title: PU.1 ChIP-Seq NOD/ShiLtJ no treatment

city: La Jolla

first: Casey

last: Romanoski

address: 9500 Gliman Dr.

institute: UCSD

description:
formaldehyde cross-linked
processed data: N/A

data_processing:
For ChIP-Seq, RNA-Seq and GRO-Seq samples, reads were aligned to the mm9 genome as well as BALB/cJ contigs using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location in both genomes, while allowing 3 mismatches in the first 28 bases, and at least 5 high-quality mismatches overall. The NOD PU.1 notx ChIP-Seq sample was only mapped to mm9 according to the same criteria. To identify allele-specific reads in CB6F1J, the initial mapping to strain-specific regions in both genomes defined in the parental inbred strains was performed with the leftmost 33 bases allowing no mismatch, and reads that mapped to both genomes were discarded. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study. Genetic variation analyses were performed using custom R scripts.
Genome_build: mm9, BALB/cJ de novo assemblies (Keane, T. M. et al., Nature 477, 289-294 (2011), the initial published version) were downloaded from the Sanger Institute website: http://www.sanger.ac.uk/resources/mouse/genomes/
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), rpkm text files (RNA-Seq, GRO-Seq expression data).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

growth_protocol: Peritoneal macrophages were harvested by peritoneal lavage with 20 ml ice-cold PBS 4 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells seeded in 10% fetal calf serum (FCS)/RPMI-1640 containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS.

extract_protocol: ChIP-Seq: Media was decanted and cells were fixed at room temperature with either 1% formaldehyde/PBS for 10 minutes (for PU.1, C/EBPα ChIPs) or 2 mM disuccinimidylglutarate (DSG, Pierce)/10% DMSO/PBS for 30 minutes followed by 1% formaldehyde/PBS for another 15 minutes. After quenching the reaction by adding glycine to 0.125 M, cells were scraped into the supernatant using a rubber policeman, pelleted, washed twice with PBS and snap-frozen in dry-ice/methanol. ChIPs for PU.1 and C/EBPα were performed exactly as described previously (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)). Briefly, 7e6-20e6 cells were incubated for 5 min in 1 ml 0.5% IGEPAL CA-630-containing 10 mM HEPES pH 7.9/85 mM KCl/1 mM EDTA on ice, centrifuged, sonicated on wet ice with a Misonix 3000 sonicator in 500 µl 1% SDS/0.5% EmpigenBB/50 mM Tris pH7.4/10 mM EDTA/1x protease inhibitor cocktail/1 mM PMSF for 6 cycles of 10s/30s break, lysates were cleared for 5 min, 20000 x g, 4°C, and the supernatant diluted with 1.5 volumes dilution buffer (0.5 % Triton X-100/20 mM Tris pH 7.4/100 mM NaCl/2 mM EDTA). Diluted chromatin was precleared for 1 h with 120 µl 50% slurry of CL-4B sepharose blocked (washed twice with TE buffer, blocked for 60 min in 0.5% BSA/20 µg/ml glycogen/TE, washed twice with TE, resuspended in original volume of TE), then immunoprecipitated overnight by adding 2.5 µg antibody, and capture with 50 µl protein A-sepharose (GE Healthcare Life Sciences, blocked as above, but overnight). Immunoprecipitates were washed twice each with ice-cold wash buffer I (150 mM NaCl/1% Triton X-100/0.1% SDS), II (450 mM NaCl/1% Triton X-100) , III (250 LiCl/1% IGEPAL CA-630/1% Deoxycholate) and TE, and eluted with 1% SDS/TE at room temperature. After addition of NaCl to 300 mM final Na+ concentration, crosslinks were reversed overnight in a hot air oven, RNA digested for 2 h at 37°C with 0.33 mg/ml RNase A, proteins digested for 2 h at 50°C with 0.5 mg/ml proteinase K, and DNA extracted using Qiagen QiaQuick columns. The H3K27Ac ChIPs were performed in the presence of 1mM  (C57BL/6J and BALB/cJ) or 5 mM (CB6F1J) butyric acid in all buffers, using sepharose as described above for the C57BL/6J and BALB/c experiments, while for the CB6F1J experiment 5 µg antibody pre-bound to 50 µl Protein A Dynabeads (Life Technologies) were used, and the preclearing step was omitted. For p65, IP conditions were identical to the ones described before, except that pre-clearing was omitted, and the ChIP was performed with 5 µg antibody pre-bound to 50 µl Protein A Dynabeads for 30 minutes in 0.5% BSA, beads were washed thrice with WB I and thrice with WBIII containg only 0.7% deoxycholate, and a final wash with TE/50 mM NaCl was added before elution. ChIPs for H3K4me2 were performed on MNase-digested chromatin as described previously (Barski et al. Cell 129, 823-837 (2007)) on 20e6 cells digested in two 10e6 cell batches with 5 and 10 U MNase (Worthington) for 5 min at 37°C, s adding stop buffer containing 10 mM each of EDTA/EGTA, brief sonication in a Bioruptor 200, dialysis against two changes of RIPA buffer, and overnight IP with antibody-bound, block protein A-Dynabeads (Life Technologies) at 4°C. After two washes each with RIPA buffer, 0.3 M NaCl/RIPA buffer, 0.5% deoxycholate/0.5% IGEPAL CA-630-containing buffer and TE, DNA was eluted with 0.3% SDS/TE and 0.9 mg/ml proteinase K overnight at 65°C overnight, and DNA was isolated by phenol/chloroform extraction and ethanol precipitation. To control for open chromatin and library biases, input chromatin libraries after sonication were sequenced for each strain, crosslinking condition and ChIP lysis protocol. Sequencing libraries were prepared by blunting, A-tailing, adapter ligation as previously described (Heinz, S. et al. Molecular Cell 38, 576-589 (2010)) using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 12-14 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2000 (Illumina) for 51 cycles.

treatment_protocol: Cells were treated by replacing the seeding media with fresh, warm media ("notx") or fresh, warm media containing 100 ng/ml KDO2-lipid A (KLA) for the indicated times.

value: NOD/ShiLtJ

value: no treatment

tag: chip (antibody)

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


title: RNA-Seq BALBc/J no treatment

status: Public on Oct 15 2013

type: SRA

state: CA

country: USA

description: GeneExpression.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

extract_protocol: RNA-Seq: PolyA-selected RNA (MicroPoly(A)Purist kit (Ambion)) was hydrolyzed with Fragmentation Buffer (Ambion) for 10 min at 70°C and re-buffered to 10 mM Tris pH 7.4 using P-30 size exclusion columns (Bio-Rad). Thirty nanograms RNA were de-capped for 2 h at 37°C with 0.5 µl (10 U/µl) TAP (Epicentre) in 20 µl TAP buffer containing 1 U/µl SUPERase-IN. Samples were 3’ dephosphorylated for 50’ at 37°C with 1 µl PNK (Enzymatics), 0.5 µl 10x TAP buffer, 1.5 µl water, 0.5 μl 0.25 M MgCl2 (3 mM free Mg2+ final), 0.5 μl 10 mM ATP (0.2 μM final to protect PNK). Subsequently, RNA was 5’-phosphorylated for 60 min at 37°C by adding 2 μl (10 U/µl) PNK, 10 μl 10x T4 DNA ligase buffer and 63 μl water. RNA was extracted with Trizol LS, precipitated in the presence of Glycoblue (Ambion), and dissolved in 4.5 µl water. 0.5 µl 9 µM of a 5’-adenylated sRNA3'MPX adapter /5Phos/AG ATC GGA AGA GCA CAC GTC TGA /3AmMO/ (IDT, desalted;  adenylated with Mth ligase (NEB) according to the manufacturer’s instructions, phenol-chloroform/chloroform-extracted, ethanol-precipitated with glycogen and dissolved in water at 9 µM) were heat-denatured together with the RNA for 2 minutes at 70°C, and ligated with 100 U truncated T4RNA ligase 2 K227Q (NEB) in 10 µl 1x T4 RNA ligase buffer without ATP, containing 10 U SUPERase-In and 15% PEG8000 for 2 hours at 16°C. To reduce adapter dimer formation, 0.5 μl 10 μM MPX_ RT primer    5’-GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T-3’ (IDT, desalted) was added and annealed to the ligation product by incubating at 75°C for 2 minutes, then 37°C for 30 minutes, then 25°C for 15 minutes. Finally, 0.5 µl 5 µM hybrid DNA/RNA sRNA5'h adapter 5’-GTT CAG AGT TCT ACA rGrUrC rCrGrA rCrGrA rUrC-3’ (IDT) were ligated to previously capped RNA 5’ ends by adding 2 µl T4 RNA ligase buffer, 6 µl 50% PEG8000 (15% final), 1 µl 10 mM ATP, 9.5 µl water and 0.5 µl (5 U) T4 RNA ligase 1 for 90 minutes at 20°C. To 15 μl ligation reaction, an additional 0.5 μl 10 μM MPX_ RT primer were added, reactions were denatured at to 70°C for 1 minute, then placed on ice. RNA was reverse-transcribed by adding 3 µl 10x first strand buffer, 4.5 µl water, 1.5 µl 10 mM dNTP, 3 µl 0.1 M DTT, 1.5 µl RNaseOUT and 1 µl Superscript III reverse transcriptase (Invitrogen), and incubating for 30 minutes at at 50°C. Complementary DNA was isolated by adding 35 µl AMPure XL beads (Beckman), binding and washing according to manufacturer’s instructions and dissolved in 40 µl TET. Libraries were PCR-amplified for 11 cycles with 0.75 µM primers oNTI201 (5'-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3' and TruSeq-compatible indexed primers (e.g. 5’-CAA GCA GAA GAC GGC ATA CGA GAT iii iii GTG ACT GGA GTT CAG ACG TGT GCT CTT-3’ (desalted, IDT, i signifies index nucleotides) using Phusion Hot Start II (Thermo Scientific) in HF buffer containing 0.5 M betaine (98°C, 30s/12x(98°C, 10s/57°C, 25s/72°C, 20s)/ 72°C, 1min/4°C, ∞), 175-225 bp fragments were size-selected on 10% PAGE gels and sequenced for 51 cycles on a HiSeq 2000 sequencer (Illumina) with small RNA sequencing primer 5’-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3’ and TruSeq Index sequencing primer (Illumina).

tag: strain

value: BALBc/J

tag: treatment


title: RNA-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: GeneExpression.txt

value: 100 ng/ml Kdo2-LipidA 1 hr


title: GRO-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: GeneExpression.txt

data_processing:
Library strategy: GRO-Seq
For ChIP-Seq, RNA-Seq and GRO-Seq samples, reads were aligned to the mm9 genome as well as BALB/cJ contigs using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location in both genomes, while allowing 3 mismatches in the first 28 bases, and at least 5 high-quality mismatches overall. The NOD PU.1 notx ChIP-Seq sample was only mapped to mm9 according to the same criteria. To identify allele-specific reads in CB6F1J, the initial mapping to strain-specific regions in both genomes defined in the parental inbred strains was performed with the leftmost 33 bases allowing no mismatch, and reads that mapped to both genomes were discarded. Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study. Genetic variation analyses were performed using custom R scripts.
Genome_build: mm9, BALB/cJ de novo assemblies (Keane, T. M. et al., Nature 477, 289-294 (2011), the initial published version) were downloaded from the Sanger Institute website: http://www.sanger.ac.uk/resources/mouse/genomes/
Supplementary_files_format_and_content: Processed files include BED-like files (ChIP-Seq peak positions), rpkm text files (RNA-Seq, GRO-Seq expression data).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

molecule: total RNA

extract_protocol: GRO-Seq: GRO-Seq was performed as described (Core, L.J., Waterfall, J.J., and Lis, J.T., Science 322, 1845-1848 (2008)) with minor modifications. Briefly, 10 million peritoneal macrophages were washed with ice-cold PBS. The nuclei was allowed to swell on ice for 5 min in buffer containing 10 mM Tris-cl pH 7.5, 2 mM MgCl2 and 3 mM CaCl2. Cells were scraped and pelleted for 10 min at 400 g. Supernatant was removed and cells suspended to 500 µl of Swelling buffer + 10 % glycerol + 2 U/ml Superase-In (Ambion). The cells were vortexed slowly while adding 500 µl of Swelling buffer + 10 % glycerol + 1 % Igepal drop by drop. Nuclei were washed twice with 10 ml of lysis buffer (swelling buffer, 0.5% Igepal, 10% glycerol, 2 U/ml SUPERase-In (Ambion)) and once with 1 ml of freezing buffer (50 mM Tris-CL pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA) before counting. Nuclei were centrifuged for 6 min at 900 g and suspended to a concentration of 5 x 10e6 nuclei per 100 µl of freezing buffer. Nuclei were mixed with an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.4 µM CTP) and the reaction was allowed to proceed for 5 min at 30°C. The reaction was stopped and RNA isolated using Trizol LS (Invitrogen). RNA was treated with TURBO DNase (Ambion). Base hydrolysis was performed using RNA fragmentation Reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). Samples were dephosphorylated with Antarctic phosphatase and immunopurified using Anti-deoxyBrU beads (Santa Cruz). E. coli Poly(A) Polymerase (NEB) was used to create a priming site for cDNA synthesis. Reverse transcription was carried out using Superscript III reagents (Invitrogen) and oligonucleotide 5’-pi2GATCGTCGGACTGTAGAACTCTxCAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN (p indicates 5’ phosphorylation, x indicates the abasic dSpacer furan and V, N indicates degenerate nucleotides, i2 is a two-nucleotide index for multiplexing). Excess RT primer was digested with Exonuclease I (NEB), the RNA was hydrolyzed by NaOH treatment and cDNA extracted from a 10% TBE-Urea Gel (Invitrogen) followed by ethanol precipitation. cDNA was circularized using CircLigase (Epicentre) and linearized using APE1 (New England Biolabs). cDNA was amplified by 8 cycles of PCR using the Phusion High-Fidelity enzyme (NEB) and Small RNA PCR primers (Illumina). Reactions were separated on a non-denaturing 8% polyacrylamide gel and the recovered libraries were sequenced for 51 cycles on an Illumina HiSeq2000 according to the manufacturer’s instructions.


title: RNA-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: GeneExpression.txt


title: GRO-Seq BALBc/J no treatment

description: GeneExpression.txt


title: RNA-Seq C57BL6/J no treatment

description: GeneExpression.txt


title: GRO-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: GeneExpression.txt


title: Sample_N8

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description:
The transgenic mice express the fluorescent ubiquitination-based cell cycle indicator,  Fucci  probe mAG-hGem (1/110) driven by the ubiquitously expressed cytomegalovirus (CMV) promoter (Sakaue-Sawano et al. Cell 2008).The fluorescent probe, mAG-hGem (1/110), consisting of a green fluorescent protein, mAG (monomeric Azami Green) fused to ubiquitination domains (110 amino acid residues at the N-terminus) of human DNA replication factor, Geminin (hGem). Male hemizygous (Tg/-) transgenic adult mice were backcrossed with female wildtype C57/BL6  to generate about 50% F1 transgenic and wildtype control littermates.
processed data file: CIRTs_cardio.txt

data_processing:
For dendrite and soma samples Illumina Casave 1.3 software for base-calling
For BAT and cardiomyocyte samples Illumina Casave 1.8.1 software for base-calling
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome (for mouse samples) and rn4 whole genome for rat samples using RUM 2.0.3_04 pipeline for the dendritic ans soma sample, RUM 1.09 for BAT samples and RUM 1.11 for cardiomyocytes with default parameters
Reads mapping the intronic regions of genes by paired-end alignment were counted
Genome_build: mm9 for mouse and rn4 for rat
Supplementary_files_format_and_content: tab-delimited text file containing the processed putative cytoplasmically retained intronic contig coordinates along with the #reads mapping to each

extract_protocol:
single cells and dendrites were harvested by mechanical isolation, RNA was extracted using the freeze/thaw method, and aRNA amplified
RNA libraries were prepared for sequencing using standard Illumina protocols

value: transgenic C57BL/6

tag: age

value: Embryonic 14.5D

tag: tissue

value: Cardiomyocyte

tag: amplification

value: 3x aRNA


title: GRO-Seq C57BL6/J no treatment

description: GeneExpression.txt


title: H3K27Ac ChIP-Seq CB6F1/J F1 Hybrids no treatment

library_source: genomic

molecule: genomic DNA

value: CB6F1/J F1 Hybrids


title: PU.1 ChIP-Seq CB6F1/J F1 Hybrids no treatment


title: input DNA for MNase ChIP-Seq BALBc/J no treatment

description:
Mnase-treated genomic DNA
processed data: N/A


title: C/EBPa ChIP-Seq CB6F1/J F1 Hybrids no treatment

value: C/EBPa (Vendor:Santa Cruz, cat# sc-61, lot# D0108)


title: input DNA for MNase ChIP-Seq C57BL6/J no treatment


title: input DNA for ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr DSG + formaldehyde

description:
Disuccinimidyl glutarate (DSG) and formaldehyde cross-linked
processed data: N/A


title: Sample_N21


title: RNA-Seq BALBc/J 100 ng/ml Kdo2-LipidA 4 hr

description: GeneExpression.txt

value: 100 ng/ml Kdo2-LipidA 4 hr


title: input DNA for ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr formaldehyde


title: input DNA for ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr DSG + formaldehyde


title: input DNA for ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr formaldehyde


title: p65 ChIP-Seq replicate 2 BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: Disuccinimidyl glutarate (DSG) and formaldehyde cross-linked

value: p65 (Vendor:Santa Cruz, cat# sc-372, lot#H2609)


title: p65 ChIP-Seq replicate 1 C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr


title: H3K27Ac ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked

value: H3K27Ac (Vendor:Abcam, cat# ab4729, lot# GR45787-1)


title: H3K27Ac ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked


title: H3K27Ac ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: RNA-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 4 hr

description: GeneExpression.txt


title: H3K4me2 ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: Mnase-treated genomic DNA

value: H3K4me2 (Vendor:Millipore, cat# 07-030, lot# DAM1724042)


title: p65 ChIP-Seq replicate 2 C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr


title: H3K4me2 ChIP-Seq BALBc/J no treatment

description: Mnase-treated genomic DNA


title: C/EBPa ChIP-Seq BALBc/J no treatment

description: formaldehyde cross-linked


title: H3K4me2 ChIP-Seq C57BL6/J no treatment

description: Mnase-treated genomic DNA


title: C/EBPa ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked


title: C/EBPa ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: PU.1 ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked


title: PU.1 ChIP-Seq BALBc/J no treatment

description: formaldehyde cross-linked


title: PU.1 ChIP-Seq C57BL6/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked


title: H3K27Ac ChIP-Seq BALBc/J no treatment

description: formaldehyde cross-linked


title: p65 ChIP-Seq replicate 1 BALBc/J 100 ng/ml Kdo2-LipidA 1 hr


title: H3K4me2 ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: Mnase-treated genomic DNA


title: PU.1 ChIP-Seq C57BL6/J no treatment

description: formaldehyde cross-linked


title: Gata2 FDCPmix N [ChIP-seq]

city: Lund

first: Shamit

last: Soneji

address: Sölvegatan 19

country: Sweden

institute: BMC

description: Sample 7

data_processing:
Reads were mapped to the mm9 genome using bowtie (v0.12.3)
Peaks were called against an IgG control with MACS (v1.3.7.1, mfold=15,bw=100) and Peakranger (v1.02, b=100,p=0.01,t=4) where a peak was called so if found by both algorithms within 90bp.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: FDCPmix

growth_protocol: FDCPmix were routinely maintained in Fischer's medium. For differentiation cells were washed and cultured in IMDM plus 10% FCS and low IL-3 with either Epo+hemin (erythoid) or GCSF+SCF (myeloid)

extract_protocol:
FDCPmix cells were cross-linked with 1% formaldehyde and sonicated so that the bulk of the chromatin was between 100-500 bp. ChIP was essentially performed by standard procedures
Libraries were made using the ChIP-Seq sample preparation kit (cat# IP-102-1001, Illumina, San Diego, CA, USA) as per manufacture’s instruction.

treatment_protocol: For differentiation, cells were washed and then triplicate samples were cultured in IMDM plus 10% FCS and low IL-3 supplemented with either Epo and hemin (erythroid output) or G-CSF and SCF (neutrophil output). GATA1ERT and Pu.1ERT were subcloned into the pHR-SIN-CSGWEmGFP lentiviral expression construct under control of the SFFV promoter. Gata2 and Pu.1 shRNAs were subcloned into Lentilox 3.7.

tag: cell line

value: FDCPmix

tag: Stage

value: 5 days neutrophil differentiation

tag: chip antibody

tag: chip antibody vendor

value: santa cruz biotechnology

tag: chip antibody cat.#


title: Gata2 FDCPmix E3 [ChIP-seq]

description: Sample 13

value: 3 days neutrophil differentiation


title: Pu1 FDCPmix N [ChIP-seq]

description: Sample 8


title: Gata1 FDCPmix Gata1ER 24hrtam [ChIP-seq]

description: Sample 15

value: Multipotential

value: sc1234x and sc265x


title: Gata1 FDCPmix E3 [ChIP-seq]

description: Sample 11

value: 3 days erythroid differentiation


title: Pu1 FDCPmix MP [ChIP-seq]

description: Sample 3


title: Gata2 FDCPmix E1 [ChIP-seq]

description: Sample 12

value: 1 days erythroid differentiation


title: Gata1 FDCPmix E [ChIP-seq]

description: Sample 5

value: 5 days erythroid differentiation


title: C/EBPa ChIP-Seq BALBc/J 100 ng/ml Kdo2-LipidA 1 hr

description: formaldehyde cross-linked

value: BALBc/J

value: 100 ng/ml Kdo2-LipidA 1 hr


title: Gata1 FDCPmix E1 [ChIP-seq]

description: Sample 10


title: Gata1 FDCPmix Gata1ER notam [ChIP-seq]

description: Sample 14


title: Pu1 FDCPmix E [ChIP-seq]

description: Sample 6


title: Igg FDCPmix [ChIP-seq]

description: Sample 9

value: IgG

value: Millipore


title: Gata2 FDCPmix Gata1ER notam [ChIP-seq]

description: Sample 16


title: Gata2 FDCPmix MP [ChIP-seq]

description: Sample 1


title: Sample_2-3

description: processed data file: CIRTs_BAT.txt

source_name: mouse_Interscapular BAT

value: Embryonic 17.5D

value: Interscapular brown adipose tissue (BAT)

value: 3x aRNA


title: Sample_1-4

description: processed data file: CIRTs_BAT.txt


title: Sample_1-5

description: processed data file: CIRTs_BAT.txt


title: Sample_1-3

description: processed data file: CIRTs_BAT.txt


title: Gata2 FDCPmix Gata1ER 24hrtam [ChIP-seq]

description: Sample 17


title: Sample_1-1

description: processed data file: CIRTs_BAT.txt


title: Sample_1-2

description: processed data file: CIRTs_BAT.txt


title: MM0447

description: processed data file: CIRTs_MmDend.txt

source_name: mouse_hippocampus dendrite

value: Embryonic 18D

value: Hippocampus Dendrite


title: MM0450

description: processed data file: CIRTs_MmSoma.txt

source_name: mouse_hippocampus soma

value: Hippocampus Soma


title: MM0449

description: processed data file: CIRTs_MmSoma.txt


title: Gata2 FDCPmix E [ChIP-seq]

description: Sample 4

value: FDCPmix

value: santa cruz biotechnology


title: MM0448

description: processed data file: CIRTs_MmSoma.txt


title: MM0445

description: processed data file: CIRTs_MmDend.txt


title: MM0446

description: processed data file: CIRTs_MmDend.txt


title: RN0018

description: processed data file: CIRTs_RnSoma.txt

organism: Rattus norvegicus

source_name: rat_hippocampus soma

value: Sprague-Dawley


title: Gata1 FDCPmix MP [ChIP-seq]

description: Sample 2

value: Multipotential

value: sc1234x and sc265x


title: RN0016

description: processed data file: CIRTs_RnSoma.txt


title: RN0013

description: processed data file: CIRTs_RnDend.txt

source_name: rat_hippocampus dendrite


title: EB_48h_shKdm5b

status: Public on Oct 14 2013

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: RNA-Seq

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries). See BED files included in this submission.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: mm8

source_name: shKdm5b EB 48h

growth_protocol: ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For embryoid body (EB) formation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.

extract_protocol:
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell type

value: embryonic stem


title: EB_d6_shKdm5b

description: RNA-Seq

source_name: shKdm5b EB day 6


title: EB_d6_shLuc_ctrl

description: RNA-Seq

source_name: shLuc EB day 6


title: shLuc_4TF-MEF_Input_48h

description: Direct sequencing following sonication of x-linked chromatin

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries). See BED files included in this submission.
The RBPM measure (reads per base per million reads) was used to generate bedgraph files.
Genome_build: mm8

source_name: shLuc 4TF-MEFs

growth_protocol: shLuc and shKdm5b 4TF-MEFs were grown in ESC media (LIF and GSK3i) without feeders and in the presence of 2ug/mL doxycyclin.

extract_protocol:
4TF-MEFs were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: mouse embryonic fibroblasts

tag: antibody


title: EB_24h_shLuc_ctrl

description: RNA-Seq

source_name: shLuc EB 24h


title: shKdm5b_4TF-MEF_Input_48h

source_name: shKdm5b 4TF-MEFs


title: mES_shLuc_ctrl

description: RNA-Seq

source_name: shLuc ES cells


title: RN0017

description: processed data file: CIRTs_RnSoma.txt


title: shKdm5b_4TF-MEF_H3K4me3_48h

description: Chromatin IP against H3K4me3


title: EB_48h_shLuc_ctrl

description: RNA-Seq

source_name: shLuc EB 48h


title: shKdm5b_4TF-MEF_H3K4me2_48h

description: Chromatin IP against H3K4me2

value: Anti-H3K4me2 antibody (Abcam:ab32356)


title: Rrp5CTD

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

data_processing:
barcodes3.pl M=0 barcode_list.txt input.fq. Custom script to demultiplex fastq file.
fastq_preprpcessing.sh -Q 33 -L TGGAATTCTC -M 15 NNNbarcode_input.txt. Custom script to clip linkers and apply quality filters. Based on fastx toolkit   novoalign -f NNNbarcode_input.fq -d Saccharomices_cerevisiae_EF3_64.1.0.novoindex   -h 150 -F STDFQ (or ILFMQ) -r Random. Map reads to Saccharomyces cerevisiae S288C genome (SGD R63-1-1 or R64-1-1) using novoalign.
pyReadCounters.py -f input.novo generated sgr files. Custom program used to generate hit tables and plots of read density. From the pyCRAC software package (sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html).
Genome_build: R64-1-1
Supplementary_files_format_and_content: SGR files (.sgr): Tab-delimited graph format. Sequence graph files that show base coordinate scores. These files are generated by CNAT (the Affymetrix Chromosome Copy Number Analysis Tool software). The format of .sgr text files is: chromosome identification, base position, and score.

organism: Saccharomyces cerevisiae BY4741

source_name: yeast cells, C-terminal domain

growth_protocol: Cells were grown in YMM, glucose media without tryptophan.

extract_protocol:
Lysates were clarified and the histidine-tagged proteins were purified on nickel columns (Qiagen Ni-NTA agarose). A two-step IP was performed with one in denaturing condition (6M guanidinium). RNA-Rrp5 complexes were separated by SDS-PAGE, transferred to a nitrocelluose membrane and extracted. Protein was removed by Proteinase K digestion and RNAs purified by phenol:chloroform extraction.
Extracted RNAs were converted to cDNA and PCR amplified. PCR products between ~150 and 250 bp were gel extracted and submitted for Solexa sequencing.

treatment_protocol:
Cells were grown in minimum media and directly cross-linked in the culture media using the Megatron approach at 30°C.
After cross-linking, cells were centrifuged and frozen at -80°C.

tag: genotype

value: MATa; his3-delta-1; met15-delta-0; GAL1::3HA::RRP5; pSLD4;  pSLD5; ; KanR; Leu+, Ura+

tag: protein-tag

tag: uv-crosslink

value: Megatron


title: Rrp5NTD

source_name: yeast cells, N-terminal domain

value: MATa; his3-delta-1; met15-delta-0; GAL1::3HA::RRP5; pSLD3;  pSLD6; ; KanR; Leu+, Ura+


title: shLuc_4TF-MEF_H3K4me3_48h

description: Chromatin IP against H3K4me3


title: Rrp5FLinvivo

source_name: yeast cells, full-length, in vivo

value: MAT-alpha; ura3-52; leu2-3,112; his3-delta-200; lys2-delta-201; GAL2;  RRP5-HTP-TRP1


title: pap1-D/SSU_hpCHS

city: Sydney

first: Marcus

last: McHale

state: NSW

address: Lvl 8 Biochemistry Bldg G08, University of Sydney

department: School of Molecular Biology

country: Australia

institute: University of Sydney

data_processing:
Illumina (CASAVA 1.8.2)
fastx_clipper to remove barcodes
bowtie alignment
samtools (sorting, indexing, counting)
UEA sRNA toolkit phasing analysis against TAIR10 cDNA representative
Genome_build: TAIR10
Supplementary_files_format_and_content: SSU_hpCHS.csv,nd SSU_amiR21-CHS.csv and SSU_amiR21-CHS.csv contain tables describing abundance of 21-, 22- and 24-nt sRNAs in regions surrounding the  the described hairpin RNA and artificial micro-RNA target sites in lines expressing the corresponding transgene. amiRNA-abundance.csv describes the abundance of a number of forms of the articial miRNA present in these samples. locuslist.csv and srnas.txt are the output of UEA sRNA toolkit phasing analysis. The data in these files is presented in supplementary material of the Plant Journal publication associated with this submission (McHale et al.  2013).

organism: Arabidopsis thaliana

source_name: 3- week old plants grown on MSN

growth_protocol: 16 hour light on MS media for 3 weeks

extract_protocol:
Trizol
Library prep was per the TruSeq small RNA protocol (performed by the Australian Genome Research Facility) with an input of 3ug of RNA and 11 amplification cycles.

tag: background

tag: tissue-type

value: aerial


title: pap1-D/SSU_amiR21-CHS


title: pap1-D/SSU_amiR22-CHS


title: Rrp5FLinvitro

data_processing:
barcodes3.pl M=0 barcode_list.txt input.fq. Custom script to demultiplex fastq file.
fastq_preprpcessing.sh -Q 33 -L TGGAATTCTC -M 15 NNNbarcode_input.txt. Custom script to clip linkers and apply quality filters. Based on fastx toolkit   novoalign -f NNNbarcode_input.fq -d Saccharomices_cerevisiae_EF3_64.1.0.novoindex   -h 150 -F STDFQ (or ILFMQ) -r Random. Map reads to Saccharomyces cerevisiae S288C genome (SGD R63-1-1 or R64-1-1) using novoalign.
pyReadCounters.py -f input.novo generated sgr files. Custom program used to generate hit tables and plots of read density. From the pyCRAC software package (sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html).
Genome_build: R63-1-1
Supplementary_files_format_and_content: SGR files (.sgr): Tab-delimited graph format. Sequence graph files that show base coordinate scores. These files are generated by CNAT (the Affymetrix Chromosome Copy Number Analysis Tool software). The format of .sgr text files is: chromosome identification, base position, and score.

source_name: yeast cells, full-length, in vitro

treatment_protocol:
Cells were pelleted, washed and re-suspended in cold PBS (4°C) before being cross-linked.
After cross-linking, cells were centrifuged and frozen at -80°C.

tag: strain

value: Stratalinker


title: pap1-D


title: EB_d14_shKdm5b

description: RNA-Seq

source_name: shKdm5b EB d14


title: EB_24h_shKdm5b

description: RNA-Seq

source_name: shKdm5b EB 24h


title: EB_d10_shKdm5b

description: RNA-Seq

source_name: shKdm5b EB day 10


title: EB_d10_shLuc_ctrl

description: RNA-Seq

source_name: shLuc EB day 10


title: Arabidopsis thaliana-spl7-root-Copper-sufficient

city: Bochum

first: Ute

last: Kramer

address: Gebaude ND Nord Raum 3/30, Universitatsstrase 150

department: Department of Plant Physiology

country: Germany

institute: Ruhr University Bochum

description: Illumina's RNA-Seq oligo-dT primed transcriptome analysis

data_processing:
RNA-Seq sequence reads were aligned against the TAIR v7.0 assembly of the Arabidopsis genome using SOAP (Li et al. 2008 Bioinformatics 24: 713-714). A tolerance of up to two-mismatches was employed and reads with more than one match to the reference sequences were eliminated. For those sequences that did not align to the genome a second round of alignment was performed in which we recursively trim one base at a time (up to 21-mers) at either the 5’ or 3’ end of the reads until we found a (perfect) unique match to the genome.
Alignments from both rounds were tagged as either unique or not unique and combined. The most 5’ position of each alignment is recorded along with the length of the alignment. For differential expression analysis, per-base unique hits from both strands were pooled and summed across the genome to obtain gene counts. Additional normalization was performed to estimate gene expression levels.

source_name: Arabidopsis thaliana spl7-2 seeds

growth_protocol: Seeds from all lines were placed on a layer of (0.8% w/v) solidified Noble agar (Bio101, Vista, CA, USA) in black 0.5-ml Eppendorf tubes clipped at the bottom and germinated for a week . Upon germination, plants were grown for 2 weeks in a half-concentrated 0.25-strength Hoagland solution described in Becher et al. (2004) . After germination, solutions were exchanged weekly. In all experiments, each culture vessel of 400 mL of hydroponic solution contained two individual plants. A subset of plants were subsequently transferred to the same solution lacking added Cu and grown for an additional 3 weeks. Plants were grown in a growth cabinet in short days (11 h light at 150 µmol m-2 s-1, and 13 h dark) at day/night temperatures of 22°C/18°C and 45%rH . 48 h before harvest of root and shoot tissues of 6-week-old plants ( ZG time 2), plants were transferred to long day conditions (16 h light/ 8 h dark) by extending the light period at the end.  RNA-Seq was conducted for two independent experiments in one channel per experiment for each combination of tissue, genotype and treatment.

extract_protocol: To generate mRNA expression profiles, total RNA was isolated from 100-mg subsamples of shoot and root tissues. RNase-free DNase set for on-column DNase digest and RNeasy spin columns (Qiagen, Hilden, Germany) were used according to the manufacturer’s instructions for subsequent digestion of genomic DNA and RNA purification. Ten µg of total RNA per sample were used to generate the cDNA Colony Template Libraries (CTL) for high-throughput DNA sequencing using Illumina technology according to the Whole Transcriptome Shotgun protocol (Fasteris SA, Genome Analyzer Service, Switzerland). CTLs were sequenced to obtain a library of 35 base-pair long reads. poly-A purification, oligo dT priming

treatment_protocol: Copper deficiency treatments were initiated when plants were 3 weeks old and lasted for 3 weeks. For copper deficiency, CuSO4 was omitted from the hydroponic solution (the copper content was below detection limits of ICP-AES); the Cu-sufficient control solution contained 0.25 µM CuSO4.

tag: ecotype

value: Columbia Col-0

value: Roots

tag: treatment

value: Copper-sufficient


title: Arabidopsis thaliana-spl7-root-Copper-deficient

tag: tissue

value: Copper-deficient


title: Arabidopsis thaliana-WT-root-Copper-sufficient

source_name: Arabidopsis thaliana WT seeds

value: WT


title: Arabidopsis thaliana-WT-shoot-Copper-sufficient

value: Shoots


title: Control_2

status: Public on Oct 11 2013

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description: Negative control RNAseq dataset, biological replicate

data_processing:
Illumina Casava 1.7 software used for basecalling.
Reference sequences and GTF annotation files were obtained from ENSEMBL (www.ensembl.org). Raw reads (fastq) were pre-processed using the fastx_toolkit (hannonlab.cshl.edu/fastx_toolkit/) to remove read artifacts, adapter sequences, low quality read and duplicate sequences. Reads were mapped to the Saccharomyces cerevisiae genome (version EF2.59) using novoalign 2.05 (www.novocraft) and only cDNAs that were mapped to a single genomic location were considered. A list of intron -containing genes was generated using information provided by SGD (www.yeastgenome.org), the Ares intron database (http://compbio.soe.ucsc.edu/yeast_introns.html) and via literature searches. An inhouse Python tool suite (pyCRAC; Webb, Hector, Kudla, and Granneman, submitted (version 1.1, which can be downloaded from https://bitbucket.org/sgrann/pycrac) was used to calculate the number of reads overlapping with genomic features. Bedtools (http://code.google.com/p/bedtools/) was used to convert the mapping data into the bedgraph format and the USCS genome browser (genome.ucsc.edu/) was used to visualize the data.
Genome_build: S. cerevisiae EF2.59 (ENSEMBL)
Supplementary_files_format_and_content: bedgraph only contains data from reads with unique chromosomal mapping positions and GTF files
Supplementary_files_format_and_content: GTF files contains interval coordinates for reads with unique mapping positions and overlapping genomic features. Control* and SMD*.gtf files were generated from immunoprecipation sequencing data.

organism: Saccharomyces cerevisiae

source_name: Control

growth_protocol: yeast were grown in YPDA medium at 30ºC to an OD600 of 0.5, rapidly shifted to 37ºC and then grown for another two hours at this temperature. Cells were harvested and snap frozen in liquid nitrogen.

extract_protocol:
RNA was extracted using standard Guanidium Thiocyanate - Phenol extraction protocols
All directional cDNA libraries were prepared using the Epicentre ScriptSeq kit, as described by the manufacturer’s procedures. 250 ng of RNA was used for ScriptSeq cDNA library preparation and 50 base pairs of each cDNA were sequenced on the Illumina GAIIX system. To prepare the total RNA sequencing libraries, the prp40-1, rrp6 and BY4741 were grown in YPD to an OD=0.3 and subsequently shifted to 37°C for two hours. Prior to preparing the RNA seq cDNA libraries, 4 μg of total RNA was treated with turbo DNase I (Ambion) to remove chromosomal DNA. To enrich for mRNAs, rRNAs were depleted using the RiboMinus kit (Invitrogen). After each step, the integrity of the RNA was analyzed on an Agilent Bioanalyzer 2100. Subsequently, 250 ng of mRNA enriched RNA was used for cDNA library preparation and cDNAs were sequenced on the Illumina HiSeq 2000 v3 platform using the 100 bp paired-end protocol according to manufacturer’s procedures. Samples were multiplexed using the Illumina indexing barcodes. The following barcodes were used for preparation of multiplexed libraries:
ATCACG SmD1-TAP_1
CGATGT Control_1
TTAGGC SmD1-TAP_2
TGACCA Control_2
CGATGT BY4741
TTAGGC Rrp6
TGACCA Prp40

tag: strain background

tag: genotype/variation

value: parental strain

tag: molecule subtype

value: Immunoprecipitated RNA


title: Control_1

description: Negative control RNAseq dataset


title: Arabidopsis thaliana-spl7-shoot-Copper-deficient


title: SmD1_TAP_2

description: SmD1 IP RNAseq dataset, biological replicate

value: SmD1-TAP strain


title: IgG_ChIPSeq_Undifferentiated_Rep2

city: Boston

first: Sebastien

last: Vigneau

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
The image analysis and base calling of ChIP-seq data was performed using the Illumina Pipeline software.
Sequence alignment to the mm9 mouse genome was performed using Bowtie (Langmead et al., Genome Biol. 2009;10(3):R25).
Only uniquely aligned sequence tags, with up to two mismatches, were considered for further analysis. Tags aligned to blacklisted areas (the ENCODE consortium blacklist was downloaded from http://genome.ucsc.edu/cgibin/hgFileUi?db=hg19&g=wgEncodeMapability) were also removed before the peak calling step.
The significant peak identification was performed using a two steps procedure, as previously described (Pal et al., Genome Res. 2011 Aug;21(8):1260-72). In the first step, statistically significant enriched genomic regions (of length 1 kb) were identified. A region is defined as statistically significant if the difference in number of reads between experiment (CTCF) and control (IgG) samples within the region is higher than a given cutoff read count, calculated using a p-value of 0.001. Each ChIP-Seq read distribution in the genome can be considered as a Poisson distribution and the difference of two Poisson distributions is given by the Skellam distribution. Skellam probability mass function is given by equation 1 (sup. file “Equations.pdf”). For each of the statistically significant enriched regions, ChIP-seq read overlapping profiles were created by extending the sequence reads from the 5' end to the 3' end of the reads up to 250 bp (the average length of the ChIP-DNA fragment sequenced with Illumina standard ChIP-seq protocol) for the experiment sample. Then, within each enriched region, the significant enriched peaks in experimental data are identified based on a threshold read count, obtained using a cutoff p-value ≤ 0.01.
Peak score was calculated within significant regions by moving average of extended CTCF ChIP-Seq reads in 500bp windows.
Genome_build: mm9
Supplementary_files_format_and_content: Description for the undifferentiated ES cells biological replicate: The file “ctcf_peaks_undifferentiated_rep2.tsv” file lists CTCF peaks position in mouse mm9 genome assembly (columns 1 to 3) and enrichment score (column 4).   The “ctcf_reads_undifferentiated_rep2.bed”, “igg_reads_undifferentiated_rep2.bed” and “input_reads_undifferentiated_rep2.bed” files list reads position in the mouse mm9 genome assembly (columns 1-3), with their orientation (column 6), for CTCF, IgG and input samples.   The “ctcf_undifferentiated_rep2.wig” and “igg_undifferentiated_rep2.wig” files show CTCF binding and IgG background profiles.

source_name: Undifferentiated mouse ES cells

growth_protocol: Protocol for the undifferentiated ES cells biological replicate: E14 mouse ES cells were grown in Dulbecco’s Modified Eagle’s Medium, High Glucose (DMEM, GIBCO® #11965-084), 15% Fetal Bovine Serum (FBS, HyClone #SH30071.03), 2 mM L-Glutamine (GIBCO® #25030-081), 0.1% 2-Mercaptoethanol (GIBCO® #21985-023) and 1000 u/ml ESGRO® supplement containing Leukemia Inhibitory Factor  (Chemicon/Millipore #ESG1107), on mitomycin C treated mouse embryonic fibroblasts (MEF) plated on gelatinized cell culture plates. Prior to collection for chromatin preparation, ES cells were dissociated into single cell suspension using 0.25% Trypsin-EDTA (GIBCO® #25200056), and adsorbed twice, for 45 minutes each time, to remove MEF.  Residual MEF contamination was estimated to be below 0.25% by visually inspecting using a hematocytometer.

extract_protocol: Protocol for the undifferentiated ES cells biological replicate: Chromatin immunoprecipitation was performed as previously described (Nelson & Denisenko, Nat Protoc. 2006;1(1):179-85). After cross-linking cells for 10 min with 1% formaldehyde and sonicating chromatin with a Diagenode Bioruptor, chromatin was immunoprecipitated using 25 µl (~25 µg) of CTCF antibody (Millipore 07-729, lot 2054523) or 25 µg of IgG (Santa Cruz Biotechnology, Sc-2027) for 20E6 cells. 10 ng of CTCF immunoprecipitated DNA, IgG immunoprecipitated DNA or input were used for library preparation according to NEBNext ChIP-Seq library protocol (NEB #E6200S/L) using AMPure XP Beads (Agencourt #A63880) and with 14 cycles PCR enrichment using index primers for multiplexing. Indexes were as follows: CTCF, acagtg; IgG, cgatgt; input, tgacca. DNA fragment size was verified using a Bioanalyzer (Agilent #5067-4626) and the libraries were sequenced as 50 bp single-reads with the Illumina hiSeq sequencing system.

value: mouse ES cells

tag: passage

tag: chip antibody

value: IgG (Santa Cruz Biotechnology, Sc-2027)


title: shLuc_4TF-MEF_H3K4me2_48h

description: Chromatin IP against H3K4me2

source_name: shLuc 4TF-MEFs

value: mouse embryonic fibroblasts

value: Anti-H3K4me2 antibody (Abcam:ab32356)


title: Arabidopsis thaliana-WT-shoot-Copper-deficient


title: Arabidopsis thaliana-WT-root-Copper-deficient


title: CTCF_ChIPSeq_Undifferentiated_Rep2


title: mES_shKdm5b

description: RNA-Seq

source_name: shKdm5b ES cells

tag: cell line

value: embryonic stem


title: Input_ChIPSeq_Undifferentiated_Rep2

tag: cell type


title: Arabidopsis thaliana-spl7-shoot-Copper-sufficient


title: RN0014

description: processed data file: CIRTs_RnDend.txt

source_name: rat_hippocampus dendrite

value: Sprague-Dawley

tag: age

value: Embryonic 18D

value: Hippocampus Dendrite

tag: amplification

value: 3x aRNA


title: SmD1_TAP_1

description: SmD1 IP RNAseq dataset


title: resting_Smc3_CHIP-seq

city: Illkirch

first: Anne-Sophie

last: THOMAS

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: CD43- B cells extracted from spleen

growth_protocol: Resting B cells were isolated from the spleen of 8-12 week-old wild-type mice (C57BL/6J) with anti-CD43 Microbeads (anti-Ly48; Miltenyi Biotech) and were cultured for 60 h with LPS (50 μg/ml; Sigma Aldrich) and IL-4 (5 ng/ml; Sigma Aldrich).

extract_protocol: ChIP-seq libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen).

treatment_protocol: Cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by quenching with 0.125 M glycine (final concentration). After lysis, chromatin was sonicated to generate 0.2–0.5 kb DNA fragments using a Covaris sonicator (Covaris). After dilution in ChIP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, and 167 mM NaCl), chromatin was precleared by rotating 1 hour at 4°C with 400µl of dynabeads protein A (Invitrogen). Dynabeads were coupled with specific or control antibodies for 1h at room temperature. Pre-cleared chromatin was precipitated overnight with the dynabeads coupled with the antibodies (10 × 106 cell equivalents were used as input, and 100 × 106 cell equivalents were used for ChIP) and processed according to the Millipore protocol.

value: Smc3 (Abcam ref:ab9263 lot:GR81379-1)


title: resting_IgG_CHIP-seq

value: Rabbit IgG (Bethyl, ref:P120-101 lot:P120-101-8)


title: resting_CTCF_CHIP-seq

value: CTCF (Millipore ref:07-729 lot:DAM1772428)


title: resting_Smc1_CHIP-seq


title: stimulated_CTCF_CHIP-seq


title: stimulated_Smc3_CHIP-seq


title: stimulated_IgG_CHIP-seq


title: EB_d14_shLuc_ctrl

description: RNA-Seq

source_name: shLuc EB day 14


title: stimulated_Smc1_CHIP-seq


title: RNASeq_Differentiated

data_processing:
We used a multi-step procedure to align the reads as previously described (Pal et al., Genome Res. 2011 Aug;21(8):1260-72.). In brief the following steps were taken. (1) Contamination removal – Reads matching to the mitochondrial genome sequence, ribosomal-like RNAs, and adapter sequences were removed. (2) Alignment to transcriptome – We generated a non-redundant combined transcriptome model using RefSeq, UCSC, Vega, Ensembl and MGI transcripts. The unaligned reads from the previous step were aligned to the combined transcriptome model. (3) Alignment to Aceview gene model – The unaligned reads from the previous step were mapped to the Aceview gene model (Thierry-Mieg and Thierry-Mieg, Genome Biol. 2006;7 Suppl 1:S12.1-14). (4) Alignment to genome – The unmapped reads from the previous steps were aligned directly to the genome. Reads were aligned allowing up to 2 mismatches and only the uniquely mapped reads were used for estimating expression.
Expression levels by transcript were calculated using the IsoformEx software (Kim et al., BMC Bioinformatics. 2011 Jul 27;12:305) and expressed as RPKM.
The expression for non-polyA tailed RNA class genes (miRNA, snoRNA, snRNA, rRNA, tRNA, scRNA) were removed from further analysis.
For transcripts sharing the same promoter, RPKM values were summed to obtain the expression by promoter. Transcripts were considered as originating from the same promoter if their first exon overlapped. Similarly, the expression for a given gene is the sum of the RPKM values of all the transcripts defining that gene.
Genome_build: mm9
Supplementary_files_format_and_content: The files "rnaseq_undifferentiated_lane1.wig" and "rnaseq_undifferentiated_lane2.wig" contain expression profiles in undifferentiated cells for sequencing lanes 1 and 2, respectively.  The files "rnaseq_differentiated_lane1.wig" and "rnaseq_differentiated_lane2.wig" contain expression profiles in differentiated cells for sequencing lanes 1 and 2, respectively.  The file "rnaseq_transcript_expression.tsv" indicates RPKM expression values by transcript, with col. 1-3, transcript location in mouse mm9 genome assembly; col. 4, transcript orientation; col. 5, transcript identifier(s); col. 6, corresponding gene name; col. 7, RPKM expression value in undifferentiated cells calculated from lane 1; col. 8, RPKM expression value in undifferentiated cells calculated from lane 2; col. 9, RPKM expression value in differentiated cells calculated from lane 1; col. 10, RPKM expression value in differentiated cells calculated from lane 2; col. 11, average RPKM expression value in undifferentiated cells, calculated from lanes 1 and 2; col. 12, average RPKM expression value in differentiated cells, calculated from lanes 1 and 2.  The file "rnaseq_gene_expression.tsv" indicates RPKM expression values by gene, with col. 1-3, gene location in mouse mm9 genome assembly; col. 4, gene name; col. 5, gene orientation; col. 6, RPKM expression value in undifferentiated cells calculated from lane 1; col. 7, RPKM expression value in undifferentiated cells calculated from lane 2; col. 8, RPKM expression value in differentiated cells calculated from lane 1; col. 9, RPKM expression value in differentiated cells calculated from lane 2; col. 10, average RPKM expression value in undifferentiated cells, calculated from lanes 1 and 2; col. 11, average RPKM expression value in differentiated cells, calculated from lanes 1 and 2.  The file "rnaseq_promoter_expression.tsv" indicates RPKM expression values by promoter, with col. 1-3, location  in mouse mm9 genome assembly of the shared first exon between transcripts originating from the same promoter; col. 4, transcript(s) orientation; col. 5, corresponding gene name; col. 6, transcript(s) identifier(s); col. 7, RPKM expression value in undifferentiated cells calculated from lane 1; col. 8, RPKM expression value in undifferentiated cells calculated from lane 2; col. 9, RPKM expression value in differentiated cells calculated from lane 1; col. 10, RPKM expression value in differentiated cells calculated from lane 2; col. 11, average RPKM expression value in undifferentiated cells, calculated from lanes 1 and 2; col. 12, average RPKM expression value in differentiated cells, calculated from lanes 1 and 2.

source_name: Differentiated mouse ES cells

growth_protocol: E14 mouse ES cells were grown in Dulbecco’s Modified Eagle’s Medium, High Glucose (DMEM, GIBCO® #11965-084), 15% Fetal Bovine Serum (FBS, HyClone #SH30071.03), 2 mM L-Glutamine (GIBCO® #25030-081), 0.1% 2-Mercaptoethanol (GIBCO® #21985-023) and 1000 u/ml ESGRO® supplement containing Leukemia Inhibitory Factor  (Chemicon/Millipore #ESG1107), on mitomycin C treated mouse embryonic fibroblasts (MEF) plated on gelatinized cell culture plates. Prior to differentiation and to collection for RNA or chromatin preparation, ES cells were dissociated into single cell suspension using 0.25% Trypsin-EDTA (GIBCO® #25200056), and adsorbed twice, for 45 minutes each time, to remove MEF.  Residual MEF contamination was estimated to be below 0.25% by visually inspecting using a hematocytometer.  For ES cells differentiation, ES cells were plated at 10E4 cells/cm2 on gelatinized cell culture plates and grown in DMEM, 10% FBS, 2 mM glutamine, 0.1% 2-Mercaptoethanol and 0.1 µM all-trans-Retinoic acid (Sigma #R2625). After 4.5 days, cells were dissociated using 0.25 % Trypsin-EDTA and collected for chromatin or RNA preparation. In the cells collected for ChIP-seq and RNA-seq, cell death was estimated around 2% in undifferentiated cells and 8% in differentiated cells, using Trypan Blue staining.

extract_protocol: RNA was extracted and purified using Trizol Reagent (Ambion®, #15596-026), according to manufacturer's instructions. The quality of total RNA was verified on a Bioanalyzer 2100 using the RNA 6000 Nano Total RNA kit (Agilent #5067-1511). Then, starting from 5 µg of total RNA, samples were prepared according to the Illumina mRNA sequencing sample preparation protocol (# RS-930-1001), with purification of ~250 bp cDNA templates from 2% agarose gel run at 100 V for 1 h. Two lanes were sequenced for each biological sample, with 36 bp single-end reads, on an Illumina Genome Analyzer IIx using Cluster Generation kits (v4) and Sequencing kits (v4).

value: mixed differentiated cell population derived from mouse ES cells after 4.5 days in vitro differentiation induced by retinoic acid


title: RNASeq_Undifferentiated


title: Prp40

description: rRNA depleted yeast total RNA

value: temperature-sensitive splicing mutant (prp40-1)

value: rRNA depleted yeast total RNA


title: CTCF_ChIPSeq_Undifferentiated

data_processing:
The image analysis and base calling of ChIP-seq data was performed using the Illumina Pipeline software.
Sequence alignment to the mm9 mouse genome was performed using Bowtie (Langmead et al., Genome Biol. 2009;10(3):R25).
Only uniquely aligned sequence tags, with up to two mismatches, were considered for further analysis. Tags aligned to blacklisted areas (the ENCODE consortium blacklist was downloaded from http://genome.ucsc.edu/cgibin/hgFileUi?db=hg19&g=wgEncodeMapability) were also removed before the peak calling step.
The significant peak identification was performed using a two steps procedure, as previously described (Pal et al., Genome Res. 2011 Aug;21(8):1260-72). In the first step, statistically significant enriched genomic regions (of length 1 kb) were identified. A region is defined as statistically significant if the difference in number of reads between experiment (CTCF) and control (IgG) samples within the region is higher than a given cutoff read count, calculated using a p-value of 0.001. Each ChIP-Seq read distribution in the genome can be considered as a Poisson distribution and the difference of two Poisson distributions is given by the Skellam distribution. Skellam probability mass function is given by equation 1 (sup. file “Equations.pdf”). For each of the statistically significant enriched regions, ChIP-Seq reads overlapping profiles were created by extending the sequence reads from the 5' end to the 3' end of the reads up to 250 bp (the average length of the ChIP-DNA fragment sequenced from the Solexa GA with Illumina standard ChIP-seq protocol) for the experiment sample. Then, within each enriched region, the significant enriched peaks in experimental data are identified based on a threshold read count, obtained using a cutoff p-value ≤ 0.01.
Peak score was calculated within significant regions by moving average of extended CTCF ChIP-Seq reads in 500bp windows.
Genome_build: mm9
Supplementary_files_format_and_content: The "ctcf_peaks_*.tsv" files list CTCF peaks position in mouse mm9 genome assembly (columns 1 and 2) and, for each peak, CTCF peak score (column 3), the tag count for CTCF immunoprecipitation (column 4) and the tag count for the IgG control (column 5). The files "ctcf_peaks_undifferentiated.tsv" and "ctcf_peaks_differentiated.tsv" are for undifferentiated and differentiated cells, respectively.  The "*_reads_*.tsv" files list reads position in the mouse mm9 genome assembly (columns 1-3), with their orientation (column 4). The files "ctcf_reads_undifferentiated.tsv" and "ctcf_reads_differentiated.tsv" list reads from CTCF ChIP-Seq in undifferentiated and differentiated cells, respectively. The files "igg_reads_undifferentiated.tsv" and "igg_reads_differentiated.tsv" list reads from the IgG ChIP-seq control in undifferentiated and differentiated cells, respectively.  The "ctcf_undifferentiated.wig" and "ctcf_differentiated.wig" files show CTCF binding profiles after substraction of IgG background, in undifferentiated and differentiated cells, respectively.

extract_protocol: Chromatin immunoprecipitation was performed as previously described (Nelson & Denisenko, Nat Protoc. 2006;1(1):179-85). After cross-linking cells for 15 min with 1% formaldehyde and sonicating chromatin with a Diagenode Bioruptor, chromatin was immunoprecipitated using 10 µg of CTCF antibody (Millipore 07-729, lot DAM1682158) or 10 µg of IgG (Santa Cruz Biotechnology, Sc-2027) for 50E6 cells. In each case, for both undifferentiated and differentiated cells, ~15 ng of CTCF or IgG immunoprecipitated DNA were recovered after combining two technical replicates from the same biological sample. DNA fragments of ~150-300 bp range were isolated by agarose gel purification, ligated to primers, and then subject to Solexa sequencing using manufacturer's recommendations (Illumina, Inc.).

value: CTCF (Millipore, 07-729, lot DAM1682158)


title: Rrp6

description: rRNA depleted yeast total RNA

value: exosome mutant (rrp6-delta)


title: IgG_ChIPSeq_Undifferentiated

value: mouse ES cells


title: B2-T2.CATG

status: Public on Oct 10 2013

city: Köln

first: Christiane

last: Gebhardt

address: Carl-von-Linné-Weg 10

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Library strategy: SuperSAGE
RTA SCS.2.6, GERALD.1.6
GenXPro SuperSAGE-Tag analysis pipeline „GenXProgram v1.2“
Annotation to S.tuberosum and P. infestans cDNA
Genome_build: STGI.042210 for potato transcripts ( http://compbio.dfci.harvard.edu/tgi/) and /NCBI/ENTREZ/NCBI_P.infestans_mRNA+REFSEQAUG10/NCBI_P.infestans_mRNA+REFSEQ.Fasta, BROAD_Ins/phytophthora_infestans_t30-4_1_genes.fasta, and BROAD_Ins/phytophthora_infestans_t30-4_1_transcripts.fasta
Supplementary_files_format_and_content: Excel files that contain raw data tag counts, the tag counts related/normalized to 1 million, the pairwise comparison of different conditions and information about differentially expressed tags (including p-value and fold change).

organism: Solanum tuberosum

growth_protocol: 29 genotypes were multiplied by shoot cuttings. Six to seven weeks old plants (three plants per genotype) were transferred to a growth chamber (Snijders Scientific B.V., Tilburg, Netherlands), and acclimated for few days to 16h light at 22°C and 8h dark at 20°C before infection with P. infestans. P. infestans was propagated on detached leaflets of 6-10 weeks old susceptible plants (cvs. Désireé or Grata) or on tuber slices of the susceptible variety Grata. Inoculum was prepared as described (Gyetvai et al. 2012).

extract_protocol:
For each time point (T0, T1 and T2) one leaflet each of 14, 6 and 9 genotypes in genotypic groups A1, A2 and B2, respectively, were pooled. Frozen pooled leaf tissue was powdered in a CryoMill (Retsch, Haan, Germany). Total RNA was extracted from powdered tissue using the Plant RNA Isolation Kit of Invitrogen (Karlsruhe, Germany) following the manufacturer’s protocol. RNA purification, removal of genomic DNA contamination, concentration measurements and quality tests were performed as described (Draffehn et al. 2010). RNA integrity was additionally assessed by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).
SuperSAGE libraries were generated at GenXPro GmbH (Frankfurt, Germany) essentially as described (Matsumura et al. 2010). To prevent amplification biases the TrueQuant technology was applied as described by B. Rotter (Patent application Nr. WO2009152928). Besides NlaIII (recognition site: 5’-CATG-3’), DpnII (recognition site: 5’-GATC-3’) was used as second anchoring enzyme, to capture transcripts without a NlaIII site. Therefore, the 26 bp tags carry either CATG or GATC at their 5’ end. The libraries were pooled and sequenced by Solexa/Illumina technology (Illumina, Inc., USA).

treatment_protocol: Three compound leaves per plant (3rd, 4th and 5th from the top) were spray inoculated on the abaxial side each with 200-400µl sporangia suspension (20 000 sporangia/ml, 65 000-130 000 zoospores/ml) using a pump glass flask. The plants were then covered with clear plastic bags to insure high humidity for optimal growth of P. infestans. Inoculations and tissue sampling were performed between 8:00 and 11:30 A.M. Individual leaflets of similar size were collected from the 4th and 5th compound leaf just before inoculation (T0), one (T1) and two (T2) days post inoculation. Leaflets were immediately frozen in liquid nitrogen. The 3rd compound leaf served as infection control. Infection symptoms were observed between the fourth and seventh day post inoculation. For each time point, leaf tissue was harvested from a different plant to avoid wounding and priming effects. The infection experiment was repeated five times with new batches of plants and inoculum (biological replicates). The best three experiments were chosen for further analysis.

tag: anchor

value: DpnII

tag: infection

value: infected

value: leaf


title: CTCF_ChIPSeq_Differentiated


title: B2-T1.GATC

value: NlaIII


title: B2-T2.GATC


title: BY4741

description: rRNA depleted yeast total RNA

value: wild type


title: B2-T0.GATC

value: uninfected


title: B2-T0.CATG


title: B2-T1.CATG


title: A2-T1.CATG


title: A2-T0.GATC


title: A2-T1.GATC


title: A2-T2.GATC


title: A2-T2.CATG


title: A1-T2.GATC


title: A2-T0.CATG


title: A1-T1.CATG


title: A1-T1.GATC


title: A1-T0.GATC


title: SmoA1 [RRBS]

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

description: RRBS

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) as part of the Sequence Control Software (on Illumina IIGAx) or HiSeq Control Software(on Illumina HiSeq2000).
Alignment and Methylation calls: reads were mapped to human (hg18) and mouse (mm9) genomes using BSMAP (version 2.74), with the option -q 20 A AGATCGGAAGAGC to trim adaptor sequences and low quality base calls. The methylation calls were performed using python script methratio.py in the BSMAP package. CpG statistics: the number of cytosines covered, and the average coverage on covered cytosines for each sample were reported by BSMAP. The average CpG methylation ratios were computed from estimated methylation ratios, weighted by the corresponding coverage.
Genome_build: mm9
Supplementary_files_format_and_content: A file (.ratio) was generated for each sample as standard out from BSMAP (version 2.74).

source_name: medulloblastoma

extract_protocol:
Genomic DNA from all sources was isolated using the DNeasy Blood and Tissue Kit (Qiagen).
EpiQuest libraries were prepared from 500 ng genomic DNA. The DNA was digested with 60 units of TaqI and 30 units of MspI (NEB) sequentially. Size-selected TaqI-MspI fragments (40–120bp and 120–350bp) were filled-in and 30-terminal-A extended, extracted with Zymo Research DNA Clean and Concentrator(tm) kit. Ligation to pre-annealed adaptors containing 50-methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor-ligated fragments were bisulphite treated using the EZ DNA Methylation-Direct(tm) Kit (Zymo Research). Preparative-scale PCR was performed and DNA Clean and Concentrator-purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 or 210–460bp in size were excised. Library material was recovered from the gel (Zymoclean(tm) Gel DNA Recovery Kit) and sequenced on an Illumina GAIIx genome analyzer.

tag: background strain

value: medulloblastoma

tag: genotype

value: SmoA1 -/+


title: WTCbl_Smo [RRBS]

description: RRBS

source_name: normal cerebellum

value: normal cerebellum


title: SmoA2 [RRBS]

description: RRBS

value: SmoA2 -/+


title: ICRF reps1-2

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

description: FAIRE-seq

data_processing:
For all the sequenced samples reads were aligned to Mouse genome (mm9) using Bowtie with default parameters.  Fseq was used to call peaks from aligned data using default parameters. All the samples were merged together and potential candidate peaks were called on merged sample to make sure that we get same genomic coordinates for all the peaks. Once the candidate peaks were identified, these peaks were filtered out by caluculating enrichment ratios and only peaks showing at least 1.5 fold enrichment were considered for analysis.
Genome_build: mm9
Supplementary_files_format_and_content: FSeq_PotentialPeaks.bed (linked as a supplementary file on the Series record) represents potential candidate peaks.

source_name: mESCs

growth_protocol: Wild type cells were grown as previously described (Bibel et al. 2004; Plachta et al. 2004; Bibel et al. 2007)

extract_protocol: FAIRESeq libraries were prepared by using standard ChIP library protocol for sequencing using standard Illumina protocols

treatment_protocol: Feeder-free ESCs were seeded at a density of 3.3 *10^6 cells in 10 cm dishes, medium was changed after 24 h and cells were treated after 32 h for 16 h with 500nM ICRF-193 (Sigma) or DMSO as a control.

tag: strain

value: Embryonic Stem Cells (ESCs)

tag: agent

value: ICRF


title: IgG_ChIPSeq_Differentiated

value: mixed differentiated cell population derived from mouse ES cells after 4.5 days in vitro differentiation induced by retinoic acid

value: IgG (Santa Cruz Biotechnology, Sc-2027)


title: DMSO reps1-2

description: FAIRE-seq

value: DMSO


title: ES Input

description: FAIRE-seq


title: Nestin-retic, rep2

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

data_processing:
Pre-processing of the RNA-seq reads was performed by Otogenetic Corporation. The RNA-seq reads were aligned to mm9 using TopHat (version 1.3.3) and levels of gene expression were quantified using Cufflinks (version 1.3.0).
Genome_build: MGSCv37
Supplementary_files_format_and_content: Tab-delimited text file contains differential expression analysis results generated by Cuffdiff.

source_name: bone marrow stromal cells, Nestin-retic

extract_protocol:
Total RNA from sorted Nes-peri and Nes-retic cells was extracted using the RNAqueous kit (Life Technologies, Grand Island, NY USA) and concentrated using RNA Clean and Concentrator columns (Zymo Research Corporation, Irvine, CA USA).
cDNA was generated using a Clontech SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech Laboratories, Inc., Mountain View, CA USA) from 100pg-1ng of total RNA. cDNA was fragmented using Covaris (Covaris, Inc., Woburn, MA USA), profiled using an Agilent Bioanalyzer, and subjected to Illumina library preparation using NEBNext reagents (New England Biolabs, Ipswich, MA USA, catalog# E6040).

tag: developmental stage

value: adult

value: bone marrow stromal cells

tag: cell population

value: Nestin-retic


title: Nestin-retic, rep1


title: Nestin-peri, rep1

source_name: bone marrow stromal cells, Nestin-peri

value: Nestin-peri


title: Nestin-peri, rep2


title: Nestin-peri, rep3


title: Nestin-retic, rep3


title: MYCN tumor 1 [RRBS]

description: RRBS

tag: tissue


title: ICRF reps1-3

data_processing:
For all the sequenced samples low complexity reads were filtered out and remaining reads were aligned to Mouse genome (mm9) using TopHat with default parameters. The aligned reads were then provided as an input to HTSeq_count utility from HTSeq package. The raw read count files obtained from HTSeq-count were then processed for differential expression using DESeq package. The raw read counts were normalized for library size differences using estimateSizeFactors function from DESeq package.
Genome_build: mm9
Supplementary_files_format_and_content: ICRFVsDMSO.txt reports normalized counts, fold-change, pval, padj.

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: A1-T0.CATG

value: DpnII

value: leaf


title: A1-T2.CATG

value: infected


title: DMSO reps1-3

value: wild type


title: ES_NoV

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

country: Switzerland

institute: ETHZ

description: E14 ES cells infected with NoV and total RNA extracted 2.5 days post-infection

data_processing:
Basecalls performed using HiSeq Control Soft. v. 1.5.15, RTA 1.13.48 and CASAVA 1.8.2
sRNAseq reads were aligned to the mm9 genome assembly using ncPRO pipeline after filtering out the reads of size lower than 19nt.
Genome_build: mm9
Supplementary_files_format_and_content: Sequence count for virus derived small RNAs

source_name: embryonic stem cells

growth_protocol: Male E14 Embryonic Stem (ES) cell line was cultured in Glasgow MEM medium (Invitrogen), containing 15% FCS (Bio West), 1000 U/ml LIF (Chemicon), 0.1 mM beta-mercaptoethanol (Invitrogen), 0.05 mg/ml of streptomycin (Invitrogen) and 50 U/ml of penicillin (Invitrogen), 2 mM L-Glutamine, 1mM Sodium Pyruvate MEM and 1X MEM Amino Acid on a gelatin-coated support in the absence of feeder cells. Dicer Flx/Flx and Dicer -/- were cultured in Dulbecco’s Modified Eagle Media (DMEM) (Invitrogen), containing 15% FCS (Bio West), 1000 U/ml LIF (Chemicon), 0.1 mM beta-mercaptoethanol (Invitrogen), 0.05 mg/ml of streptomycin (Invitrogen) and 50 U/ml of penicillin (Invitrogen) on a gelatin-coated support in the absence of feeder cells. The culture medium was changed daily. All cells were grown at 37°C in 8% CO2.

extract_protocol:
Total RNA was isolated with Trizol.
Libraries construction was contracted out to Fasteris SA. At Fasteris SA, barcoded libraries were prepared such that four samples could be run per lane. Libraries were prepared according to Illumina's instructions accompanying the sequencing Kit TruSeq(TM) SBS v5.

value: embryonic stem cells

tag: virus

value: Nodamura virus

value: WT


title: Input DNA

city: Seoul

first: Hyun Mu

last: Shin

address: Biomedical Science Building 202, 103 Daehakro, Jongro-gu

department: Biomedical Sciences

country: South Korea

institute: Seoul National University College of Medicine

data_processing:
Sequence reads were obtained and mapped to a mouse reference genome (mm9) using the Illumina Genome Analyzer Pipeline.
All reads mapping with two or fewer mismatches were retained, applied to a Cisgenome 2.0 integrated software system (Hongkai et, 2008) and converted to browser extensible data (BED) files for viewing the data in the UCSC or Cisgenome browser.
The parameters used in Cisgenome were Read Extension Length E=150bp, Bin Size B=50bp, Half Window Size W=3, Max Gap=50bp, Min Peak Length=100bp, Win Stat Cutoff C>=3.
Following this, peak enrichment regions that fell below the false discovery rate (FDR<0.1) and within 10kb of the transcription start site or the transcription end site were considered for further analysis.
Blimp-1 target genes were classified by functional group using the Ingenuity pathway database.
Genome_build: mm9
Supplementary_files_format_and_content: Gene list of Blimp1 binding enrichments.txt contains enrichment scores by total normalized counts and maximun log2 scaled values, peak lengths, false discovery rates (FDR) and gene descriptions with coordiates and functional annotations.
Supplementary_files_format_and_content: BED files are tab-delimited files with one line for each genomic region
Supplementary_files_format_and_content: WIG files were generated by each chromosome and compressed as a one file

source_name: mouse CD8+ T cells

extract_protocol:
10 million cells were harvested, crosslinked with 1% formaldehyde, sonicated, and then subjected to chromatin immunoprecipitation with anti-Blimp-1 antibody. 300-500 bp DNA fragments were obtained after reverse-crosslinking.
To generate libraries, DNA fragments were ligated to Illumina’s adapters according to Illumina’s instructions. Briefly, DNA fragments were end-repaired using an END-IT DNA REPAIR KIT#ER0720 Epicentre. The blunt, phosphorylated DNAs were treated with Klenow fragment (Exo-minus, NEB M0212M 50U/ul) and dATP to generate A base overhang. These fragments were ligated with Illumina adapters using a FAST LINK KIT #LK11025 Epicentre. After adapter ligation, DNAs were PCR-amplified with Illumina primers (Primer1.1 and Primer2.1) for 17 cycles and library fragments of 300-500 bp were extracted from an agarose gel.

value: OT-I TCR transgenic Rag1-/- mice

value: in vitro stimulated CD8+ T cells

tag: tagchip antibody


title: ES_NoVΔB2

description: E14 ES cells infected with mutant NoVΔB2 and total RNA extracted 2.5 days post-infection

value: Nodamura virus ΔB2


title: Blimp-1 ChIPSeq

value: Blimp-1 (SantaCruz, sc-66015, lot I2909)


title: MYCN tumor 2 [RRBS]

description: RRBS

value: medulloblastoma


title: IP_mAGO2_INF

description: Immunoprecipitation of endogenous mouse AGO2 (mAGO2) using specific antibody in E14 ES cells infected for 6 hours with EMCV

value: Encephalomyocarditis virus (EMCV) strain BEL-2887A/91

tag: antibody

value: Rat anti-mouse AGO2 clone 6F4 (kind gift from Prof. Gunter Meister)


title: mouse IgG

value: mouse IgG (SantaCruz, sc-2025, lot G0910)


title: ES_D10 INF

description: E14 ES cells were induced spontaneously to differentiate into LIF-free DMEM, 10% FCS medium for 10 days, infected with EMCV and total RNA extracted 6 hours post-infection

value: Differentiated E14


title: ES_D10 NI

description: Non-infected E14 ES cells were induced spontaneously to differentiate into LIF-free DMEM, 10% FCS medium and total RNA extracted at 10 days (D10) of differentiation


title: N6-144hr

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: 200-400bp in length

data_processing:
Illumina Casava1.7 software used for basecalling.
We used Tophat v1.2.0 (Trapnell et al. 2009) to perform spliced alignments of the reads against the Neurospora crassa reference genome. Only reads that mapped to a single unique location  with in the genome with a maximum of two mismatches in the anchor region of the spliced alignment were reported in these results. We used the default settings for all other Tophat options.
To obtain a tally of the number of the reads that overlapped the exons of a gene, we analyzed the aligned reads with HTSeq v0.4.5p6 and the gene structure annotation file for the reference genome.
The tally for each sample was then processed with LOX v1.6 (Zhang et al. 2010) to statistically analyze the gene expression levels.
Genome_build: Neurospora crassa reference genome NC10 (Assembly ASM18292v1 http://www.ncbi.nlm.nih.gov/assembly/GCF_000182925.1/)
Supplementary_files_format_and_content: Tabulated tables (.txt) with the normalized expression levels (as outputed from LOX software)

organism: Neurospora crassa

source_name: N. crassa perithecia

growth_protocol: Two strains of N. crassa of complementary mating types MAT-a (FGSC4200) and MAT-A (FGSC2489) were kindly provided by the Fungal Genetics Stock Center (McCluskey et al., 2010). The strains were grown on Carrot Agar (CA, Klittich and Leslie, 1988), covered by a cellophane membrane at a constant temperature of 26°C and under constant artificial light provided by several Ecolux bulbs (F17T8.SP41-ECO, General Electric Company) that provided a net intensity of 14µMol/m2S at the media surface, measured at wavelengths between 400nm to 700nm. Conidia from the MAT-a strain were collected and suspended in 2.5% Tween 60. Cultures of the MAT-A strain were examined using a stereomicroscope for the formation of protoperithecia in 7 days, and areas of evenly distributed protoperithecia of similar size were marked out on the bottom of the plate. Crosses were performed by applying 1 ml Mat-a conidial suspension (105 -106 conidia /ml with 2.5% Tween 60) to the surface of the MAT-A protoperithecia plates. Subsequent sexual development occurred under the same culture conditions as before the crossing. Tissues were collected from the plate surface with a razor blade for the CA cultures of the MAT-A strain in the marked areas right before the crossing, and at 2, 24, 48, and 72 hours after crossing. All tissues/perithecia collected from the same plate was counted as one biological replicate, and three to five biological replicates were prepared for each sampled time-point. Perithecia at similar development stages (based on size and color under stereomicroscope) were collected from the plate surface with razor blade for cultures of the MAT-A mated perithecial plates within the marked areas at 96, 120, and 144 hours after crossing.  All tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, and stored at -80°C.

extract_protocol: Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen).  About 100ng of purified mRNA (9ul) were mixed with 10X fragmentation buffer (Ambion) and incubated at 70C for 5min before adding 1ul stop buffer (Ambion). Fragmented mRNA was precipitated using 100% ethanol with glycogen (Ambion) at -80C. A multi-targeting primer (MTP -- VWNVNNBDKGGC) was used for reverse transcription of the first strand cDNA, and random hexamers (N6, Invitrogen) were used to recover the second strand cDNA. As technique replicates, a common cDNA preparation using N6 was followed for samples of all time-points. After ligation of standard adaptors for Illumina sequencing, gel purification was applied to all samples with 2% low melting point agarose gel, and a gel band corresponding to 200 – 400bp processed cDNA fragments was cut and purified with a Qiaquick gel extraction kit (Qiagen). Selected cDNA samples were enriched with PCR using Pfx DNA polymerase (Invitrogen), and 15 cycles of PCR steps including 98C for 10sec, 65C for 30sec, and 68C for 30sec. Purified PCR products of all 16 samples were checked with bioanalyzer and samples from MTP and N6 preparation were sequenced separately for only one end with 35bp in length on eight lanes of an Illumina Genome Analyzer at Yale Center for Genomic Analysis (YCGA).

value: surface perithecia

tag: time (after crossing)

tag: priming strategy


title: N6-120hr

description: 200-400bp in length


title: N6-72hr

description: 200-400bp in length


title: N6-96hr

description: 200-400bp in length


title: N6-48hr

description: 200-400bp in length


title: ES_EMCV 3hrs

description: E14 ES cells infected with EMCV and total RNA extracted 3 hours post-infection with EMCV

tag: cell type


title: ES_EMCV 6hrs

description: E14 ES cells infected with EMCV and total RNA extracted 6 hours post-infection with EMCV

tag: age


title: N6-24hr

description: 200-400bp in length

source_name: N. crassa crossing material

value: surface perithecia with surrounding myceilia


title: WTCbl_MYCN [RRBS]

description: RRBS

value: normal cerebellum


title: MTP-144hr

description: 200-400bp in length

value: MTP


title: SNU668

city: Daejeon

first: Seongmin

last: Park

address: 111 Gwahangno, Yuseong-gu

institute: KRIBB

data_processing:
BclConverter (version 1.7.1) software was used for basecalling.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using TopHat (version 1.3.1) and assembled using Cufflinks (version 1.0.3).
FPKM (fragments per kilobase of exon per million fragments mapped) value were provide by Cufflinks.
Genome_build: hg18
Supplementary_files_format_and_content: transcript.gtf file provied by Cufflinks

organism: Homo sapiens

source_name: gastric cancer cell line

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) or RNeasy kit (QIAGEN) according to the manufacturer’s instructions.
Total RNA (3 μg) was selected for poly(A)+ RNA using Sera-Mag oligo(dT) beads (Thermo Scientific), and paired-end next-generation sequencing libraries were prepared using Illumina-supplied universal adaptor oligos and PCR primers (Illumina).

tag: cell line


title: SNU601


title: MTP-120hr

description: 200-400bp in length


title: SNU484


title: MTP-96hr

description: 200-400bp in length


title: Primary gastric tumor-2 (38627)

source_name: primary cell cultrue

value: primary cell culture  from gastric cancer tissue


title: Primary gastric tumor-3 (40703)


title: ES_D0 INF

description: E14 ES cells infected with EMCV at day 0 (D0) before induction of differentiation. Total RNA was extracted 6 hours post-infection with EMCV

value: embryonic stem cells


title: MTP-24hr

description: 200-400bp in length


title: hWTCbl [RRBS]

description: RRBS

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) as part of the Sequence Control Software (on Illumina IIGAx) or HiSeq Control Software(on Illumina HiSeq2000).
Alignment and Methylation calls: reads were mapped to human (hg18) and mouse (mm9) genomes using BSMAP (version 2.74), with the option -q 20 A AGATCGGAAGAGC to trim adaptor sequences and low quality base calls. The methylation calls were performed using python script methratio.py in the BSMAP package. CpG statistics: the number of cytosines covered, and the average coverage on covered cytosines for each sample were reported by BSMAP. The average CpG methylation ratios were computed from estimated methylation ratios, weighted by the corresponding coverage.
Genome_build: hg18
Supplementary_files_format_and_content: A file (.ratio) was generated for each sample as standard out from BSMAP (version 2.74).


title: Gastric normal (CGC-457)

source_name: gastric normal tissue

value: normal gastric tissue


title: MTP-48hr

description: 200-400bp in length


title: MTP-0hr

description: 200-400bp in length

source_name: N. crassa protoperithecia

value: surface protoperithecia with surrounding myceilia


title: MTP-2hr

description: 200-400bp in length


title: Gastric normal (CGC-140)


title: Primary gastric tumor-1 (36291)


title: hMB [RRBS]

description: RRBS


title: RPS19+p53 MO

status: Public on Oct 09 2013

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

country: China

institute: Beijing Institute of Genomics

description: Sample 3

data_processing:
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements (FPKM values) for each sample

organism: Danio rerio

source_name: RPS19+p53 MO_embryo

growth_protocol: Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the Illumina mRNA-Seq library preparation kit according to the manufacturer’s instructions.

treatment_protocol: Zebrafish embryos at the one-cell stage were injected with the MOs using an Microinjector (WPI SYS-PV830). Based on initial injection trials, 2-5 ng MO and control MO was chosen as the optimal concentration.

tag: genotype/variation

value: RPS19 and p53 morpholino double knockdown

value: embryo


title: RPS19 MO

description: Sample 2

source_name: RPS19 MO_embryo

value: RPS19 morpholino knockdown (RPS19 MO)


title: morpholino control

description: Sample 1

source_name: morpholino control_embryo

value: control


title: N6-0hr

description: 200-400bp in length


title: N6-2hr

description: 200-400bp in length


title: chiifu-Stem

city: Shenzhen

first: Zhangyan

last: Wu

address: Yantian district, Shenzhen

institute: Beijing Genomics Institute

description: Sequenced reads were generated from stem tissue of 7-week old Brassica rapa plant

data_processing:
use Brassica rapa genome as reference,  sequenced reads were aligned onto the corresponding reference using TopHat-1.0.13 with default parameters except -N 1, -r 20, -p 4, --coverage-search, --microexon-search
Supplementary_files_format_and_content: bedgraph and fpkm

organism: Brassica rapa

source_name: Stem tissues of Brassica rapa

growth_protocol: The flower, leaf, root, silique and stem from the Brassica rapa plants, which were grown in the greenhouse under condition of temperature,15-25℃ and sunlight. The tissue of Callus were generated in the illumination box under the 25℃ using tissue culture. All the tissues were generated by Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,China in 2010.

extract_protocol: For RNA-seq, poly-A+ RNA was isolated with  30  oligo-dT-coupled beads from 20 μg total RNA of each sample. First strand cDNA synthesis was  performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second  strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with  Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp  fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE  adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR  amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end  sequencing module.

treatment_protocol: total RNA is extracted by TRIzol Reagent

value: stem

value: 7-week old


title: chiifu-Root1

description: Sequenced reads were generated from root tissue (Biological replicates 1) of 7-week old Brassica rapa plant

source_name: Root tissues of Brassica rapa

value: root


title: chiifu-Root2

description: Sequenced reads were generated from root tissue (Biological replicates 2) of 7-week old Brassica rapa plant


title: chiifu-Silique

description: Sequenced reads were generated from Silique tissue of 15-day after pollination

source_name: Silique tissues of Brassica rapa

value: silique

value: 15-day after pollination


title: ES_NI

description: Non-infected E14 ES cells

value: WT


title: MTP-72hr

description: 200-400bp in length

value: surface perithecia


title: chiifu-Leaf2

description: Sequenced reads were generated from leaf tissue (Biological replicates 2)of 7-week old Brassica rapa plant

source_name: Leaf tissues of Brassica rapa

value: leaf


title: chiifu-Leaf1

description: Sequenced reads were generated from leaf tissue (Biological replicates 1) of 7-week old Brassica rapa plant


title: chiifu-Callus

description: Sequenced reads were generated from callus tissue using tissue culture

source_name: Callus tissues of Brassica rapa

value: callus

value: tissue culture


title: Third trimester Placenta 3T.4

city: Wenzhou

first: Chunming

last: Ding

state: Zhejiang

address: School of Laboratory Medicine and Life Sciences

institute: Wenzhou Medical University

data_processing:
paired-end 36-base pair (bp) reads were filtered based on qseq score
reads were aligned to CpG Islands in the bisulfite-converted human genome (UCSC Build hg19, GRCh37, Feb 2009) using Bowtie
Partially methylated regions (30-70% methylation) were selected
Concordance was calculated based on whether the neighbouring CpG site showed the same methylation pattern
Genome_build: hg19
Supplementary_files_format_and_content: Series supplementary files contain Allele-specific partially methylated regions in human placental tissue with concordance >85%; numbers represent the concordance value)

source_name: Third trimester Placenta

extract_protocol: Modified Illumina RRBS Sample Preparation Protocol

value: Fetal placenta tissue

value: third trimester


title: Third trimester Placenta 3T.6 (RNA-Seq)

data_processing:
Illumina RNA-seq pipeline (CASAVA 1.7)
Genome_build: hg19
Supplementary_files_format_and_content: Series supplementary file contains RNA expression level in RPKM

extract_protocol: Illumina mRNA-Seq Sample Preparation Protocol


title: Third trimester Placenta 3T.3


title: chiifu-Flower

description: Sequenced reads were generated from flower tissue, blooming in the same day without floral shoot

source_name: Flower tissues of Brassica rapa

value: flower

value: blooming stage


title: Third trimester Placenta 3T.1


title: Third trimester Placenta 3T.2


title: First trimester CVS 1T.5

source_name: First trimester CVS

value: CVS tissue

value: first trimester


title: First trimester CVS 1T.4


title: First trimester CVS 1T.3


title: First trimester CVS 1T.2


title: First trimester CVS 1T.1


title: ChIP-seq_spt6-1_Swd1-myc_I

first: Peter

middle: J

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing:
ChIP-seq reads were aligned to S. Pombe assembly ASM294v2 using bowtie with ‘-m 10 --best’ options.
The samples were normalized with BEADS. The fragments were extended in the 3’ end direction to be 100 bp long ("beads extend -threePrim <100-read length>”).  Spp defined broad enrichment clusters (z=3) were excluded in the BEADS calculation.  Downstream ChIP-seq analysis was performed in 10 bp bins as out by BEADS (“beads tagCount -base 10”).
The input samples were normalized to per 1M fragments over nuclear chromosomes.
The IP samples were normalized such that the median fold enrichment over input is set to 1.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig files at 10bp resolution show fold enrichment for IP samples and normalized tag counts for input samples

organism: Schizosaccharomyces pombe

growth_protocol: Strains were cultured at 30°C, using Yeast Extract Supplemented (YES) medium

extract_protocol:
100 ml cultures grown to 1-2 x 107 cells/ml were crosslinked (1% formaldehyde, 30 min) and lysed by bead beating.  The chromatin fraction was isolated and sheared to 200-500 bp fragments using a Bioruptor sonicator (Diagenode) or Sonicator 3000 (Misonix).  Immunoprecipitations (IPs) were performed overnight at 4°C with 1 μg of anti-H3 (ab1791; Abcam), 2 μg of anti-H2B (ab1970; Abcam), 3 μg of anti-H3K36me3 (ab9050; Abcam), 5 μg of anti-H3K4me3 (ab8580; Abcam), 5 μL of anti-Rpb1 (8WG16; Covance), 5 μg of anti-HA (ab9110; Abcam), or 5 μL of anti-Myc (9E10; Santa Cruz Biotechnology).  IPs were coupled to 50 μL of protein-G-sepharose beads (GE Healthcare Life Sciences) at 4°C for 4 hours.  Beads were washed and eluted; eluate was reverse-crosslinked overnight at 65°C and incubated with proteinase K and glycogen for 2 hours at 37°C.  DNA was purified by phenol chloroform extraction and precipitated in ethanol overnight at -20°C.
Between 1-10 ng of ChIP DNA were processed for each ChIP-seq library.  DNA was end repaired with T4 DNA Polymerase (Invitrogen), T4 PNK (NEB) and DNA Pol I, Large Klenow fragment (Invitrogen), and an 'A' base was added using Klenow 3' to 5' exo minus (NEB).  1 pmol of barcoded adaptors were ligated on with T4 DNA ligase (Roche) and the products were PCR amplified with Phusion DNA Polymerase (NEB) and size selected by purification on 2% agarose-EX E-gels (Invitrogen) for fragments between 200-600 bp.  Library size and concentration was determined by Bioanalyzer or Tapestation analysis (Agilent) and libraries were pooled equimolar amounts with up to 26 in each sequencing lane.  Pooled libraries were gel purified twice, followed by column purification on MinElute columns (Qiagen).  At least 10 nM were submitted for analysis on the Illumina Hi-Seq at Tufts University Core Facility.

value: spt6-1; spt6 mutant

tag: chip-antibody

value: Swd1-myc (anti-Myc)

tag: chip-antibody vendor

value: Santa Cruz Biotechnology

tag: chip-antibody cat. #


title: ChIP-seq_spt6-1_Swd1-myc_III


title: THP1_mRNA-seq

description: ribosomal RNA-depleted RNAs from THP1 cells

data_processing:
Sequence read alignment with human genome sequence (release 55)
Measure gene expression by the number of tags matching exon regions
The IDEG6 program was used to assess differential gene expression
Functional classifications were assigned according to Gene Ontology (GO) using WebGestalt online software
Biological pathways of differentially expressed genes were assigned according to the updated Kyoto Encyclopedia of Genes and Genomes (KEGG) database
Genome_build: human genome sequence (release 55)
Supplementary_files_format_and_content: Excel files include RPKM values for each sample

source_name: Peripheral blood

growth_protocol: HL-60 and THP1 cells were culture  in the culture flask containing RPMI 1640 medium (Gibco) supplied with 10% fetal bovine serum (Hylone) and penicillin (100 U/ml)-streptomycin (0.1 mg/ml) (Invitrogen, Carlsbad, CA)

extract_protocol:
Total RNA was extracted from HL-60 and THP1 cells using TRIzol® Reagent (Invitrogen) as per manufacturer’s instruction.
SOLiD RNA-seq with invitrogen ribominus kit

value: monocyte

tag: passage


title: ChIP-seq_spt6-1_Input_Swd1-Myc_III


title: HL-60_mRNA-seq

description: ribosomal RNA-depleted RNAs from HL-60 cells

value: promyeloblast


title: ChIP-seq_spt6-1_Input_Set2-myc_I


title: ChIP-seq_spt6-1_Input_Set2-myc_II


title: ChIP-seq_spt6-1_Input_Swd1-Myc_I