title: [E-TABM-722] do259_Input_liver_none_mdo3_CRI01

description:
do259_Input_liver_none_mdo3_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
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.2009.03.001


title: [E-TABM-722] do81_CEBPA_liver_sc91314c18_mdo_CRI01_h0_t0

status: Public on Jun 02 2010

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

description:
do81_CEBPA_liver_sc91314c18_mdo_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: CEBPA

library_source: genomic

molecule: genomic DNA

organism: Monodelphis domestica

source_name: mdo

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

value: male

tag: individual

value: mdo

tag: chip antibody

value: CEBPA

tag: chip catalog number


title: [E-TABM-722] do107_Input_liver_none_cfa4_CRI01_h0_t0

description:
do107_Input_liver_none_cfa4_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: input_DNA

organism: Canis lupus familiaris

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.2009.03.002

value: none, input DNA


title: [E-TABM-722] do61_CEBPA_liver_sc91314C18_cfa4_CRI01_h0_t1

description:
do61_CEBPA_liver_sc91314C18_cfa4_CRI01_h0_t1.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do163_CEBPA_liver_sc9314_gga_CRI02

description:
do163_CEBPA_liver_sc9314_gga_CRI02.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
Factor Value [IMMUNOPRECIPITATE]: CEBPA

organism: Gallus gallus

source_name: gga

value: female

value: gga


title: [E-TABM-722] do162_Input_liver_none_gga_CRI01

description:
do162_Input_liver_none_gga_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
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.2009.03.007


title: [E-TABM-722] do247_CEBPA_liver_sc9314_mdo3_CRI01

description:
do247_CEBPA_liver_sc9314_mdo3_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: CEBPA


title: [E-TABM-722] do100_Input_liver_none_cfa4_CRI01

description:
do100_Input_liver_none_cfa4_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
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 gland 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.2009.03.001


title: Stat3fl/fl FoxP3-GFP<STAT3 wild type>, STAT3-ChIPSeq

status: Public on May 30 2010

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

country: USA

institute: National Institutes of Health

description: Chromatin IP against phospho-STAT3

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 to create summary windows.
Peaks: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958)

organism: Mus musculus

source_name: in vitro polarized Th17 T cells

growth_protocol: Control (STAT3fl/fl) and STAT3-/- (CD4 Cre; STAT3fl/fl) naïve CD4+CD44-CD62L+ T cells were isolated and sorted on the FACSAria flow cytometer. Cells were cultured for 72h with platebound anti-CD3, anti-CD28 (5 mg/ml each), IL-6 (10 ng/ml) and TGF-b (2.5ng/ml) with blocking antibodies to IL-2, IL-4 and IFN-g (all at 10 mg/ml). Cells were restimulated for 1h with IL-6 (10 ng/ml) and then processed for ChIP-Seq.

extract_protocol: Lysates were clarified from sonicated nuclei 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 3 day culture in vitro, cells were restimulated for 1h with IL-6 (10 ng/ml) and then processed for ChIP-Seq.

tag: strain

value: Stat3fl/fl FoxP3-GFP<STAT3 wild type>

tag: cell type

value: WT-Th17 polazied T cells from naive

tag: passages

value: mouse primary T cells cultured in vitro for 3 days and restimulated with IL6

tag: antibody manufacturer

value: Cell Signaling

tag: antibody catalog number


title: Stat3fl/fl FoxP3-GFP<STAT3 wild type>, H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: AbCam


title: Stat3fl/fl FoxP3-GFP, CD4-Cre<STAT3 deficient>, H3K4me3_ChIPSeq

description: Chromatin IP against H3K4me3

value: STAT3-deficient-Th17 polarized T cells from naïve


title: mouse testicular tissue [09-002]

status: Public on Jun 07 2010

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

library_source: transcriptomic

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.

molecule: total RNA

source_name: Mouse Testes

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

tag: tissue

value: testes


title: Arabidopsis H3 ChIP-Seq

status: Public on May 29 2010

city: Los Angeles

first: matteo

last: Pellegrini

state: CA

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

description: Sonicated chromatin was immunoprecipitated by anti-Histone H3 antibody

data_processing: For MNase samples, Bowtie was used to align the reads to the TAIR7 genome.  Alignments with greater than 3 mismatches were filtered and only unique alignments were included.  The processed file indicates the position, strand, and number of reads alingning to that position.  For the ChIPSeq sample, reads were mapped to the TAIR7 genome using a probabilistic algorithm previously described (Cokus et al. 2008 Nature 452: 215-219) .  The processed file indicates the position, strand, and number of reads alingning to that position. BS-seq was analyzed similarly as previously described (Cokus et al. 2008 Nature 452: 215-219).  The processed file indicates the chromosome, strand, position, fraction methylated, and total number of counts (methylated Cs and unmethylated Cs).  All processed files indicate one-based positions (i.e. first base of the chromosome corresponds to position 1).

organism: Arabidopsis thaliana

source_name: Arabidopsis shoot tissue

growth_protocol: For MNase and ChIP-Seq samples, Arabidopsis plants were grown under continuous light for three weeks.

extract_protocol: For MNase samples, Arabidopsis nuclei were prepared as described previously (Bernatavichute et al. 2008 PLoS ONE 3: e3156) with the following modifications.  After spinning the nuclei pellet at 3000 rpm for 5 min (SS-34, Sorvall), the pellet was resuspended in 5 ml of HBB buffer (25 mM Tris-Cl pH 7.6, 0.44 M sucrose, 10 mM MgCl2, 0.1% Triton-X, 10 mM beta-mercaptoethanol), applied to a 40/60% Percoll (GE Healthcare) gradient in HBB and spun 2000 rpm for 20 min (SS-34, Sorvall).  Isolated nuclei were washed two times in HBB buffer and flash frozen in liquid nitrogen in HBC buffer (25 mM Tris-Cl pH 7.6, 25 mM Tris-Cl pH 7.6, 440 mM sucrose, 10 mM MgCl2 and 0.1% Triton-X, 10 mM beta-mercaptoethanol, 20% glycerol). Nuclei from 1/5 of each preparation were treated with four ul of RNAse A, 10 ug/ul, (Qiagen) and digested with 0.02 U/ul (final concentration) of Micrococcal Nuclease (Takara), 3 min. Digestion was done in digestion buffer (16 mM Tris-Cl, pH 7.6, 50 mM NaCl, 2.5 mM CaCl2, 0.01 mM PMSF and EDTA-free protease inhibitor cocktail (Roche)) and stopped with 10 mM EDTA and treated with Proteinase K (Roche). DNA was purified either with phenol:chlorophorm extraction and precipitated with salts and ethanol or with ChIP DNA  Clean and Concentrator kit (Zymo Research). Purified DNA was run on 2% agarose gel and bands corresponding to ~150 bp were cut and purified with a Gel Purification kit (Qiagen). Approximately 300ng of MNase digested mononucleosome DNA were used for library generation following manufacturer protocols (Illumina). Libraries were sequenced according to manufacturer instructions (Illumina).  For H3-ChIPSeq samples, chromatin was immunoprecipitated using an antibody against histone H3 as previously described (Bernatavichute et al. 2008 PLoS ONE 3: e3156).  Libraries were constructed and DNA was sequenced according to manufacturer instructions (Illumina).   For BS-seq samples, the HSF1 hESC line was cultured as described previously (Xiao et al. 1999 Embo J 18: 5943-5952). BS-Seq DNA library construction, high-throughput Illumina sequencing by and analysis were performed similar to that previously described (Cokus et al. 2008 Nature 452: 215-219).

treatment_protocol: Arabidopsis shoot tissues were obtained.

tag: genotype

value: wild type

value: shoots

tag: antibody vendor

value: Abcam

tag: catalog number

value: #1791 polyclonal anti-H3

tag: lot number

value: unknown


title: Arabidopsis Mnase-Seq (qseq)

description: MNase digested DNA was size selected for the mononucleosome fraction


title: Human HSF1 BS-Seq

description: Bisulfite conversion of unmethylated cytosines

organism: Homo sapiens

source_name: Human HSF1 embryonic stem cells

value: ES cells


title: mouse B cells activated in vitro with LPS/IL4 replicate 1 [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: male

tag: source

value: spleen

tag: isolation

value: CD43 negative magnetic beads selection


title: mouse germinal center B cells (lymph node) [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, Lymph Nodes, FACS

value: lymph nodes

value: fluorescence activated cell sorting


title: H3K27me3 WIBR2 20% O2

status: Public on May 28 2010

city: Cambridge

first: Garrett

middle: M

last: Frampton

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

description: Chromatin IP against H3K27me3

data_processing:
ChIP-Seq reads were aligned to the March 2006 build of the human genome sequence (NCBI36/hg18) with the software Bowtie (Langmead et al., 2009) using the following settings: -e 70 -k 1 -m 1 -n 2 --best.
The genome was divided into bins 100 base pairs in width, beginning at the first base of each chromosome.  Each ChIP-Seq read was shifted 100 bp from its mapped genomic position and strand to the approximate middle of the sequenced DNA fragment.  The ChIP-Seq density within each genomic bin was then calculated as the number of ChIP-Seq reads mapping within a 1kb window (+/- 500bp) surrounding the middle of that genomic bin.
In order to facilitate comparison of ChIP-Seq datasets a quantile normalization method was used.  In each ChIP-Seq dataset the genomic bin with the greatest ChIP-Seq density was identified.  The mean of these values was calculated and the bin with the greatest signal in each dataset was assigned this mean value.  This was repeated for all genomic bins from the greatest signal to the least, assigning each the average ChIP-Seq signal for all bins of that rank across all datasets.  H3K4me3 and H3K27me3 ChIP-Seq datasets were subjected to quantile normalization as separate groups.

source_name: hES line WIBR2 20% O2

growth_protocol:
Embryos were graded as described (Gardner et al., 2000): no blastocoel (grade 2), blastocyst not expanded (grade 3), expanded blastocyst (grade 4), hatching blastocyst (grade 5), hatched blastocyst (grade 6). ICM grade: tightly packed, many cells (grade A), loosely grouped, not many cells (grade B), no ICM visible (grade C). Trophectoderm (TE) was graded as well: many cell forming a cohesive epithelium (grade A), few cells forming a loose epithelium (grade B), very few large cells  (grade C).
ICM isolation was carried out first by removing the zona pelucida (ZP) by 30-40 seconds of treatment with 0.5 mg/ml protease (Sigma, St. Louis MO) in embryo culture media (LifeGlobal, Guelph, ON, Canada) under microscopic observation. Then trophectodermal cells were removed by incubating in human anti-placental alkaline phosphatase antibody diluted 1:10 for 40 min. TE cells were lysed by incubating in guinea pig complement (Invitrogen, Carsbad CA), diluted 1:4 in embryo culture medium and removed using a fire polished Pasteur pipette 100-120 um in diameter.  The isolated ICM was then plated in 5% O2 on a feeder layer of freshly plated mitomycin C-inactivated mouse embryonic fibroblasts (MEFs) in human ES cell derivation media.  This hESC derivation media consisted of 75% DMEM/F12 (Invitrogen, Carsbad CA), 7% Fetal Bovine Serum (FBS) (HyClone, ThermoFischer, Waltham, MA), 7% KO serum replacement (KSR) (Invitrogen, Carsbad CA), 7% human Plasmonate (Bayer, Leverkusen, Germany), 2mM L-glutamine, 1% non-essential amino acids, 50 units/ml penicillin and 50 ug/ml streptomycin (Invitrogen, Carsbad CA), 0.1mM b-mercaptoethanol (Invitrogen, Carsbad CA), 4ng/ml bFGF (R&D, Minneapolis, MN), human LIF (Chemicon, Millipore, Billerica, MA).  These procedures were carried out in a 5% O2 working cabinet (Biospherix, NY, NY).  7-15 days after plating, ICM outgrowth was mechanically dispersed and plated onto two fresh MEF feeder cell layer with hES derivation media (passage 1). One half of the ICM outgrowth was placed in the same physiologic oxygen culture condition (5%O2, 3%CO2 and 92%N2) while the other half was introduced into atmospheric oxygen incubators (20%O2, 5%CO2).  Secondary colonies resulting from ICM outgrowth were dispersed similarly until passage 2-5.  The Plasmonate content of the media and human LIF were eliminated during these initial passages while the content of FBS was increased to 15% and KSR reduced to 5%.  All Whitehead Institute cell lines are named according to their order of derivation as “WI-MIT-1, 2, 3, 4, 5, 6”.
All hESCs were maintained on MEFs and passaged mechanically without the use of enzymatic dissociation. For RNA analysis, hESC colonies were mechanically isolated and pooled for RNA extraction. Compounds used in oxidative stress protection experiments and cellular stress experiments were obtained from Sigma (Sigma, St. Louis MO). For in vitro differentiation, hESC colonies were harvested with 1 mg/ml collagenase type IV (Invitrogen, Carlsbad, CA), separated from MEFs by differential plating, gently triturated, and cultured for 5 days in nonadherent suspension culture dishes (Corning, Lowell, MA) in DMEM supplemented with 20% FBS to promote embryoid body (EB) formation. After 5 days. EBs were trypsinised to single cells and plated on tissue culture plates and were allowed to differentiate further for 10-12 days.

extract_protocol:
Human ESCs were grown to a final count of ~5x107 cells to obtain starting material for six chromatin immunoprecipitations.  Cells were chemically cross-linked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 15 minutes at room temperature.  Cells were rinsed twice with 1X PBS, harvested by centrifugation, and flash frozen in liquid nitrogen.  Cross-linked cells were stored at –80oC prior to use.
Cells were re-suspended, lysed and sonicated to solubilize and shear cross-linked DNA.  Sonication was performed using a Misonix Sonicator 3000 at a power of 27W for ten 30 second pulses with a 90 second pause between each pulse.  Samples were kept on ice at all times.
The resulting whole cell extract was incubated overnight at 4 degrees C with 10µl of Dynal Protein G magnetic beads that had been pre-incubated with approximately 3 µg of the appropriate antibody.  Each individual immunoprecipitation used 1/6 of the 3ml total, or ~8 x106 cells per IP.  The immunoprecipitation was allowed to proceed overnight.  Beads were washed three times (3 x 1.5ml) with RIPA buffer and one time (1x 1.5ml) with TE containing 50 mM NaCl.  Bound complexes were eluted from the beads by heating at 65 degrees C with occasional vortexing and cross-linking was reversed by overnight incubation at 65 degrees C.  Whole cell extract DNA (reserved from the sonication step) was also treated for cross-link reversal.  Immunoprecipitated DNA and whole cell extract DNA were then purified by treatment with RNAse A, proteinase K and 2x phenol:chloroform:isoamyl alcohol extractions.
The ChIP antibodies used were ab8580 (Abcam, Cambridge, MA) for H3K4me3 and ab6002 (Abcam) for H3K27me3.
Purified ChIP DNA was prepared for sequencing according to a modified version of the Illumina/Solexa Genomic DNA protocol. Approximately 50-200ng of IP DNA was prepared for ligation of Solexa linkers by repairing the ends and adding a single adenine nucleotide overhang to allow for directional ligation.  A 1:100 dilution of the Adaptor Oligo Mix (Illumina) was used in the ligation step.  A subsequent PCR step with 18 amplification cycles added additional linker sequence to the fragments to prepare them for annealing to the Genome Analyzer flow-cell.  Amplified material was purified by Qiaquick MinElute (Qaigen) and a narrow range of fragment sizes was selected by separation on a 2% agarose gel and excision of a band between 150-300 bp, representing IP fragments between 50 and 200nt in length and ~100bp of primer sequence.  The DNA was purified from the agarose and diluted to 10 nM for loading on the flow cell.
The DNA library (2-4 pM) was applied to one lane of the flow-cell (eight samples per flow-cell) using a Cluster Station device (Illumina).  The concentration of library applied to the flow-cell was calibrated so that polonies generated in the bridge amplification step originate from single strands of DNA.  Multiple rounds of amplification reagents were flowed across the cell in the bridge amplification step to generate polonies of approximately 1,000 strands in 1µm diameter spots.  Double stranded polonies were visually checked for density and morphology by staining with a 1:5000 dilution of SYBR Green I (Invitrogen) and visualizing with a microscope under fluorescent illumination. Validated flow-cells were stored at 4 degrees C until sequencing.
Flow-cells were removed from storage and subjected to linearization and annealing of sequencing primer on the Cluster Station.  Primed flow-cells were loaded into the Genome Analyzer 1G (Illumina).  After the first base was incorporated in the sequencing-by-synthesis reaction the process was paused for a key quality control checkpoint.  A small section of each lane was imaged and the average intensity value for all four bases was compared to minimum thresholds.  Flow-cells with low first base intensities were re-primed and if signal was not recovered the flow-cell was aborted.  Flow-cells with signal intensities meeting the minimum thresholds were resumed and sequenced for 26-36 cycles.
Images acquired from the Genome Analyzer were processed through the bundled image extraction pipeline (Illumina), which identified polony positions, performed base-calling and generated QC statistics.

treatment_protocol: One half of the ICM outgrowth was placed in physiologic oxygen culture condition (5%O2, 3%CO2 and 92%N2) while the other half was introduced into atmospheric oxygen incubators (20%O2, 5%CO2).

tag: cell line

value: hES cell line WIBR2

tag: oxygen concentration


title: H3K27me3 WIBR3 20% O2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR3 20% O2

value: hES cell line WIBR3

tag: chip antibody


title: Arabidopsis Mnase-Seq (seq, prb)


title: H3K27me3 WIBR1 20% O2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR1 20% O2

value: hES cell line WIBR1


title: H3K27me3 WIBR3 5% O2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR3 5% O2


title: PUER-1h-MNase-Seq

status: Public on May 27 2010

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: Mononucleosome sequencing in PUER cells after 1h Tamoxifen treatment

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: PUER cells

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, DNA was phenol/chloroform-extracted from MNase-treated nuclei, and 134-154 bp long fragments were extractred from a 2% agarose gel. 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, ChIP DNA was PCR-amplified with Illumina primers for 12-16 cycles and library fragments of 200-300 bp (ChIP) (insert plus adaptor and PCR primer sequences) were isolated from a 2% agarose gel. For MNase-Seq, size-selected mononucleosome-derived DNA fragments were ligated to modified adapters that incorporate both the adapter sequence as well as the primer landing sites for the flow cell-conjugated primers. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer or Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Tamoxifen, 1h

value: PUER cells

tag: treatment

value: Tamoxifen, 1h

tag: transgenes

tag: genotype/variation


title: H3K27me3 WIBR2 5% O2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR2 5% O2


title: H3K27me3 WIBR1 5% O2

description: Chromatin IP against H3K27me3

source_name: hES line WIBR1 5% O2


title: PUER-0h-MNase-Seq

description: Mononucleosome sequencing in PUER cells after 0h Tamoxifen treatment

growth_protocol: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.

tag: cell type

tag: strain


title: H3K4me3 WIBR1 5% O2

description: Chromatin IP against H3K4me3


title: H3K4me3 WIBR3 20% O2

description: Chromatin IP against H3K4me3


title: H3K4me3 WIBR2 5% O2

description: Chromatin IP against H3K4me3


title: H3K4me3 WIBR2 20% O2

description: Chromatin IP against H3K4me3


title: H3K4me3 WIBR1 20% O2

description: Chromatin IP against H3K4me3


title: H3K4me3 WIBR3 5% O2

description: Chromatin IP against H3K4me3


title: Yeast_Tbf1_Chip_seq

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing: Sequence reads were mapped onto the yeast genome (SGD1.01/sacCer2 build) using Bowtie (version 0.11.3 with options -n 3 --best --strata -a -m 10). Multiple matches were kept but contributing 1/#hits to the tag density at each matching locus, and strand specificity of the matches was retained. The resulting ChIP/control ratio densities were analyzed for a configuration expected for ChIP sites, namely, a peak on each strand separated by the expected fragment size. Specifically, Gaussian shapes were fitted to the densities at each genomic position on each strand separately, and position were retained where the Gaussian would explain more than 60% of the variance in windows of 2000 bp centered at each position. The resulting set of positions were then clustered using hierarchical clustering on each strand. The tree was cut at a height of 500 bp to identify individual clusters. Each cluster was assigned a position equal to the median of the positions in each group. Finally, ChIP sites were defined as pairs of clusters, one on the plus and one on the minus strand, spaced by less than 200 bp.

organism: Saccharomyces cerevisiae

source_name: whole organism, tagged

growth_protocol: Strains were grown in liquid rich media (YPAD) for 3 hours in order to reach exponential phase.

extract_protocol: Crosslinked cells were processed in 18 separate sonication/immunoprecipitation procedures using a monoclonal anti-Myc antibody (9E10). The resulting purified DNAs were pooled, and DNA sequencing was carried out according to the manufacturer’s protocols on an Illumina GA machine at Fasteris, S.A. (Geneva).

treatment_protocol: 18 aliquots (40 ml) from three independent cultures of each strain were crosslinked for 5 min with 1% formaldehyde.

value: W303-1A TBF1-13xMyc::HIS3

tag: antibody

value: monoclonal anti-Myc antibody 9E10


title: Yeast_Untagged_control

source_name: whole organism, untagged


title: [E-TABM-722] do81_CEBPA_liver_sc91314c18_mdo_CRI02_h0_t0

description:
do81_CEBPA_liver_sc91314c18_mdo_CRI02_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Monodelphis domestica
Factor Value [IMMUNOPRECIPITATE]: CEBPA

source_name: mdo

tag: developmentalstage

value: adult

tag: organismpart

value: liver

tag: sex

tag: individual

value: mdo

value: CEBPA

tag: chip catalog number


title: PUER-H3K4me1-24h-ChIP-Seq

description: Chromatin IP against H3K4me1 in PUER cells after 24h Tamoxifen treatment

treatment_protocol: Tamoxifen, 24h

value: Tamoxifen, 24h

value: H3K4me1 (Vendor:Abcam, cat# ab8895, lot# 721955)


title: BMDM.LXRDKO-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in LXRa/b-/- BMDM

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

value: macrophage

value: LXRa/b-/-


title: BMDM-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in BMDM

value: wild-type


title: BLRP-LXRb-GW-ChIP-Seq

description: Chromatin IP against BLRP-LXRb in RAW264.7 cells treated with GW3965

source_name: BirA/BLRP-LXRb RAW264.7 cells

growth_protocol: RAW264.7 Macrophage cell line was cultured in RPMI 1640 containing 10% FCS and 100 U/ml penicillin/streptomycin then treated for 1 hour with 1 µM GW3965.

value: RAW264.7 Macrophage cell line

value: Biotin-tagged LXRb/Streptavidin

value: LXRb-BLRP, BirA

value: Biotin-tagged LXRb bound to NanoLink Streptavidin Magnetic Microspheres (Vendor:SoluLink, cat# M1002-010, lot# LM041609)


title: BMDM.LXRDKO-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in LXRa/b-/- BMDM

value: PU.1 (Vendor:Santa Cruz, cat# sc-352, lot# F1808)


title: BMDM-PU.1-ChIP-Seq

description: Chromatin IP against PU.1 in BMDM


title: BirA-input-GW-ChIP-Seq

description: Chromatin IP with streptavidin (no BLRP transgene [control]) in RAW264.7 cells treated with GW3965

source_name: BirA RAW264.7 cells

value: Streptavidin

value: BirA

value: Streptavidin (NanoLink Streptavidin Magnetic Microspheres (Vendor:SoluLink, cat# M1002-010, lot# LM041609))


title: PU.1KO-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in PU.1-/- myloid cells

source_name: PU.1-/- myloid cell

growth_protocol: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

value: PU.1-/- myloid cell


title: PUER-H3K4me1-1h-ChIP-Seq

description: Chromatin IP against H3K4me1 in PUER cells after 1h Tamoxifen treatment

value: PUER cells

value: Tamoxifen, 1h


title: PUER-H3K4me1-0h-ChIP-Seq

description: Chromatin IP against H3K4me1 in PUER cells after 0h Tamoxifen treatment

growth_protocol: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.


title: mouse B cells activated in vitro with LPS/IL4 replicate 2 [09-002]

tag: gender

value: male

value: spleen

value: CD43 negative magnetic beads selection


title: ThioMac-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in ThioMac

growth_protocol: Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

value: macrophage

value: H3K4me1 (Vendor:Abcam, cat# ab8895, lot# 721955)


title: Bcell-H3K4me1-ChIP-Seq

description: Chromatin IP against H3K4me1 in immature B cells

source_name: resting splenic B cells

growth_protocol: Splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells (Miltenyi, Bergisch Gladbach, Germany).

value: resting splenic B cells


title: Rh_N2_CO2_MA2_6

status: Public on May 22 2010

city: Saint Louis

first: Jeremiah

middle: J

last: Faith

state: MO

address: Campus Box 8510

institute: Washington University in St. Louis

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes;N2/CO2 headspace), in defined minimal medium containing glucose and Sodium Formate (4.5mM).   Cells were harvested at A600= 0.25

data_processing: After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm. Minimum score thresholds for ssaha were selected based on the distribution of scores for all mapped reads of a 32nt barcoded sample and a 36-nt non-barcoded sample (29 was selected as the minimum score for 32nt barcoded samples; 33 was the minimum score used for 36-nt non-barcoded samples). Although an 18-nt read is sufficient to map more than 90% of the sequencing reads, even at 32-36nt there is a large fraction of the reads that map to multiple locations within a genome or across genomes. Reads that map non-uniquely were added to each gene in proportion to each gene‚Äôs fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth, although clearly a more appropriate model-based approach to smooth lower expression values is needed in the future, particularly with mixed species samples where one or more species is clearly undersampled. Raw counts were normalized to reads/kb/million mapped reads

organism: Blautia hydrogenotrophica DSM 10507

source_name: in vitro culture

growth_protocol: Cecal and fecal samples obtained from mice at the time that they were sacrificed, as well as bacteria in vitro cultures, were immediately frozen at -80¬∞C and maintained at this temperature prior to processing. All samples were treated with RNAProtect (Qiagen).

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample Kit. Briefly, cDNA was sonicated in a biorupter sonicator, cleaned up/concentrated through a Qiagen PCR column, and end-repaired. The blunt DNA was treated with Klenow fragment (exo minus) to add an A-overhang, and ligated to the relevant Illumina adapter sequence (either with our without a barcode).  Adaptered-DNA was then size-selected on a agarose gel and PCR amplified. The purified PCR was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.library strategy

tag: sample type

value: in vitro culture


title: Rh_N2-CO2_valine_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Valine as a carbon source. Cells were harvested at  A600~0.5


title: MitoPLD+/+ E16.5 small RNA

city: NewHaven

first: Toshiaki

last: Watanabe

state: CT

address: 10 Amistad

institute: Yale University

description: small RNA cloning by length

data_processing: small RNAs were mapped to the genome (UCSC 2007, mm9), and mapped sequences were annotated.

source_name: E16.5 testes

extract_protocol: small RNA ranging from 20 nt to 40 nt were gel purified. Libraries are prepared according to small RNA Sample prep kit (Illumina).

value: MitoPLD+/+


title: Rh_N2-CO2_Glucose_exp_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~0.5


title: Rh_N2_CO2_MA2_3

description: Blautia hydrogenotrophica grown anaerobically (125-ml serum bottle tubes; N2/CO2 in headspace), in MA2 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~0.25


title: Rh_N2-CO2_Pyruvate_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Pyruvate as a carbon source. Cells were harvested at  A600~0.5


title: Rh_N2-CO2_Isoleucine_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Isoleucine as a carbon source. Cells were harvested at  A600~0.5


title: Rh_N2_only_MA3_3

description: Blautia hydrogenotrophica grown anaerobically (125-ml serum bottle tubes; N2 in headspace), in MA3 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~0.25


title: Rh_N2-CO2_Ribose_1

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Ribose as a carbon source. Cells were harvested at  A600~0.5


title: Rh_H2_CO2_MA2_8

description: Blautia hydrogenotrophica grown anaerobically (125-ml serum bottle tubes; H2/CO2 in headspace), in MA2 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~0.25


title: Rh_N2-CO2_Glucose_exp_1


title: Rh_N2_only_MA3_1

description: Blautia hydrogenotrophica grown anaerobically (125-ml serum bottle ; N2 in headspace), in MA3 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~0.25


title: Rh_N2-CO2_Ribose_2


title: Rh_N2-CO2_valine_1


title: Rh_N2-CO2_Phenylalanine_1

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Phenylalanine as a carbon source. Cells were harvested at  A600~0.5


title: NAM-RNAi_sRNA_library

city: Davis

first: Dario

last: Cantu

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

description: Small RNA profiling.

data_processing:
Sequencing reads were filtered for quality, and then trimmed to remove the sequence of the 3’ adapters.  Filtering and trimming scripts are available from http://code.google.com/p/atgc-illumina/.  Only the high-quality reads with detectable 3’ adapter were used for the analysis. The filtered and trimmed sequence reads are provided in fastq format in the supplementary file
'GSM548032_wheat_gpc_rnai_sRNA_TRIMMED.fastq.txt'.

The Sample data table lists the unique sRNA sequences with their abundance counts.

The supplementary file 'GSM548032_TaNAM_perfect_matches.txt' lists the sRNAs perfectly matching the NAM gene (DQ869673.1), which is the target of the RNAi. To detect perfect matches, a program was written that consists of a scrolling window with frame size between 18 and 33 bp that scans through the entire query sequence with a 1 nt increment after each read. When the scanner finds a region of the query sequence that exactly matches a sRNA in the database, the program returns the matching sRNA sequence, the length of the sequence (18-33 nt), the coordinate within the queried region, the library of origin, and the total counts in the sRNA database.

organism: Triticum aestivum

source_name: Flag-leaves, NAM-RNAi

growth_protocol: Transgenic plants for the NAM RNAi construct were grown under long-days (LD, 16 h light 8 h dark).

extract_protocol: The sRNA library (designated as TAE4 in the publication) was prepared using Illumina Small RNA Library Sample Prep protocol version 1.5.  Total RNA (10 ug) was used as input material. The 3’ adaptor (Illumina, San Diego, CA, USA) was ligated to RNAs.  The v1.5 3’ adapter predominantly ligates to microRNAs and other small RNAs that have a 3’ hydroxyl group. The 3' ligation products were then ligated to the 5' small RNA adapter (Illumina). The ligation products were reverse transcribed followed by PCR amplification. The amplification products from 18 – 30 nt long RNAs were excised from a Novex 6% TBE PAGE gel (Invitrogen). The purified DNA fragments were submitted for 45 cycles of sequencing on the Illumina Genome Analyzer.

treatment_protocol: At anthesis, spikes were labelled and after 12 days, flag leaves samples from four plants were pooled and used for RNA extraction.

tag: cultivar

value: Bobwhite

tag: tissue

value: flag-leaves

tag: developmental stage

value: 12 days after anthesis

tag: rnai

value: no apical meristem (NAM)


title: Rh_N2-CO2_Pyruvate_1_noDeplete

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Pyruvate as a carbon source. Cells were harvested at  A600~1.8; total RNA was NOT depleted


title: MVH-/- E16.5 small RNA

description: small RNA cloning by length

tag: development stage

tag: tissue type

value: testes

value: MVH-/-


title: Rh_N2-CO2_Pyruvate_1

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Pyruvate as a carbon source. Cells were harvested at  A600~1.8


title: Rh_N2_only_1


title: Rh_H2_CO2_MA2_7


title: Rh_N2_only_2


title: Rh_N2_CO2_MA2_1


title: Rh_H2_CO2_MA2_1


title: Rh_N2_only_MA3_2


title: Rh_H2_CO2_MA2_2


title: Rh_N2-CO2_Isoleucine_1


title: Rh_N2-CO2_Fructose_2_noDeplete

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Pyruvate as a carbon source. Cells were harvested at  A600~0.5; total RNA was NOT depleted


title: Rh_N2-CO2_Fructose_1

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Fructose as a carbon source. Cells were harvested at  A600~0.5


title: Rh_N2-CO2_Glucose_stat_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 1% Glucose as a carbon source. Cells were harvested at  A600~1.8


title: Rh_N2-CO2_Fructose_2


title: Rh_N2_CO2_MA2_5


title: Rh_N2-CO2_Glucose_3


title: Rh_N2-CO2_Tryptone_2

description: Blautia hydrogenotrophica grown anaerobically (Bach tubes; N2/CO2), in MA4 medium containing 2% Tryptone as a carbon source. Cells were harvested at  A600~0.5


title: BtRh8_CC

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica. Mouse was fed a polysaccharide rich diet (BK chow).

organism:
Bacteroides thetaiotaomicron VPI-5482
Blautia hydrogenotrophica DSM 10507

source_name: mouse cecal contents

value: mouse cecal contents


title: Rh_N2-CO2_Glucose_stat_1


title: Rh_N2-CO2_Tryptone_1


title: BtRh_FP7

description: Fecal pellet from mice (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica . Mouse was fed a polysaccharide rich diet (BK chow).

source_name: mouse feces

value: mouse feces


title: BtRh7_CC


title: BtRh7.B2

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica. Mouse was fed a polysaccharide rich diet (BK chow). Technical replicate of BtRh_CC7 (not used to calculate fold-changes)


title: Rh_N2-CO2_Phenylalanine_2


title: Bt_MC_EtOH_noDeplete

description: total RNA prepped with MEGAClear (1x) and EtOH preciptation; with no depletion; TYG media; log phase

organism: Bacteroides thetaiotaomicron VPI-5482


title: BtRh8_FP


title: BtRh_CC9


title: Bt_MC2x_ME2x_custom2x

description: total RNA prepped with MEGAClear (2x); depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: FA5_10ug_noDeplete

description: 10 ug total RNA prepped with MEGAClear (2x); not depleted; TYG media; log phase


title: FA4_2.5ug_ME2x_custom2x

description: 2.5 total RNA prepped with MEGAClear (2x); depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: Bt_CC2

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482). Mouse was fed a polysaccharide rich diet (BK chow).


title: Bt_MC_EtOH_MEbeads

description: total RNA prepped with MEGAClear (1x) and EtOH precipitation; elution from MICROBExpress rRNA capture beads; TYG media; log phase


title: RNA-A1

status: Public on Jun 04 2010

city: Qingdao

first: Naihao

last: Ye

address: Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences, Qingdao, 266071, China

country: China

data_processing:
Low-quality reads were filtered strictly. 3' adaptor sequences were trimmed and 5' adaptor contaminants were removed. Too small and polyA sequences were removed.
Small RNA fragments were compared with the sequences of non-coding RNAs (rRNA, tRNA, snRNA, snoRNA) available in Rfam and the GenBank database.

The Sample data table includes counts for clean tags, 18-30 nt. The supplementary file 'GSM516100_small.txt' contains counts for tags less than 18 nt.

organism: Pyropia yezoensis

source_name: Filamentous sporophytes of Porphyra yezoensis

growth_protocol: Filamentous sporophytes of P. yezoensis were grown in seawater medium at 16°C in the laboratory. The medium was renewed weekly.

extract_protocol: The samples were subjected to 15% denaturing polyacrylamide gel electrophoresis, after which the small RNA fragments of 18-28 nt were isolated from the gel and purified. Next, the small RNA molecules were ligated to a 5′ adaptor and a 3′ adaptor sequentially and then converted to cDNA by RT-PCR. The products of RT-PCR were then sequenced directly on a Solexa sequencing machine.

value: filamentous sporophyte


title: [E-TABM-722] do260_Input_liver_none_gga2_CRI01

description:
do260_Input_liver_none_gga2_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Gallus gallus
Factor Value [IMMUNOPRECIPITATE]: input_DNA

value: adult

value: liver

value: female

tag: chip antibody

value: none, input DNA


title: Bt_RE_ME2x_custom2x

description: total RNA prepped with RNAEasy (1x); depleted using the MICROBExpress kit (2x); TYG media, log phase


title: Bt_MC_EtOH_ME2x_custom2x

description: total RNA prepped with MEGAClear (1x) and EtOH preciptation; depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: FA7_10ug_ME2x

description: 10 ug total RNA prepped with MEGAClear (2x); depleted using MICROBExpress (2x); TYG media; log phase


title: FA6_10ug_custom2x

description: 10 ug total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); TYG media; log phase


title: BtRh10_FP

description: Fecal pellet from a mouse(c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica . Mouse was fed a polysaccharide rich diet (BK chow).


title: Bt_RE_EtOH_MEbeads

description: total RNA prepped with RNAEasy (1x) and EtOH precipitation; elution from MICROBExpress rRNA capture beads; TYG media; log phase


title: Ec_RE_noDeplete_2

description: total RNA prepped with RNAEasy (1x); with no depletion; LB media, log phase

organism: Escherichia coli str. K-12 substr. MG1655


title: Bt_RE_MC_ME2x_custom2x

description: total RNA prepped with RNAEasy (1x) followed by MEGAClear (1x); depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: Ec_RE_Exo_custom2x

description: total RNA prepped with RNAEasy (1x); depleted using the mRNA-ONLY (epicenter) exonuclease; LB media, log phase


title: FA8_10ug_ME2x_custom2x

description: 10 ug total RNA prepped with MEGAClear (2x); depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: Bf_glucose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Glucose as a carbon source. Cells were harvested at A600~0.4

organism: Marvinbryantia formatexigens DSM 14469


title: Bt_RE_EtOH_ME2x_custom2x

description: total RNA prepped with RNAEasy (1x) and EtOH precipitation; depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: FA2_2.5ug_custom2x

description: 2.5 ug total RNA prepped with MEGAClear (2x); depleted using custom depletion oligos (2x); TYG media; log phase


title: Bt_MC_RE_ME2x_custom2x

description: total RNA prepped with MEGAClear (1x) followed by RNAEasy; depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: Bf_maltose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltose as a carbon source. Cells were harvested at A600~0.4


title: Bf_stachyose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Stachyose as a carbon source. Cells were harvested at A600~0.4


title: Bf_glucose_stat_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Glucose as a carbon source. Cells were harvested at A600~1.8


title: FA3_2.5ug_ME2x

description: 2.5 ug total RNA prepped with MEGAClear (2x); depleted using MICROBExpress (2x); TYG media; log phase


title: Bf_Maltotriose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltotriose as a carbon source. Cells were harvested at A600~0.4


title: Bt_FP1

description: Fecal pellet from mice (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482). Mouse was fed a polysaccharide rich diet (BK chow).


title: Bt_FP4


title: Bf_Trehalose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Trehalose as a carbon source. Cells were harvested at A600~0.4


title: Bf_Maltodextrin_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltodextrin as a carbon source. Cells were harvested at A600~0.4


title: Bt_RE_EtOH_noDeplete

description: total RNA prepped with RNAEasy (1x) and EtOH precipitation; with no depletion; TYG media; log phase


title: Bt_RE2x_ME2x_custom2x

description: total RNA prepped with RNAEasy (2x); depleted using MICROBExpress (2x) and custom depletion oligos (2x); TYG media; log phase


title: Bf_glucose_stat_2


title: Bf_Glucose_1_noDeplete

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% glucose as a carbon source. Cells were harvested at A600~0.4; total RNA was NOT depleted


title: Bt_RE_polyA_custom2x

description: total RNA prepped with RNAEasy (1x); depleted using a poly-A selection and custom depletion oligos (2x); TYG media, log phase


title: Bf_raffinose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Raffinose as a carbon source. Cells were harvested at A600~0.4


title: Bt_RE_Exo_custom2x

description: total RNA prepped with RNAEasy (1x); depleted using the mRNA-ONLY (epicenter) exonuclease and custom depletion oligos (2x); TYG media, log phase


title: FA1_2.5ug_noDeplete

description: 2.5 total RNA prepped with MEGAClear (2x); not depleted; TYG media; log phase


title: Bf_raffinose_2


title: Bf_NAG_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% N-Acetyl Glucosamine as a carbon source. Cells were harvested at A600~0.4


title: Bf_xylose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Xilose as a carbon source. Cells were harvested at A600~0.4


title: Bt_RE_noDeplete

description: total RNA prepped with RNAEasy (1x); with no depletion; TYG media; log phase


title: Bf_galactose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Galactose as a carbon source. Cells were harvested at A600~0.4


title: Bt2_CC

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482). Mouse was fed a polysaccharide rich diet (BK chow). not used to calculate


title: Bt_CC3

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482). Mouse was fed a polysaccharide rich diet (BK chow).


title: Bf_MM_45mM_F_6

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes;N2/CO2 headspace), in defined minimal medium containing glucose and Sodium Formate (45mM).   Cells were harvested at A600= 0.25


title: Bf_stachyose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Stachyose as a carbon source. Cells were harvested at A600~0.4


title: Bf_sucrose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Sucrose as a carbon source. Cells were harvested at A600~0.4


title: Bt1_CC


title: Bf_lactose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Lactose as a carbon source. Cells were harvested at A600~0.4


title: Bf_MM_45mM_F_5


title: Bf_arabinose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Arabinose as a carbon source. Cells were harvested at A600~0.4


title: Bf_MM_4.5mM_F_3

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes;N2/CO2 headspace), in defined minimal medium containing glucose and Sodium Formate (4.5mM).   Cells were harvested at A600= 0.25


title: Bf_cellobiose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Cellobiose as a carbon source. Cells were harvested at A600~0.4


title: Bf_fructose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% fructose as a carbon source. Cells were harvested at A600~0.4


title: Bf_NAG_2


title: Bf_lactose_2


title: Bf_galactose_2


title: Bf_mellibiose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Melibiose as a carbon source. Cells were harvested at A600~0.4


title: Bf_xylose_2_noDeplete

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Xilose as a carbon source. Cells were harvested at A600~0.4; total RNA was NOT depleted


title: Bf_xylose_1


title: Bf_Trehalose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Trehalose as a carbon source. Cells were harvested at A600~0.4


title: BtBf11.B2

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica. Mouse was fed a polysaccharide rich diet (BK chow). Technical replicate of BtBf11_CC (not used to calculate fold-changes)

organism:
Bacteroides thetaiotaomicron VPI-5482
Marvinbryantia formatexigens DSM 14469


title: Bf_maltose_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltose as a carbon source. Cells were harvested at A600~0.4


title: Bf_MM_No_F_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes;N2/CO2 headspace), in defined minimal medium containing glucose as the sole source of carbon (Sodium Formate was not added).   Cells were harvested at A600= 0.25


title: BtBf_FP13

description: Fecal pellet from mice (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Marvinbryantia formatexigens. Mouse was fed a polysaccharide rich diet (BK chow).


title: Bf_mellbiose_1


title: BtBf_CC13

description: Cecal contents from mice (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Marvinbryantia formatexigens. Mouse was fed a polysaccharide rich diet (BK chow).


title: Bf_Maltodextrin_2

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltodextrin as a carbon source. Cells were harvested at A600~0.4


title: Bf_sucrose_1


title: Bf_MM_No_F_2


title: Bf_MM_4.5mM_F_4


title: Bf_Fructose_1


title: BtBf11_CC

description: Cecal contents from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Blautia hydrogenotrophica. Mouse was fed a polysaccharide rich diet (BK chow).


title: input_DNA

status: Public on May 21 2010

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Control Input DNA.

data_processing:
Alignment: Sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174, Illumina pipeline version 1.3). All reads that map uniquely to the genome with two or fewer mismatches were kept. 76-bp reads were trimmed at the 3' end using different cutoffs in order to obtain the highest number of mappable reads onto the genome. In this way, the first 30bp at the 5' end for the untreated sample and the first 45bp at the 5' end for the LPS treated sample were kept.

Peaks: Analyses were performed using MACS (PMID: 18798982) with a p-value threshold of 10^-5. Both ChIPs were normalized against input DNA (GSM487453).

source_name: Primary bone marrow-derived macrophages (BMDM) from Fvb mice, untreated, input

growth_protocol: Bone marrow cells isolated from female Fvb mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting of blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 10 ng/ml).

value: Fvb

tag: cell type

value: BMDM cells (7th day of differentiation)

tag: treatment


title: UT

data_processing:
Alignment: sequence reads were mapped to the mouse mm9 genome using TopHat (PMID: 19289445, Illumina pipeline version 1.3). All reads that map uniquely to the genome with two or fewer mismatches were kept. Lanes 1 and 2 were sequenced up to 76bp while lanes 3 and 4 up to 55bp. For this reason all the reads were trimmed to 55bp before aligning.
Transcripts discovery and quantification was performed using Cufflinks 0.8.0 (unpublished, http://cufflinks.cbcb.umd.edu/).

source_name: Primary bone marrow-derived macrophages (BMDM) from Fvb mice

extract_protocol: Cells were lysed in HB buffer (10% glycerol, 60 mM KCl, 15 mM NaCl, 1.5 mM HEPES pH 7.9, 0.5 mM EDTA) containing 0.3M sucrose and 0.8% NP40. Nuclei were then pelleted through a 0.9M sucrose cushion in HB buffer and then resuspended in 100 ml of NRB (75 mM NaCl, 20 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 50% glycerol). Transcripts were extracted by Trizol (Invitrogen) followed by manufacturer's instructions. RNA is then fragmented using divalent cations under elevated temperature. Then the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process, the addition of a single 'A' base, and then ligation of the adapters. These products are then purified and enriched with PCR to create the final cDNA library.


title: polII_ser5.LPS_2h

description: Chromatin IP against polII ser5 2hrs post LPS treatment.

source_name: Primary bone marrow-derived macrophages (BMDM) from Fvb mice, 2hrs LPS, ChIP

tag: strain

tag: antibody

value: RNA polymerase II CTD repeat YSPTSPS (phospho S5) – Abcam (ab5131)

value: LPS (10 ng/ml) for 2hrs


title: polII_ser5.UT

description: Chromatin IP against polII ser5.

source_name: Primary bone marrow-derived macrophages (BMDM) from Fvb mice, untreated, ChIP


title: Bf_cellobiose_1

value: in vitro culture


title: Bf_arabinose_2


title: BtBf14_FP

description: Fecal pellet from a mouse (c57Bl6) colonized with Bacteroides thetaiotaomicron (VPI-5482) and Marvinbryantia formatexigens. Mouse was fed a polysaccharide rich diet (BK chow).


title: Bf_Glucose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% glucose as a carbon source. Cells were harvested at A600~0.4


title: TNRC6C

city: New York

first: Markus

last: Hafner

state: NY

address: 1230 York Ave, Box 186

department: Laboratory of RNA Molecular Biology

institute: The Rockefeller University

description:
HEK293 cells stably expressing FLAG/HA-tagged TNRC6C.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
TNRC6C_1: 19-24
TNRC6C_2: 19-24

Processed data from combined TNRC6C_1 and _2 PAR-CLIP experiment.

data_processing: The basic method for removing adaptors and assigning a functional annotation to the sequence reads was described in (Berninger et al., 2008). Briefly, we used an in-house ends-free local alignment algorithm (score parameters: 2 for match, -3 for mismatch, -2 for gap opening, -3 for gap extension) to align the Solexa adapter to the 3' end of each sequence read, allowing for the possibility that the adapter was not completely sequenced (Software can be downloaded from http://www.mirz.unibas.ch/restricted/clipdata/RESULTS/index.html). We removed from the reads the fragments that aligned to the adaptor as long as the number of matches exceeded that of mismatches by at least 3. Sequences that were either too short (less than 20 nt) or too repetitive (using a cut-off of 0.7 and 1.5 in the entropy of the mono- and dinucleotide distributions, respectively, of individual sequence reads (Berninger et al., 2008)) were discarded because they would probably map to multiple genomic locations. The remaining sequences were mapped to the hg18 version of the human genome assembly that was downloaded from the University of California at Santa Cruz (http://genome.cse.ucsc.edu) and to a database of sequences whose function (rRNA, tRNA, sn/snoRNA, miRNA, mRNA, etc.) is already known. These were obtained from the sources specified in (Berninger et al., 2008). The Oligomap algorithm (Berninger et al., 2008) was used for this purpose, and all the perfect and 1-error (mismatch or insertion or deletion (indel) mappings were obtained. Based on the GMAP (Wu and Watanabe, 2005) genome mapping of human mRNA transcripts from NCBI downloaded on November 4th, 2008, we determined whether the sequence reads mapped to intronic or exonic regions of genes. Based on the coding region annotation of transcripts in GenBank, we determined whether the exonic sequence reads originated from the 5'UTR, CDS or 3'UTR. Detailed bioinformatics procedure can be found in the Supplement to PMID 20371350.

source_name: cultured cells, TNRC6C

growth_protocol: HEK293 T-REx Flp-In cells (Invitrogen) were grown in D-MEM high glucose with 10% (v/v) fetal bovine serum, 1% (v/v) 2 mM L-glutamine, 1% (v/v) 10,000 U/ml penicillin/10,000 µg/ml streptomycin, 100 µg/ml zeocin and 15 µg/ml blasticidin. Cell lines stably expressing FLAG/HA-tagged proteins were generated by co-transfection of pFRT/TO/FLAG/HA or pFRT/FLAG/HA constructs with pOG44 (Invitrogen). Cells were selected by exchanging zeocin with 100 µg/ml hygromycin. Expression of FLAG/HA-IGF2BP1, -2, -3 and TNRC6A, B and C was induced by addition of 250 ng/ml doxycycline 15 to 20 h before crosslinking. Detailed experimental procedure can be found in the Supplement to PMID 20371350.

extract_protocol:
The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g. RNase T1 (Fermentas) was added to the cleared cell lysates and the reaction mixture was incubated at 22ºC for 15 min and subsequently cooled for 5 min on ice before addition of antibody-conjugated magnetic beads.
The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008). The first step, 3' adapter ligation, was carried out as described on a 20 ul scale using 10.5 ul of the recovered RNA. UV 365 nm crosslinked sample RNAs were processed using Solexa sequencing adapter sets. Depending on the amount of RNA recovered, 5'-adapter-3'-adapter products without inserts may be detected after amplification of the cDNA as additional PCR bands. In such case, the longer PCR product of expected size was excised from a 3% NuSieve low-melting point agarose gel, eluted from the gel pieces with the Illustra GFX-PCR purification kit (GE Healthcare) and Solexa sequenced. Detailed experimental procedure can be found in the Supplement to PMID 20371350.

treatment_protocol: For UV crosslinking, cells were washed once with ice-cold PBS while still attached to the plates. PBS was removed completely and cells were irradiated on ice with 365 nm UV light in a Stratalinker 2400 (Stratagene). Cells were scraped off with a rubber policeman in 1 ml PBS per plate and collected by centrifugation at 500×g for 5 min. Detailed experimental procedure can be found in the Supplement to PMID 20371350.

tag: cell line

value: HEK 293

tag: crosslinker and crosslinking wavelength

value: anti-FLAG antibody

tag: antibody vendor

value: Sigma

tag: antibody catalog #

tag: immunoprecipitated protein

tag: weight of protein recovered

value: ca. 200 kDa


title: TNRC6B

description:
HEK293 cells stably expressing FLAG/HA-tagged TNRC6B.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
TNRC6B_1: 19-24
TNRC6B_2: 19-24

Processed data from combined TNRC6B_1 and _2 PAR-CLIP experiment.

source_name: cultured cells, TNRC6B


title: BtBf_FP15

tag: sample type


title: Bf_Maltotriose_1

description: Marvinbryantia formatexigens grown anaerobically (Balch tubes), in MBf medium containing 1% Maltotriose as a carbon source. Cells were harvested at A600~0.4


title: AGO4

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO4.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
Ago4_1: 19-24
Ago4_2: 19-24

Combined processed data from AGO4 libraries.

source_name: cultured cells, AGO4

value: 100 kDa


title: AGO3

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO3.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
Ago3_1: 19-24
Ago3_2: 19-24

Combined processed data from AGO3 libraries.

source_name: cultured cells, AGO3


title: H9 Oct4 technical replicate 2

status: Public on May 20 2010

first: Richard

middle: A

last: Young

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against Oct4.H9

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
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 reads per million are shown.

source_name: Embyonic stem cells

growth_protocol: H9 (WA09) human ES cells were grown in mTESR1 media (Stem Cell Technologies) on matrigel (BD Biosciences) in the absence of feeders.

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts for 20 second pulses for a total of 3 minutes. 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.

treatment_protocol: Cross-linking was performed with 1% paraformaldehyde

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog number


title: AGO2, miR124

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO2.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
miR-124: 19-24

Processed data from miR-124 transfection experiment.

source_name: cultured cells, AGO2


title: TNRC6A

description:
HEK293 cells stably expressing FLAG/HA-tagged TNRC6A.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
TNRC6A_1: 19-24
TNRC6A_2: 19-24

Processed data from combined TNRC6A_1 and _2 PAR-CLIP experiment.

source_name: cultured cells, TNRC6A


title: H9 Oct4 technical replicate 1

description: Chromatin IP against Oct4 in H9 cells


title: Pumilio2

description:
HEK293 cells stably expressing FLAG/HA-tagged PUM2.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
Pum_2_High: 24-100
Pum_2_Low: 19-24

Combined processed data from Pum2_High and Pum2_low.

source_name: cultured cells, Pumilio2

value: 130 kDa


title: H9 IgG

description: Chromatin IP against IgG in H9 human ES cells

value: IgG

value: Upstate


title: RNA Polymerase II phospho Ser7 CTD ChIPseq in mES cells

description: Chromatin IP against Pol2Ser7

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie.
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.
Genome build: mm8

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: RNA Pol II (Ser7 phospho CTD)

value: Dirk Eick DIRK EICK LABORATORY

value: V6.5 embryonic stem cells


title: IGF2BP1

description:
HEK293 cells stably expressing FLAG/HA-tagged IGF2BP1. Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
IGF2BP1_1: 19-24
IGF2BP1_2: 24-40
IGF2BP1_3: 40-70
IGF2BP1_4: 70-150
IGF2BP1_5: >150
IGF2BP1_U_SMA_8: 15-50

Combined processed data from IGF2BP1_1-5 and IGF2BP1_U_SMA8.

source_name: cultured cells, IGF2BP1

value: 75 kDa


title: IGF2BP3

description:
HEK293 cells stably expressing FLAG/HA-tagged IGF2BP3.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
IGF2BP3_1: 19-24
IGF2BP3_2: 24-40
IGF2BP3_3: 40-70
IGF2BP3_4: 70-150
IGF2BP3_5: >150

Combined processed data from IGF2BP3_1-5.

source_name: cultured cells, IGF2BP3


title: 3T3-L1_240hr_Input

city: Philadelphia

first: David

last: Steger

state: PA

address: 415 Curie Blvd

institute: University of Pennsylvania

description: Input; no peak file

data_processing: Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.

growth_protocol: 3T3-L1 cells were obtained from American Type Culture Collection and differentiated to adipocytes according to standard protocol. All cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: ChIP samples were amplified using the ChIP-Seq Sample Prep Kit (Illumina) according to manufacturer's instructions. Sequence reads of 36 bp were obtained using the Solexa Analysis Pipeline, and mapped to the mouse genome (mm8) using ELAND allowing up to two mismatches. Uniquely positioned reads were included for further analysis such that each start coordinate was represented once.

treatment_protocol: ChIP was performed as described using cross-linked 3T3-L1 nuclear lysates.

tag: developmental stage

value: 10 days after inducing differentiation


title: 3T3-L1_6hr_Input

description: Input; no peak file

value: 6 hr after inducing differentiation


title: QKI

description:
HEK293 cells stably expressing FLAG/HA-tagged QKI.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
QKI_1_1: >50
QKI_1_2: >50
QKI_2: 24-50
QKI_3: 19-24

Combined processed data from all QKI libraries.

source_name: cultured cells, QKI

value: QKI

value: 50 kDa


title: AGO1

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO1.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
Ago1: 19-24

Processed data from AGO1 library.

source_name: cultured cells, AGO1

value: HEK 293


title: 3T3-L1_24hr_Input

description: Input; no peak file

value: 24 hr after inducing differentiation


title: 3T3-L1_240hr_H3K9ac

description: Peak file reports regions outside of TSS and differentially enriched for H3K9ac at 240 hr relative to 0 or 24 hr of differentiation

data_processing:
Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.

Input sample: GSM544725: 3T3-L1_240hr_Input

source_name: Chromatin IP against acetylated H3 lysine 9

value: H3K9ac (Upstate Biotechnologies, 06-942)


title: 3T3-L1_0hr_CEBPb

description: Peak file reports enriched regions at 0h

data_processing:
Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.

Input sample: GSM544726: 3T3-L1_6hr_Input

source_name: Chromatin IP against CEBPb

value: undifferentiated

value: CEBPβ (Santa Cruz Biotechnologies, sc-150)


title: IGF2BP2

description:
HEK293 cells stably expressing FLAG/HA-tagged IGF2BP2.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
IGF2BP2_1: 19-24
IGF2BP2_2: 24-40
IGF2BP2_3: 40-70
IGF2BP2_4: 70-150
IGF2BP2_5: >150

Combined processed data from IGF2BP2_1-5.

source_name: cultured cells, IGF2BP2

value: anti-FLAG antibody

value: Sigma


title: 3T3-L1_6hr_CEBPb

description: Peak file reports enriched regions at 6h


title: 3T3-L1_0hr_Input

description: Input; no peak file


title: 3T3-L1_6hr_GR

source_name: Chromatin IP against GR

value: GR (Santa Cruz Biotechnologies, sc-1004; and Affinity BioReagents, PA1-511A)


title: 3T3-L1_24hr_H3K9ac

description: Peak file reports regions outside of TSS and differentially enriched for H3K9ac at 24 hr relative to 0 or 240 hr of differentiation

data_processing:
Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.

Input sample: GSM544724: 3T3-L1_24hr_Input


title: AGO2, miR7

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO2.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
miR-7: 19-24

Processed data from miR-7 transfection experiment.

value: 100 kDa


title: H9 Oct4 replicate 2

description: Chromatin IP against Oct4 in H9 cells

value: Santa Cruz


title: AGO2

description:
HEK293 cells stably expressing FLAG/HA-tagged AGO2.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
Ago2_1: 19-24
Ago2_2: 19-24

Combined processed data from AGO2 libraries.


title: RER SCL no AB

status: Public on May 18 2010

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

description: ChIP enriched

data_processing: wig files were made from maq pileup data and incorporated into GBrowse htt

source_name: fetal liver erythroblasts

growth_protocol: mouse E12.5 fetal liver cells were expanded in vitro for 3 days in the presence of growth factors then ter119 purified. Ter119- populations were processed for ChIP experiments.

extract_protocol: Protein-DNA cross-linking was performed on 1 x 10^7 Ter119– cells with 1% formaldehyde for 10 min at room temperature. Glycine (0.125 M) was added to quench the reaction. Cells were washed twice in phosphate-buffered saline containing protease inhibitors (Complete; Roche). Nuclei were lysed in lysis buffer (ChIP assay kit; Upstate Biotechnology) and sheared by sonication to reduce the chromatin fragments to 200 to 500 base pairs. Immunoprecipitation of cross-linked chromatin was performed using anti-SCL and ready-made buffers (ChIP assay kit; Upstate Biotechnology). Control samples were treated exactly as the anti-SCL ChIP smaples except no antibody was added to the crosslinked and sonicated chromatin.

treatment_protocol: no treatments applied

value: fetal liver erythroblast

tag: genotype

value: RER SCL mutant


title: RER SCL

description: ChIP enriched


title: 3T3-L1_0hr_H3K9ac

description: Peak file reports regions outside of TSS and differentially enriched for H3K9ac at 0 hr relative to 24 or 240 hr of differentiation

data_processing:
Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.

Input sample: GSM544723: 3T3-L1_0hr_Input


title: WT SCL

description: ChIP enriched

value: wild type


title: WT no AB

description: ChIP enriched


title: IGF2BP1_6SG

description:
HEK293 cells stably expressing FLAG/HA-tagged IGF2BP1.  Protein was immunoprecipitated by anti-FLAG antibody, Sigma F1854.

Sample: Length of RNA-segment (nt) used for cDNA generation
IGF2BP1_6SG: 15-50

Processed data from IGF2BP1_6SG.

value: 75 kDa


title: LNCaP 0h-R1881

city: Chicago

first: Jindan

last: Yu

state: IL

address: 303 E. Superior St.

department: Medicine - Hem/Onc

institute: Northwestern University

data_processing: Reads were aligned to the reference genome using Eland software   (Illumina). Enriched intervals were identified by a Hidden Markov   Model-based program named HPeak (Qin et al. unpublished).

source_name: LnCaP - R1881 - LNCaP cells hormone starved for 24 hrs, and treated with R1881 for 0h

growth_protocol: Prostate cell lines were maintained in appropriate medium.  For androgen treatment experiment, LNCaP and VCaP cells were hormone starved for 48 hours prior to treatment with ethanol control or synthetic androgen R1881.  For RNA interference of ERG, VCaP cells were grown in regular medium and subjected to non-silencing control siRNA or siRNA specific for targeting ERG on two continuous days.  At 48 hour after the last siRNA transfection, cells were harvested for ChIP analysis.

extract_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.


title: LNCaP 24h-R1881

source_name: LnCaP - R1881 - LNCaP cells hormone starved for 24 hrs, and treated with R1881 for 24h


title: tissue_H3K4me3

description: Chromatin IP against H3K4me3

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against H3K4me3

tag: metastatic prostate cancer tissue


title: tissue_H3K27me3

description: Chromatin IP against H3K27me3

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against H3K27me3


title: tissue_AR

description: Chromatin IP against AR

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against AR


title: tissue_H3K9me3

description: Chromatin IP against H3K9me3

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against H3K9me3


title: RWPE+GUS_ERG_jy16

description: Chromatin IP against ERG

source_name: RWPE - GUS control stable cell line - Chromatin IP against ERG

tag: GUS control stable cell line


title: tissue_ERG

description: Chromatin IP against ERG

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against ERG


title: tissue_PolII

description: Chromatin IP against PolII

source_name: tissue - metastatic prostate cancer tissue - Chromatin IP against PolII


title: 22RV1_no_treat_AR

description: Chromatin IP against AR

source_name: 22RV1 - no treat - Chromatin IP against AR

tag: no treat


title: LnCaP_1nmR_AR

description: Chromatin IP against AR

source_name: LnCaP - 1nm R - Chromatin IP against AR

tag: 1nm R


title: VCaP_ethl_AR_jy11

description: Chromatin IP against AR

source_name: VCaP - Ethanol - Chromatin IP against AR

tag: Ethanol


title: VCaP_ERG_jy13

description: Chromatin IP against ERG

source_name: VCaP - regular medium - Chromatin IP against ERG

tag: regular medium


title: LNCaP_R1881_AR_jy10

description: Chromatin IP against AR

source_name: LNCaP - R1881 - Chromatin IP against AR


title: LNCaP_ERG_jy14

description: Chromatin IP against ERG

source_name: LNCaP - regular medium - Chromatin IP against ERG


title: VCaP_NT_ERG

description: Chromatin IP against ERG

source_name: VCaP - NT - Chromatin IP against ERG

tag: NT


title: LNCaP 48h-R1881

source_name: LnCaP - R1881 - LNCaP cells hormone starved for 24 hrs, and treated with R1881 for 48h


title: VCaP_NT_AR

description: Chromatin IP against AR

source_name: VCaP - NT - Chromatin IP against AR


title: LnCaP_regular_medium_H3K4me1

description: Chromatin IP against H3K4me1

source_name: LnCaP - regular medium - Chromatin IP against H3K4me1


title: LnCaP_regular_medium_H3K4me2

description: Chromatin IP against H3K4me2

source_name: LnCaP - regular medium - Chromatin IP against H3K4me2


title: LnCaP_regular_medium_FoxA1

description: Chromatin IP against FoxA1

source_name: LnCaP - regular medium - Chromatin IP against FoxA1


title: VCaP_siERG_AR

description: Chromatin IP against AR

source_name: VCaP - siERG - Chromatin IP against AR

tag: siERG


title: VCaP_regular_medium_H3K4me2

description: Chromatin IP against H3K4me2

source_name: VCaP - regular medium - Chromatin IP against H3K4me2


title: VCaP_regular_medium_FoxA1

description: Chromatin IP against FoxA1

source_name: VCaP - regular medium - Chromatin IP against FoxA1


title: VCaP_regular_medium_H3K4me1

description: Chromatin IP against H3K4me1

source_name: VCaP - regular medium - Chromatin IP against H3K4me1


title: RWPE+ERG_ERG_jy15

description: Chromatin IP against ERG

source_name: RWPE - ERG overexpression stable cell lline - Chromatin IP against ERG

tag: ERG overexpression stable cell lline


title: LNCaP_ethl_AR_jy9

description: Chromatin IP against AR

source_name: LNCaP - Ethanol - Chromatin IP against AR


title: LnCaP_10nmR_AR

description: Chromatin IP against AR

source_name: LnCaP - 10nm R - Chromatin IP against AR

tag: 10nm R


title: VCaP_R1881_AR_jy12

description: Chromatin IP against AR

source_name: VCaP - R1881 - Chromatin IP against AR


title: VCaP_regular_medium_Ace_H3

description: Chromatin IP against Ace-H3

source_name: VCaP - regular medium - Chromatin IP against Ace-H3


title: LnCaP_regular_medium_H3K36me3

description: Chromatin IP against H3K36me3

source_name: LnCaP - regular medium - Chromatin IP against H3K36me3


title: VCaP_regular_medium_H3K36me3

description: Chromatin IP against H3K36me3

source_name: VCaP - regular medium - Chromatin IP against H3K36me3


title: VCaP_regular_medium_Pan_H3

description: Chromatin IP against Pan-H3

source_name: VCaP - regular medium - Chromatin IP against Pan-H3


title: LnCaP_regular_medium_H3K4me3

description: Chromatin IP against H3K4me3

source_name: LnCaP - regular medium - Chromatin IP against H3K4me3


title: CS58.LnCaP_R1881_H3K4me3

description: Chromatin IP against H3K4me3

source_name: LnCaP - R1881 - Chromatin IP against H3K4me3


title: LnCaP_Ethl_Polll

description: Chromatin IP against Polll

source_name: LnCaP - Ethanol - Chromatin IP against Polll


title: LnCaP_R1881_Polll

description: Chromatin IP against Polll

source_name: LnCaP - R1881 - Chromatin IP against Polll


title: VCaP_regular_medium_H3K9me3

description: Chromatin IP against H3K9me3

source_name: VCaP - regular medium - Chromatin IP against H3K9me3


title: LnCaP_R1881_H3K4me3

description: Chromatin IP against H3K4me3


title: LnCaP_regular_medium_Ace_H3

description: Chromatin IP against Ace-H3

source_name: LnCaP - regular medium - Chromatin IP against Ace-H3


title: VCaP_siERG_ERG

description: Chromatin IP against ERG

source_name: VCaP - siERG - Chromatin IP against ERG


title: LnCaP_regular_medium_H3K9me3

description: Chromatin IP against H3K9me3

source_name: LnCaP - regular medium - Chromatin IP against H3K9me3


title: CS57.LnCaP_Ethl_H3K4me3

description: Chromatin IP against H3K4me3

source_name: LnCaP - Ethanol - Chromatin IP against H3K4me3


title: LnCaP_R1881_H3K27me3

description: Chromatin IP against H3K27me3

source_name: LnCaP - R1881 - Chromatin IP against H3K27me3


title: LnCaP_R1881_H3K9me3

description: Chromatin IP against H3K9me3

source_name: LnCaP - R1881 - Chromatin IP against H3K9me3


title: LnCaP_Ethl_H3K27me3

description: Chromatin IP against H3K27me3

source_name: LnCaP - Ethanol - Chromatin IP against H3K27me3


title: LnCaP_Ethl_H3K9me3

description: Chromatin IP against H3K9me3

source_name: LnCaP - Ethanol - Chromatin IP against H3K9me3


title: VCaP_Ethl_Polll

description: Chromatin IP against Polll

source_name: VCaP - Ethanol - Chromatin IP against Polll


title: VCaP_R1881_Polll

description: Chromatin IP against Polll

source_name: VCaP - R1881 - Chromatin IP against Polll


title: LnCaP_Ethl_H3K4me3

description: Chromatin IP against H3K4me3


title: VCaP_R1881_H3K27me3

description: Chromatin IP against H3K27me3

source_name: VCaP - R1881 - Chromatin IP against H3K27me3


title: VCaP_R1881_H3K4me3

description: Chromatin IP against H3K4me3

source_name: VCaP - R1881 - Chromatin IP against H3K4me3


title: VCaP_Ethl_H3K27me3

description: Chromatin IP against H3K27me3

source_name: VCaP - Ethanol - Chromatin IP against H3K27me3


title: VCaP_Ethl_H3K4me3

description: Chromatin IP against H3K4me3

source_name: VCaP - Ethanol - Chromatin IP against H3K4me3


title: VCaP_regular_medium_Polll

description: Chromatin IP against Polll

source_name: VCaP - regular medium - Chromatin IP against Polll


title: VCaP_Ethl_H3K9me3

description: Chromatin IP against H3K9me3

source_name: VCaP - Ethanol - Chromatin IP against H3K9me3


title: VCaP_regular_medium_H3K27me3

description: Chromatin IP against H3K27me3

source_name: VCaP - regular medium - Chromatin IP against H3K27me3


title: VCaP_regular_medium_H3K4me3

description: Chromatin IP against H3K4me3

source_name: VCaP - regular medium - Chromatin IP against H3K4me3