title: 3T3-Control-RNAseq


title: 3T3-8hrs-mild-HS-Riboseq-rep2

status: Public on Jan 03 2013

type: SRA

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

library_source: transcriptomic

data_processing: RNAseq: mapping was performed using bowtie v. 12.3 with the following parameters: "-m 1 --best --strata -m 1 -n 2 --best --strata --sam" with a sam format output. reads were uniquely mapped to the mm9 genome, with the addition of splice junctions and ribosomal RNA. the 2 ends of each library were further combined to a single sam file.  RNA Seq bowtie files for the combined replicates of control, HS8M, and HS2S are provided as supplementary files on the Series record.

molecule: total RNA

organism: Mus musculus

source_name: 3T3 cells

extract_protocol: RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009

treatment_protocol: Mild HS: 8 hours in 42 deg C, Severe HS: 2 hours in 44 deg C.

tag: treatment

value: mild heat shock

tag: cell line

value: 3T3 cells

tag: assay type

value: Riboseq


title: 5-683

status: Public on Jan 04 2013

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostOestrus_3.counts.txt: bt4

molecule: polyA RNA

organism: Bos taurus

source_name: Cervix

growth_protocol: The estrous cycles of Limousin heifers (n = 30) were synchronized by insertion of a controlled internal drug release (CIDR) device (1.94 g progesterone; Pfizer Animal Health) placed into the vagina for 8 days. A 0.5 mg intramuscular injection of a prostaglandin F2α (PG) analogue (PG, Estrumate, Shering-Plough Animal Health, Hertfordshire, UK) was administered 1 day before CIDR removal.  Heifers were checked for standing  estrus  and only those exhibiting  estrus  (Day 0) were used.

extract_protocol: The standard Illumina protocol for generating single read RNAseq data was followed. Version 2 illumina sequencing kits were used.

treatment_protocol: Cervical tissues were collected at slaughter from heifers 12h after CIDR removal (Group 1: CIDR + 12 h, n = 6), 24h after CIDR removal (Group 2: CIDR + 24 h, n = 6), at the onset of  estrus  (Group 3: Estrus, n = 4), 12 h after the onset of  estrus  (Group 4:  estrus  + 12 h, n = 5), 48 h after the onset of  estrus  (Group 5: Estrus+48h, n = 4) and on day 7 after the onset of  estrus  (Group 6: Luteal phase, n = 5).

tag: Stage

tag: animaltype

value: Heifer

tag: animalid

tag: timepoint


title: PP (RNA-Seq)

status: Public on Jan 02 2013

city: Lisbon

first: Angela

last: Inácio

address: Campo Grande

country: Portugal

institute: centro de Biologia Ambiental

description: Library based on 3 individuals.

data_processing:
Base-calling: Sequence data called raw data or raw reads is stored in the *.fq file by software trim developed by BGI (Beijing Genomics Institute).
Filtering: Removed small tags, contamination formed by adaptor-adaptor ligation, 3' adaptor and low-quality data. Trim Software was developed by BGI.
Mapping: Small RNA tags were mapped to the Zv9 genome by SOAP using the Ensembl database (ftp://ftp.ensembl.org/pub/release-64/fasta/danio_rerio/dna/).
Annotation: Annotation was made using the version 14 miRBase database (http://www.mirbase.org/) for the precursor/mature miRNAs and GenBank (http://www.ncbi.nlm.nih.gov/) and Rfam (http://www.sanger.ac.uk/software/Rfam) databases for other categories of RNA.
Abundance measurement: Each miRNA was normalized by dividing the number of reads for that miRNA by the number of total reads of annotated miRNAs in the same library multiplied by 10000000000. No special software was used. Calculations were made in Excel.
Genome_build: Zv9
Supplementary_files_format_and_content: *_miRNA_expression.txt: The expression value of each miRNA.
Supplementary_files_format_and_content: lengthVSnumber*.txt: The number of reads per length in the library between sizes 14 and 30 nucleotides.

organism: Squalius pyrenaicus

source_name: PP liver, brain, and muscle

growth_protocol: Fish were acclimatized in a proper aquarium for 15 days in the animal house of the institution prior to sacrifice.

extract_protocol: Tri-Reagent® (Ambion) was used for total RNA extraction. Libaries were constructed using the Illumina kit Small RNA v1.5.

treatment_protocol: All fish were in the same aquarium with controlled temperature and light conditions.

tag: genomic composition

value: PP

tag: tissue

value: liver, brain, muscle

tag: ploidy

tag: nuclear hybridization

value: absent


title: ChIP Sequencing Pho7-TAP -Pi

city: Cambridge

first: Ian

middle: O'Brien

last: Carter-O'Connell

state: MA

address: 52 Oxford St. NW 440

department: MCB

country: USA

institute: Harvard University

description: ChIP Sequencing

library_source: genomic

data_processing:
Sequenced reads were aligned to the S. pombe 972 h- genome using ELAND. Uniquely mappable reads with a maximum of 3 mismatches were mapped to the genome. Reads were then extended 80 base-pairs to cover the average length of insert DNA between sequencing adaptors as determined by the Agilent Bioanalyzer. WIG files for ChIP normalized such that the genome average is 100 reads/nucleotide.
Genome_build: S. pombe 972 h-
Supplementary_files_format_and_content: WIG files for each chromosome

molecule: genomic DNA

organism: Schizosaccharomyces pombe 972h-

growth_protocol: S. pombe cells were maintained in previously described YES or EMM media. Prior to starvation, cells were grown at 30°C, 220RPM to mid-log phase (OD600~0.2) in 90%SD-10%EMM media supplemented with 10 mM KH2PO4 (high-Pi media).

extract_protocol: Cells were lysed by bead beating (6 x 2 min on, 2 min off) and chromatin was sheared to 300-600 bp fragments using a Misonix Sonicator 3000. Immunoprecipitation was performed with 100 uL of Protein G Dynabeads (Invitrogen) coupled to 4 uL of anti-Protein A antibody (Sigma). Protein concentrations were measured using a Bradford Assay (Bio-Rad). Following the generation of ChIP lysate three aliquots of 650 μg soluble protein were subject to immunoprecipitation and pooled just prior to elution from the beads. Samples were processed following the Illumina HTS guidelines with libraries of 200-300 bp selected via 2% agarose DNA gels. Libraries were amplified by PCR and purity was determined using an Agilent High-Sensitivity DNA kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina HighSeq 2000 using a 50 bp read length.

treatment_protocol: Following growth in high-Pi media, cells were split into either 200 mL of high-Pi or no-Pi media and grown for 2 hours at 30°C, 220RPM. Formaldehyde (Sigma) was added to a final concentration of 1% (v/v) to cross-link chromatin, and the reaction was allowed to proceed for 15 minutes. Glycine (Sigma) was then added to a final concentration of 125 mM and incubated for 5 minutes to quench cross-linking. Cells were collected by centrifugation and washed once with cold PBS buffer, pH 7.4. The cell pellet was snap frozen in liquid nitrogen and stored in −80 °C.

tag: phosphate concentration

value: 0 mM KH2PO4

tag: chip antibody

value: anti-Protein A (Sigma)

tag: time

value: 2 hours post-starvation


title: ChIP Sequencing mock -Pi

description: ChIP Sequencing


title: ChIP Sequencing Pho7-TAP +Pi

description: ChIP Sequencing

value: 10 mM KH2PO4


title: thymocyte_53BP1ko_RPAip_a

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing: Image analysis, base calling, quality filtering: Standard Illumina tools (different versions); ***Raw data***: Fastq files contain full length reads that passed the chastity filter. ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum. Redundancy was capped at 3 reads per position and shifted reads were counted in 400 nt bins across the genome. Counts were normalized to the reduced redundancy library size and bin size such that the final units are reads per kb per million (RPKM).

source_name: thymocyte

extract_protocol: Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-CTCF antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol and sequenced on a Genome Analyzer II or HiSeq2000.

tag: chip antibody manufacturer

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

value: multiple lots

tag: cell type

value: thymocyte

tag: strain

tag: genotype

value: RPA


title: activatedB_53BP1ko_ATMi_SG2M_RPA_combined

source_name: in vitro activated B cells

growth_protocol: CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.

value: in vitro activated B cells

tag: cell cycle

tag: cell treatment

value: ATM inhibitor


title: Pancreatic Islets paternal control

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Immunoprecipitation using antibodies against 5mC followed by deep sequencing

data_processing:
Basecalls performed using CASAVA version 1.4, with default parameters.
MeDIP-Seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2.
Peaks were called using PeaksFind version 2.2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited excel files include peak scores for each sample

source_name: Pancreatic Islets

growth_protocol: Male F0 founders were weaned from mothers at 3 weeks of age, and sibling males were put into cages with high-fat diet (33% energy as fat) or control diet until 12 weeks of age, at which point mice fed with HFD were injected intraperitoneally with a low dose of STZ and kept on the same diet for 4 weeks. Fasting blood glucose was examined each week post-STZ for 4 weeks, and only glucose level at 7~11 mM was considered as T2D. Females were always raised on standard diet. At 16 weeks, male F0 founders were mated with females. After 1 or 2 days, males were removed, and pregnant females were left alone until their litters were 3 weeks of age. Pancreatic islets were collected from 6 control and 6 T2D offspring. Sperm were collected from 6 control and 6 T2D male F0 founders.

extract_protocol:
For pancreatic islets, genomic DNA was extracted by DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instructions. For sperm, caudal epididymis was dissected from sacrificed animals, punctured, and incubated for 30 minutes in M2 media (Sigma) at 37 C. Supernatant was removed, pelleted (3,000g for 5 minutes), and washed 2× with PBS, 1× in water, and incubated in Somatic Cell Lysis buffer, and then subjected to DNeasy Blood & Tissue Kit (Qiagen). The 5mC antibody was included in the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode), with the Cat. No. of mc-magme-048.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Paternal T2D vs control, the pancreatic islets or sperm methylome was analysed through MeDIP-Seq.

value: ICR

value: Pancreatic Islets

tag: age

value: 3 weeks

tag: condition

value: paternal control


title: ChIP Sequencing Pho7-TAP, csk1Δ +Pi

description: ChIP Sequencing


title: thymocyte_WT_RPAip_b

value: WT


title: thymocyte_53BP1ko_ATMko_RPAip_b


title: thymocyte_53BP1ko_ATMko_RPAip_a


title: 8-259

data_processing:
Reads were processed with the standard Illumina pipeline IPAR v1.0. Reads were aligned against the BosTau4 genome with ELAND using standard parameters. Pseudochromosomes incorporating the known splice sites in the version 54 of the bovine trnascriptome were also included. Only reads aligning to a single unique position with less than 2 mismatches were included. CASAVA v1.0 was used to generate transcript counts.
Genome Build:
cervix_12hrPostCIDR_7.counts.txt: bt4

tag: Stage

tag: animaltype

value: Heifer

tag: animalid

tag: timepoint


title: activatedB_WT_S_gH2AXip_a

value: Epitomics

value: S


title: ChIP Sequencing mock +Pi

description: ChIP Sequencing

tag: phosphate concentration

value: anti-Protein A (Sigma)


title: thymocyte_WT_RPAip_a

tag: chip antibody


title: activatedB_WT_G1_gH2AXip_a


title: activatedB_IsceI_53BP1ko_AIDko_RPAip


title: activatedB_H2AXko_UNGko_MSH2ko_RPAip_a


title: activatedB_IsceI_53BP1ko_AIDko_RPAip_ExoI_a

tag: chip dna treatment

value: ExoI


title: activatedB_IsceI_53BP1ko_AIDko_RPAip_RecJf_a

tag: chip antibody manufacturer

value: RecJf


title: activatedB_H2AXko_S_RPAip_a

value: Calbiochem

tag: chip antibody catalog #


title: activatedB_H2AXko_RPAip_a

tag: chip antibody lot #

value: multiple lots


title: activatedB_H2AXko_G2M_RPAip_a

tag: cell type


title: 3T3-Control-Riboseq-rep2

tag: treatment

value: control

tag: cell line

value: 3T3 cells

tag: assay type

value: Riboseq


title: activatedB_H2AXko_G1_gH2AXip_a

value: in vitro activated B cells

tag: strain

tag: genotype

tag: cell cycle


title: activatedB_ER-IsceI_53BP1ko_AIDko_RPAip_3h

value: RPA

tag: cell treatment

value: TAM 3h


title: activatedB_H2AXko_G1_RPAip_a


title: activatedB_ER-IsceI_53BP1ko_AIDko_RPAip_30min

value: TAM 30min


title: activatedB_ER-IsceI_53BP1ko_AIDko_RPAip_24h

value: TAM 24h


title: thymocyte_53BP1ko_RPAip_b

value: thymocyte


title: activatedB_ER-IsceI_53BP1ko_AIDko_RPAip_0min

value: TAM 0h


title: activatedB_53BP1ko_RPAip_a


title: activatedB_53BP1ko_RPAip_b


title: activatedB_AIDtg_53BP1ko_RAD51ip_combined

value: Santa Cruz


title: activatedB_AIDtg_53BP1ko_RPAip_ExoI


title: activatedB_53BP1ko_ATMko_RPAip_b


title: activatedB_53BP1ko_G1_gH2AXip_a

value: Epitomics


title: activatedB_AIDwt_RAD51ip

value: AIDwt


title: activatedB_53BP1ko_ATMko_RPAip_a


title: activatedB_AIDtg_53BP1ko_RPAip_a


title: MEF_I-PpoI_53BP1ko_RPAip

source_name: MEF

value: MEF


title: activatedB_53BP1ko_SG2M_RPA_c


title: MM1.S_RNA_POL2_DMSO

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against RNA Pol II in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_4.CAGATC
Barcode (already removed): CAGATC

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

organism: Homo sapiens

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

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

treatment_protocol: 0.05% DMSO for 6h

value: RNA Pol II (Rpb1 N-terminus)

tag: chip antibody details

value: Santa Cruz SC-899

tag: duration

value: DMSO

tag: concentration


title: U87_BRD4

description:
Chromatin IP against BRD4 in U87 glioblastoma
Sample name: 01272012_D0NF2ACXX_8.GCCAAT
Barcode (already removed): GCCAAT

source_name: Glioblastoma

growth_protocol: RPMI 1640 + FBS

value: Bethyl A301-985A


title: activatedB_53BP1ko_SG2M_RAD51ip


title: activatedB_53BP1ko_S_RPAip_a

value: Calbiochem

value: multiple lots

value: S


title: activatedB_53BP1ko_SG2M_RPA_b

value: in vitro activated B cells

value: RPA


title: activatedB_53BP1ko_RPAip_c


title: activatedB_53BP1ko_G2M_gH2AXip_a


title: activatedB_53BP1ko_RAD51ip


title: MM1.S_MED1_DMSO

description:
Chromatin IP against MED1 in MM1.S multiple myeloma
Sample name: 08282012_C1260ACXX_4.AGTCAA
Barcode (already removed): AGTCAA

value: Bethyl A300-793A


title: activatedB_53BP1ko_G1_RPA_b


title: activatedB_53BP1ko_G1_RPA_c


title: activatedB_53BP1ko_G1_RPAip_a


title: MM1.S_BRD4_DMSO

description:
Chromatin IP against BRD4 in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_2.ATCACG
Barcode (already removed): ATCACG


title: activatedB_53BP1ko_ATMi_G1_RPA_c

value: ATM inhibitor


title: MM1.S_BRD4_5uM_JQ1

description:
Chromatin IP against BRD4 in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_3.GCCAAT
Barcode (already removed): GCCAAT

treatment_protocol: 5uM JQ1 treatment for 6hr


title: activatedB_53BP1ko_ATMi_G1_RPA_b


title: MM1.S_BRD4_5nM_JQ1

description:
Chromatin IP against BRD4 in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_2.CGATGT
Barcode (already removed): CGATGT

treatment_protocol: 5nM JQ1 treatment for 6hr


title: activatedB_53BP1ko_S_gH2AXip_a


title: activatedB_AIDtg_53BP1ko_RPAip_RecJf

value: RecJf


title: H2171_BRD4

description:
Chromatin IP against BRD4 in H2171 small cell lung cancer
Sample name: 01272012_D0NF2ACXX_8.ACAGTG
Barcode (already removed): ACAGTG

source_name: Small Cell Lung Carcinoma


title: ChIP-Seq_MED1_48HR

description:
Chromatin IP against MED1 in ZHBTc4 ESCs
Sample name: 10192012_D1FMEACXX_3.CAGATC
Barcode (already removed): CAGATC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all ChIP-Seq samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 1 -n 2 --best --sam. Seed length (-l) was set to read length for each dataset.
For all RNA-Seq samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 2 -n 2 --best --sam. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all ChIP-Seq samples, wiggle files were produced by MACS 1.4 with --space=50.
Supplementary_files_format_and_content: RNA-Seq RPKM expression values were computed for each gene and normalized to the included ERCC controls. Details can be found with the associated manuscript.

source_name: ZHBTc4 ES cells

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media. Oct4 shutdown was induced by addition of 2ug doxycycline for 48 hours.

value: Med1/TRAP220 (Bethyl, Catalog No.A300-793A)

value: Embryonic stem cells

value: 2 ug/mL

tag: drug

value: dox

tag: duration of treatment

value: 48 hr


title: GroSeq_1hr_1-2

data_processing:
Library strategy: Gro-Seq
For all Gro_Seq samples, reads were first cut to 40bp, then trimmed to remover linker sequence. Reads shorter than 24bp after trimming were removed. The remaining reads were aligned to their indicated build using bowtie with parameters -e 70 -k 1 -m 10 -n 2  --best --strata, with the additional -l parameter set to the read lengths. See Manuscript for additional details.
supplementary_files_format_and_content: WIG files: For Gro-Seq samples, replicates were merged and combined aligned sequences were extended 10bp and allocated into 10bp bins. Reads from plus and minus strans were processed into separate tracks. Counts were normalized to reads per million, and bins with at least 0.1 read per million are shown.
Images analysis and base calling was done using the solexa pipeline.
Genome_build: hg18

source_name: GRO-seq H1-hESC-1hr-Activin

growth_protocol: H1 cells were grown to confluence in mTESR1 media. Cells were then rested for 24 hours in RPMI-B27 and then treated with Activin 50ng/ml for 1 hour

extract_protocol: Nuclei were isolated from hESC and differentiating hESC. GRO-seq libraries were prepared from 5 million cells based on previously published protocols (Core et al., 2008). Libraries were sequenced on Illumina Hi-Seq 2000.

value: H1 embryonic stem cells

tag: chip antibody

value: BrdU

tag: antibody catalog number

value: Santa Cruz 32323-ac

value: TCGTATGCCGTCTTCTGCTTG

tag: drug treatment

value: Activin

tag: drug concentration


title: Med1 Pro Bcell_ChipSeq

description:
Chromatin IP against Med1 Pro Bcell
Sample name: 10032012_C1605ACXX_2.TTAGGC
Barcode (already removed): TTAGGC

source_name: pro-B cell

growth_protocol: 38B9 (pro-B) cells were grown under typical conditions in RPMI media with 10% FCS.

tag: cell type

value: 38B9 cells


title: ChIP-Seq_WCE_0HR

description:
Chromatin IP against WCE in ZHBTc4 ESCs
Sample name: 10192012_D1FMEACXX_4.ACTTGA
Barcode (already removed): ACTTGA

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media.


title: AA (RNA-Seq)

description: Library based on 3 individuals.

organism: Squalius alburnoides

source_name: AA liver, brain, and muscle

tag: genomic composition

value: AA

tag: tissue

value: liver, brain, muscle

tag: ploidy

tag: nuclear hybridization

value: absent


title: MM1.S_BRD4_50nM_JQ1

description:
Chromatin IP against BRD4 in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_2.TTAGGC
Barcode (already removed): TTAGGC

treatment_protocol: 50nM JQ1 treatment for 6hr

value: Bethyl A301-985A

tag: treatment


title: MM1.S_BRD4_500nM_JQ1

description:
Chromatin IP against BRD4 in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_3.ACAGTG
Barcode (already removed): ACAGTG

treatment_protocol: 500nM JQ1 treatment for 6hr


title: GroSeq_0hr_1-2

source_name: GRO-seq H1-hESC-RPMI

growth_protocol: H1 cells were grown on matrigel in mTESR1 media.


title: PAA (RNA-Seq)

description: Library based on 3 individuals.

source_name: PAA liver, brain, and muscle

value: PAA

value: present


title: PA (RNA-Seq)

description: Library based on 3 individuals.

source_name: PA liver, brain, and muscle

value: PA


title: RNA_Seq_48hr_2

data_processing:
For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying splicing.
supplementary_files_format_and_content: RPKM: The average (combining hESC or 48hr replicates) reads per kilobase of exonic length per million (RPKM) for each gene or lncRNA (see manuscript for details) was calculated and reported.
Images analysis and base calling was done using the solexa pipeline.
Genome_build: hg18

source_name: RNA-seq H1-hESC-48hr-Activin

growth_protocol: H1 cells were grown to confluence in mTESR1 media. Cells were then differentiated for 48 hours in RPMI-B27 plus 50 ng/ml Activin

extract_protocol: Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free™ DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a modified Illumina mRNA-Seq protocol. Polyadenylated RNA was fragmented and sequenced according to modified version of standard Illumina RNA-seq protocol. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis. RNA-seq libraries were sequenced on Illumina HiSeq 2000.


title: MM1.S_RNA_POL2_500nM_JQ1

description:
Chromatin IP against RNA Pol II in MM1.S multiple myeloma
Sample name: 05242012_D0WUYACXX_5.GGCTAC
Barcode (already removed): GGCTAC

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899


title: RNA_Seq_48hr_1


title: RNA_Seq_hESC_2

source_name: RNA-seq H1-hESC


title: ChIP-Seq_Med1_0HR

description:
Chromatin IP against MED1 in ZHBTc4 ESCs
Sample name: 10192012_D1FMEACXX_3.TTAGGC
Barcode (already removed): TTAGGC

tag: strain

value: Med1/TRAP220 (Bethyl, Catalog No.A300-793A)

value: Embryonic stem cells


title: RNA-Seq_0HR

description:
RNA-Seq from ZHBTc4 cells after 0HR of treatment
Sample name: L22_1534
Barcode (already removed): CGATGT

extract_protocol: Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions. Synthetic RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added to each population based on cell number. See manuscript for details.  Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a standard Illumina mRNA-Seq protocol with the following modifications. Briefly, polyadenylated RNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis.


title: GroSeq_hESC_1-3

source_name: GRO-seq H1-hESC

value: H1 embryonic stem cells


title: 48hr_IgG_ChipSeq

data_processing:
For all ChIP-Seq reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 10 -n 2 -l 40 --best --strata.
supplementary_files_format_and_content: WIG files: For the ChIP-Seq samples, reads were extended 200 bp upstream and 0bp downstream (with respect to strand) and reads from both strands were allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 0.5 read per million are shown.
Images analysis and base calling was done using the solexa pipeline.
Genome_build: hg18

source_name: Chromatin IP against 48hr_IgG

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Sample was divided into 6 aliquots after sonication. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: IgG

value: Millipore 12-370


title: 48hr_H3K27ac_ChipSeq

source_name: Chromatin IP against 48hr_H3K27ac

value: Abcam AB4729


title: RNA-Seq 48HR

description:
RNA-Seq from ZHBTc4 cells after 48HR of treatment
Sample name: L22_1538

value: 2 ug/mL

value: dox

value: 48 hr


title: ChIP-Seq_WCE_48HR

description:
Chromatin IP against 48HR WCE
Sample name: 10192012_D1FMEACXX_4.CTTGTA
Barcode (already removed): CTTGTA


title: 38b9 WCE

description:
WCE for 38B9 cells
Sample name: 07242009_42E6LAAXX_B8

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. 1x10^8 cells were sonicated at 21 watts in 20 second pulses for 3 min of sonication time. The chromatin extracts containing DNA fragments with an average size of 500 bp were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: 38B9 cells


title: GroSeq_48hr_1-2

source_name: GRO-seq H1-hESC-48hr-Activin

growth_protocol: H1 cells were grown to confluence in mTESR1 media. Cells were then rested for 24 hours in RPMI-B27 and then treated with Activin 50ng/ml for 48 hours

value: BrdU

value: Santa Cruz 32323-ac

value: TCGTATGCCGTCTTCTGCTTG

value: Activin


title: WCE Pro Bcell

description:
WCE Pro Bcell
Sample name: 10032012_C1605ACXX_2.TGACCA
Barcode (already removed): TGACCA


title: Normalized Max

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Sequences were mapped to the human genome (hg18) using the Eland alignment program. ChIP-Seq data was scored based on sequence reads (length ~30 bps) that align uniquely to the human genome. From the mapped tags a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
The sequenced reads were extended accordingly and allocated into 25 bases bins. The data from each bin were combined to generate the wiggle (WIG) files.
Max and Myc datasets of HeLa were further normalized for the total number of reads and the normalized Myc dataset was subtracted from normalized Max to identify the genomic regions having extra Max compared to Myc.
A genome-wide search of canonical and non-canonical Myc binding sequences was conducted using EMBOSS. 275994, 108479, 387331, 89966, 235264, 2173124 binding sites were identified for CACGTG, CAACGTG, CACGAG, CACGCG, CATGCG, CATGTG, respectively.
Genome_build: hg18
Supplementary_files_format_and_content: wgEncodeYaleChIPseqAlignmentsHelas3CmycV2_norm2.wig.gz: Normalized Myc data for the total number of reads
Supplementary_files_format_and_content: wgEncodeYaleChIPseqAlignmentsHelas3MaxV2_norm2.wig.gz: Normalized Max data for the total number of reads
Supplementary_files_format_and_content: Max-Myc.wig.gz: Normalized Myc data was subtracted from normalized Max data
Supplementary_files_format_and_content: cmyc_6_binding_sites.bed.gz: BED file including 6 Myc binding sites across human genome
Supplementary_files_format_and_content: Max-Myc.sort+_Peaks.wig.gz: extra Max peaks identified from Max-Myc dataset

source_name: HeLa

growth_protocol: ENCODE cell culture protocol

extract_protocol: Cells were cross-linked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using a Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.

tag: cell line

value: HeLa

tag: antibody

value: anti-Max (Santa Cruz sc-197)


title: Co-limited Culture

status: Public on Jan 01 2013

city: Woods Hole

first: Sonya

last: Dyhrman

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

description: Illumina (SAGE-NlaIII)

data_processing:
RNA was sent to Illumina and converted to cDNA. Illumina library construction included a polyA selection and digestion with NlaIII.
This resulted in 21 bp sequence reads called tags that should map to the most 3' NlaIII site in each transcript, but often map to alternative sites likely due to incomplete digestion during library construction.
Tags were mapped to the T. pseudonana genome (sequence data available at NCBI, AAFD00000000) using a pipeline developed by Genesifter Inc., which required the 21-base pair tags to match with 100% identity.  All tags which fell within a gene model were pooled and the pooled tag frequency was normalized to the total tags sequenced and is reported as tags per million (tpm)).  Tags that mapped to more than one location and could not be unambiguously mapped, as well as those tags that mapped to antisense gene models were excluded from further analyses.  Statistical significance of differential expression was evaluated by Analysis of Sequence Counts (ASC; Wu et al., 2010) on pairwise comparisons between the treatments and the control.
Genome_build: NCBI, AAFD00000000
Supplementary_files_format_and_content: Tab-delimited text files include raw count and TPM  values for each sample

organism: Thalassiosira pseudonana CCMP1335

source_name: Co-limited Culture

growth_protocol: Axenic T. pseudonana CCMP 1335 was grown at 14°C under 24 hour light (120 µmol photons m-2 s-1) after Dyhrman et al. (2012) in f/2 plus silica chelated media made from surface Sargasso Sea water.

extract_protocol:
Biomass was harvested onto 0.2 µm filters and flash frozen in liquid nitrogen and total RNA was extracted as described in Dyhrman et al. (2012) [PMID: 22479440]. Tag-seq sequencing of the transcriptome was performed by Illumina with a polyA selection and NlaIII digestion, resulting in 21 bp sequence reads or tags (Dyhrman et al., 2012). Libraries were of varied sizes as follows: replete (~12 million), P-limited (~13 million), Fe-limited (~23 million), and Co-limited (~26 million). Tags were mapped to gene models (predicted protein coding regions) with a pipeline designed by Genesifter Inc., requiring 100% identity and covering 9759 genes. Tag counts within a gene were pooled and normalized to the size of the library, with resulting data expressed in tags per million (tpm). Genes with normalized tag counts less than 2.5 tpm for each of the four treatments were excluded (Figure S1) , leaving 7380 genes in the analysis.
library strategy: OTHER: SAGE (NlaIII Digest)

treatment_protocol: Nitrate, silica, vitamins, and trace metals were at f/2 concentrations (Guillard and Ryther 1962), while iron and phosphate were modified across treatments. In brief, triplicate cultures of replete (36 µM PO4, 400 nM Fe), P-limited (0.4 µM PO4, 400 nM Fe), Fe-limited (36 µM PO4, 40 nM Fe), and Co-limited (0.4 µM PO4, 40 nM Fe) treatments were harvested when growth deviated from the replete control. Growth was monitored by cell counts.

tag: iron concentration

value: 40 nM

tag: phosphorus concentration


title: RNA_Seq_hESC_1


title: Phosphorus-limited Culture

description: Illumina (SAGE-NlaIII)

source_name: Phosphorus-limited Culture


title: Replete Culture

description: Illumina (SAGE-NlaIII)

source_name: Replete Culture

value: 36 uM


title: Iron-limited Culture

description: Illumina (SAGE-NlaIII)

source_name: Iron-limited Culture


title: set3 hypha Rep1

city: Vienna

first: Denes

last: Hnisz

address: Dr Bohr-gasse

department: Medical Biochemistry

country: Austria

institute: Max F Perutz Laboratories

description: Sample 10

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were mapped onto the Assembly 21 of the C. albicans genome containing only the coding sequences using TopHat (Trapnell C, Bioinfromatics, 2009) with default parameters, and allowing only for uniquely mapping reads.
Fragment Per Kilobase in a Million mapped reads (FPKM) values were calculated with Cufflinks (Trapnell C, Nat Biotechnology, 2010) including quartile normalization (removing top 25% of genes from the FPKM denominator) and bias correction. The transcript coordinates were fixed as in the annotation of the coding sequence assembly.
Genome_build: Assembly 21
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Candida albicans

source_name: set3Δ/Δ_hyphal phase

extract_protocol: RNA was isolated by the hot phenol method after which RNA was further purified by the SV Total RNA isolation system (Promega) according to the manufacturer’s instructions. 5μg total RNA was depleted of rRNAs using the RiboMinus kit (Invitrogen) and cDNA was synthesized and amplified with the SMARTer cDNA synthesis kit (Clonetech) according to the manufacturer’s instructions.

tag: genotype/variation

tag: morphological phase

value: hyphal phase


title: set3 hypha Rep2

description: Sample 11


title: wt yeast Rep2

description: Sample 2

source_name: wild type_yeast phase

value: wild type

value: yeast phase


title: wt yeast Rep3

description: Sample 3


title: wt hypha Rep2

description: Sample 8


title: E14_AbaSeq_rep2

city: Ipswich

first: Yu

last: Zheng

address: 240 County Road

institute: New England Biolabs

data_processing:
Library strategy: Aba-Seq
CASAVA version 1.8.2 was used for basecalling
Aba-seq reads were mapped to the mouse reference (UCSC mm9) using the Bowtie aligner with parameters (-v 2 –m 1)
Neighboring sequences of the aligned AbaSI cleavage sites were interrogated in search of putative 5hmC sites at expected distance (-CN11-13 or +N9-11G).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing genomic position (bed-format) and sequencing depth of 5hmC sites

source_name: embryonic stem cell (E14)

extract_protocol:
100 ng E14 genomic DNA was glucosylated and then was digested by AbaSI.
biotinylated Ilumina's adapters were ligated onto the AbaSI digested DNA. Ligated DNA was then sonicated to a range around 300bp and captured by streptavidin beads. End-repair and A-tailing were done consecutively by using the NEBNext® End Repair Module (NEB: E6050S) and the NEBNext® dA-Tailing Module (NEB:  E6053S) on the DNA-bound beads. The second Illumina's adapter was ligated onto the biotin-free end of dA-tailed DNA. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

value: embryonic stem cell

tag: passage


title: set3 yeast Rep3

description: Sample 6


title: wt hypha Rep1

description: Sample 7


title: wt yeast Rep1

description: Sample 1


title: set3 hypha Rep3

description: Sample 12


title: set3 yeast Rep2

description: Sample 5


title: set3 yeast Rep1

description: Sample 4


title: E14 basal 3Seq, resequenced

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

description: FACS setting: K14h2BGFP high, Itga-PE staining high

data_processing:
Reads alignment by Bowtie, allowing maximum 2 mismatches and only unique mapping
Peak calling by MACS, and PeakSplitter
Assign peaks to genes using RefSeq and Ensembl annotation (Apr 9th download)
Filtering internal primed peaks by motif combination
Determine polyadenylation signal for each filtered peak
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files (BED)

source_name: Epidermal progenitor cells

growth_protocol: in vitro cultured primary keratinocytes are cultuired in low Calcium medium (0.05mM)

extract_protocol: E14 mouse embryos are dissected from uterus, and epidermis is carefully isolated under dissection microscope. E14 epidermal basal and suprabasal cell populations are FACS isolated. Total RNA is extracted and polyA purified and fragmented. Anchored oligo(dT) probe is used to capture polyadenylated RNA fragment followed by first strand synthesis. Second strand DNA is synthesized using RNase H-based method. Double strand DNA library is further constructed using Illumina standard protocol.

tag: age

value: embryonic day 14

value: epidermis, basal cells


title: E14 suprabasal 3Seq, resequenced

description: FACS setting: K14h2BGFP low, Itga-PE staining low

value: epidermis, suprabasal cells


title: E14_AbaSeq_rep1


title: feeder2

city: Toronto

last: Liu

state: ON

address: 600 University Ave

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Illumina CASAVA 1.8 was used to perform basecalling
The first 15 bases of each read were trimmed
Top-Hat 1.3 was used to align to mm9 genome
Reads mapped to multiple location in the genome were dicarded
RPKM were calculated for protein coding gene using exon union model.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file of RPKM

source_name: Mouse embryonic fibroblasts

growth_protocol: Secondary MEFs were isolated and treated with doxycycline to induce reprogramming

extract_protocol:
mRNA was purified using Qiagen RNAeasy kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

treatment_protocol: Secondary MEFs were treated with doxycycline for 14, 21, 22, 23 or 27 days

tag: day of dox treatment

tag: days cultured without doxycycline

value: Mouse embryonic fibroblasts


title: feeder3

tag: cell type


title: SI4-d23

source_name: secondary reprogramming cells

value: secondary reprogramming cells


title: 48hr_H3K4me3_ChipSeq

source_name: Chromatin IP against 48hr_H3K4me3

growth_protocol: H1 cells were grown to confluence in mTESR1 media.  Cells were then differentiated for 48 hours in RPMI-B27 plus 50 ng/ml Activin

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Sample was divided into 6 aliquots after sonication.  Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: H1 embryonic stem cells

tag: chip antibody

tag: antibody catalog number

value: Millipore 07-473

tag: drug treatment

tag: drug concentration

tag: duration of treatment


title: feeder1


title: SI4-d22


title: Normalized Myc

value: anti-Myc (Santa Cruz sc-764)


title: SI4-d21


title: SI4-d14


title: SI3-d27


title: SI3-d21


title: SI3-d14


title: SI2-d27


title: SI2-d22


title: SI3-d23


title: SI2-d23


title: activatedB_AIDtg_53BP1ko_RPAip_Mbnuc

source_name: in vitro activated B cells

tag: chip antibody manufacturer

value: Calbiochem

tag: chip antibody catalog #

tag: chip antibody lot #

value: multiple lots

value: in vitro activated B cells

tag: strain

tag: genotype

value: RPA

tag: chip dna treatment

value: Mbnuc


title: SI1-d14


title: SI2-d14


title: SI1-d23


title: SI1-d21


title: SC4-d27


title: SC4-iPS

source_name: secondary iPS cells

value: secondary iPS cells


title: SI2-d21


title: SI4-d27


title: SI1-d27


title: SI3-d22


title: SC3-d27


title: SC4-d14


title: SC3-d23


title: SC4-d21


title: SC3-d22


title: SC4-d22


title: SC3-d21


title: SC3-d14


title: SC2-iPS


title: SC2-d27


title: SC1-d27


title: SC1-d23


title: SC4-d23


title: SC2-d21


title: SC1-d21


title: SC2-d14


title: SC2-d22


title: SC1-d22


title: SI1-d22


title: U87DK_DNaseSeq_rep2

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

institute: New York University

data_processing:
For DNase-Seq, the sequencing reads of 35 bp were aligned to the hg18 genome by Illumina's Eland extended software with maximum two mismatches in the first 25 bp.
The reads from two biological replicates of each cell line were first concatenated.
Regions more hyperensitive in U87DK than in U87H were detected by running the Model-based Analysis of ChIP-Seq (MACS version 1.4.0rc2) algorithm (http://liulab.dfci.harvard.edu/MACS/) with reads from U87DK as treatment and reads from U87H as control, with mfold parameter set to 10,30 and p-value cutoff of 1e-6.
Regions more hyperensitive in U87H than in U87DK were detected by running the Model-based Analysis of ChIP-Seq (MACS version 1.4.0rc2) algorithm (http://liulab.dfci.harvard.edu/MACS/) with reads from U87H as treatment and reads from U87DK as control, with mfold parameter set to 10,30 and p-value cutoff of 1e-6.
Subpeak summits were computed from the MACS peaks by the PeakSplitter program (http://www.ebi.ac.uk/bertone/software/PeakSplitter_usage.txt).
For ChIP-Seq, the sequencing reads of 36 bp were aligned to the hg18 genome by the short reads aligner bowtie version 0.12.5 suppressing all alignments for reads that align to more than one location (-m 1).
ChIP-Seq peak detection was performed by Model-based Analysis of ChIP-Seq (MACS version 1.4.0rc2) algorithm (http://liulab.dfci.harvard.edu/MACS/), with parameter mfold of 10,30, bandwidth of 150, and p value cutoff 1e-5.
Genome_build: hg18
Supplementary_files_format_and_content: BED file of subpeak summits of regions that are more hypersensitive in U87DK cells than in U87H cells
Supplementary_files_format_and_content: BED file of subpeak summits of regions that are more hypersensitive in U87H cells than in U87DK cells
Supplementary_files_format_and_content: MACS output BED file of p300 bound regions

source_name: U87MG cell line, kinase dead EGFRvIII

growth_protocol: Cell were cultured in DMEM supplemented with 10% fetal bovine serum, 100 units/mL penicillin,  100 mg/mL streptomycin, 4 mM L-glutamine and in a 95% air/5% carbon dioxide humidified atmosphere at 37 degree Celsius.  Expression of EGFRvIII and DK receptors were selected by 400 mg/mL G418.

extract_protocol: For each of the two biological replicates of each cell line, intact nuclei were extracted from 50 million cells by incubating with NP-40 detergent and then digested with DNaseI.  Sequencing libraries were prepared with the Illumina sample preparation kit, specifically selecting the 100 to 300 bp fragments by gel electrophoresis.  Each biological replicate was sequenced in one lane on a Genome Analyzer II sequencer (Illumina).

treatment_protocol: Cells were wahsed with PBS and grown in serum free media for 24 hours before harvesting.

tag: cell line

value: glioblastoma

tag: genotype/variation

value: kinase dead EGFRvIII


title: U87H_DNaseSeq_rep1

source_name: U87MG cell line, 2 million EGFRvIII

value: 2 million copies of EGFRvIII receptor per cell


title: U87DK_DNaseSeq_rep1


title: U87H_DNaseSeq_rep2


title: Primary goat mammary epithelial cell (pgMEC), sample 1, control Goat_1_control

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

data_processing: De-multiplexed fastq files (Qphred+64 quality values) were generated from the RTA output using the Genome Analyzer Pipeline Software (version 1.5, Illumina) allowing a single mismatch during demultiplexing. The Burrows-Wheeler Alligner (BWA, version 0.5.7) was used to map the obtained 50 bp sequences against the latest version (24.5.2010) of NCBI's Bos Taurus RefSeq sequence database (version 24.5.2010). Frequence tables were prepared from each mapped fastq file by summing the reads mapping to individual RefSeq accessions. An expression matrix was prepared by summing the frequences for each gene across replicated sequence runs within each of the 12 samples. Differential expression analysis of the mapped reads was performed in the R statistical environment (version 2.11.0) using the  Bioconductor package edgeR (version 1.6.5). A negative binomial model were fitted and dispersion estimates were obtained using the quantile-adjusted conditional maximum likelihood (qCML) method. This was followed by an estimation of the moderated tagwise dispersions using a value of the weight parameter prior.n. of 10. Differentially expressed genes between each of the time points (3, 12 and 24 hours post infection) and the controls were identified using the exact test. Genes with a p-value of less than 0.05 after adjusting for multiple testing using the Benjamini and Hochberg method for controlling the FDR, were considered significantly affected.

organism: Capra hircus

growth_protocol: Lactating Saanen goat (Capra hircus) was slaughtered and whole mammary gland was removed for processing. The mammary gland was rinsed with 70% ethanol, aseptically cut into larger pieces and washed in HBSS containing penicillin (200 µg/ml), streptomycin (200 µg/ml), and ampicilin (200 µg/ml). The tissue pieces were minced using surgical scissors and digested in 100 ml of collagenase and hyaluronidase solution (400 U/ml of each) prepared in HBSS with HEPES (4-(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid) also containing the above listed antibiotics in the same concentrations. Digestion was carried out at 37°C during gentle shaking. The digesta were collected after 60, 120 and 180 minutes and filtered through a steel mesh. The filtrates were put in a 50 ml tube and washed with HBSS followed by centrifuging at 300 x g for 5 minutes. After washing, the resuspended cells were filtered through a 40 µm mesh, centrifuged, and resuspended in growth medium or in 90 % FBS and 10 % DMSO for freezing in liquid nitrogen. Aliquots of cell suspensions were plated on Geltrex covered plastic flasks in growth medium RPMI-1640 supplemented with 0,1 mM L-methionine, 0,4 mM L-lysine, NaHCO3 (2g/L), 0.01mM Na-pyruvate, 2 mM glutamine, 10% fetal bovine serum (FBS), insulin (1 µg/ml), hydrocortisone (1 µg/ml), and prolactin (1 µg/ml), and incubated at 37°C with 5% CO2 and saturated humidity. The medium was changed every 2 days. Myoepithelial cells were removed by selective trypsinization using 0,05 % trypsin-EDTA. Primary goat mammary epithelial cell (pgMEC) culture was characterized using immunocytochemistry (ICC) and milk protein mRNA expression. For ICC pgMECs were seeded in 6-well plates on Geltrex coated coverslips. Attached cells were washed with cold phosphate buffered saline (PBS) and fixed in a mixture of cooled acetone and methanol (dilution 1:1) at - 20°C. Monoclonal antibodies against smooth muscle ?-actin (sc-58669), and cytokeratin 18 (sc-51582) were used to distinguish between myoepithelial-like and luminal cell types. The coverslips were covered with solution of primary antibodies (dilution 1:200) in PBS with BSA (3%) and incubated overnight at room temperature. For unspecific binding control the cells were incubated with PBS-BSA (3%) alone. Antibodies were visualized using secondary goat anti-mouse fluorescin isothyocyanate (FITC)-conjugated antibodies at dilution 1:500 in PBS-BSA (3%). Incubation was carried out in dark for 1 hour. Cells were observed under fluorescent microscope Nikon Eclipse TE, 2000. To confirm the luminal character and hormone responsivness of our pGMECs we designed primers against beta casein (CSN2), the most abundant milk protein in goats (CSN2-F: 5'-ACAGCCTCCCACAAAACATC-3', CSN2-R: 5'-AGGAAGGTGCAGCTTTTCAA-3'). OneStep reverese transcription polymerase chain reaction (RT-PCR) kit was used to detect potentially present CSN2 mRNA in the total DNAse treated RNA extract from postconfluent second passage pGMECs, grown on thin layer of Geltrex in lactogenic growth medium. The derived PCR fragments were extracted from agarose gel using gel extraction kit and sequenced (Macrogen Inc.).

extract_protocol: pgMEC cells were washed with HBSS followed by addition of 3 mL of Tri-Reagent (Ambion) for direct lysis. Total RNA was extracted from the samples using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and concentrations and purity were measured using NanoVue (GE Healtcare) spectrophotometer. Approximately 10 µg of total RNA from each of the 12 samples was used for indexed mRNA-Seq library construction by combining the protocol supplied with the mRNA-Seq Sample Prep Kit (Illumina, protocol version 1004898 Rev. D, September 2009) and the Multiplexing Sample Preparation Oliogonucleotide Kit. Briefly, poly-dA containing mRNA was purified selected using poly-dT oligonucleotide-attached magnetic beads and fragmented using divalent cations under elevated temperature. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. The short cDNA fragments were “end-repaired” using T4 DNA polymerase and Klenow DNA polymerase and single A bases were added to the cDNA fragments by using 3’ to 5’ exonuclease. This was followed by ligation of Illumina adaptors from the Multiplexing Sample Preparation Oliogonucleotide Kit and by gel purification of fragments of approximately 200 bp in size. The libraries were finally indexed (12-plexed) and enriched by PCR for 18 cycles using the primers from the Multiplexing Sample Preparation Oliogonucleotide Kit. The concentrations of the libraries were determined using a Qubit fluorometer (Invitrogen) and the size and purity were determined using an Agilent 2100 Bioanalyzer using Agilent DNA 1000 Kit. Equimolar amounts of each of the 12 libraries were pooled, diluted in buffer EB (Qiagen) to 10 nM, denaturated with 2 N NaOH to a final concentration of 1.0 nM, further diluted with pre-chilled hybridization buffer (Illumina) and loaded into lanes of single-read flow cells (v2, 1.4 mm). All 12 samples were hence loaded in each lane and a total of five lanes in three flow cells were used. A single lane of the Multiplexing PhiX Control library (Illumina) was included in each flow cell and was used to estimate phasing and matrix correction for all other lanes to compensate for the skewed base compositions in the lanes containing the mRNA-Seq libraries. Clustering were conducted on an Illumina Cluster Station followed by 51+7 cycle sequencing on an Illumina Genome Analyzer (version IIx, SCS2.5/RTA) using the Genomic DNA Sequencing Primer and the Index Seq Primer in combination with clustering and sequencing kits (SBS v3), all supplied by Illumina.

treatment_protocol: Challenging pgMECs with Mycoplasma agalactiae. First passage pgMECs cultured in antibiotic-free growth medium were grown on Geltrex coated flasks (75 cm2) almost to the confluent state (approx. 8-9 x 106 cells/flask). Pathogenic M. agalactiae (PG2 strain) was grown in LB broth with 10% serum until the exponential phase of growth (approx. 1010  mycoplasmas). The mycoplasmas were centrifuged, washed and finally resuspended in 10mL of pgMECs antibyotic-free growth medium. Cells were challenged with 900 µL (approx 9 x 108) of resuspended mycoplasmas, which is equivalent to multiplicity of infection of approximatelly 100, while 3 flasks were kept as uninfected controls. The infected pgMECs were incubated in triplicate for each time-point and collected 3, 12, and 24 h PI . The successfulness of the infection and purity of the controls was verified by PCR based detection of mycoplasma specific sequences, using universal 16S ribosomal primers (U4-F: 5’-GTAGTCCACGCCGTAACG-3’, U8-R: 5’-CACAGGAAACAGCTATGACC-3’) (Johansson et al., 1998).

tag: gender

value: female

tag: tissue

value: mammary gland

tag: aliquot #

tag: time

value: control


title: Primary goat mammary epithelial cell (pgMEC), sample 5, 3 hrs post-infection Goat_5_3h_PI

tag: cell type

value: 3 hours post infection

tag: infection

value: Mycoplasma agalactiae PG2 strain


title: Primary goat mammary epithelial cell (pgMEC), sample 12, 24 hrs post-infection Goat_12_24h_PI

value: 24 hours post infection


title: Primary goat mammary epithelial cell (pgMEC), sample 3, control Goat_3_control


title: Primary goat mammary epithelial cell (pgMEC), sample 4, 3 hrs post-infection Goat_4_3h_PI


title: bladder tissue from human s2, paracancerous

city: haikou

first: shufang

last: zhang

address: people avenue NO.43

institute: haikou people hospital

description: Sample 2

data_processing: We used TopHat 1.31 software to align the sequence reads to reference genome (hg19). Then we used the cufflink program of Cufflinks 1.0.3 to call the expression values (FPKM, Fragments Per Kilobase of exon model per Million mapped fragments) of mapped human genes and the cuffdiff program of Cufflinks 1.0.3 to detect differentially expressed genes and the differentially expressed isoforms.

source_name: bladder tissue, paracancerous

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit. The RNA extraction is Trizol.Briefly, 10 ug of each total RNA sample was used for polyA mRNA selection using streptavidin-coated magnetic beads, followed by thermal mRNA fragmentation. The fragmented mRNA was subjected to cDNA synthesis using reverse transcriptase (Super- Script II) and random primers. The cDNA was further converted into double stranded cDNA and, after an end repair process (Klenow fragment, T4 polynucleotide kinase and T4 polymerase) and 3-'A' add process (Klenow exo- fragment), was finally ligated to Illumina Truseq adaptors. Size selection was performed using a 2% agarose gel, generating cDNA libraries ranging in size 380 bp. Finally, the libraries were enriched using 15 cycles of PCR and purified by the QIAquick PCR purification kit (Qiagen). The enriched libraries were diluted with Elution Buffer to a final concentration of 10 nM. Each library was run at a concentration of 11 pM on one Genome Analyzer (GAIIx) lane using 115 bp sequencing. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: bladder

tag: disease state

value: paracancerous


title: Primary goat mammary epithelial cell (pgMEC), sample 8, 12 hrs post-infection Goat_8_12h_PI

value: 12 hours post infection


title: bladder tissue from human s3, cancerous

description: Sample 3

source_name: bladder tissue, cancerous

value: cancerous


title: Primary goat mammary epithelial cell (pgMEC), sample 2, control Goat_2_control


title: Primary goat mammary epithelial cell (pgMEC), sample 9, 12 hrs post-infection Goat_9_12h_PI


title: Primary goat mammary epithelial cell (pgMEC), sample 7, 12 hrs post-infection Goat_7_12h_PI


title: Primary goat mammary epithelial cell (pgMEC), sample 10, 24 hrs post-infection Goat_10_24h_PI


title: wt hypha Rep3

description: Sample 9

value: wild type

tag: morphological phase

value: yeast phase


title: SC2-d23

tag: day of dox treatment

tag: days cultured without doxycycline

value: secondary reprogramming cells


title: SC1-d14


title: WT RNA-seq

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: transcriptome profiling of WT (wild type)

data_processing:
ChIP-seq Data Analysis: ChIPed DNA was subjected to library preparation for Illumina GAII. In brief, Illumina single end genome sequencing adaptor was ligated with ChIPed DNA and then the fragments around 300bp was gel purified following by PCR to amplify the adapter-modified DNA fragments and sequence according to standard protocols (single end 36 cycles). The raw reads from Illumina GAII with a single-end reads of 36 nt in length were aligned to TIGR 6.1 genome using Bowtie (Langmead et al., 2009) allowing up to two mismatches. MASC program (Zhang et al., 2008) was used to shift the reads and convert the data to WIG format. Integrated Genome Browser (IGB) (Nicol et al., 2009) was employed to visualize the WIG file. ChIPDiff program (Xu et al., 2008) was used for quantitative comparison of H3K4me3 level in WT and jmj703. Region with more than 1.5 fold change were kept for downstream analysis. Reads with multiple location on genome were also used to avoid improper deletion of reads from transposon regions. The gene list in table S1 was finally manually checked to avoid false positive caused by the 1kb window size used in ChIPDiff program. RNA-seq Data Analysis: Rice genome sequences and annotated gene models were downloaded from TIGR6.1 (http://rice.plantbiology.msu.edu/). The single end reads were aligned to genome sequences using TopHat (Trapnell et al., 2009) allowing up to two mismatches. Splice junction sequences required at least four bases on each side of the junction. Reads mapped to multiple locations as well as only uniquely mapped reads were used and compared with each other to avoid the improper deletion of reads for subsequent analysis. The gene expression levels were measured in reads per kilobase of exon model per million mapped reads (RPKM), which indicated that the total exons of a gene were detected when they met the criterion of more than 3 RPKM (Mortazavi et al., 2008). The differential expressed genes were identified using DEGseq (Wang et al., 2010). Genes with more than 1.5 fold change and p-value < 0.01 were regarded as differential expressed genes.
Genome_build: Orazy TIGR6.1
Supplementary_files_format_and_content: wig files were generated using MACS program

organism: Oryza sativa

source_name: 7DAG seedlings

growth_protocol: Rice plants used in the study were Orazy sativa spp japonica cv Dongjin. All the transgenic plants were regenerated from transformed calli. Plants used for phenotypic investigation were grown in the field until maturity and the ones used for ChIP-sequencing and RNA-sequencing analysis were 7DAG seedlings cultivated in the incubator with 9 h 30 min of light at 27 °C and followed by 14 h 30 min of dark at 23° C. The relative humidity of the incubator was kept at 85%.

extract_protocol:
Total RNAs were extracted from 7DAG seedlings leaves of wild type and jmj703 same to the samples used in ChIP-seq analysis with TRIzol Reagent (15596–026; Invitrogen).
ChIP was performed as previously described with minor modification (58). Briefly, 1 g leaves of 7DAG seedling grown on long day condition were fixed with formaldehyde followed by immunoprecipitation with anti-H3K4me3 (Millipore 07-473) and anti-H3 (Abcam ab1791) antibodies. After de-crosslink and proteinase K and RNase treatment, the immunoprecipitated DNA was purified by phenol/chloroform for the further experiment including Illumina single end sequencing or quantitative PCR. Total RNAs were extracted from 7DAG seedlings leaves of wild type and jmj703 same to the samples used in ChIP-seq analysis with TRIzol Reagent (15596–026; Invitrogen). Polyadenylated RNAs were isolated using Dynabeads® mRNA Purification Kit (Invitrogen). The RNA-Seq libraries were prepared using Illumina Directional mRNA-Seq Library Prep. v1.0 protocol and sequenced on Illumina GAII to generate high-quality single-end reads of 80 nt in length.

tag: cultivar

value: Dongjin

value: WT

tag: age

value: 7DAG seedlings

value: seedling


title: jmj703 RNA-seq

description: transcriptome profiling of jmj703 (mutant)


title: U87H_p300_ChipSeq

extract_protocol: For each biological replicate, 50 million cells were cross-linked in 1% formaldehyde for 10 minutes and lysed.  Sonication was performed on a Bioruptor NextGen sonication system (Diagenode) with 10 cycles of 30 sec on, 30 sec off at high power setting.  p300 ChIP was done on the SX-8G IPStar Automated System (Diagenode) with buffers from the Auto Transcription ChIP kit (Diagenode) following instruction manual version V1_07-10-10.  The pre-set IP protocol "ChIP 22hr IPure16 200vol" was used with 5 hours of antibody coating and 16 hours of ChIP reaction at 4 degree Celsius.  3µg of the Santa Cruz antibody sc-585x Lot#E2610 was used on 25 µL of the sonicated chromatin diluted with 75 µL of ChIP Buffer T.  The ChIP products were reverse crosslinked at 65 °C for 6 hours with occasional vortexing.  ChIP DNA was purified by reagents in the Auto IPure kit (Diagenode) but done manually following the IPure kit (Diagenode) instruction manual version V2_12-05-10.  Sequencing library was prepared from the purified DNA by the SPRI-te Nucleic Acid extractor (Beckman Coulter) with SPRIworks Fragment Library System I cartridges according to manufacturer's protocol.  Enrichment was done with 2x Phusion Master Mix, PE PCR primer 1.0 (Illumina) and a barcoded paired-end PCR primer 2.0.  Each biological replicate was sequenced in one paired-end (PE) lane on Illumina Genome Analyzer II.

value: glioblastoma

value: 2 million copies of EGFRvIII receptor per cell


title: Primary goat mammary epithelial cell (pgMEC), sample 6, 3 hrs post-infection Goat_6_3h_PI

value: female

value: mammary gland


title: jmj703 H3K4me3 ChIP-seq

description: high-throughput profiling of H3K4me3 in jmj703 (mutant)

tag: chip antibody manufactuer

value: Millipore

tag: chip antibody catalog #

tag: chip antibody


title: Primary goat mammary epithelial cell (pgMEC), sample 11, 24 hrs post-infection Goat_11_24h_PI

value: 24 hours post infection

value: Mycoplasma agalactiae PG2 strain


title: HUVEC H3K27Ac DMSO 24hr normoxia

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

description: Chromatin IP against H3K27Ac. The ChIP antibody used in this experiment was generated and kindly provided by Dr. Kimura (Cell Struct Funct. <http://www.ncbi.nlm.nih.gov/pubmed/18227620#> 2008;33(1):61-73. Epub 2008 Jan 28.)

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) and alignment files (.bed) were generated using QuEST 2.4 with the following parameters.
positive_region_size               :  1000
KDE_bandwidth                      :  100
ChIP_seeding_fold_enrchment        :  30
ChIP_extension_fold_enrichment     :  3
ChIP_to_background_fold_enrichment :  3
Genome_build: hg18

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were cultured in EGM2MV medium (Lonza).  HUVECs were used within the first 6 passages.

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

treatment_protocol: 3x10^6 HUVEC cells were plated in 15cm2 culture plate, and cultivated for 3 days.  HUVECs were treated with or without hypoxia (1%O2) for 24hours.  Normoxia was used as a control condition.

value: Human umbilical vein cells

tag: passage

value: within 6 passage

tag: treatment

value: normoxia 24h


title: HUVEC_p65_TNF30min_ChIP seq

description: Chromatin IP against p65

data_processing:
HUVEC_p65_TNF30min.wig; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) were generated using QuEST 2.4 with the following parameters.
For Pol II - positive_region_size: 600,  KDE_bandwidth: 60, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment:  3
For p65 - positive_region_size: 300, KDE_bandwidth:  30, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment: 3

source_name: HUVEC_p65_10 ng/ml_TNF_30min

treatment_protocol: 3x10^6 HUVEC cells were plated in 15cm2 culture plate, and cultivated for 3 days. Cells were starved before stimulation longer than 16 hours. HUVECs were treated with or without 10 ng/ml of TNF alpha for 30 mins.

value: Human umbilical vein endothelial cells

tag: chip antibody vendor

value: abcam

tag: chip antibody cat#


title: bladder tissue from human s1, normal

description: Sample 1

source_name: bladder tissue, normal

tag: tissue

value: bladder

value: normal


title: HUVEC_PolII_TNF30min_ChIP seq

description: Chromatin IP against PolII

data_processing:
HUVEC_PolII_TNF30min.wig; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) were generated using QuEST 2.4 with the following parameters.
For Pol II - positive_region_size: 600,  KDE_bandwidth: 60, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment:  3
For p65 - positive_region_size: 300, KDE_bandwidth:  30, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment: 3

source_name: HUVEC_PolII_10 ng/ml_TNF_30min

value: PolII (S2, S5 in CTD were both phosphorylated)


title: HUVEC_p65_TNF00min_ChIP seq

description: Chromatin IP against p65

data_processing:
HUVEC_p65_TNF00min.wig; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) were generated using QuEST 2.4 with the following parameters.
For Pol II - positive_region_size: 600,  KDE_bandwidth: 60, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment:  3
For p65 - positive_region_size: 300, KDE_bandwidth:  30, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment: 3


title: HUVEC H3K27Ac DMSO 24hr hypoxia

value: hypoxia 24h


title: HUVEC_PolII_TNF00min_ChIP seq

description: Chromatin IP against PolII

data_processing:
HUVEC_PolII_TNF00min.wig; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) were generated using QuEST 2.4 with the following parameters.
For Pol II - positive_region_size: 600,  KDE_bandwidth: 60, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment:  3
For p65 - positive_region_size: 300, KDE_bandwidth:  30, ChIP_seeding_fold_enrchment: 30, ChIP_extension_fold_enrichment: 3, ChIP_to_background_fold_enrichment: 3


title: VACV dsGFP control

city: Philadelphia

first: Sara

last: Cherry

address: 304K Lynch Labs

institute: University of Pennsylvania

description: VACV dsGFP control

data_processing:
Sequence information was extracted from the image files with the Illumina base calling software package (GAPipeline version 1.4).
Prior to alignment of the smRNA reads, ‘‘vectorstrip’’ in the EMBOSS package was used to identify the first eight bases of the 3’ adaptor sequence, and the sequencing read was truncated up to the junction with the adaptor sequence. No further analysis was performed on reads that did not contain adaptor sequence, as those reads lacking an adaptor cannot be precisely sized.
The smRNA reads were reduced to a list of only non-redundant (NR) sequences to minimize the computational requirement in all following procedures. It is of note that the number of times each smRNA was sequenced is maintained during this reduction step.
The NR smRNA reads with perfect matches of length 15 – 29 nt were aligned and parsed using in-house Perl scripts to obtain the genomic location of smRNAs on the viral genome
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files; contain the small RNA ID, viral genome, strand of viral genome the small RNA maps to, start and end position of small RNA relative to viral genome, number of mismatches, and number of independent reads that were cloned of that sequence

organism: Drosophila melanogaster

source_name: DL1 cells

growth_protocol: Drosophila DL1 cells were grown and maintained at 25°C in Schneider’s Drosophila media (Gibco) supplemented with FBS, pen/strep and L-glut. Cells were split every 3-4 days.

extract_protocol:
Cells were resuspended and pelleted, then total RNA was extracted from the pellet using Trizol reagent (Invitrogen).
40 ug of total RNA was separated on a 15% TBE-urea gel and small RNAs ~15-29 nt were excised and eluted. Following ethanol precipitation, small RNA-seq libraries were produced using the Small RNA Sample Prep v1.5 kit (Illumina, San Diego, CA) as per manufacturer’s instructions.

treatment_protocol: To knock down factors of interest, cells were passaged in serum-free media containing dsRNA, and complete media was added after 1 hour of bathing. After three days of knockdown, cells were infected with the indicated virus by adding the virus inoculum directly to the medium. Infection was allowed to proceed for 4 days.

tag: cell line

tag: dsrna treatment (knockdown)

value: GFP dsRNA

tag: virus infection

value: Vaccinia virus


title: uninfected dsDCV

description: uninfected dsDCV

value: DCV capsid dsRNA


title: DCV dsAgo1

description: DCV dsAgo1

value: Argonaute 1 dsRNA

value: Drosophila C virus


title: RVFV dsDrosha

description: RVFV dsDrosha

value: Drosha dsRNA

value: Rift Valley Fever Virus


title: DCV dsDcr-2

description: DCV dsDcr-2

value: Dicer-2 dsRNA


title: DCV dsBgal control

description: DCV dsBgal control

value: Bgal dsRNA


title: VACV dsAgo2

description: VACV dsAgo2

value: Argonaute 2 dsRNA


title: VACV dsAgo1

description: VACV dsAgo1


title: RVFV dsAgo2

description: RVFV dsAgo2


title: RVFV dsAgo1

description: RVFV dsAgo1


title: H3K27Ac NS ChIP seq

description: Chromatin IP against H3K27ac

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (UCSC human genome hg18, March, 2006) genomes using the Illumina Genome Analyzer Pipeline (ELAND). All reads mapping with two or fewer mismatches were retained.
Peak files (.wig) and alignment files (.bed) were generated using QuEST 2.4 with the following parameters.
For MEF2C
positive_region_size               :  300
KDE_bandwidth                      :  30
ChIP_seeding_fold_enrchment        :  30
ChIP_extension_fold_enrichment     :  3
ChIP_to_background_fold_enrichment :  3
For H3K27Ac
positive_region_size               :  1000
KDE_bandwidth                      :  100
ChIP_seeding_fold_enrchment        :  30
ChIP_extension_fold_enrichment     :  3
ChIP_to_background_fold_enrichment :  3

treatment_protocol: 3x10^6 HUVEC cells were plated in 15cm2 culture plate, and cultivated for 3 days. For MEF2C study, cells were stimulated with pitavastatin at a concentration of 1 micro M for 4 hours, and same concentration of DMSO was used as a control sample.  For H3K27ac study, cells were harvested without stimulation.

tag: cell type

value: Human umbilical vein cells

value: within 6 passage


title: VSV dsAgo2

description: VSV dsAgo2

value: Vesicular Stomatitis Virus


title: WT H3K4me3 ChIP-seq

description: high-throughput profiling of H3K4me3 in WT (wild type)

value: Millipore

value: Dongjin

tag: genotype

value: WT

value: 7DAG seedlings

value: seedling


title: VACV dsDrosha

description: VACV dsDrosha

value: Vaccinia virus


title: RVFV dsDcr-2

description: RVFV dsDcr-2


title: VACV dsDcr-1

description: VACV dsDcr-1

value: Dicer-1 dsRNA


title: RVFV dsDcr-1

description: RVFV dsDcr-1


title: VACV dsDcr-2

description: VACV dsDcr-2


title: VSV dsAgo1

description: VSV dsAgo1

value: Argonaute 1 dsRNA


title: VSV dsDrosha

description: VSV dsDrosha


title: VSV dsDcr-1

description: VSV dsDcr-1


title: VSV dsDcr-2

description: VSV dsDcr-2


title: MEF2C statin ChIP seq

description: Chromatin IP against MEF2C

value: statin for 4 hr


title: MEF2C control ChIP seq

description: Chromatin IP against MEF2C

value: DMSO for 4 hr


title: VSV dsBgal control

description: VSV dsBgal control


title: DCV dsAgo2

description: DCV dsAgo2

value: Drosophila C virus


title: N-input

city: LA

first: jueng soo

last: You

state: CA

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
AGTCAA_KEL656A63_peaks.bed: hg19

source_name: embryonic carcinoma NCCIT

growth_protocol: NCCIT cells were routinely subcultured using opimal media

extract_protocol: Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: We transfected the exogenous SNF5 for overexpression and harvest the cells at post 72 hrs transfection.

value: pluripotent cells

tag: ChIP

value: none, control, input


title: DCV dsDcr-1

description: DCV dsDcr-1


title: DCV dsDrosha

description: DCV dsDrosha

value: Drosha dsRNA


title: RVFV dsBgal control

description: RVFV dsBgal control

value: Bgal dsRNA

value: Rift Valley Fever Virus


title: SNF5overexpression-OCT4 ChIP seq

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
CCGTCC_KEL656A75_peaks.bed: hg19

value: SNF5 overexpressed cells

tag: antibody catalog#

tag: antibody vendor

value: Abcam


title: SNF5overexpression-SNF5 ChIP seq

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
AGTTCC_KEL656A73_peaks.bed: hg19


title: N-OCT4 ChIP seq

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
s_3_AGTTCC_N-OCT4_1e-3_peaks.bed: hg19


title: N-SNF5 ChIP seq

data_processing:
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
Genome Build:
s_3_GTGGCC_N-SNF5_1e-3_peaks.bed: hg19


title: Input

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequencing and alignment: Sequencing was done by the Functional Genomics Core at the University of Pennsylvania. Sequence reads were processed and mapped to the mouse genome (mm8) using ELAND pipeline. Before subsequent analysis, redundant reads in each genomic position were condenced into one to avoid possible PCR bias or each sample.
Peak Calling: Then two WT samples (WT and GFP) were pooled into one as single WT sample. Peak calling was performed by Homer with default parameters then 1rpm cut-off was applied, where maximum two reads were counted in WT samples due to the pooling, and one read were considered in NS-DADm sample.
Genome_build: mm8
Supplementary_files_format_and_content: Peak calling results for WT and NS-DADm samples in bed format.

source_name: Liver tissue

growth_protocol: 10-12 week old male C57Bl/6 mice has been housed in regular 12h light/12h dark cycles on normal chow.

extract_protocol:
Liver samples were cross-linked with 1% formaldehyde, and used for ChIP with specififed antibody(ies).
Nuclei were lysed and sonicated. Protein-DNA complexes were isolated from lysates using antibodies, and DNA were extracted. For each condition, ChIP was performed on lysates from 4-5 different mice, and ChIPed DNA or input DNA samples were pooled for sequencing.

treatment_protocol: Mice were euthanized and livers were removed at ZT10, 5pm.

tag: strain

value: Liver

tag: time

value: none (Input)


title: HDAC3 NS-DADm

value: HDAC3 (Abcam, catalog# 7030)


title: LK2(GS/GS)-ipsNSC(p15)

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

country: Switzerland

institute: Uiversity Hospital Zurich

data_processing: Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline. Reads were mapped to human hg18 with Bowtie. Unique monoclonal reads were selected and reported as bed files. Read densities across the genome were obtained using BEDtools and bigWig were created for genome browser display.

source_name: iPSC-derived NSCs bearing homozygous LRRK2(G2019S) mutation at passage 15

growth_protocol: iPSCs were cultured in mTeSR medium, and NSCs were maintained in NSMM

treatment_protocol: iPSCs were obtained by reprogramming of patient fibroblasts, and NSCs were differentiated from iPSCs

value: NSCs


title: HDAC3 WT (pooled)

description:
Two WT samples (HDAC3 WT and HDAC3 GFP) were pooled into one as single WT sample.
The 'HDAC3 GFP' sample is prepared from HDAC3f/f AAV-GFP liver, which serves as a control for HDAC3 KO


title: LK2(+/+)-iPSC

source_name: wild-type iPSCs

value: iPSCs


title: RYBP_ChIPSeq

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

description: Chromatin IP against RYBP

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.3.7.1 (for Suz12 and Ring1B and and IgG_old as control) 40 bp and 1.4.1 (for Cbx7, RYBP and IgG as control)
Genome_build: mm9
Supplementary_files_format_and_content: excel file containing peak coordinates

source_name: Embryonic stem cells (E14)

growth_protocol: Wild-type (E14Tg2A) ES cells were cultured feeder-free in plates coated with 0.1% of gelatin in Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).

extract_protocol:
ESCs were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 0.125 M glycine for 5 min. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 14 min in a Bioruptor. ChIP-Seq experiments were performed as previously described (Morey et al, Cell Stem Cell. 2012, 10: 47-62)
It was performed using the NEBNext DNA Sample Prep Reagents Set 1

tag: antibody

value: Millipore, #3637

value: Embryonic stem cells (E14)


title: IgG_old_ChIPSeq

description: Chromatin IP against IgG

value: Rabbit IgG- ab37415


title: LK2(+/+)-ipsNSC(p15)

source_name: wild-type iPSC-derived NSCs at passage 15


title: LK2(+/+)-ipsNSC(p10)

source_name: wild-type iPSC-derived NSCs at passage 10


title: LK2(GS/GS)-ipsNSC(p10)

source_name: iPSC-derived NSCs bearing homozygous LRRK2(G2019S) mutation at passage 10


title: IgG_ChIPSeq_2

description: Chromatin IP against IgG

tag: originally submitted as


title: LK2(GS/GS)-iPSC

source_name: iPSCs bearing homozygous LRRK2(G2019S) mutation


title: H23_N31_Oct4_EGFP_anti-K4m2_0hr

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

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

institute: CyberomiX Inc

data_processing:
Basecalls performed using CASAVA version 1.8.1
Data were filtered using Illumina's Quality Filtering and 76th bases in reads were not used.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.6.2 with default parameters.
Peaks were detected using MACS version 1.4.2 with default parameter and without control samples.
Genome_build: mm9
Supplementary_files_format_and_content: Text files which contain peak information were generated using MACS version 1.4.2.

source_name: Neural progenitor like cells

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to New England Biolabs's instructions accompanying the NEBNext ChIP-seq Library Prep Reagent. Briefly, 10 ng of DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated by Caliper XT(Perkinelmer). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 107 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixed cells were lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche, 04693159001), centrifuged at 950g for 10 min and re-suspended in 0.2% SDS, 10 mM EDTA, 140 mM NaCl and 10 mM Tris-HCl. Cells were then fragmented with a Covaris Sonicater (model E210) at 8 °C to a size range between 200–500 bp, and precipitated by centrifugation.

value: ES-derived neural progenitor like cells

tag: passages

tag: chip antibody

value: Histone H3 dimethyl Lys4 antibody (ACTIVE MOTIF, 39141)


title: H38_NS-F-Etv6

value: Monoclonal ANTI-FLAG M2, Clone M2 (SIGMA, F1804)


title: Cbx7_ChIPSeq

description: Chromatin IP against Cbx7

value: Abcam, ab21873


title: Suz12_ChIPSeq_2

description: Chromatin IP against Suz12

value: Abcam, ab12073


title: H36_NS-F-Pax6


title: H32_N31_EGFP_OK_flag_2


title: 521_RNA-polII_CHIP-seq

city: ILLKIRCH Cedex

first: Stephanie

last: Le Gras

address: 1, rue Laurent Fries

country: France

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: liver

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: Total liver from the indicated mouse genetic backgrounds was homogenized by douncing in buffer with 25mM Hepes pH=7,8, 1,5mM MgCL2, 10mM KCl, and 0,1% NP40. Nuclei were purified by centrifugation (4000 rpm, 5 min) and resuspended in fixation buffer (PBS1X, PIC PMSF and DTT, 1% PFA) and incubated 15 min at RT. Cold glycine was added to stop the reaction and nuclei were subsequently washed twice in PBS1X followed by centrifugation (4000 rpm, 5min). Nuclei were incubated 10min at 4°C in lysis buffer (EDTA 10mM, Tris HCl pH=8,0 50mM, SDS 1% +PIC +PMSF) and sonicated to average fragment size of 200-1000 nt. ChIP experiments were performed as previously described (Choukrallah et al., 2011).

value: Trim24-/- mouse

tag: age

value: 5 Week old

value: Pol II :Santa-Cruz (Sc9001)


title: 521_H3K4Me3_CHIP-seq

value: H3K4me3 :Millipore (04-745)


title: Primary keratinocytes sample 2

description:
3SEQ
Primary keratinocytes isolated from back skin of neonatal mice.

data_processing:
Reads alignment by Bowtie, allowing maximum 2 mismatches and only unique mapping.
Peak calling by MACS, and PeakSplitter.
Assign peaks to genes using RefSeq and Ensembl annotation (Apr 9th download).
Filtering internal primed peaks by motif combination.
Determine polyadenylation signal for each filtered peak.
Genome_build: mm9
Supplementary_files_format_and_content: BED files; for content details, see the README.txt file that is linked to the Series record as a supplementary file.

source_name: Low passage in vitro cultured primary keratinocytes

growth_protocol: in vitro cultured primary keratinocytes are cultured in low-calcium medium (0.05mM).

extract_protocol: E14 mouse embryos are dissected from the uterus, and epidermis is carefully isolated under the dissection microscope. E14 epidermal basal and suprabasal cell populations are FACS isolated. Total RNA is extracted and polyA purified and fragmented. An anchored oligo(dT) probe is used to capture polyadenylated RNA fragments, followed by first strand synthesis. Second-strand DNA is synthesized using the RNase H-based method. The double strand DNA library is further constructed using the Illumina standard protocol.

value: neonatal

value: primary keratinocytes isolated from back skin

tag: passage


title: 8_KO_RNA-seq

data_processing:
Both libraries (WT and KO) were sequenced twice. Illumina Casava v1.7 (1st sequencing) and v1.8 (2nd sequencing) software were used for basecalling.
Sequence reads mapped to reference genome mm9/NCBI37 using Tophat (Trapnell et al., 2009) v1.0.12 (1st sequencing) and v1.4.1 (2nd sequencing).
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using the Wiggles program supplied by Tophat.

extract_protocol: Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.

treatment_protocol: Total RNA was extracted from liver tissue samples by Trizol reagent (Invitrogen) using manufacturer’s instructions. Further purification of the RNA was achieved by RNase-free DNase (Roche) treatment (10U for 20 μg RNA). 1,5 μg of RNA was reverse transcribed using a mix 1/1 of SuperScript II RNase H-reverse transcriptase (Invitrogen) and AMV retrotranscriptase (Roche) with 500 ng of oligodT22 primer, hexanucleotides or specific primers according to the manufacter’s instructions.

tag: tissue

value: liver

value: 5 week old


title: 511_H3K4Me3_CHIP-seq

value: Wild-type 129/SV mouse


title: Ring1B_ChIPSeq

description: Chromatin IP against Ring1B

value: Ab generated in Di Croce´s lab


title: 483_wt_RNA-seq

value: Wild-type


title: P4 hair follicle 3Seq

source_name: Hair follicle cells

value: postnatal day 4

value: hair follicle


title: Primary keratinocytes sample 1


title: E14 suprabasal 3Seq

description:
3SEQ
FACS setting: K14h2BGFP low, Itga-PE staining low.

source_name: Epidermal progenitor cells

value: embryonic day 14

value: epidermis, suprabasal cells


title: E14 basal 3Seq

description:
3SEQ
FACS setting: K14h2BGFP high, Itga-PE staining high.

value: epidermis, basal cells


title: Input_CT6_ChIPSeq

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

description: Chromatin IP against Input

data_processing: Raw paired-end 50bp reads (in FASTQ format) were aligned to the UCSC mm9 genome build with Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) using pre-built indexes downloaded from the host website. Parameters were optimised to utilise the software’s multi-threading capabilities (we typically used a 128-core cluster for alignments). Alignment files were then converted from the standard Bowtie output format to ALN files (for use with Cisgenome) using a custom Perl script. Alignments were then analysed using a 2-sample comparison (ChIPed sample vs. Input control for each time-point) with Cisgenome v1, using a cut-off false discovery rate of 10% and a sliding window size of 100. Output files were converted into various formats for browsing datasets and to display data. The Cisgenome and UCSC browsers were used for data visualisation, using custom tracks

extract_protocol: Chromatin was sheared using a Diagenode Bioruptor at 4oC, using conditions optimised to produce 150-300bp fragments with the use of 15 ml Falcon tubes holding 2ml of lysate each (30 cycles of 30 secs on HIGH, 30 secs OFF). Sheared chromatin was transferred to 1.5 ml microcentrifuge tubes and spun at 14,000 rpm for 15 min at 4°C to pellet debris. Cleared supernatants were transferred to clean microcentrifuge tubes and 100 µl from each sample lysate was saved for use as an input control for sequencing and to check fragment size distribution. standard Illumina indexing primers were used, as per the manufacturer’s instructions. All libraries were multiplexed, and 4 indexed pooled samples (corresponding to four time-points, CT0, 6, 12, 18) sequenced per lane.

value: Liver

tag: time point


title: Input_CT12_ChIPSeq

description: Chromatin IP against Input


title: Input_CT18_ChIPSeq

description: Chromatin IP against Input


title: Input_CT0_ChIPSeq

description: Chromatin IP against Input