title: CAGE_T9-3

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

institute: Leiden University Medical Center

description: DeepCAGE (5' sequencing)

data_processing: Illumina GAPipeline, GAPSS analysis (www.lgtc.nl/GAPSS_R), custom Perl and R scripts

source_name: Mouse C2C12 myoblasts

growth_protocol: Proliferating C2C12 mouse myoblasts were grown out on collagen coated plates in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: For DeepCAGE, we used the protocol of Valenet al. 2009, but we used modified adapters in the 5' and 3' end ligation steps that have linker sequences (proliferating – CCGACAGGTTCAGAGTTCTACAGAGACAGCAG and differentiated - CCGACAGGTTCAGAGTTCTACAGCTTCAGCAG)  for Illumina Genome Analyzer II sequencing and have a recognition site for EcoP15I used instead of MmeI.  For DeepSAGE we used a FC-102-1005 DGE-Tag Profiling NlaIII SamplePrepKit from Illumina

treatment_protocol: To induce fusion into myotubes, proliferating cells were serum deprived by changing to a medium of DMEM supplemented with 2% FBS

tag: time

value: T9 (days)

tag: cell type

value: Mouse C2C12 myoblasts

value: CAGE


title: Saccharomyces bayanus genome-wide nucleosome data

status: Public on Jul 06 2010

type: SRA

city: Boston

first: Alex

middle: M

last: Tsankov

state: MA

address: 155 Bay State

country: USA

institute: MIT

description: Mnase digested DNA and size selected for mononucleosomes (~150bp)

library_source: genomic

data_processing:
Read Extended Nucleosome Map: Each uniquely mapped read was then extended to a length of 100bp.  To generate a genomic nucleosome occupancy landscape, we cumulatively summed all extended reads covering each base pair.  The *.wig files use the WIGGLE fixed_step format.
Alignment: Sequence reads were mapped to the appropriate reference genome (fasta file attached) using BLAT. All reads mapping to a unique location in the genome with 4 or fewer mismatches were retained.  *.read files are tab delimited text files containing each uniques reads chromosomal coordinates.  The files have 4 columns and the following headers: readChrom, readStart, readStop, onForwardStrand (1=forward strand or +, 0=reverse strand or -).
Genomes: The version of the species' genomic sequences used in this study are attached as fasta files (*.fsa).

molecule: genomic DNA

organism: Saccharomyces bayanus

source_name: in vivo cells

growth_protocol: Overnight cultures for each species were grown in 450ml of media at 220 RPM in a New Brunswick Scientific air-shaker at 30°C until reaching mid log-phase.

extract_protocol:
Libraries were prepared according to standard Illumina instructions. Briefly, DNA was end-repaired. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 19 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Mnase digestion and gel purification of mononucleosomal DNA

treatment_protocol: Formaldehyde crosslink, shearing with MNase, isolation of mononucleosomal DNA using gel purification of DNA band ~150bp.

tag: strain


title: CAGE_T9-2

country: Netherlands

description: DeepCAGE (5' sequencing)

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: protocol


title: CAGE_T9-1_duplo

description: DeepCAGE (5' sequencing)


title: Saccharomyces castellii genome-wide nucleosome data

organism: Naumovozyma castellii


title: Saccharomyces mikatae genome-wide nucleosome data

organism: Saccharomyces mikatae


title: CAGE_T0-3

description: DeepCAGE (5' sequencing)

value: T0 (days)


title: SAGE_T9-3

description: DeepSAGE (3' sequencing)

value: SAGE


title: CAGE_T0-1

description: DeepCAGE (5' sequencing)


title: CAGE_T0-2

description: DeepCAGE (5' sequencing)


title: Saccharomyces paradoxus genome-wide nucleosome data

organism: Saccharomyces paradoxus


title: SAGE_T0-2

description: DeepSAGE (3' sequencing)


title: SAGE_T9-2

description: DeepSAGE (3' sequencing)


title: Chlamydomonas-D66-Sulfur-Replete

status: Public on Jul 08 2010

city: Stanford

first: Arthur

last: Grossman

state: CA

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institute for Science

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Processed sequence files from the Solexa pipeline output were aligned against the v.3.1 assembly of the Chlamydomonas genome. The SOAP alignment program (Li et al., 2008) was used to map the short reads in two steps. In a first alignment round, the raw 35-mers sequences were aligned to the genomic sequence with a tolerance of up to two mismatches and no indels. For those sequences that did not align to the genome a second round alignment was performed in which we recursively trim one base at a time (up to 21-mers) at either the 5’ or 3’ end of the reads until we found a (perfect) match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment.
Reference sequence: Chlamydomonas V3.1 unmasked assembly (JGI's Chlre3_1.fasta.gz, md5: c14cb6c004b90983e3a82404b1902173)  with a total of 1266 scaffolds. Global genomic coordinates in the accompanying processed files refer to the first base of scaffold_1 when the reference sequence is sorted as in Chlre3_1.fasta.gz.
Processed files: k-hits files. Format (tab delimited). Headers: Global genomic position - length of the alignment - number of unique hits

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cells were cultured under continuous light of ~60 μmol photon m-2s-1 at 23ºC in liquid and on solid Tris-Acetate-Phosphate (TAP) medium.

extract_protocol: Cell aliquots were collected for RNA isolation just prior to and 1, 6 and 24 h after being transferred to TAP and TAP-S medium. Total RNA from cells after 0 and 6 h of being transferred to -S medium were submitted to Illumina for sequencing.

treatment_protocol: To impose S deprivation, cells in mid-logarithmic growth phase were washed twice with liquid TAP medium without S (TAP-S), and equal numbers of cells were resuspended in TAP or TAP-S.

tag: medium

value: TAP


title: Saccharomyces kluyveryii genome-wide nucleosome data

organism: Lachancea kluyveri NRRL Y-12651


title: SAGE_T0-3

description: DeepSAGE (3' sequencing)


title: Yarrowia lipolytica genome-wide nucleosome data

organism: Yarrowia lipolytica

value: CLIB 89


title: SAGE_T9-1

description: DeepSAGE (3' sequencing)


title: Kluyveromyces lactis genome-wide nucleosome data

organism: Kluyveromyces lactis

value: CLIB 209


title: SAGE_T0-1

description: DeepSAGE (3' sequencing)


title: Saccharomyces cerevisiae genome-wide nucleosome data

organism: Saccharomyces cerevisiae


title: Debaryomyces hansenii genome-wide nucleosome data

organism: Debaryomyces hansenii

value: NCYC 2572


title: Candida glabrata genome-wide nucleosome data Dec0908

organism: Nakaseomyces glabratus

value: CLIB 138


title: 5-8F_nucleus

status: Public on Jul 14 2010

city: Guangzhou

first: Jian-You

last: Liao

address: XinGang West Road

country: China

institute: Sun Yat-Sen University

data_processing: txt: The 3' linker, CTGTAGGCACCATCAAT, was identified and stripped out of the raw reads using a dynamic programming algorithm, which request at least 5nt overlap between 35nt reads and 3' adaptor sequence.

molecule: nuclear RNA

organism: Homo sapiens

growth_protocol: Human Nasopharyngeal carcinoma cell lines 5-8F was maintained at 37°C in DMEM containing 10% FBS.

extract_protocol: sRNAs ranging from 18 to 30-nt were gel-purified and ligated to the 39 adaptor (5'-pUCGUAUGCCGUCUUCUGCUUGidT-3'; p, phosphate; idT, inverted deoxythymidine) and 5' adaptor (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3'). Ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5'-CAAGCAGAAGACGGCATACGA-3'; 5'-AATGATACGGCGACCACCGA-3'). Samples were sequenced on an Illumina 1G Genome Analyzer.

value: nasopharyngeal carcinoma cell line


title: CAGE_T9-1

description: DeepCAGE (5' sequencing)


title: Candida glabrata genome-wide nucleosome data Jan2809


title: CAGE_T0-1_duplo

description: DeepCAGE (5' sequencing)


title: Pancreatic islets-pregnant-rp2

status: Public on Jul 02 2010

city: San Francisco

first: Hail

last: Kim

address: 513 Parnassus avenue HSW1090

department: Diabetes Center

institute: University of California San Francisco

description: 13 weeks old pregnant (G13~15)

data_processing: 31-bp reads were mapped to the Refseq collection of mouse transcripts generated from mouse genome build MM9 using Seqmap34. Mapped reads were quantified using the reads per kilobase exon model metric. Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group. The quantified transcription levels were expressed as reads per kilobase of exon model per million mapped reads (RPKM).

source_name: pancreatic islets

growth_protocol: C57BL/6J mice were housed on a 12-h light/dark cycle in climate-controlled, pathogen-free barrier facilities. Mating was confirmed by the presence of a vaginal plug the next morning, designated day 0 of gestation (G0).

extract_protocol: Total RNA from pooled islets from 4 non-pregnant or pregnant (G13−G15) mice was converted into a library of template molecules using mRNA-Seq Sample Prep Kit (Illumina) according to manufacturer’s protocol. Poly(A)+ mRNA purified using poly-dT oligo-attached Dynal magnetic beads (Invitrogen) was fragmented in RNA fragmentation buffer (Ambion) at 94 ˚C for 5 minutes. First strand cDNA synthesis from the RNA fragments using Superscript III (Invitrogen) and random hexamers was followed by second strand synthesis using DNA Polymerase I and RNaseH, addition of a 3’deoxyadenosine, and ligation of adaptors.  Double stranded cDNAs of 200 ± 25 bp were purified by electrophoresis through a 2% low melting-point agarose gel, extracted using the QIAquick Gel Extraction Kit (Qiagen) and further purified using a QiaQuick PCR purification kit (Qiagen). Libraries were expanded with the Illumina Cluster generation protocol and sequenced at the UCSF Genomics Core Facility using the 36 cycle sequencing kit v3 (Illumina). Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group.

tag: organ

value: pancreatic islets

tag: pregnancy

value: adult prengnat female


title: Pancreatic islets-nonpregnant-rp3

description: 12 weeks old non-pregnant

value: adult normal female


title: Pancreatic islets-pregnant-rp3

description: 14 weeks old pregnant (G13~15)


title: Pancreatic islets-nonpregnant-rp1

description: 12 weeks old non-pregnant


title: Pancreatic islets-nonpregnant-rp2

description: 12 weeks old non-pregnant


title: 5-8F_cytoplasm

molecule: cytoplasmic RNA


title: H3K36me3 ChIP-Seq-LSK cells R1

status: Public on Jul 01 2010

first: Jiang

last: Zhu

address: 185 Cambridge Street

institute: Massachusetts General Hospital, Harvard Medical School and Broad Institute

description: Chromatin is immunoprecipitated with antibody against indicated epitope

data_processing: Illumina reads were post-processed and aligned to the reference genome (UCSC, mm8) from the 10th base using MAQ. Reads mapped to more than one position in the genome were filtered out. Multiple reads mapping to the same position were only counted once to remove potential bias from PCR. Aligned reads were extended by 300 bases to roughly approximate the average size of sequenced fragments, and a 25 bp resolution density map was established by counting the number of fragments that overlap each position. Positions in the density map where less than 50% of the flanking 200 bp are alignable were masked as repetitive and discarded from further analysis.

source_name: Hematopoietic stem and progenitor cells

growth_protocol: ES cells were grown in culture according usual labarotory practices. LSK cells were isolated from mouse bone marrow and FACS sorted for the presence of Lin-, Sca+, Kit+.

extract_protocol: Low cell number ChIP-Seq library preparation: The library method described here consists of three main steps. Step 1: ChIP DNA (estimated at 10-50 picograms) is primed with a universal primer for four cycles (Primer 1, below) to create template DNA with common sequences incorporated at the ends. Primer 1 contains a common sequence for PCR, a restriction site for BciVI (underlined) and a random 9-mer at the 3’end. Priming is achieved using Sequenase V2.0 (US Biochemical 70775), a polymerase with strand displacement capability but no 3’→5’ exonuclease activity, as described7. First, we incubated 7 μl of ChIP DNA with 1 μl of Primer 1 (2 mM stock) and 2 μl of Sequenase buffer at 98 deg C briefly, and then annealed at 8 deg C for 5 min. We then added 5.5 μl of Sequenase Enzyme mix containing 1.5μl of 3nM dNTPs, 0.75μl 0.1M DTT, 1.5μl 500mg/ml BSA and 0.3μl 13U/μl Sequenase. The temperature was gradually increased to 370C and incubated for 8 min. The whole cycle was then repeated with the addition of 1.2 μl of diluted Sequenase (1:4) instead of the enzyme mix. After four cycles of priming, excess Primer 1 was cleaned up by exonuclease and alkaline phosphatase treatment as follows: 3 μl of ExoSAP-IT reagent (USB, Cat#: 78250) was added to 15 μl of step 1 reaction and incubated for 15 min at 37 deg C. The enzymes were then heat-inactivated at 85 deg C for 15 minutes. Step 2: Product from the priming reaction was PCR amplified using Primer 2 (below). The template DNA from step 1 was diluted by addition of 43 μl of water. Four parallel PCR reactions (50μl total volume each) were set up with 15 μl template DNA from Step 1, 1μl of Primer 2 (5 mM stock), 1.5μl of Phusion DNA Polymerase (NEB), 15μl of high GC buffer (NEB) and 1% DMSO. The amplification consisted of 15 cycles of denaturation (98 deg C for 30 sec), annealing (40 deg C for 30 sec and 50 deg C for 30 sec) and extension (72 deg C for 1 min).  Step 3: PCR Product was column purified using the MinElute reaction clean up kit (Qiagen) and restricted overnight with BciVI (NEB) to yield 3’A overhangs at each end. Restricted fragments were ligated to Illumina adapters using the Quick Ligation Kit (NEB). This approach eliminates several standard library preparation steps, significantly reducing material loss. Ligation products were amplified for 18 cycles using standard Illumina primers and then size selected on 2 % agarose, retaining fragments between 275 and 600 bp. The resulting libraries were hybridized to flowcells, subjected to cluster amplification and sequenced on the Illumina Genome Analyzer using standard procedures.  Primer 1: 5'-GACATGTATCCGGATGTNNNNNNNNN-3' Primer 2: 5'-GACATGTATCCGGATGT-3’

value: Bone marrow isolated

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number

tag: antibody lot number


title: H3K27me3 ChIP-Seq-LSK cells R1

value: Millipore


title: H3K27me3 ChIP-Seq-LSK cells R2


title: H3K4me3 ChIP-Seq-LSK cells R1


title: H3K4me3 ChIP-Seq-LSK cells R2


title: THP1_cyto_sRNAs

city: St Lucia

first: Ryan

middle: J

last: Taft

state: QLD

address: 80 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: Small RNA deep sequencing of cytoplasmic THP-1 RNA

data_processing: FASTQ files were converted to FASTA and adaptor trimmed. The format of the FASTA headers is <LibName>_<internalTagID>_<tagCount>_<tagLength>. Alignment BED files are also provided.

source_name: monocytic leukemia cell line

growth_protocol: THP-1 cells were grown in suspension culture according to previously published methods (Suzuki et al Nature Genetics 2009) and harvested. Growth media was aspirated and the pellets were resuspended and washed twice in equivalent volumes of ice-cold PBS. The cells were then split into two equal volumes for the extraction of total RNA and the extraction of nuclear and cytoplasmic RNA. Total RNA was extracted using TRIzol (Invitrogen), according to the manufacturer’s instructions. Nuclear and cytoplasmic RNA was isolated as previously described (Hwang et al Science 2007), except that each wash was carried out using 1ml of wash buffer and tween-40 was substituted for tween-20 in the final wash. Additionally, to ensure complete clearing of any intact cells or nuclei, the cytoplasmic fraction was subjected to an additional centrifugation step at 1000 X g for 5 minutes at 4ºC, after which the supernatant was transferred to clean tubes for RNA extraction. To validate the integrity of the cytoplasmic fraction an aliquot was aspirated and inspected under an inverted light microscope to confirm that it was free from intact cells or nuclei. The nuclear fraction was similarly confirmed free from intact cells under an inverted light microscope by comparing an aliquot of nuclei after the final wash step to an aliquot of intact cells. RNA was extracted using the TRIzol (Invitrogen) according to the manufacturer’s instructions and the resulting RNA pellets were resuspended in equal volumes of ultra-pure water to obtain cell-equivalent concentrations.

extract_protocol: Prior to deep sequencing 2.4 x 10^-6 pmol and 2.4 x 10^-7 pmol of three 21mer and three 18mer synthetic RNA spike-ins with 5’ phosphate and 3’ hydroxyl groups, respectively, were added to the cytoplasmic, nuclear, and total RNA pools in equal quantities. Deep sequencing of the THP-1 small RNA samples was performed by GeneWorks (Adelaide, Australia) on the Illumina GAII. Library preparation and sequencing was completed according to the manufacturer’s instructions with one modification. Sample isolation from the PAGE gel after adaptor ligation was performed with a modified set of size markers to facilitate sequencing of small RNAs greater than or equal to 15 nt, allowing detection and quantification of tiRNAs and other very small RNA species.

tag: passages


title: QDE-2_IP Solexa sequencing

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
CIP PNK cloning
QDE-2 IP associated RNA profiling

data_processing:
Raw sequences are processed using a customized PERL script: sequences were identified using the first 6nt of the 3' linker, CTGTAG. Then, the perfect matches to Neurospora crassa Assembly 7 were obtained using a PERL hash method. Sequences matching serval loci of the genome were normalized based on the matches. Please request the script by emailing weifeng.gu@umassmed.edu
Alignment files provided in .txt and .gff formats.
Multi-alignments that match at the same loci by the same solexa sequences are collapsed by signing a score in the gff format column 6, indicating how many  such identical sequences we got. For example, mir-1 are sequences 10000 times and matched one unique locus. This locus was represented only once as a feature containing a score 10000.

organism: Neurospora crassa

source_name: QDE-2 IP

growth_protocol: constant light, 1x Vogel's 2% sucrose, 25 C

extract_protocol:
Isolating MycQDE-2 associated RNAs: Myc-QDE-2 expressing strain was grown liquid culture of in the presence or absence of histidine (100 ug/ml), and harvested 40 hours after inoculation. Cell extracts were prepared in a buffer containing 25 mM Tris (pH 7.5), 150 mM NaCl, 1.5 mM MgCl2, 1% NP40, 1mM DTT, protease inhibitors, and 100 U/mL RNase inhibitor (RNaseOut, Invitrogen). Cell extracts were then pre-cleaned by incubation with 20 uL of Protein G Sepharose (GE Healthcare) for 1 h at 4°C. For immunoprecipitation of Myc-QDE-2, the precleaned extracts were incubated first with 5ug Myc monoclonal antibody overnight at 4°C and followed with 25 uL of Protein G Sepharose for 2 h at 4°C. Immunoprecipitated beads were washed five times using the extraction buffer. The beads were then resuspended in 150 uL proteinase K buffer and treated with 1mg/ml proteinase K (RNA grade, Invitrogen) at 65°C for 1 hr. QDE-2 associated RNAs were recovered by phenol/chloroform extraction and ethanol precipitation.
QDE-2 IP associated small RNA cloning: RNAs associated with QDE-2 IP were resolved in a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 26-nt) in separate lanes. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated using 20mg of glycogen as the carrier. Gel purified RNA was treated with 1 Unit/µl of Alkaline Phosphatase, Calf Intestine (NEB) in 100mM NaCl, 50mM Tris-HCl, 10mM MgCl2, 1mM Dithiothreitol, pH 7.9 at 25°C and 1 Unit/µl SuperRNaseIn (Ambion) for 1 hour at 37 °C. After phenol extraction, the gel purified RNA and 1µM of each standard were incubated with 20µM of 3'-end linker, 1 Unit/µl of SuperRNaseIN, 10% DMSO and 3 Units/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2, 6mg/mL BSA, 10mM DTT).  The 3' ligated products were gel purified and treated with 1 Unit/µl Polynucleotide Kinase in 1x Polynucleotide Kinase buffer (70mM Tris-HCl, 10mM MgCl2, 5mM Dithiothreitol, pH 7.6 at 25°C), 2mM ATP, 1 Unit/µl SuperRNAseIN. After phenol extraction, RNAs were incubated in the presence of 30µM of 5' adapter oligonucleotide, 1 Unit/µl SuperRNaseIN (Ambion) and 3 Units/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO. The ligated products were gel purified as described above and reverse transcribed in a standard 50µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 10% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.)

tag: fraction

value: IP fraction

tag: genotype/variation

value: wild type

value: Myc monoclonal antibody (Roche, Anti-c-myc, Cat.No.11667203001) to pull down MycQDE-2 protein


title: THP1_nuc_sRNAs

description: Small RNA deep sequencing of nuclear THP-1 RNA


title: Whole Brain Degradome 2

status: Public on Jun 25 2010

city: Cambridge

first: Jin-Wu

last: Nam

address: Nine Cambridge Center

institute: Whitehead Institute

description: PolyA selection

data_processing:
Linker sequences were removed, requiring a match to at least five of the six most proximal linker nucleotides.  After filtering out tags shorter than 20 nt, degradome tags were mapped to RNAs annotated in the ENSEMBL (http://www.ensembl.org/), requiring a perfect match.  To find “multiple loci tags,” and tags that did not map to annotated RNAs, filtered tags were mapped to the human genome (hg18, http://genome.ucsc.edu/).
sequence reads are summarized as frequency counts

source_name: Whole Brain

tag: data type

value: Degradome

tag: tissue

value: brain


title: Whole Brain Degradome 3

description: PolyA selection

extract_protocol: Linker sequences were removed, requiring a match to at least five of the six most proximal linker nucleotides.  After filtering out tags shorter than 20 nt, degradome tags were mapped to RNAs annotated in the ENSEMBL (http://www.ensembl.org/), requiring a perfect match.  To find “multiple loci tags,” and tags that did not map to annotated RNAs, filtered tags were mapped to the human genome (hg18, http://genome.ucsc.edu/).


title: Whole Brain Degradome 1

description: PolyA selection


title: TSS_FWAF_logphase

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

data_processing:
Alignment: The data were aligned onto the G. sulfurreducens PCA genome (NC_002939.4) using the Mosaik Aligner (http://bioinformatics.bc.edu/marthlab/Mosaik), hash size = 15, mismatch=0. These data are in the *bed files.

5' end: the 5' end of unique aligned reads were counted and considered as potential transcription start sites. These data are in the *wig files.

organism: Geobacter sulfurreducens PCA

source_name: G. sulfurreducens PCA, grown in FWAF medium, mid-log phase

growth_protocol: G. sulfurreducens PCA strain was cultured in FWAF medium, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with a Thermo NanoDrop 1000.

RNA with 5’-monophosphate end was removed with 5’-phosphate-dependent exonuclease. The 5’-triphosphate end of primary RNA was then converted to 5’-monophosphate end with RNA 5’ polyphosphatase. 5’ sRNA adapter was ligated to the 5’ end of mRNA. cDNAs were then synthesized from the adapter-ligated mRNA using 3’-adapter. Fraction of the cDNA between 100 bp and 300 bp was then gel purified and PCR amplified.

value: PCA

tag: genotype

tag: condition

value: fresh water acetate-fumarate (FWAF) medium


title: TSS_N2_logphase

source_name: G. sulfurreducens PCA, grown in FWAF medium with N2 as nitrogen source, mid-log phase

growth_protocol: G. sulfurreducens PCA strain was cultured in FWAF medium with N2 as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.

tag: strain

value: fresh water acetate-fumarate (FWAF) medium with N2


title: TSS_electrode

source_name: G. sulfurreducens PCA, grown on electrode, one week

growth_protocol: G. sulfurreducens PCA strain was cultured on electrode, under strictly anoxic conditions at 30°C, and harvested one week after growth.

value: electrode


title: HeLa Degradome 2

description: PolyA selection

source_name: HeLa cell

tag: rnai treatment

tag: cell line

value: HeLa


title: HeLa Degradome 5

description: PolyA selection


title: H3K36me3 ChIP-Seq-LSK cells R2

tag: cell type


title: HeLa Degradome 1

description: PolyA selection


title: H3K4me3 ChIP-Seq-10K ESC

source_name: Embryonic stem cells

value: ES cells line


title: mouse_granulocyte_nuclei_smallRNAs

description: Small RNA deep sequencing of primary mouse granulocyte nuclei

data_processing: For the primary granulocyte nuclei small RNA profiling FASTQ files were converted to FASTA and adaptor trimmed. The format of the FASTA headers is <LibName>_<internalTagID>_<tagCount>_<tagLength>. Additional information with respect to spliRNA expression in granulocyte cells (i.e. alignment BED files) can be found at http://jsm-research.imb.uq.edu.au/groupwiki/index.php?title=NuclearTinyRNAs.

source_name: mouse primary granulocyte nuclei

growth_protocol: C57BL/6J mice were obtained from the Animal Resource Centre (Perth, Australia), with all animal experiments performed in a pathogen free facility according to national and institutional guidelines. Bone marrow was harvested from the femur, tibia and spine using a mortar and pestle in PBS supplemented with 2% fetal calf serum (FCS) as previously described (Holst et al Nat Protoc 2006). Bone marrow cells were passed through a 70 mm filter to ensure a single cell suspension, and incubated with lineage specific antibodies (B220, CD19, CD3, Sca–1; BioLegend), conjugated to biotin, together with anti–Gr–1–fluorescein isothiocyanate (FITC; Biolegend), anti–cKit–phycoerythrin (PE; Becton Dickinson), anti–CD34–Alexafluor 647 (eBioscience) and anti–CD16/32–PerCP/Cy5.5 (Becton Dickinson) antibodies. Cells were washed twice in PBS with 2% FCS and incubated with streptavidin–APC–Cy7 (Biolegend). Control stains for FITC, PE, PerCP/Cy5.5, Alexafluor 647 and APC–Cy7 were used to determine compensation settings and gating for each population. Mature granulocytes were purified as shown previously (Guibal et al Blood 2009), using fluorescence activated cell sorting (FACS) on a Becton Dickinson Aria II. After purification, a small sample of the cells was reanalyzed for purity by flow cytometry, and a separate sample was stained using May-Grünwald Giemsa following a cytospin. Purification of the nucleus from sorted cells was carried out using the PARIS kit (Ambion) with modifications to minimise RNA degradation. In order to confirm the purity of the nuclear fraction, SDS-PAGE and Western blots were carried out to detect the known cytoplasmic protein GAPDH, and the ubiquitous protein b–actin, on whole cell and nuclear lysates to ensure absent cytoplasmic contamination of the nuclear fraction. RNA was extracted from the nuclear fraction using Trizol prior to deep sequencing.

extract_protocol: Deep sequencing of small RNAs was performed by GeneWorks (Adelaide, Australia) on the Illumina GAII. Library preparation and sequencing was completed according to the manufacturers’ instructions.

value: granulocyte


title: HeLa Degradome 4

description: PolyA selection


title: HeLa Degradome 3

description: PolyA selection


title: THP1_total_sRNAs

description: Small RNA deep sequencing of total THP-1 RNA


title: Zebrafish Embryo small RNAs

description: Size fraction(18-30nt)

data_processing:
Small RNA sequences from same total RNA samples were mapped to the human genome (hg18), requiring a perfect match, and reads co-localizing to annotated miRNA loci (miRBase, version 11.0) were counted.
sequence reads are summarized as frequency counts

organism: Danio rerio

source_name: Embryo Cells

extract_protocol: The small RNA cDNA libraries were made as described (Grimson et al. 2008), except for the 3' adaptor ligation, which was 5' adenylated pTCGTATGCCGTCTTCTGCTTGidT. For a detailed protocol, see http://web.wi.mit.edu/bartel/pub/protocols.html.

value: small RNAs

value: embryo


title: white_cells-1

city: Foster City

first: Brian

last: Tuch

address: 850 Lincoln Center Dr.

institute: Life Technologies

description:
Strand-specific RNA-Seq.
Strain QMY23 (PMID: 17351132).
Poly(A) RNA.
Biological replicate 1 of 2.

data_processing:
AB WT Analysis Pipeline.

The reads were aligned to the Candida albicans Assembly 21 (Ca21) genome (from Candida Genome Database [CGD]: www.candidagenome.org) using the alignment algorithm provided by the WT Pipeline v1.2 (Life Technologies) and documented in their manual. The reads were filtered against a database containing rDNA, tRNA, repetitive element, CEN and adapter sequences. Alignments are provided in MAX format. A MAX specification file is available on the Series GSE21291 record.

The WIG files were generated by counting the number of uniquely aligned reads covering each position in the genome. The coverage on the plus and minus strands are provided in the *plus.wig and *minus.wig files, respectively.

organism: Candida albicans

source_name: Candida albicans white cells

growth_protocol: 23°C; SC medium (PMID: 12073320) with 100 mg/l uridine; log-phase growth (OD600=1).

extract_protocol:
Total RNA was extracted from the yeast cells (Hernday AD, Noble SM, Mitrovich QM, Johnson AD (2010) Genetics and Molecular Biology in Candida albicans. Methods in Enzymology: Elsevier Inc. pp. 737-758).

Two rounds of poly(A) selection with Poly(A)Purist MAG kit (Ambion). SOLiD whole transcriptome (WT) protocol applied to poly(A)-selected RNA.

treatment_protocol: None.

tag: isolate

value: MTLa/MTLa

value: white

tag: rna preparation

value: poly(A) RNA selection


title: opaque_cells-2

description:
Strand-specific RNA-Seq.
Strain QMY23 (PMID: 17351132).
Poly(A) RNA.
Biological replicate 2 of 2.

source_name: Candida albicans opaque cells

value: opaque


title: Tbrucei_ShortStumpy_SLT (GDG-10)

city: Bern

first: Daniel

last: Nilsson

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description:
Instrument: GA-II, EAS210R
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.4.0
protocol: Spliced Leader Trapping
GDG-10
polyA RNA

data_processing:
Base calling was performed using the Genome Analyzer Pipeline (Illumina). Linker sequences were removed while separating reads according to identified barcodes. Only sequence reads of inserts with a length of at least 24 nt were retained. A pipeline was set up using languages with open source interpreters (bash, perl and R) to automate the following analysis. The reads were mapped to the genome sequence of T. brucei TREU927 (build TriTrypDB 2.0) using maq (http://maq.sourceforge.net) with n=3 and an effective first read length of 24. Single mapping reads were separated from multi mapping reads by an alignment quality threshold of 30. Tags ending in the same position were joined together, and their counts were added (using bioperl). Tag counts were normalized to the library size (number of reads of length 24 or more) and scaled linearly to reflect counts of tags per million (TPM). Mapped tags were assigned to the downstream annotated protein coding gene. Tags mapping internally to a coding sequence (CDS) were assigned to it as internal splice sites.

The 3'adaptor and barcode of GDG-2 -- GDG-10 were as follow.
3' adaptor: <barcode>AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
where barcode is one of:
GDG-2 CCTG
GDG-3 CGAC
GDG-4 GTCT
GDG-5 CAGT
GDG-6 CTCA
GDG-7 GTCT
GDG-9 CTTT
GDG-10 CGGA
GDG-21 (normal Illumina RNAseq run, one channel) had the 3' adaptor CTGTAGGCACCATCAATCGTA.

Processed data file type for this sample: GFF

organism: Trypanosoma brucei

source_name: Trypanosoma brucei cell culture

growth_protocol: Bloodstream form parasites were grown in mice, insect stage parasites in SDM79 medium supplemented with 10% FCS.

extract_protocol: RNA was extracted using TriPure (Roche, Switzerland) according to the manufacturer. PolyA mRNA was purified from 7.5 μg total RNA using Dynabeads oligo-(dT) beads according to the manufacturer (Invitrogen, USA). First strand cDNA was synthesized from polyA RNA using random hexamers and Superscript II reverse transcriptase (Invitrogen, USA) in a final volume of 20 μl for 1 hour at 42ºC. Half of the first strand mix was used for second strand synthesis (10 μl 1st strand mix, 1 μl RNaseH, 15 minutes at 37ºC). Second strand synthesis was done using 2 μl 10x Thermopol buffer (New England BioLabs), 1 μl dNTPs 10mM, 1 μl 2nd strand primer 10μM ([BIOT]5'- AATGATACGGCGACCACCGAGATCTACAGTTTCTGTACTATATTG -3'), 2 units Taq polymerase (New England BioLabs, USA) and 4.5 μl H2O by incubation for 5 minutes at 50ºC and then 5 minutes at 72ºC. The cDNA was purified on a Qiagen MinElute column (Qiagen, USA) and eluted in 10ul TE buffer. Adapter ligation to the purified dsDNA was done using (10.0 μl DNA, 2.5 μl 10X Ligase Buffer (New England BioLabs), 10.0 μl H2O, 1.0 μl Fasteris customized bar-coded paired-end Illumina adapter, 600 units T4 DNA Ligase (New England BioLabs, USA) for 1hour at room temperature. The ligation mix was purified from unligated linker with Streptavidin beads (Dynabeads). After incubation at room temperature for 15 minutes beads were separated on a magnetic stand, and washed twice and then resuspended in 20 μl 10mM Tris buffer. 5 μl was used for PCR amplification with primers (5'- AATGATACGGCGACCACCGA -3'/ 5'-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAAC -3') following the standard Illumina mRNA-SEQ library amplification protocol. Fragments in the range 120-160 bp were separated on a 2% agarose-TBE gel and subsequently purified on Qiagen Gel Extraction MinElute columns (Qiagen, USA). Quality control for insert size was performed by TOPO cloning and subsequent ABI sequencing.

tag: life cycle stage

value: Short stumpy bloodstream form

tag: culture condition

value: Mice

tag: rna interference target

tag: tetracycline induced


title: white_cells-1_riboMinus

description:
Strand-specific RNA-Seq.
Strain QMY23 (PMID: 17351132).
Ribo-depleted total RNA.

data_processing:
AB WT Analysis Pipeline.

The reads were aligned to the Candida albicans Assembly 21 (Ca21) genome (from Candida Genome Database [CGD]: www.candidagenome.org) using the alignment algorithm provided by the WT Pipeline v1.2 (Life Technologies) and documented in their manual. The reads were filtered against a database containing rDNA, tRNA, repetitive element, CEN and adapter sequences. Alignments are provided in MAX format. A MAX specification file is available on the Series GSE21291 record.

The WIG files were generated by counting the number of uniquely aligned reads covering each position in the genome. The coverage on the plus and minus strands are provided in the *plusStrand.wig and *minusStrand.wig files, respectively.

extract_protocol:
Total RNA was extracted from the yeast cells (Hernday AD, Noble SM, Mitrovich QM, Johnson AD (2010) Genetics and Molecular Biology in Candida albicans. Methods in Enzymology: Elsevier Inc. pp. 737-758).

Small RNA depletion with mirVana miRNA isolation kit (Ambion; alternative protocol), followed by two rounds of rRNA depletion with RiboMinus Eukaryote Kit for RNA-seq (Invitrogen). SOLiD whole transcriptome (WT) protocol applied to ribo-depleted total RNA.

value: ribodepletion


title: white_cells-2


title: Tbrucei_PC_late02_RNAseq (GDG-21)

description:
Instrument: GA-IIx, EAS210R
Sequencing Kit: Chrysalis 36cycles v 4.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.6.0
protocol: RNA-Seq
GDG-21
polyA RNA

data_processing:
Base calling was performed using the Genome Analyzer Pipeline (Illumina). Linker sequences were removed while separating reads according to identified barcodes. Only sequence reads of inserts with a length of at least 24 nt were retained. A pipeline was set up using languages with open source interpreters (bash, perl and R) to automate the following analysis. The reads were mapped to the genome sequence of T. brucei TREU927 (build TriTrypDB 2.0) using maq (http://maq.sourceforge.net) with n=3 and an effective first read length of 24. Single mapping reads were separated from multi mapping reads by an alignment quality threshold of 30. Tags ending in the same position were joined together, and their counts were added (using bioperl). Tag counts were normalized to the library size (number of reads of length 24 or more) and scaled linearly to reflect counts of tags per million (TPM). Mapped tags were assigned to the downstream annotated protein coding gene. Tags mapping internally to a coding sequence (CDS) were assigned to it as internal splice sites.

The 3'adaptor and barcode of GDG-2 -- GDG-10 were as follow.
3' adaptor: <barcode>AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
where barcode is one of:
GDG-2 CCTG
GDG-3 CGAC
GDG-4 GTCT
GDG-5 CAGT
GDG-6 CTCA
GDG-7 GTCT
GDG-9 CTTT
GDG-10 CGGA
GDG-21 (normal Illumina RNAseq run, one channel) had the 3' adaptor CTGTAGGCACCATCAATCGTA.

Processed data file type for this sample: WIG

value: Procyclic, late

value: SDM79 supplemented with 10% FBS


title: Tbrucei_PC_late_SLT (GDG-7)

description:
Instrument: GA-II, EAS210R
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.4.0
protocol: Spliced Leader Trapping
GDG-7
polyA RNA


title: Tbrucei_LongSlender_SLT (GDG-9)

description:
Instrument: GA-II, EAS210R
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.4.0
protocol: Spliced Leader Trapping
GDG-9
polyA RNA

value: Long slender bloodstream form


title: mESC-mock

city: Illkirch

first: Laszlo

last: Tora

email: tora@igbmc.fr, krebs@igbmc.fr

address: 1, rue Laurent Fries

department: Functional Genomics

country: France

institute: IGBMC

description: Chromatin IP with no Ab

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with one or fewer mismatches were retained.

organism: Mus musculus

source_name: embryonic stem cells E14

growth_protocol: standard feeder free mES cells growing protocol

extract_protocol: library was created on a sequencing platform

tag: passage

tag: ab

value: no Ab


title: mESC-LUZP1

description: Chromatin IP against LUZP1

value: LUZP1 Rabbit sera


title: Cord blood CD4+_Act_4h

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Chromatin IP against STAT6

data_processing: Sequencing was performed on an Illumina Genome Analyzer and 27bp reads were aligned to the human reference genome (NCBI v36) using the short oligonucleotide alignment program SOAP (Li et al., Bioinformatics 24, 2008), allowing at most two mismatches. Only uniquely mapped reads were retained.

source_name: human cord blood CD4+ cell, activated, 4h

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturer's instructions.

extract_protocol: Cells were fixed using formaldehyde solution, lysed and sonicated to obtain chromatin fragments of 100-500bp size. The sonicated chromatin was then subjected to immunoprecipitation with polyclonal anti-STAT6 antibody (rabbit polyclonal αSTAT6 M-20, Santa Cruz Biotechnology, Inc.). The STAT6 bound chromatin was isolated using Dynal magnetic beads coated with secondary antibody anti-rabbit IgG (Dynal Biotech). The immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen minielute columns. The sample preparation for Solexa sequencing was performed according to Illumina's recommendations by Illumina service provider, Fasteris Life Sciences, Switzerland. Briefly, the ChIP DNA was end-repaired with T4 DNA polymerase, Klenow and PNK, and after purification with Qiagen minielute columns, a 3´-A was added using Klenow (exo-). The -A tailed DNA samples were purified and ligated with Illumina paired ends adaptors. After adapter ligation, fragments of size range of 200-300bp were purified from agarose gel and subjected to PCR amplification using Phusion polymerase with paired ends primers for 18 cycles. The libraries were quantified using PicoGreen Assay (Q-bit Invitrogen) before in situ amplification on the Illumina Cluster Station to generate DNA colonies according to the manufacturer's standard recommended protocol. Sequencing was performed on an Illumina Genome Analyzer “GAII” for 36 cycles using sequencing kit V-1.0 with scanning buffers V-2.0 and GA data analysis pipeline 1.0rc4. Each library was sequenced in a single read channel that produced between 4 to 5.2 million reads.

treatment_protocol: Cells were activated through the T cell receptor (plate bound antiCD3 500 ng/24-well or proportially scaled up or down according to culturing well dimension, and soluble antiCD28 500 ng/ml, Immunotech, France), and to half of the samples IL-4 was added (10ng/ml, R&D Systems). Cells were cultured in Yssel´s medium. Cells were harvested at 1 and 4 h timepoints. Naive cells without any treatment were collected as control.

value: cord blood

value: CD4+ T cells


title: Cord blood CD4+_Act+IL-4_4h

description: Chromatin IP against STAT6

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 4h


title: Tbrucei_Alba1_N_SLT (GDG-5)

description:
Instrument: GA-II, EAS210R
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.4.0
protocol: Spliced Leader Trapping
GDG-5
polyA RNA

value: Procyclic

value: non-induced


title: Tbrucei_BS_427_SLT (GDG-4)

description:
Instrument: GA-II, EAS038
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline1.3.2
protocol: Spliced Leader Trapping
GDG-4
polyA RNA

value: Bloodstream


title: MZdicer mutant2 hu896

city: New Haven

first: Antonio

middle: J.

last: Giraldez

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: RNA size from 18 to 35 nt.

data_processing: Alignment: Sequence reads were mapped to Zebrafish (Zv8/danRer6) precursor miRNA sequences using Bowtie software (version 0.12.1) with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.

source_name: 48hpf embryo, Mzdicer mutant

growth_protocol: Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hours post-fertilization, embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.

extract_protocol: Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions (Part # 1004239 Rev. A) accompanying the small RNA Sample Kit. Briefly, total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18-35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: mixed AB, TU, TL,TLF background

tag: developmental stage

value: 48h post-fertilization embryo

value: MZdicer hu896/hu896


title: WT2

description: RNA size from 18 to 35 nt.

source_name: 48hpf embryo, WT

value: wild type


title: Cord blood CD4+_0h

description: Chromatin IP against STAT6

source_name: human cord blood CD4+ cell, 0h


title: Tbrucei_Alba34_N_SLT (GDG-2)

description:
Instrument: GA-II, EAS038
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline1.3.2
protocol: Spliced Leader Trapping
GDG-2
polyA RNA

value: Alba3 and Alba4


title: Cord blood CD4+_Act_1h

description: Chromatin IP against STAT6

source_name: human cord blood CD4+ cell, activated, 1h


title: Cord blood CD4+_Act+IL-4_1h

description: Chromatin IP against STAT6

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 1h


title: MZdicer mutant1 hu715

description: RNA size from 18 to 35 nt.

value: MZdicer hu715/hu715


title: Tbrucei_Alba34_I_SLT (GDG-3)

description:
Instrument: GA-II, EAS038
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline1.3.2
protocol: Spliced Leader Trapping
GDG-3
polyA RNA

value: induced


title: MZago2 mutant YΔ90

description: RNA size from 18 to 35 nt.

source_name: 48hpf embryo, MZago2 mutant

value: MZago2 Δ90/Δ90


title: opaque_cells-1

value: MTLa/MTLa

value: opaque

value: poly(A) RNA selection


title: Tbrucei_Alba34_I_SLT (GDG-6)

description:
Instrument: GA-II, EAS210R
Sequencing Kit: Chrysalis 36cycles v 3.0
Cycles: 76
Initial Data Analysis Pipeline: GAPipeline-1.4.0
protocol: Spliced Leader Trapping
GDG-6
polyA RNA

value: SDM79 supplemented with 10% FBS


title: Mitotic Input DNA

status: Public on Jun 24 2010

city: Los Angeles

first: Benjamin

last: Berman

department: USC Epigenome Center

institute: University of Southern California

description:
Input DNA
input_mit

data_processing: Illumina GA-Pipeline 1.4.0, Maq (Li et. al. 2008) with default command line parameters

source_name: Mitotic T24 Cells

growth_protocol: Mitotic T24 cells were grown to ~50% confluency at which time 100ng/ml Nocodazole was added for 20 hours. Mitotic cells were then  harvested by shaking and ppoured into falcon tube.  G0/G1 cells were obtained by growing cells to confluency and then serum starving them for 24 hours in media containing 0.1% FBS.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp-700 (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 100ng/ml Nocodazole was added for 20 hours to mitotic T24 cells at ~50% confluency

value: T24 bladder cancer cells

tag: antibody

tag: fraction

value: Input


title: G0/G1 Input DNA

description:
Input DNA
input_nonmit

source_name: G0/G1 T24 Cells


title: H2A.Z_G0/G1_ChIPSeq

description:
Chromatin IP against H2A.Z
H2AZ_nonmit

value: IP


title: H2A.Z_Mitotic_ChIPSeq

description:
Chromatin IP against H2A.Z
H2AZ_mit


title: WT1

description: RNA size from 18 to 35 nt.

tag: genotype


title: IgG-ChIP-Seq, Nrl ko, 1

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

country: Germany

institute: Institute of Human Genetics

description: Chromatin IP against IgG.

data_processing:
Mapping: 36 bp tags were mapped to the mouse genome (NCBI Build 37, mm9) using the Genomatix mapping algorithm allowing one mismatch.

Clustering: Peak (Cluster) detection was performed with the Genomatix NGS Analyzer.

source_name: Retina, Nrl ko, IgG ChIP

growth_protocol: Retinas were isolated from adult C57BL/6 and Nrl-/- mice, and Crx-ChIP-Seq and IgG-ChIP-Seq were performed.

extract_protocol: Crx-DNA complexes were isolated from retinal lysates with anti-Crx-antibody.  Anti-IgG-antibody was used as a control. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Nrl-/-

tag: age

value: 8 weeks

tag: tissue

value: retina

tag: chip antibody

value: IgG


title: Crx-ChIP-Seq, Nrl ko, 2

description: Chromatin IP against Crx.

source_name: Retina, Nrl ko, Crx ChIP

tag: strain

value: Crx


title: HeLa_ANS

city: Philadelphia

first: Jeongsik

last: Yong

state: PA

address: 415 Curie Blvd.

department: Biochemistry and Biophysics

institute: University of Pennsylvania School of Medicine/HHMI

description:
RNA IP against Gemin5
Sequencing of immunoprecipitated snRNAs

data_processing: Raw reads from Illumina were converted to Fastq formats. These reads were then trimmed to remove the trailing adapter sequence, allowing for 0-2 mismatches in the adapter sequences. Remaining reads were then filtered by length. Any read with length 15-30bp was kept and others were discarded. These resulting reads were then aligned to the custom sequences using Eland and allowing no mismatches in the read (no quality information is used). Any reads that do not align were then aligned again using Eland to the genome and allowing no mismatches. The final results of this alignment are in ProcessedSequences.bed.

source_name: HeLa PV cells

growth_protocol: HeLa PV cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Cells were havested and crosslinked by 0.2% formaldehyde for 10 min. Extracts were prepared in the IP buffer (20 mM Tris, 500 mM NaCl, 2.5 mM MgCl2, 1% Empigen) and the immunoprecipitation was carried out using anti-Gemin5 antibody. IPed RNAs were treated with limited RNase T1 followed by extensive washing. The resulting RNAs were used for the construction of cDNA library for Illumina genome analyzer according to the supplier's instructions.

treatment_protocol: Cells were treated with Anisomycin for 4 hours

tag: cell line

value: HeLa PV cells

tag: ip antibody


title: Crx-ChIP-Seq, Nrl ko, 1

description: Chromatin IP against Crx.


title: IgG-ChIP-Seq, Nrl ko, 2

description: Chromatin IP against IgG.


title: p300_ChIPSeq

status: Public on Jun 22 2010

city: Cleveland

first: Mike

middle: Paul

last: Schnetz

state: OH

address: 10900 Eulid Ave

institute: Case Western Reserve University

description: Chromatin IP against p300

data_processing: The Eland software (Illumina) was used to align reads with up to two mismatches against the mm8 reference genome. Regions significantly enriched for CHD7 or p300 binding were identified using F-seq, a feature density estimator for high-throughput sequence tags. Genomic regions found to have an unexpectedly high percentage of reads aligning to the sample positions, indicating PCR artifacts, were eliminated from the analysis. Also excluded from the analysis were CHD7 and p300 peaks in which the midpoint overlapped a repetitive region.

source_name: mouse ES cells

growth_protocol: R-1 ES cells were cultured under feeder free conditions according to standard procotols.

extract_protocol: ChIP, DNA purification, and library preparation for Illumina sequencing were performed as described (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, et al. (2009) ChIP-seq: using high throughput sequencing to discover protein-DNA interactions. Methods 48: 240-248) . ChIP was performed using commercially available antibodies to CHD7 (Abcam, ab31824, batch #215651) and P300 (Santa Cruz, sc-585, batch # unknown). Sequencing was done on an Illumina GAII instrument according to the manufacturer’s protocol.

tag: cell type

value: ES cells


title: Crx-ChIP-Seq, wt, 2

description: Chromatin IP against Crx.

source_name: Retina, wt, Crx ChIP

value: WT


title: Crx-ChIP-Seq, wt, 1

description: Chromatin IP against Crx.


title: CHD7_ChIPSeq

description: Chromatin IP against CHD7


title: GM10861_vitaminD_rep2

city: Oxford

first: Sreeram

last: Ramagopalan

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description:
ChIP against VDR.
08_861_D3_R2

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied.

Alignment: Reads were aligned to human genome hg18 (NCBI Build 36) using Eland software (Illumina pipeline).

Peaks: MACS peak-calling algorithm was used with a cut-off of pvalue = 1.00e-09 (http://liulab.dfci.harvard.edu/MACS/). MACS peaks were filtered by removing a small number of peaks in locations where the Input sample had peaks with >12 overlapping reads.

source_name: lymphoblastoid, GM10861, vitamin D

growth_protocol: Cells were grown in RPMI-1640 medium supplemented with 10% FBS, 0.2 mM L-glutamine at 37 degrees Celsius in 5% humidified CO2.

extract_protocol: Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-VDR antibody sc-1008 (Santa Cruz Biotech; lot# B1809). ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.

treatment_protocol: Cell lines were either stimulated for 36 hours with calcitriol or unstimulated.

value: lymphoblastoid

tag: treatment

value: calcitriol

value: anti-VDR

tag: antibody name

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number

tag: antibody lot number


title: GM10861_vitaminD_rep1

description:
ChIP against VDR.
07_861_D3_R1


title: GM10861_unstimulated_rep2

description:
ChIP against VDR.
06_861_Unstim_R2

source_name: lymphoblastoid, GM10861, unstimulated

value: unstimulated


title: GM10861_Input

description:
Input.
10_861_Input

source_name: lymphoblastoid, GM10861, input

tag: sample type

value: mixture of equal amounts of DNA from samples 05-08


title: GM10855_unstimulated_rep2

description:
ChIP against VDR.
02_855_Unstim_R2

source_name: lymphoblastoid, GM10855, unstimulated


title: GM10855_unstimulated_rep1

description:
ChIP against VDR.
01_855_Unstim_R1


title: GM10855_vitaminD_rep1

description:
ChIP against VDR.
03_855_D3_R1

source_name: lymphoblastoid, GM10855, vitamin D


title: GM10855_vitaminD_rep2

description:
ChIP against VDR.
04_855_D3_R2


title: GM10861_unstimulated_rep1

description:
ChIP against VDR.
05_861_Unstim_R1


title: smallRNA-HA_AGO1_IP-rep2

status: Public on Jun 21 2010

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description:
Small RNA from IP sample
library selection: RT-PCR

data_processing:
Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary (the first six nucleotides of the 3' adaptor: CTGTAG) and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline. Only sequences that mapped perfectly to the A. thaliana genome were included in the analysis.
Processed data presented in .gff files.  A .gff README file is linked to Series GSE22252 record.

organism: Arabidopsis thaliana

source_name: Flowers (stage 1-12)

extract_protocol: Small RNA were extracted from total RNA or HA-AGO1 complexes immunoprecipitated with anti-HA antibody (Roche clone 12CA5, catalog # 11583816001) by size fractionation using polyacrylamide gel electrophoresis. Small RNA were converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.

value: Col-0 pAGO1:HA-AGO1

value: Flowers

tag: developmental stage

value: stage 1-12

tag: sample source

value: HA-AGO1 co-immunoprecipitated RNA

tag: ChIP-seq antibody


title: smallRNA-total_RNA-rep2

description:
Small RNA from IP input sample
library selection: RT-PCR

value: Total RNA


title: IgG-ChIP-Seq, wt, 1

description: Chromatin IP against IgG.

source_name: Retina, wt, IgG ChIP

tag: genotype

value: 8 weeks

value: retina


title: smallRNA-total_RNA-rep1


title: GM10855_Input

description:
Input.
09_855_Input

source_name: lymphoblastoid, GM10855, input

value: mixture of equal amounts of DNA from samples 01-04

tag: antibody


title: H3K36me3WTTh2

status: Public on Jun 18 2010

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description: Chromatin IP against H3K36me3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse mm9 genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp (SICER) or 100 bp (CisGenome) to create summary windows.
Peaks: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958) for epigenetics modifcations and CisGenome ( Nature Biotechnology, 26: 1293-1300) for Stats

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Control and STAT-deficient naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured for 72h with platebound anti-CD3, anti-CD28 (10 mg/ml each), IL-12 (20 ng/ml) and anti-IL-4 (10 mg/ml) for 3 days, followed by IL-2 (50 U/ml) and IL-12 (10 ng/ml) for 4 days (Th1 conditions), or anti-CD3, anti-CD28 (10 mg/ml each), IL-4 (10 ng/ml) and anti-IFN-g (10 mg/ml) for 3 days, followed by IL-2 (50 U/ml) and IL-4 (10 ng/ml) for 4 days (Th2 conditions).

extract_protocol: Cell lysates were made by 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 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: After 7 day culture in vitro, cells were restimulated for 2hr with plate-bound anti-CD3, anti-CD28 (10 mg each) and IL-12 (20 ng/ml) for Th1 condition or IL-4 (10 ng/ml) for Th2 condition before chemically cross linked by 1% formaldehyde.

value: C57BL/6J (wild type)

value: in vitro polarized T helper2 cells for 7 days

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th2 condition and restimulated with plate-bound CD3/28 +IL4 for 2 hrs


title: H3K36me3 S6KOTh2

description: Chromatin IP against H3K36me3

value: B6.129S2©-STAT6<tm1Gru>/J (STAT6KO)

tag: chip antibody


title: NRSTh2

description: Chromatin IP with normal rabbit serum

tag: strain

value: Normal Rabbit Serum<Upstate#12-370>


title: H3K27me3WTTh2

description: Chromatin IP against H3K27me3

value: H3K27me3<Millipore #07-449>


title: H3K4me3 S6KOTh2

description: Chromatin IP against H3K4me3


title: H3K27me3 S6KOTh2

description: Chromatin IP against H3K27me3


title: Stat6WTTh2

description: Chromatin IP against STAT6


title: Stat6KOTh2

description: Chromatin IP against STAT6


title: H3K4me3WTTh2

description: Chromatin IP against H3K4me3


title: H3K4me3 S4KOTh1

description: Chromatin IP against H3K4me3

value: C57BL6-STAT4<tm1> (STAT4KO)

value: in vitro polarized T helper1 cells for 7 days

value: FACS sorted naive CD4+T cells cultured in vitro for 7 days under Th1 condition and restimulated with plate-bound CD3/28 +IL12 for 2 hrs


title: H3K27me3WTTh1

description: Chromatin IP against H3K27me3


title: H3K4me3WTTh1

description: Chromatin IP against H3K4me3


title: Stat4KOTh1

description: Chromatin IP against STAT4


title: ChIP-Seq for TBP in mES cells (B6)

status: Public on Jun 15 2010

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against TBP
07242008_20A50AAXX_B6

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (mm8) using bowtie.
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.
The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie.  The file contains the locations of the bowtie aligned reads with the following format:

#BWT1 (read category BWT1)
>1  (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2  (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
(etc.)

The data from the BWT1 category is what is visualized in the uploaded WIG files

source_name: Embyonic 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 one passage off of MEFs, on gelatinized tissue-culture plates.

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.

value: TBP

value: Abcam AB818

value: V6.5 embryonic stem cells


title: Stat4WTTh1

description: Chromatin IP against STAT4


title: H3K27me3 S4KOTh1

description: Chromatin IP against H3K27me3


title: ChIP-Seq for RNA Pol2 in MEF (B4)

description:
Chromatin IP against Pol2
03192010_61HWJAAXX_B4

source_name: Mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM with 10% FBS.

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 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: RNA Pol II (8WG16)

value: Covance MMS-126R

value: MEF


title: ChIP-Seq for TBP in mES cells (B2)

description:
Chromatin IP against TBP
03172010_614ATAAXX_B2

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.


title: smallRNA-HA_AGO1_IP-rep1

value: Col-0 pAGO1:HA-AGO1

tag: tissue

value: Flowers

value: stage 1-12

value: HA-AGO1 co-immunoprecipitated RNA


title: ChIP-Seq for H3K79me2 in MEF (B7)

description:
Chromatin IP against H3K79me2
03192010_61HWJAAXX_B7

value: Abcam AB3594


title: ChIP-Seq for H3K79me2 in MEF (B6)

description:
Chromatin IP against H3K79me2
12302009_619VPAAXX_B6


title: WCE in MEF (B5)

description:
WCE in MEF
07092009_42F6GAAXX_B5
Whole Cell Extract for Mouse Embryonic Fibroblasts
Mouse embryonic fibroblasts (MEFs) are an example of an early differentiated cell type.  The whole cell extract was prepared in order to have background information for additional ChIP-Seq experiments in MEFs.
MEFs were sonicated, DNA was purified and prepared for solexa sequencing.

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build (mm8) using bowtie.
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.
The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie.  The file contains the locations of the bowtie aligned reads with the following format:

#BWT1 (read category BWT1)
>1  (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2  (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
(etc.)

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts contain DNA fragments with an average size of 500 bp. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 350bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.


title: RAG1KO-EBF-ChIP-Seq

status: Public on Jun 13 2010

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Chromatin IP against EBF in RAG1-/- pro-B cells

data_processing:
Alignment: Reads were truncated to 25 bp and aligned to the mouse mm8 genome (NCBI Build 36) using eland. Only reads that mapped to a single, unique position were used for downstream analysis.
Peak Identification: Peaks were identified using custom software (HOMER, available at http://biowhat.ucsd.edu/homer/). For transcription factors, peaks were found by identifying 200 bp regions with tag density exceeding a threshold set at a 0.1% false discovery rate (determined by tag randomization). Only peaks with >4x normalized tag density relative to control sequencing and >4x normlaized tag density to the sourrounding 10kb of region were considered for analysis.

source_name: RAG1-/- pro-B cell

growth_protocol: Pro-B cells were isolated from femoral bone marrow of Rag1 knockout mice by positive enrichment of B220+ cells using magnetic separation (Miltenyi) and expanded for 10 d in Opti-MEM medium containing 10% FCS, 2x penicillin/streptomycin/glutamine, and 50 µM ß-mercaptoethanol supplemented with IL-7 and SCF.

extract_protocol: Lysates were clarified from sonicated cells or nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers for 12-18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size selected from a 2% agarose gel or a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I or Genome Analyzer II following the manufacturer's protocols.

value: pro-B cell

tag: transgenes

tag: genetic background


title: H3K36me3 S4KOTh1

description: Chromatin IP against H3K36me3

tag: cell type


title: H3K36me3WTTh1

description: Chromatin IP against H3K36me3

value: C57BL/6J (wild type)


title: A12-E2A-6h-E47ER-ChIP-Seq

description: Chromatin IP against E2A in A12 cells expressing an tamoxifen activated E2A (E47-ER) for 6hr

source_name: A12 (E2A-/- T cell)

growth_protocol: A12 cells were cultured in RPMI Medium 1640 supplemented with 10% FCS, 50 uM beta-mercaptoethanol, penicillin, streptomycin and L-glutamine.

treatment_protocol: The cells were spin-infected with a retrovirus expressing full length E2A fused to the estrogen receptor ligand binding domain, as well as hCD25 from a second cistron. After 21 hr in culture, cells were treated with tamoxifen (1 µM final concentration) for 6 hr. Cells expressing hCD25 were then enriched magnetically (Miltenyi).

value: double-positive T cell


title: A12-H3K4me1-6h-E47ER-ChIP-Seq

description: Chromatin IP against H3K4me1 in A12 cells expressing an Tamoxifen activated E2A (E47-ER) for 6hr


title: E2AKO-H3K4me1-6h-E47ER-ChIP-Seq

description: Chromatin IP against H3K4me1 in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A (E47-ER) for 6hr

source_name: E2A-/- pre-pro-B cell

growth_protocol: E2A-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7, SCF, and FLT3 ligand in Iscove’s Modified Dulbecco’s medium and in the presence of 10% FCS, penicillin, streptomycin and L-glutamine.

value: pre-pro-B cell


title: E2AKO-E2A-1h-E47ER-ChIP-Seq

description: Chromatin IP against E2A in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A (E47-ER) for 1h

treatment_protocol: The cells were spin-infected with a retrovirus expressing full length E2A fused to the estrogen receptor ligand binding domain, as well as hCD25 from a second cistron. After 21 hr in culture, cells were treated with tamoxifen (1 µM final concentration) for 1 hr. Cells expressing hCD25 were then enriched magnetically (Miltenyi).


title: E2AKO-H3K4me1-1h-E47ER-ChIP-Seq

description: Chromatin IP against H3K4me1 in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A (E47-ER) for 1hr


title: A12-H3K4me1-6h-bHLHER-ChIP-Seq

description: Chromatin IP against H3K4me1 in A12 cells expressing an tamoxifen activated E2A mutatant lacking both transactivation domains (bHLH-ER) for 6hr

treatment_protocol: The cells were spin-infected with a retrovirus expressing truncated E2A (lacking both activation domains) fused to the estrogen receptor ligand binding domain, as well as hCD25 from a second cistron. After 21 hr in culture, cells were treated with tamoxifen (1 µM final concentration) for 6 hr. Cells expressing hCD25 were then enriched magnetically (Miltenyi).

value: bHLH-ER


title: Input2

description: Mock IP in lymphoid cells

source_name: Lymphoid cell

growth_protocol: The cells were cultured on S17 stromal cells in the presence of IL7, SCF, and FLT3 ligand in Iscove’s Modified Dulbecco’s medium and in the presence of 10% FCS, penicillin, streptomycin and L-glutamine.

value: Lymphoid cell

value: WT


title: E2AKO-E2A-6h-E47ER-ChIP-Seq

description: Chromatin IP against E2A in E2A-/- pre-pro-B cells expressing an Tamoxifen activated E2A (E47-ER) for 6hr


title: RAG1KO-FOXO1-ChIP-Seq

description: Chromatin IP against FOXO1 in RAG1-/- pro-B cells


title: E2AKO-H3K4me1-6h-bHLHER-ChIP-Seq

description: Chromatin IP against H3K4me1 in E2A-/- pre-pro-B cells expressing an tamoxifen activated E2A mutatant lacking both transactivation domains (bHLH-ER) for 6hr


title: ChIP-Seq for RNA Pol2 in MEF (B6)

description:
Chromatin IP against Pol2
09112009_folder42TUFAAXX_B6


title: EBFKO-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in EBF-/- pre-pro-B cells

source_name: EBF-/- pre-pro-B cell

growth_protocol: EBF-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7, SCF, and FLT3 ligand in Iscove’s Modified Dulbecco’s medium and in the presence of 10% FCS, penicillin, streptomycin and L-glutamine.

value: EBF-/-


title: 18-32 nt total small RNAs (Mov10l+/-)

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

description:
Mov10l-associated small RNAs and total 18-32 nt small RNAs extracted after PAGE separation.
This sample represents total small RNAs

data_processing: In-house programs developed by Alexander Stark and Ravi Sachidanandam. Barcoded dataset (5' GUUCAGAGUUCUACAGUCCGACGAUCGAUC; barcode GAUC is at 3' end) was first sorted into respective libraries and then mapped to the genome (July 2007, mm9 assembly).

source_name: Testes

growth_protocol: Mice were maintained and genotyped as per standard procedures

extract_protocol:
Mov10L1 was immunoprecipitated from mouse testes extracts, small RNAs recovered by phenol-choloroform extraction, 5'-end labelled with gamma-ATP and gel extracted.
Total RNA was separated by 15% Urea-PAGE and RNAs in the range of 18-32 nt were gel extracted. RNA libraries were prepared with Digital Gene Expression for Small RNA kit from Illumina.

treatment_protocol: Testes were extracted from euthanized animals of indicated ages

value: Mov10l+/- mutant

tag: age

value: 10 dpp

value: Total small RNAs


title: RAG1KO-CTCF-ChIP-Seq

description: Chromatin IP against CTCF in RAG1-/- pro-B cells


title: 18-32 nt total small RNAs (Mov10l-/-)

data_processing: In-house programs developed by Alexander Stark and Ravi Sachidanandam. Barcoded dataset (5' GUUCAGAGUUCUACAGUCCGACGAUCCGAC; barcode CGAC is at 3' end) was first sorted into respective libraries and then mapped to the genome (July 2007, mm9 assembly).

value: Mov10l-/- mutant


title: mouse heart tissue [09-002]

status: Public on Jun 07 2010

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

data_processing: Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.0-1.4 using PhiX control; Fastq files contain full length reads (26 or 36 nts) that passed the chastity filter. Qualities are in phred64 format for all files.  Alignments were done with a custom software that used bowtie 0.9.9.3 to find the longest, mismatch-free alignable prefix of each read, trimmed any remaining adapter sequence, and then stored the unique sequence reads and their frequency.  This data is given in the data table, which therefore gives frequencies only for alignable reads.  For further analysis, the alignments were matched up with annotation to determine where the small RNA reads originated from and to profile miRNA expression in different tissues.  These tab-delimited files (supplied as supplementary files below) have a header line and give the expression level of each miRNA (previously described and putatively new) in tags per million miRNA tags.  No expression level cutoff was applied, so all miRNAs are included if there were any reads detected.

source_name: Mouse Heart

extract_protocol: RNA isolation method: Trizol. Small RNA library preparation: Illumina protocol "Preparing Samples for Analysis of Small RNA" (Part # 11251913 Rev. A)

tag: gender

value: male

value: heart


title: mouse muscle tissue [09-002]

source_name: Mouse Skeletal Muscle

value: skeletal muscle


title: mouse lung tissue [09-002]

source_name: Mouse Lung

value: lung


title: mouse liver tissue [09-002]

source_name: Mouse Liver

value: liver


title: mouse iTreg cells [09-002]

source_name: Mouse Naive CD4 positive T cells, in vitro iTreg polarized

growth_protocol: Sorted naive CD4+CD62L+CD44lowCD25- T cells were polarized in vitro as described in Wei G et al.,  Immunity 2009, 16;30(1):155-67

tag: source

value: lymph nodes/spleen


title: mouse salivary gland tissue [09-002]

source_name: Mouse Salivary Glands

value: salivary glands


title: mouse pancreatic tissue [09-002]

source_name: Mouse Pancreas

value: pancreas


title: mouse ovaries [09-002]

source_name: Mouse Ovaries

value: female

value: ovaries


title: mouse CD8+ T cells (spleen) [09-002]

description: Cell surface markers used for cell sorting: CD3+CD8+CD4-

source_name: Mouse CD8 positive T cells, Spleen, FACS

value: spleen


title: mouse embryonic stem cells [09-002]

description: Marson A, et al., Cell 2008, 8;134(3):521-33.

source_name: Mouse Embryonic Stem Cells, cultured


title: mouse Th1 cells [09-002]

source_name: Mouse Naive CD4 positive T cells, in vitro Th1 polarized


title: mouse Th17 cells [09-002]

source_name: Mouse Naive CD4 positive T cells, in vitro Th17  polarized

growth_protocol: Sorted naive CD4+CD62L+CD44lowCD25- T cells  were polarized in vitro as described in the Th17 II protocol by Shi G. et al., J Immunol 2008, 15;181(10):7205-13 with one modification: cells were polyclonally stimulated in the absence of antigen presenting cells and in the presence of plate bound anti-CD3 and anti-CD28 (10mcg/ml)


title: mouse kidney tissue [09-002]

source_name: Mouse Kidney

value: kidney


title: mouse CD4+ T cells (spleen) [09-002]

description: Cell surface markers used for cell sorting: CD4+CD62L+CD44lowCD25-

source_name: Mouse Naive CD4 positive T cells, Spleen, FACS


title: mouse BclXL B activated with LPS/IL4 [BalbC] [09-002]

source_name: Mouse Mature B cells, Spleen, in vitro LPS/IL-4 activated

growth_protocol: Culture of CD43 depleted splenocytes with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs

value: BclXL transgenic BalbC


title: mouse brain tissue [09-002]

source_name: Mouse Brain

value: brain


title: mouse BclXL germinal center B cells [BalbC] [09-002]

description: Isolation of draining lymph nodes seven days after foodpad immunization with chicken-IgY in complete Freund's Adjuvant. Cell surface markers used for cell sorting: CD19+CD95high

source_name: Mouse Germinal Center B cells, Lympn Nodes, FACS

value: lymph nodes


title: mouse neutrophil cells replicate 2 [09-002]

description: Cells isolated by Percoll ultracentrifugation of peritoneal lavage cells harvested after Casein Injection eitheen and three hours prior to lavage. Purity 88% as determined by Ly-6G staining and flow cytometry

source_name: Mouse Neutrophils, Peritoneal Lavage

value: peritoneal lavage


title: mouse embryonic fibroblast cells [09-002]

description: Passage 2

source_name: Mouse Embryonic Fibroblasts, cultured


title: mouse skin tissue [09-002]

source_name: Mouse Skin

value: skin


title: mouse dendritic cells [09-002]

description: Reference: Lutz MB et al. J Immunol Methods 1999, 223(1):77-92

source_name: Mouse Macrophage-derived Dendritic Cells, Bone Marrow,  in vitro differentiated

growth_protocol: Culture of bone marrow cells in complete RPMI 1640 supplemented with GM-CSF (20 ng/ml). Half the culture volume replaced by new medium and GM-CSF every third day. Cells in the removed culture supernatant were harvested by centrifugation and added back to the culture. Nonadherent dendritic cells were harvested after 12 days of culture.

value: male

value: bone marrow


title: mouse macrophages [09-002]

description: Reference: Cunnick J. et al. J Immunol Methods 2006, 311(1-2):96-105

source_name: Mouse Macrophages, Bone Marrow, in vitro culture

growth_protocol: Culture of bone marrow cells in complete RPMI 1640 supplemented with GM-CSF (10ng/ml) and IL-3 (10ng/ml). Medium was changed every third day and adherent cells were harvested at 14 days.


title: mouse mast cells [09-002]

source_name: Mouse Mast cells, Bone Marrow, in vitro differentiated

growth_protocol: Culture of bone marrow cells in complete RPMI 1640 supplemented with  IL3 (20ng/ml) and  SCF (20ng/ml) for 8 weeks


title: mouse neutrophil cells replicate 1 [09-002]


title: Pancreatic islets-pregnant-rp1

city: San Francisco

first: Hail

last: Kim

address: 513 Parnassus avenue HSW1090

institute: University of California San Francisco

description: 12 weeks old pregnant (G13~15)

data_processing: 31-bp reads were mapped to the Refseq collection of mouse transcripts generated from mouse genome build MM9 using Seqmap34. Mapped reads were quantified using the reads per kilobase exon model metric. Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group. The quantified transcription levels were expressed as reads per kilobase of exon model per million mapped reads (RPKM).

source_name: pancreatic islets

growth_protocol: C57BL/6J mice were housed on a 12-h light/dark cycle in climate-controlled, pathogen-free barrier facilities. Mating was confirmed by the presence of a vaginal plug the next morning, designated day 0 of gestation (G0).

extract_protocol: Total RNA from pooled islets from 4 non-pregnant or pregnant (G13−G15) mice was converted into a library of template molecules using mRNA-Seq Sample Prep Kit (Illumina) according to manufacturer’s protocol. Poly(A)+ mRNA purified using poly-dT oligo-attached Dynal magnetic beads (Invitrogen) was fragmented in RNA fragmentation buffer (Ambion) at 94 ˚C for 5 minutes. First strand cDNA synthesis from the RNA fragments using Superscript III (Invitrogen) and random hexamers was followed by second strand synthesis using DNA Polymerase I and RNaseH, addition of a 3’deoxyadenosine, and ligation of adaptors.  Double stranded cDNAs of 200 ± 25 bp were purified by electrophoresis through a 2% low melting-point agarose gel, extracted using the QIAquick Gel Extraction Kit (Qiagen) and further purified using a QiaQuick PCR purification kit (Qiagen). Libraries were expanded with the Illumina Cluster generation protocol and sequenced at the UCSF Genomics Core Facility using the 36 cycle sequencing kit v3 (Illumina). Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group.

tag: organ

value: pancreatic islets

tag: pregnancy

value: adult prengnat female


title: mouse Th2 cells [09-002]

source_name: Mouse Naive CD4 positive T cells, in vitro Th2 polarized


title: mouse B1 B cells [09-002]

description: Cell surface markers used for cell sorting: B220lowIgMhigh

source_name: Mouse B1 B cells, Peritoneal Lavage, FACS

tag: isolation

value: fluorescence activated cell sorting


title: mouse T cells activated in vitro with Concanavalin A [09-002]

source_name: Mouse T cells, Spleen, in vitro Concanavalin A activated

growth_protocol: Culture of spleen T cells with 5mg/ml Concanavalin A for 5 days


title: mouse plasma cells [09-002]

description: Cells sorted from enlarged lymph nodes of IL-6 transgenic mice. Exclusion of malignant tranformation by microscopy. Cell surface markers used for cell sorting: B220-CD138high

source_name: Mouse Plasma Cells, Lymph Nodes, FACS

value: IL-6 transgenic


title: mouse nTreg cells [09-002]

description: Cell surface markers used for cell sorting: CD4+CD25+

source_name: Mouse Natural Regulatory T cells, Lymph Nodes / Spleen, FACS

value: lymph nodes/spleen


title: mouse marginal zone B cells (spleen) [09-002]

description: Cell surface markers used for cell sorting: B220+IgMhighCD21/CD35high

source_name: Mouse Marginal Zone B cells, Spleen, FACS


title: mouse hematopoetic progenitor cells [09-002]

description: At the end of the culture 60% of cells c-Kit+ScaI+Lin- by flow cytometry

source_name: Mouse Hematopoietic Progenitor cells, Bone Marrow, in vitro expanded

growth_protocol: Culture of bone marrow cells isolated at day five after intratperitoneal injection of 5 mg 5-Fluorouracil (Adrucil) in complete DMEM supplemented with IL-3 (20 ng/ml), IL-6 (50 ng/ml), and SCF (50ng/ml) for 7 days.


title: mouse natural killer cells [09-002]

description: Reference: Mason LH et al. J Immunol 2006, 176: 6615-6623.

source_name: Mouse NK cells, Spleen, in vitro culture

growth_protocol: Splenocytes from RAG ko mice were cultured on 6-well plates in complete RPMI supplemented with IL-2 (1000 U/ml). Adherent cells were washed and medium exchanged at day three and six, and harvested at day eight

value: RAG-/-


title: mouse CD4+CD8+ T cells (thymus) [09-002]

description: Cell surface markers used for cell sorting: CD3+CD4+CD8+

source_name: Mouse CD4 and CD8 positive T cells, Thymus, FACS

value: thymus


title: mouse basophil cells [09-002]

source_name: Mouse Basophils, Bone Marrow, in vitro differentiated

growth_protocol: Flurescence activated cell sorting of CD49b+Fc_RI_+CD11b+Kit- cells from bone marrow cells cultured in complete RPMI 1640 supplemented with  IL3 (20ng/ml) for 10 days


title: mouse B cells activated in vitro with LPS/aIgD-Dextran [09-002]

source_name: Mouse Mature B cells, Spleen, in vitro LPS/anti-IgD-Dextran activated

growth_protocol: Culture of CD43 depleted splenocytes with LPS (50 mcg/ml) and Dextran-coupled anti-IgD (2.5 ng/ml) for 72 hrs

value: CD43 negative magnetic beads selection


title: AMS_ChIPSeq

status: Public on Jun 04 2010

city: Shanghai

first: dabing

last: zhang

address: Dongchuan RD 800

institute: Shanghai Jiao Tong University

description: 0.6-1.1 mm

data_processing:
Alignment: Sequence reads were obtained and mapped to the Arabidopsis genome (TAIR8) by SSAHA2 (version 2.3; http://www.sanger.ac.uk/Software/analysis/SSAHA2) All reads mapping with one mismatch in either end-1 or end-2 were retained.
Processed files: Each of AMS_SIPeS.fasta, AMS_MACS.bed has 6742698 reads which one mismatched nucleotide was allowed in either end-1 or end-2 when mapping to the genome using SSAHA2 (version 2.3). File named AMS_SIPeS.fasta is in FASTA format where the first and second term means the chromosomal start and end coordinates of the mapped mates(fragments).

source_name: plants cells, buds of Arabidopsis

growth_protocol: Plant material was sown on Levington M3 supplemented with 0.2gl-1 of Intercept and grown in controlled environmental chambers at 21-22°C under illumination of 167µmol.m-2.sec-1 with a 22h photoperiod.

extract_protocol: Chromatin was isolated from 1.5 g of formaldehyde cross-linked tissue from 0.6-1.1-mm buds of plants showing AMS expression.Briefly, Arabidopsis anthers were treated with formaldehyde, and the chromatin solution was sonicated on an Ultrasonic Crasher Noise Isolating Chamber (SCIENTZ, NingBo). The soluble chromatin fragments were obtained from isolated nuclei. Preadsorption with sheared salmon sperm DNA/protein A agarose mix (Santa Cruz, USA) was performed to remove nonspecific bound DNA. Immunoprecipitations with purified AMS-specific antiserum and preadsorption with protein A-Sepharose beads and without any serum were performed . A small aliquot of untreated sonicated chromatin was reversely cross-linked and used as the total input DNA control.

value: Columbia


title: [E-TABM-722] do73_CEBPA_liver_sc9314_mmuC57BL69_CRI03_h0_t8

status: Public on Jun 02 2010

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

institute: European Bioinformatics Institute

description:
do73_CEBPA_liver_sc9314_mmuC57BL69_CRI03_h0_t8.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
chip_seq | sequencing | The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles. doi:10.1016/j.ymeth.2009.03.001

tag: developmentalstage

value: adult

tag: organismpart

value: liver

tag: sex

tag: individual

value: CEBPA

tag: chip catalog number


title: [E-TABM-722] do73_CEBPA_liver_sc9314_mmuC57BL69_CRI01_h0_t0

description:
do73_CEBPA_liver_sc9314_mmuC57BL69_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

tag: chip antibody


title: [E-TABM-722] do73_CEBPA_liver_sc9314_mmuC57BL69_CRI02_h0_t0

description:
do73_CEBPA_liver_sc9314_mmuC57BL69_CRI02_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

tag: strain


title: [E-TABM-722] do70_CEBPA_liver_sc9314_mmuC57BL68_CRI03_h0_t11

description:
do70_CEBPA_liver_sc9314_mmuC57BL68_CRI03_h0_t11.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do70_CEBPA_liver_sc9314_mmuC57BL68_CRI02_h0_t13

description:
do70_CEBPA_liver_sc9314_mmuC57BL68_CRI02_h0_t13.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do79_CEBPA_liver_sc91314c18_cfa3_CRI02_h0_t0

description:
do79_CEBPA_liver_sc91314c18_cfa3_CRI02_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA

organism: Canis lupus familiaris


title: mouse pre B cells [09-002]

description: Cell surface markers used for cell sorting: B220+IgM-CD43-CD25+

source_name: Mouse Pre B cells, Bone Marrow, FACS


title: mouse TFHS cells [09-002]

description: Cells sorted from spleens six days after intreperitoneal injection of sheep red blood cells. Cell surface markers used for cell sorting: CD4+CD44+CXCR5highPD1high

source_name: Mouse Follicular B Helper T cells, Spleen, FACS

value: spleen


title: [E-TABM-722] do79_CEBPA_liver_sc91314c18_cfa3_CRI01_h0_t0

description:
do79_CEBPA_liver_sc91314c18_cfa3_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do79_CEBPA_liver_sc91314c18_cfa3_CRI03_h0_t8

description:
do79_CEBPA_liver_sc91314c18_cfa3_CRI03_h0_t8.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do249_CEBPA_liver_sc9314_gga2_CRI01

description:
do249_CEBPA_liver_sc9314_gga2_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

organism: Gallus gallus

value: female


title: [E-TABM-722] do61_CEBPA_liver_sc91314C18_cfa4_CRI03_h0_t0

description:
do61_CEBPA_liver_sc91314C18_cfa4_CRI03_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do131_Input_liver_none_mmuC57BL65_CRI01

description:
do131_Input_liver_none_mmuC57BL65_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: input_DNA

extract_protocol:
hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde.  After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde.  After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of  fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://dx.doi.org/10.1016/j.ymeth.2009.03.003

value: none, input DNA


title: Mov10L1-associated piRNAs

description:
Mov10l-associated small RNAs and total 18-32 nt small RNAs extracted after PAGE separation.
This sample represents Mov10L1 IP small RNAs.

data_processing: In-house programs developed by Alexander Stark and Ravi Sachidanandam. Reads mapped to the genome (July 2007, mm9 assembly).

source_name: Testes

tag: genotype

value: wild type

value: Adult

tag: antibody

value: Mov10l1 antibody (purified polyclonal)


title: mouse mature B cells (spleen) replicate 2 [09-002]

description: Cell surface markers used for cell sorting: B220+IgMlowCD21/CD35low

source_name: Mouse Mature resting B cells, Spleen, FACS

value: male


title: mouse immature B cells [09-002]

description: Cell surface markers used for cell sorting: B220+IgMhighCD21/CD35low

source_name: Mouse Immature B cells, Spleen, FACS

value: fluorescence activated cell sorting


title: mouse pro B cells [09-002]

description: Cell surface markers used for cell sorting: B220+IgM-CD43+CD25-

source_name: Mouse Pro B cells, Bone Marrow, FACS

value: bone marrow


title: [E-TABM-722] do61_CEBPA_liver_sc91314C18_cfa4_CRI02_h0_t0

description:
do61_CEBPA_liver_sc91314C18_cfa4_CRI02_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do81_CEBPA_liver_sc91314c18_mdo_CRI03_h0_t7

description:
do81_CEBPA_liver_sc91314c18_mdo_CRI03_h0_t7.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: CEBPA

organism: Monodelphis domestica

source_name: mdo

value: mdo


title: mouse B cells activated in vitro with LPS/IL4 replicate 3 [09-002]

source_name: Mouse Mature B cells, Spleen, in vitro LPS/IL-4 activated


title: mouse mature B cells (spleen) replicate 1 [09-002]

source_name: Mouse Mature Resting B cells, Spleen, FACS


title: [E-TABM-722] do163_CEBPA_liver_sc9314_gga_CRI03

description:
do163_CEBPA_liver_sc9314_gga_CRI03.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

source_name: gga

value: gga


title: [E-TABM-722] do163_CEBPA_liver_sc9314_gga_CRI01

description:
do163_CEBPA_liver_sc9314_gga_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
Factor Value [IMMUNOPRECIPITATE]: CEBPA