). The library was captured on an Illumina flow cell for cluster generation.

value: induced pluripotent stem cells TKCBV5-6 subclone 1


title: O-Sf-M

source_name: Human dermal fibroblast

value: OCT3/4, SOX2-overexpressed Human dermal fibroblast

value: anti flag antibody


title: TIG118-4f1-s7

value: induced pluripotent stem cell TIG118-4f1subclone 7


title: CD4 SP CMS-Seq IP BR2


title: TIG108-4f3-s6

value: induced pluripotent stem cell TIG108-4f3 subclone 6


title: Cit_160min

description:
ChIP-DNA
Cit ChIP-seq 160min E2 rep1

value: MCF-7 breast cancer cells


title: 451F3-s5

value: induced pluripotent stem cells 451F3 subclone 5


title: FHY1-input

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v1, default parameter
MACS for peak-calling, v1.4.4, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: BED, peaks called by MACS, Table head: chr start end length summit tags -10*LOG10(pvalue) fold_enrichment FDR(%); FHY1_chipseq_.bed contains the overlapping peaks in each sample.

source_name: Arabidopsis thaliana seedlings

growth_protocol: To determine whether phyA and FHY1 associate with the same genes upon FR irradiation, four-day old etiolated 35S: GFP-FHY1 fhy1-1 transgenic seedlings were exposed to 3hr FR. The treated plants were utilized for ChIP-seq analysis with an anti-FHY1 antibody that exhibits high specificity in the detection of FR-induced FHY1-association events. FHY1 associated-DNA samples from three distinct biological replicates and an input DNA sample (as a negative control) were subjected to high-throughput Solexa (Illumina) sequencing.

extract_protocol:
5 g of seedlings were first cross-linked with 1% formaldehyde under vacuum, and then the samples were ground to powder in liquid nitrogen. The chromatin complexes were isolated and sonicated and then incubated with  antibodies. The precipitated DNA was recovered and used to generate Illumina sequencing libraries according to the manufacturer’s instructions.
standard Illumina ChIP-seq protocol

value: 35S:GFP-FHY1, fhy1-1

value: 4 day old seedling

tag: antibody

value: none (input)


title: CD4 SP CMS-Seq Input BR1

value: thymus


title: Cit_2min

description:
ChIP-DNA
Cit ChIP-seq 2min E2 rep1

value: H3R26Cit (AbCam, catalog# ab19847, lot# 135757)


title: 201B7

value: induced pluripotent stem cells


title: p2

source_name: Intermediate reprogrammed cells

value: induced pluripotent stem cells 7 days after 2nd passage


title: 2 - macrophage + fibroblast

description: M (Fib) -

value: primary macrophages

value: co-culture with fibroblast

value: CAGATC


title: FHY1-GFP_2_ChIP-seq

value: anti-GFP

tag: antibody manufacturer

value: Clontech

tag: catalog number


title: DP CMS-Seq Input BR2

source_name: DP T cells

value: DP T cells


title: DP CMS-Seq IP BR2


title: Sample_fhy1-1-3_RNA-seq

data_processing:
Bowtie for alignment, v1, default parameter
Cufflink for expression profiling, v2.1.0, default parameter
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with different expressed genes discovered by Cufflink software package, table head : test_id gene_id gene    locus   sample_1        sample_2        status  value_1 value_2 log2(fold_change)       test_stat       p_value q_value significant

growth_protocol: The 35S: GFP-FHY1 fhy1-1 transgenic line and the fhy1-1 mutant were grown under the same light conditions used  (D4d+FR3h) for RNA preparation and sequencing. Three biologically replicates were subjected to high-throughput Solexa (Illumina) sequencing.

extract_protocol:
RNAeasy Kit
standard Illumina mRNA-seq protocol


title: p3

value: induced pluripotent stem cells 7 days after 3rd passage


title: FHY1-GFP_3_ChIP-seq


title: p1

value: induced pluripotent stem cells 7 days after TRA-1-60(+) cell sorting on day 28


title: d28

value: TRA-1-60(+) cells on day 28


title: DP CMS-Seq IP BR1


title: DP CMS-Seq Input BR1


title: Sample_fhy1-1-2_RNA-seq


title: Sample_fhy1-1-1_RNA-seq


title: d20

value: TRA-1-60(+) cells on day 20


title: Of-S-M

value: OCT3/4, SOX2-overexpressed Human dermal fibroblast

value: anti flag antibody


title: d15

value: TRA-1-60(+) cells on day 15


title: DP Input BR2 ChIP-Seq

data_processing:
The ChIP-seq sequencing libraries were mapped against mm9 using Bowtie.
Reads with identical sequences were filtered and only one was retained for subsequent analysis.
In case of biological replicates they were pooled for subsequent analysis.
The coverage tracks (RPM normalized) were generated using HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: The RPM normalized coverage tracks (bigWig)

extract_protocol:
Cells were lysed on ice in Lysis buffer (50 mM Hepes pH 7.9, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 140 mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25 % Triton, protease inhibitors and 5 mM sodium butyrate)  in order to obtain nuclei, that were washed twice with washing buffer(10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 1x protease inhibitors, 5 mM sodium butyrate)  and resuspended in shearing buffer(0.1% SDS, 1mM EDTA pH 8.0, 1x protease inhibitors, 5 mM sodium butyrate) . Then, chromatin was sheared in an average size of 200 bp using Covaris. Histones-DNA complexes were isolated using the H3K27Ac antibody.
Libraries were prepared following standard procedures. Briefly, DNA was end repaired  using the End Repair kit by Epicentre.  A-tailing was performed using the large Klenow fragment enzyme by NEB.We used the TruSeq indexed adapters by Illumina. After adapter ligation DNA was PCR amplified for  10 cycles using Kapa HiFi DNA polymerase from Kapa Biosystems. Libraries were purified twice using Ampure Beads (Beckman Coulter) and subsequently were sequenced in an Illumina HiSeq 2000 instrument.

treatment_protocol: 10 million sorted  DP T cells were washed in PBS and  fixed for 10 min in 1% Formaldehyde at room temperature. Then quenching of formaldehyde took place for 5 min  in the precence of Glycine. Cells were washed twice with PBS containing protease inhibitors (Roche) and sodium butyrate (to inhibit deacetylation).

value: Thymus


title: DP H3K27ac BR2 ChIP-Seq

value: H3K27Ac (Abcam, ab 4729)


title: DP Input BR1 ChIP-Seq


title: d11

value: TRA-1-60(+) cells on day 11


title: Sample_GF3_RNA-seq

value: 4 day old seedling

value: 35S:GFP-FHY1, fhy1-1


title: CD4 SP CMS-Seq IP BR1

value: thymus

value: CD4 SP T cells


title: DP H3K27ac BR1 ChIP-Seq


title: Sample_GF1_RNA-seq


title: FHY1-GFP_1_ChIP-seq

value: anti-GFP


title: Sample_GF2_RNA-seq


title: d3

value: SOX2-EGFP (+) cells on day 3


title: Th0.Ezh2KO.9.ChIP-seq

city: Parkville

first: Jovana

last: Maksimovic

state: Victoria

address: Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

data_processing:
The reads were mapped to the mouse reference genome (mm10) with bowtie2 (2.1.0) using the option -5 10 to trim 10bp from the 5’ end of each read.
Read counts were then summarized across genes, including 2kb upstream of the TSS, using FeatureCounts (1.4.2).
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Read counts were summarized across mm10 genes using FeatureCounts (1.4.2) producing a txt file for each sample containg the length and read count for each gene.
Supplementary_files_format_and_content: ChIP-seq: Read counts were summarized across mm10 genes using FeatureCounts (1.4.2), including 2kb upstream of the TSS, producing a txt file for each sample containg the location, strand, length and read count for each gene.

growth_protocol: Naïve CD4+T cells were flow sorted, activated with plate-bound anti-CD3 (5ug/ml), solbule anti-CD28 (1ug/ml) antibodies and rhIL-2 (50U/ml) in 10%FCS RPMI media. Cells were supplemented with rhIL2 at day 3 and harvested at day 4.

extract_protocol:
Cells were lysed with 1%SDS lysis buffer, sonicated (Branson Sonifier, 4 cycles of sonication for 30 seconds and rest for 1min) and diluted to 0.1% SDS buffer. After over night immunoprecipitation samples were washed sequentially with low salt, hight salt, LiCl and TE buffer before elution.
Illumina’s TruSeq ChIP sample preparation protocol

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperture and quenched with 1/10 1.25M Glycine for 5min, snap frozen on dry ice and stored at -80C.

value: Ezh2 fl/fl.CD4Cre

tag: genotype/variation

value: in vitro neutrally activated Th0 cell

value: Polyclonal rabbit-anti-H3K27me3 (10 μg/ChIP)

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: d0

value: Human dermal fibroblast


title: Th0.Ezh2KO.10.ChIP-seq

tag: chip antibody


title: O-S-Kf-M

value: OCT3/4, SOX2 and KLF4-overexpressed Human dermal fibroblast


title: O-Sf-K-M

value: anti flag antibody


title: Th0.Ezh2KO.175.d4.RNA-seq

data_processing:
Bases with a Phred score < 25 were trimmed from the 3’ end of reads (Trimmomatic 0.30). Reads shorter than 50bp were subsequently discarded.
Trimmed reads were mapped to the mouse genome (mm10) using TopHat (2.0.6) with default parameters; mouse gene model annotations (mm10) were supplied via the -G option, which forces reads to initially align to a virtual transcriptome, followed by genomic mapping of unaligned reads.
Read counts were then summarized across genes using FeatureCounts (1.4.2).
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Read counts were summarized across mm10 genes using FeatureCounts (1.4.2) producing a txt file for each sample containg the length and read count for each gene.
Supplementary_files_format_and_content: ChIP-seq: Read counts were summarized across mm10 genes using FeatureCounts (1.4.2), including 2kb upstream of the TSS, producing a txt file for each sample containg the location, strand, length and read count for each gene.

growth_protocol: Naïve CD4+T cells were flow sorted, activated with plate-bound anti-CD3 (5ug/ml), solbule anti-CD28 (1ug/ml) antibodies  in 10%FCS RPMI media. For Th0 cells, rhIL-2 (50U) were supplemented. For iTreg cells, rhIL-2(200U/ml) and rhTGF-b1 (5ng/ml) were supplemented.

extract_protocol:
Total RNA extracted by Rneasy Mini Kit
Illumina’s TruSeq RNA v2 sample preparation protocol

treatment_protocol: Differentiation cytokines were added at day 1 and 3, cells were harvested at day 4.

tag: strain


title: Th0.Ezh2KO.165.d4.RNA-seq


title: Th0.Ezh2ff.7.ChIP-seq

value: Ezh2 fl/fl

value: wild type


title: Th0.Ezh2KO.174.d4.RNA-seq


title: Of-S-K-M


title: GM06990 CHi-C,  replicate 1-2

city: London

first: Nicola

last: Dryden

address: 237 Fulham Road

department: Breast Cancer Research

institute: Institute of Cancer Research

description: This Sample represents 2 replicates.

data_processing:
Library strategy: Capture Hi-C
Casava software (v1.8, Illumina) was used to make base calls.
Reads failing the Illumina chastity filter were removed before further analysis.
Sequences were output in fastq format before mapping against the human reference genome (GRCh37/NCBI Build 37/hg19) and filtering to remove experimental artifacts using the publicly available Hi-C User Pipeline (HiCUP) (http://www.bioinformatics.babraham.ac.uk/).
In addition to the standard pipeline, off-target di-tags (defined as di-tags where neither end mapped to one of the capture regions) were removed from the final processed data sets.
Replicates were combined and Virtual 4C libraries were generated for each HindIII fragment within each capture region for (i) high-resolution cis interactions, (ii) high-resolution within capture region interactions, (iii) low-resolution cis interactions, and (iv) low-resolution trans interactions using SeqMonk (seqmonk_v0.23.1.dmg).
Data sets were reformatted in STATA IC11 and output as tab-delimited text files.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited txt files were generated using STATA IC 11.
Supplementary_files_format_and_content: Tab-delimited txt file of bait coordinates (baits_coordinates.txt) is linked to the Series record.

source_name: Lymphoblastoid

growth_protocol: Grown in RPMI 1640 supplemented with 15% fetal bovine serum, 50U/ml penicillin, 50μg/ml streptomycin and 2mM L-Glutamine.

extract_protocol:
Each cross-linked cell aliquot (~20 million cells) was re-suspended in 50ml of permeabilisation buffer (10mM Tris-HCl p8, 10mM NaCl, 0.2% IGEPAL CA-630), supplemented with complete mini EDTA-free tablets and incubated on ice for 30 minutes with occasional mixing. SUM44 and GM06990 cells were lysed using 10 strokes of a dounce homogeniser. BT483 cells were lysed by incubating with trypsin (0.25%, Sigma-Aldrich, St. Louis, MO, USA) at 37°C for 5 minutes. Trypsin was inactivated by addition of 500μl FBS. Permeabilised cells were centrifuged for 6 minutes at 600g and washed three times in 1ml 1.3xNEBuffer 2. Nuclei were resuspended, and chromatin digestion and Hi-C library preparation were carried out as described by van Berkum and colleagues (Hi-C: a method to study the three-dimensional architecture of genomes J.Vis exp. 2010; (39): 1869) with the following modifications: (i) cells were split into three microcentrifuge tubes instead of five, (ii) restriction fragment overhangs were filled in with biotinylated dATP instead of biotinylated dCTP, (iii) dGTP was added to the reaction mixture for the removal of biotinylated dATP from unligated ends,  (iv) we did not include an agarose gel size selection step, and  (v) after PCR amplification (6-8 cycles) of the Hi-C library bound streptavidin beads the PCR product was pooled and subjected to target enrichment (below) before paired-end sequencing.
Target enrichment was performed based on the SureSelect protocol (Agilent, Santa Clara, CA, USA) but incorporating the following modifications: (i) Biotinylated Hi-C ditags bound to streptavidin-beads were amplified pre-hybridization directly from beads using 24 parallel 25μl PCR reactions cycles with six to eight cycles using Phusion High-Fidelity DNA polymerase to yield approximately 500ng total DNA. Subsequently, PCR products were pooled, purified using Agencourt Ampure XP beads (Beckman Coulter, Brea, CA, USA) and dried using a speedvac concentrator then resuspended in 34μl of water; and (ii) Enriched fragments were amplified post-hybridization again directly from the streptavidin beads, using 13 parallel 25μl reactions of six cycles of PCR. PCR products were again pooled and purified using Agencourt Ampure XP beads (Beckman Coulter, Brea, CA, USA).

treatment_protocol: Cells were fixed in 2% formaldehyde for 5 minutes at room temperature followed by the addition of glycine to a final concentration of 150 mM.

tag: cell source

value: B-lymphocyte

tag: restriction enzyme

value: HindIII


title: Th0.Ezh2fl/fl.177.d4.RNA-seq


title: BT483 CHi-C, replicate 1-2

description: This Sample represents 2 replicates.

source_name: Breast cancer

growth_protocol: Grown in RPMI 1640 supplemented with 20% fetal bovine serum, 50U/ml penicillin, 50μg/ml streptomycin, 2mM L-Glutamine and 0.01mg/ml recombinant human insulin.

tag: cell line

value: primary invasive ductal carcinoma


title: Th0.Ezh2fl/fl.176.d4.RNA-seq

tag: cell type


title: Th0.Ezh2fl/fl.173.d4.RNA-seq


title: d7

value: TRA-1-60(+) cells on day 7


title: iTreg.Ezh2fl/fl.155.d5.RNA-seq

value: in vitro differentiated induced regulatory T cell


title: iTreg.Ezh2fl/fl.177.d5.RNA-seq


title: No Antibody IP

data_processing:
We used bowtie to align to hg19, with default parametersand the addition arguments: "-v 2 -m 1".
We used MACS14 to call peaks on the merged replicate alignments, with the following arguments: "-g hs --keep-dup=all -B -S --call-subpeaks -m 20,300000".
We normalized the shirted tags from the MACS14 output to the total read depth of each library for the submitted bigWig files.
Genome_build: hg19
Supplementary_files_format_and_content: Each bigWig file was derived from the -B option in MACS14. The shifted bedGraph files were normalized by total read depth in each library and converted to bigWig files using Jim Kent's wigToBigWig software.

extract_protocol:
To achieve high temporal resolution, ChIP crosslinking concentration of formaldehyde was 2% and crosslinking was quenched after 1 minute with 250mM glycine. The ER antibody we used for IP was Santa Cruz: sc-542.
The ends of the ChIP DNA were blunted and phosphorylated in 1X END Repair Buffer (Epicentre Biotechnologies, #ER0720), 250nM dNTPs, 1mM ATP, and 1X END-IT enzyme mix (Epicentre Biotechnologies, #ER0720) for 45 minutes. An A overhang was achieved in 1xNEB2 buffer, 200nM dATP (Invitrogen), 3units of Klenow (3¢-5¢ exo-) 5U/ml (from New England BioLabs), in 50ul volume for 30 minutes. 10nM of adapter was ligated to the DNA in 1X ligation buffer, 5ml (3000units) of UltraPure Ligase from enzymatics (Enzymatics T4 DNA Ligase #L603-HC-L) in a total volume of 50ul. Thirteen cycles of PCR with Phusion polymerase were performed to acquire the final library.


title: NS-IgG IP

value: IgG


title: ER_160min_1

value: 100nM estradiol1 60 mins

value: ER (Santa Cruz, sc-542)


title: ER_10min_1

value: 100nM estradiol 10 mins


title: SUM44 CHi-C, replicate 1-2

description: This Sample represents 2 replicates.

growth_protocol: Grown in phenol-red-free RPMI 1640 supplemented with 10% fetal bovine serum, 50U/ml penicillin, 50μg/ml streptomycin, 2mM L-Glutamine and 1 nM Estradiol.

value: plural effusion


title: ER_40min_1

value: 100nM estradiol 40 mins


title: ER_5min_1

value: 100nM estradiol 5 mins


title: iTreg.Ezh2fl/fl.154.d5.RNA-seq


title: iTreg.Ezh2KO.153.d5.RNA-seq

value: Ezh2 fl/fl.CD4Cre


title: ER_0min_1

value: 100nM estradiol 0 min


title: iTreg.Ezh2KO.165.d5.RNA-seq


title: ER_2min_1

value: 100nM estradiol 2 mins


title: Th0.Ezh2ff.33.ChIP-seq

value: Ezh2 fl/fl

value: in vitro neutrally activated Th0 cell

value: Polyclonal rabbit-anti-H3K27me3 (10 μg/ChIP)

value: Millipore


title: ZNF92_Abgent_AT4646a_ChipSeq

status: Public on Aug 03 2014

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against ZNF92_Abgent_AT4646a
05172013_D26EFACXX_4.TGACCA

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples RPE-WCE(2)_ChipSeq, RPE-H3K27ac_ChipSeq, RPE-WCE(3)_ChipSeq, RPE-CTCF_ChipSeq, RPE-E2F4_ChipSeq, RPE-POLII_ChipSeq, and ZNF92_Abgent_AT4646a_ChipSeq 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.
For samples AD-3-WCE-Retina_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Retinal pigment cells, science cell

growth_protocol: Sciencell epithelial cell medium

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.

tag: chip-seq antibody

tag: antibody catalog number

value: Abgent AP4646A

value: Retinal pigment cells #6540


title: Pol2_Jurkat_THZ-2-102_12hr_500nM_ChipSeq

description:
Chromatin IP against Pol2_Jurkat_THZ-2-102_12hr_500nM
05112012_D0WTHACXX_2.AGTTCC

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 -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL cell line

growth_protocol: Cells grown in RPMI1640+10%FBS

treatment_protocol: Treated with 500nM THZ-2-102 for 12 hours (Cdk7 covalent inhibitor - N. Gray lab).

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899

value: Jurkat


title: AD-1-WCE-astrocytes_ChipSeq

description:
Chromatin IP against AD-1-WCE-astrocytes
11062012_D1F51ACXX_2.CCGTCC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For samples MEF_WCE_ChipSeq, MEF_K27Ac_ChipSeq, 13F_WCE_ChipSeq, Sox2GFP_WCE_ChipSeq, 13F-K27Ac_ChipSeq, and Sox2GFP_K27Ac_ChipSeq 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.
For samples AD-12-Med1-Skeletal_ChipSeq and AD-1-WCE-astrocytes_ChipSeq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18 (human); mm8 (mouse)
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Spinal cord astrocytes, Sciencell

growth_protocol: Astrocyte Medium (AM, Cat. No. 1801)

tag: cll type

value: Sciencell #1820


title: Cdk7_Jurkat_DMSO_12hr_ChipSeq

description:
Chromatin IP against Cdk7_Jurkat_DMSO_12hr
05112012_D0WTHACXX_2.GGCTAC

treatment_protocol: Cells treated with DMSO/vehicle for 12 hours. Equivalent DMSO concentration to drug treatment with THZ-2-102.

value: Bethyl A300-405A


title: AD-3-WCE-Retina_ChipSeq

description:
Chromatin IP against AD-3-WCE-Retina
11062012_D1F51ACXX_2.GTGAAA

growth_protocol: Epithelial Cell Medium (EpiCM, Cat No 4101)

value: Sciencell #6540


title: iTreg.Ezh2KO.150.d5.RNA-seq

value: in vitro differentiated induced regulatory T cell


title: Cdk7_Jurkat_THZ-2-102_12hr_500nM_ChipSeq

description:
Chromatin IP against Cdk7_Jurkat_THZ-2-102_12hr_500nM
05112012_D0WTHACXX_2.CTTGTA


title: AD-12-Med1-Skeletal_ChipSeq

description:
Chromatin IP against AD-12-Med1-Skeletal
11132012_D1FATACXX_7.TTAGGC

source_name: Skeletal myoblast

growth_protocol: Skeletal Muscle Cell Medium (SkMCM, Cat. No. 3501)

value: Skeletal myoblast


title: RPE-E2F4_ChipSeq

description:
Chromatin IP against RPE-E2F4
05042013_D269BACXX_8.GATCAG

growth_protocol: sciencell epithelial cell media

value: Santa Cruz SC-1082


title: RPE-H3K27ac_ChipSeq

description:
Chromatin IP against RPE-H3K27ac
05042013_D269BACXX_6.TGACCA

growth_protocol: sciencell epithelial media

value: Abcam AB4729


title: RPE-POLII_ChipSeq

description:
Chromatin IP against RPE-POLII
05042013_D269BACXX_8.TAGCTT

growth_protocol: Scincell Epithelial media

value: Santa Cruz SC-899X


title: RPE-WCE(3)_ChipSeq

description:
Chromatin IP against RPE-WCE(3)
05042013_D269BACXX_7.ACTTGA

growth_protocol: sciencell epithelial growth media

value: Input


title: RPE-WCE(2)_ChipSeq

description:
Chromatin IP against RPE-WCE(2)
03142013_D1WLRACXX_7.CGATGT


title: Chipseq-H3K4me1

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: H3K4me1 ChIP-seq in rat GC pituitary cells

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the rn4 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

organism: Rattus norvegicus

source_name: rat GC pituitary cells

growth_protocol: GC cells are grown in Untraculture medium containing 5% FBS

extract_protocol:
For ChIP-seq, fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C overnight. For samples fixed with glutaraldehyde, proteinase K (0.3mg/ml) (Ambion) was added during de-crosslinking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) ;
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: siRNA and overexpression experiments in GC cells were performed using Neon system (Invitrogen). Conditions of 2 pulses of 1150 V with 30ms spacing were used. 100 nM siRNA and 3ug of DNA were used per 3x106 cells. Knockdown was repeated after 48h to obtain optimal depletion of the protein, verified by Western blotting.

value: rat GC pituitary cells

value: Millipore 07-436


title: phPol2_Ser7_r2_ChipSeq

description:
Chromatin IP against phPol2_Ser7_r2
08082012_C12E8ACXX_2.ATTCCT

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

value: RNA Pol II (Ser7 phospho CTD)

value: Millipore 04-1570

value: V6.5 embryonic stem cells


title: Cdk7_mES_r2_ChipSeq

description:
Chromatin IP against Cdk7_mES_r2
08082012_C12E8ACXX_2.CGTACG


title: Chipseq-SATB1

description: SATB1 ChIP-seq in rat GC pituitary cells

value: Kohwi-Shigematsu lab


title: Chipseq-HA-Pit1r271w

description: HA-Pit1R27W1 mutant ChIP-seq in rat GC pituitary cells

value: HA-Pit1R27W1 mutant