title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in hESC H9 Cells; renlab.H2BK12ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK12ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK30
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6011
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM667610_UCSD.H9.H2BK12ac.AK30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the H9 Cell Line, Library AK30 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6298
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0943
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1857
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM667610_UCSD.H9.H2BK12ac.AK30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the H9 Cell Line, Library AK30 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6640
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 H2BK12ac 30
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK12ac Library AK30 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0943
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1857
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK12ac.hESC.H9.01.01

tag: passage

tag: medium

value: Histone H2BK12ac

value: magnetic anti-rabbit


title: BC

status: Public on Mar 22 2011

type: SRA

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

country: China

institute: Zhejiang University

description: transfer to healthy tabocco plants as an control

library_source: transcriptomic

data_processing: The adapter-ligated tags are fixed on the Solexa Sequencing Chip to form single-molecule cluster, and then sequencing by synthesis is performed to generate millions of raw data with sequencing length of 35bp. Raw sequences were transformed into clean tags through removing adaptor sequence, low quality sequences. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to TPM.

molecule: total RNA

organism: Bemisia tabaci

source_name: Whitefly female adult

growth_protocol: Culture of B biotype whitefly was maintained on cotton plants.

extract_protocol: 1. mRNA is captured using the magnetic oligo(dT) beads from the extracted total RNA and first- and second-strand cDNA is synthesized. 2. Bead-bound cDNA is subsequently digested with restriction enzyme NlaIII (recognition sequence CATG). 3. The fragments apart from the 3’cDNA fragments connected to oligo(dT) beads are washed away and a special adapter containing a restriction site for MmeI is ligated to the sticky 5’end of the digested bead-bound cDNA fragments. 4. The MmeI cuts 17 bp downstream from the recognition site, then product the 21 bp tag starting with the recognition site of restriction enzyme NlaIII (CATG). 5. A second adapter is ligated at the site of MmeI cleavage. After enriched by polymerase chain reaction (PCR) amplification, the adapter-ligated tags are purified by 6% tris borate (TBE) buffer, polyacrylamide gel electrophoresis (PAGE).

treatment_protocol: Three thousands of newly emerged adults of whitefly on cotton were released onto the leaves of healthy and viruliferous tobacco plants. They were allowed to feed for 24 h. After that, non-viruliferous and viruliferous whiteflies were transferred respectively to cotton plants in different cages and allowed to feed for 120 h. Then approximately 1,000 non-viruliferous and viruliferous female adults of whitefly were collected, respectively.

tag: biotype

value: B biotype

tag: growth condition

value: maintained on cotton

tag: agent

value: no TYLCCNV


title: GR ChIP-seq 4 hours

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: GR ChIP-seq 4 hours

library_source: genomic

data_processing:
processed data file build: mm9
Bed: Areas of enrichment were identified using a newly developed hotspot algorithm.
Bedgraph: Tag density profiles were generated by the newly developed hotspot algorithm.

molecule: genomic DNA

organism: Mus musculus

source_name: Preadipocyte cell line

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum.

extract_protocol: ChIP-seq: Chromatin from various time points of 3T3-L1 differentiation was subjected to ChIP using different antibodies. Purified DNA was prepared for sequencing according to the manufacturer (Illumina). DHS-seq: Nuclei were isolated at various time points of 3T3-L1 differentiation and subjected to a limited DNase I digestion. Small DNA fragments where DNase I cut twice were isolated and prepared for sequencing according to the manufacturer (Illumina).

treatment_protocol: Two days post confluency (day 0), 3T3-L1 cells were  induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were  maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation.

tag: cell line

value: 3T3-L1 preadipocyte cell line

tag: differentiation stage

value: Early stage

tag: time

value: 4 hours

tag: chip antibody

value: GR


title: C/EBPdelta ChIP-seq 4 hours

description: C/EBPdelta ChIP-seq 4 hours

value: C/EBPdelta


title: C/EBPbeta ChIP-seq day 2

description: C/EBPbeta ChIP-seq day 2

value: Intermediate stage

value: day 2

value: C/EBPbeta


title: C/EBPbeta ChIP-seq 2 hours

description: C/EBPbeta ChIP-seq 2 hours

value: 2 hours


title: DHS-seq 4 hours

description: DHS-seq 4 hours

tag: dnase treatment

value: DNase I treated


title: DHS-seq day 6

description: DHS-seq day 6

value: Mature adipocyte

value: day 6


title: DHS-seq day 1

description: DHS-seq day 1

value: day 1


title: DHS-seq 2 hours

description: DHS-seq 2 hours


title: DHS-seq day 0

description: DHS-seq day 0

value: Preadipocyte

value: day 0


title: DHS-seq day 2

description: DHS-seq day 2


title: C/EBPbeta ChIP-seq 4 hours

description: C/EBPbeta ChIP-seq 4 hours


title: layer_reads

status: Public on Mar 18 2011

city: Beijing

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

description: short RNA

data_processing:
0. Run Solexa pipeline
Data were deposited in *.fastq files (.fq format)

1. Filter low quality reads and trimming adaptors
Data were deposited in *_clean_reads_16-30.txt files
File format: one line for one read, delimited by tab.
Column1 is the raw read.
Column2 is the corresponding quality.
Column3 is the length of read after trimming adaptor.
Column4 is the number of error base localizing in trimmed adaptor.
Column5 is the read after trimming adapter

4. Group all identical sequence reads together
Data were deposited in all_nr.fas (.fasta format)
For each id:
eg. >nr1 26(bp) L:1 B:0
>id reads-length L:reads-number-in-layer B:reads-number-in-broiler

5. Map reads to the UCSC chicken genome galGal3 by ZOOM with perfect match.
Data were deposited in all_nr_ZOOM_mm0.bed (BED format)
Column1 is the chromosome.
Column2 is the start position.
Column3 is the end position.
Column4 is the name. eg. nr136536_L0_B1  id_L(reads number in layer)_B(reads number in broiler)
Column5 is the reads length.
Column6 is the strand.

organism: Gallus gallus

source_name: layer skeletal muscle at embryonic 10 days

growth_protocol: Meat-type broiler eggs (commercial Arbor Acres) and egg-type layer eggs (White Leghorn) were incubated at 37.5°C for 10 days (E10).

extract_protocol: Total RNA was isolated from skeletal muscles using the Trizol reagent (Invitrogen) and precipitated overnight at -20°C. Approximately 20 μg of Total RNA from broiler and layer chickens were submitted to Beijing Genomics Institute (BGI) for Solexa sequencing. In brief, the sequencing was performed as follows: total RNA was fractionated by polyacrylamide gel electrophoresis (PAGE), to enrich for molecules in the range of 16-30 nt, and ligated with proprietary adapters. Following adaptor ligation, the RNA was reverse transcribed for cDNA synthesis. The cDNA was amplified with 15 PCR cycles to produce sequencing libraries that were subjected to sequencing.

treatment_protocol: skeletal muscles (pectoralis) were collected from broilers and layers at E10 stage, immediately frozen in liquid nitrogen, and stored at -80°C until RNA isolation.

tag: breed

value: White Leghorn


title: broiler_reads

description: short RNA

source_name: broiler skeletal muscle at embryonic 10 days

value: commercial Arbor Acres


title: Envirnomental contaminated aquifer sample enriched for DNA Stable Isotope Probing 1

city: Neuherberg

first: Giovanni

last: Pilloni

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz-Centre Munich

description: small rRNA were amplified from total nucleic acids extracted from environmental samples using specific PCR primers

data_processing:
Trimming was performed with the "Trim" function of Greengenes web site, with the parameters: good quality score 20, window size 40 bp, window threshold 90%. Shorter reads (<250 bp) were excluded.
quality and length trimmed fasta

molecule: other

organism: unidentified

source_name: Fresh Aquifer Sediment

extract_protocol: Nucleic acids extracted with a bead beating-phenol/chloroform protocol from sediment samples were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. Amplicons were purified and pooled as specified by the manufacturer. Emulsion PCR (emPCR), purification of DNA-enriched beads and sequencing run were performed following protocols and using a 2nd generation pyrosequencer (454 GS FLX Titanium, Roche) as recommended by the developer. Quality filtering of the pyrosequencing reads was performed using the automatic amplicon pipeline of the GS Run Processor (Roche), with a slight modification concerning the valley filter (vfScanAllFlows false instead of TiOnly) to extract the sequences. Demultiplexed raw reads from 2 runs were furhter trimmed for quality and lenght (>250 bp).

tag: electron donor

value: Fully 13C-lebelled toluene

tag: electron acceptor

value: Sulphate

tag: incubation time

value: 13 weeks


title: MCF7_DNA

status: Public on Mar 16 2011

city: Rochester

first: Zhifu

last: Sun

state: MN

address: 200 1st ST SW

department: HSR-BSI

country: USA

institute: Mayo Clinic

description: processed data is the copy number aberration segment compared to MCF10A

data_processing:
Alignment: BWA alignment of reads to the genome (Build 36)
CNA segments: CNV-seq and Partek were used to estimate copy number changes compared to MCF10A

organism: Homo sapiens

source_name: Breast Cancer Cell Line

growth_protocol: All cell lines were grown under conditions recommended by ATCC and RNA and DNA were extracted from mid log phase populations of low passage number cultures.

extract_protocol: Genomic DNA was extracted using Qiagen's QIAamp DNA Mini Kit. Genomic DNA libraries were constructed according to the standard Illumina protocol. Briefly, DNA (5?g) was fragmented using the Covaris shearing apparatus. The end of digested DNA was repaired and an adenine was added to the 3' of the DNA fragments according to the Illumina standard end repair and add_A protocol. After adaptor ligation using standard Illumina adaptor ligation protocol, ligated fragments were separated by 2% agarose gel and DNA fragments of around 400bp were selected and purified using Qiagen Gel extraction kit. Size selected DNA fragments were then amplified using standard Illumina PCR amplification protocol with 12 PCR cycles. The concentration of the final library was measured using the Agilent 2100 Bioanalyzer (Palo Alto, CA).

tag: er status

value: Pos

tag: cell type

value: Breast cancer cell lines

tag: passages

value: ATCC low passage


title: BT20_DNA

value: Neg


title: T47D_DNA


title: MDAMB231_DNA


title: MDAMB468_DNA


title: dgcr8_ko_hippocampus

status: Public on Mar 23 2011

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

description: small RNA-Seq

data_processing: Illumina Pipeline v1.3

source_name: hippocampus

extract_protocol: Libraries were constructed with the Illumina small RNA kit version 1.5

treatment_protocol: The hippocampus and cortex were manually dissected.  Total RNA was prepared with Trizol Reagent

tag: strain

tag: age

tag: genotype/variation

value: dgcr8 ko


title: ZR751_DNA


title: BT474_DNA


title: MDAMB231_Methyl

description: DNA was MspI fragmented and bisulfite treated

data_processing:
Alignment: Sequence reads and genome reference were converted before mapped to the human (March, 2006) genomes using the Illumina stand_alone Eland_extended module.
Average methylation ratio:Summarized methylation data on each CpG island were obtained from averaging all CpG sites with coverage >= 10 in a CpG island. These data represent the percentage of methylated CpGs over total number of CpGs in the island

extract_protocol: DNA extracted from cell lines was fragmented using endonuclease MspI, followed by QIAQuick purification. The end of digested DNA was repaired and an adenine was added to the 3' end of the DNA fragments according to the Illumina standard end repair and add_A protocol (Illumina, San Diego, CA). Pre-annealed forked Illumina adaptors containing 5'-methyl-cytosine instead of cytosine was ligated to both ends of DNA fragments using standard Illumina adaptor ligation protocol (Illumina). Ligated fragments were then separated by 2% agarose gel. Two size ranges, 150-175bp and 175-225bp (includes adaptor length), were selected and cut from the gel. DNA from gel slices was purified using Qiagen Gel extraction kit (Qiagen). The purified DNA was treated with EpiTect Bisulfite kit (Qiagen) with modification. The bisulfite conversion time was extended to approximately 14hr by adding 3 cycles of denaturation at 95°C for 5min followed by incubation at 60°C for 180min. The bisulfite-converted DNA was purified using the EpiTect Bisulfite kit and the protocol for DNA isolated from formaldehyde-fixed, paraffin-embedded tissue samples. The bisulfite-treated DNA was purified a second time with MinElute PCR purification kit (Qiagen) and eluted with 15ul EB buffer. The bisulfite-treated DNA fragments were PCR amplified: 15ul of eluted DNA, 5pmol of Illumina PE PCR primers 1.0 and 2.0, 62.5nM of each dNTP, and 2.5U of Pfu Turbo Cx hotstart DNA polymerase (Stratagene Products, Agilent, La Jolla, CA) in a total 50ul volume.  The amplification conditions were as follows: 5min at 95°C, 30sec at 98°C then 6X (10sec at 98°C, 30sec at 65°C, 30sec at 72°C) followed by 5min at 72°C. The PCR reaction was purified by MinElute PCR purification Kit (Qiagen) and final reduced representation bisulfite library was eluted in 15ul EB. The concentration of final library was measured using the Agilent 2100 Bioanalyzer (Palo Alto, CA). The library was sequenced on Illumina GA sequencing instrument according to standard Illumina cluster generation and sequencing protocols.


title: ZR751_Methyl


title: T47D_Methyl


title: BT474_Methyl


title: MDAMB468_Methyl


title: C/EBPbeta ChIP-seq day 0

description: C/EBPbeta ChIP-seq day 0

value: 3T3-L1 preadipocyte cell line

value: C/EBPbeta


title: Envirnomental contaminated aquifer sample enriched for DNA Stable Isotope Probing 2

value: Fe(III) oxyhydroxide


title: MCF7_Methyl


title: MCF10A_Methyl

source_name: Breast Cell Line

value: Non-tumor epithelium cell lines


title: BT20_Methyl


title: MCF10A_mRNA

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed .
Raw Gene Count: Illumina CASAVA version 1.0 and Genome studio was used to get the summaried gene count by read start method

molecule: polyA RNA

extract_protocol:
Total RNA extraction was performed using Exiqon's miRCURY RNA Isolation Kit. Long-read mRNA-seq cDNA libraries were prepared from 1ug of total RNA using a modification of the Illumina mRNA-seq protocol.  Briefly, mRNA was resolved using poly-dT oligonucleotides attached to magnetic beads, fragmented using divalent cations under elevated temperatures, and converted to cDNA using random primers. After conversion of the cleaved fragments into cDNA, the cDNA underwent blunt end repair, addition of an 'A' base to the 3' blunt ends, and ligation of adapter molecules which will be used for PCR amplification, bridge amplification, and sequencing. The cDNA library was resolved by gel electrophoresis using conventional Illumina protocols except that we cut from the gel those cDNA fragments in the range of 300-400bp. The increased fragment length is necessary to accommodate paired end sequence analysis. The gel purified cDNA fragments were amplified by PCR and sequenced using the Illumina Cluster Station and Genome Analyzer. Paired-end sequence analysis (51 cycles/end) was carried out using sequencing primers that correspond to either end of the bridge-amplified cDNA fragments so as to obtain 50nt of sequence from either end of every cDNA fragment.
The average insert sizes for the libraries are: mRNA-seq: 350bps; DNA-seq: 400bps; Mehtyl-seq: 175bps


title: MDAMB468_mRNA


title: MDAMB231_mRNA


title: BT474_mRNA


title: T47D_mRNA


title: MCF7_mRNA


title: MCF10A_DNA


title: H3K9ac at ZT10

status: Public on Mar 11 2011

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing: Sequencing reads are mapped by bowtie software. Peaks were called using MACS (version 1.4.0b) from X. Shirley Liu's lab, then splitted into subpeaks by PeakSplitter software. Wiggle files from MACS are normalized by the sequencing depth in million reads.

source_name: Liver

growth_protocol: 12 week old male C57Bl/6 mice has been housed in regular 12h light/12h dark cycles for at least 2 weeks on normal chow.

extract_protocol: Nuclei were lysed and either sonicated (for HDAC3, Rev-erbα, NCoR and Pol II ChIP) or Mnase-digested (for H3K9Ac). 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 different time of the day (ZT10, 5pm; ZT22, 5am). Liver samples were cross-linked with 1% formaldehyde, and used for ChIP with different antibodies.

tag: tissue

value: liver

tag: fragmentation methods

value: Mnase Digestion

tag: chip-seq antibody

tag: chip-seq antibody manufacturer

value: Millipore

tag: chip-seq antibody catalog #


title: H3K9ac in HDAC3 KO liver at ZT10

tag: time


title: H3K9ac at ZT22


title: Liver input at ZT22

value: Sonication


title: BT20_mRNA

tag: cell line


title: Liver input at ZT10


title: Pol II ChIP at ZT22

value: Pol II

value: santa cruz


title: Liver input at ZT22 Mnase digestion


title: Liver input at ZT10 Mnase digestion


title: Rev-erba ChIP at ZT22

value: Rev-erba

value: cell signaling


title: Pol II ChIP at ZT10


title: Rev-erba ChIP at ZT10


title: HDAC3 ChIP at ZT10-3

value: abcam


title: HDAC3 ChIP at ZT22-1


title: HDAC3 ChIP at ZT22-2


title: HDAC3 ChIP at ZT10-2


title: HDAC3 ChIP at ZT10-1


title: NCoR ChIP at ZT22

value: NCoR

value: home made rabbit polyclonal


title: ZR751_mRNA

value: Pos

value: Breast cancer cell lines

value: ATCC low passage


title: Col-WTxLer-WT_Embryo

status: Public on Mar 10 2011

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: RNA sequencing

data_processing: 76-bp Illumina reads from cDNA libraries were aligned to Col and Ler cDNA scaffolds (TAIR8) using Bowtie (ref), accepting up to three mismatches in an alignment. Reads that aligned to either Col or Ler with fewer mismatches were assigned to that ecotype.

organism: Arabidopsis thaliana

source_name: Embryo

growth_protocol: Seeds were plated on 0.5X Murashige and Skoog salts (Caisson Laboratories, Inc.), Gamborg’s Vitamins (Sigma), and 2% sucrose; stratified at 4ºC for 2 days; grown in continuous light in a growth chamber for 10 days; and then transplanted to soil and grown in greenhouse conditions (16 hr light). For crosses, flowers were emasculated 2 days before pollination. met1-6 (Col-gl ecotype, [Xiao, 2003 #848]) homozygous plants were obtained from a self-pollinated met1-6 heterozygote that had never been homozygous. fie-1 [Ohad, 1999 #490] and dme-2 [Choi, 2002 #755] heterozygous plants were Ler and Col-gl ecotypes, respectively.

extract_protocol: Seeds at the mid-torpedo stage to early maturation stage (7-9 days after pollination, ecotype Col-0) were dissected in 0.3 M sorbitol, 5 mM MES (pH 5.7) on a slide under a dissecting microscope. At this stage of development, bilaterally active genes are expressed from both maternal and paternal genomes in embryo and endosperm (S1). Embryos were washed to remove contaminating endosperm. Because the Arabidopsis seed coat has considerable tensile strength, it was possible to separate endosperm from the seed coats and extract RNA from endosperm.

tag: maternal-ecotype

tag: paternal-ecotype

value: Landsberg

tag: maternal-genotype

value: Wild-type

tag: paternal-genotype

value: embryo


title: Col-WTxLer-WT_Endosperm

description: RNA sequencing

source_name: Pure endosperm

value: endosperm


title: Ler-fiexCol-WT_Endosperm

description: RNA sequencing

value: fie (FERTILIZATION-INDEPENDENT ENDOSPERM) mutant


title: Col-WTxLer-WT_full-Endosperm

description: RNA sequencing

source_name: Full endosperm


title: Ler-WTxCol-WT_full-Endosperm

description: RNA sequencing


title: Ler-WTxCol-WT_Endosperm

description: RNA sequencing


title: Col-LCMxLer-LCM_Embryo

description: RNA sequencing


title: Ler-WTxCol-met1_Endosperm

description: RNA sequencing

value: met1 (METHYLTRANSFERASE 1) mutant


title: Ler-WTxCol-WT_Embryo

description: RNA sequencing


title: Col-LCMxLer-LCM_Endosperm

description: RNA sequencing


title: NCoR ChIP at ZT10

value: liver

value: Sonication


title: Col-dmexLer-WT_Endosperm

description: RNA sequencing

value: Columbia-gl

value: dme (DEMETER) mutant


title: dataset 1C

status: Public on Mar 07 2011

city: New York

first: Scott

last: Keeney

address: 1275 York Ave

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: Adaptor ligation and PCR amplification was carried out from the same purified Spo11 oligos with 1A.

data_processing: Adaptor sequences were removed from sequence reads, and reads were mapped to the S288C genome using the rmapper-ls program from the SHRiMP mapping package (http://compbio.cs.toronto.edu/shrimp). The specific mapping parameters we used were:  '-s 111101111 –n 1 –m -1 –i -1 –g -1 –e -1 –h 10 –o 10000'. These parameters specify the seed pattern and Smith-Waterman parameters of 1 for matches and -1 for mismatches, gap openings and gap extensions. The alignment cutoff score was 10 and we set a limit of 10,000 for the number of best matches to store. Reads that were mapped to more than one position in the genome were stored separately from unique mappers. The maps were then curated, using unique mappers. First, we identified discrepancies between the S288C map and a separately derived map against a draft assembly of the SK1 genome. Discrepancies were defined as reads that mapped to different chromosomes or to different strands on the same chromosome, and accounted for <0.8% of total mappable reads. For each discrepant read, we compared the alignment scores against the two genomes and, if the scores differed by ≥20%, the read was deleted from the map with the lower score; otherwise the discrepant reads were retained. Second, the rDNA array is represented in the S288C assembly by only 1.9 copies of the repeat unit, thus oligos that span the boundary between the repeats map to a single position in the genome even though they come from a repetitive sequence. Therefore, reads of this type were moved to the multiple mapping set. Finally, we observed 8,653 reads (<0.42% of total mappable reads) that mapped with similar alignment scores to a single position in the S288C genome but to multiple positions in SK1. Because the SK1 genome assembly is incomplete and may contain incorrect duplications, we added these reads back to the S288C map.   Reads that mapped to multiple positions in one or both genomes (with exceptions noted above) were handled separately: each such read was assigned to every position to which it mapped, normalized by the number of mapping sites. Normalized “multi-maps” were assembled separately for each reference genome, and combined with the maps of uniquely mapped reads.

organism: Saccharomyces cerevisiae

source_name: Spo11-associated oligos

growth_protocol: Synchronized meiotic cultures of diploid S. cerevisiae of strain background SK1 (SKY1874: MATα/MATa, ho::LYS2/", lys2/", ura3/", leu2::hisG/", his4X::LEU2/”, arg4-Nsp/”, nuc1∆::LEU2/”, SPO11-HA3-His6::kanMX/”) were set up as follows: A saturated YPD culture was used to inoculate 2 liters liquid YPA medium (1% yeast extract, 2% Bacto peptone, 1% potassium acetate) to OD600 = 0.2 and grown in 2.8-liter baffled Fernbach flasks (1 liter per flask) at 225 rpm at 30°C for 14 hrs. Cells were harvested, washed once, resuspended in 2 liters sporulation medium (2% potassium acetate) and shaken at 225 rpm at 30°C for 4 hrs.

extract_protocol: Spo11-oligo complexes were immunoprecipitated from denaturing meiotic nuclear lysate, electrophoresed in 7.5% SDS-PAGE, and eluted from the gel. Spo11 protein was digested with proteinase K during elution and Spo11 oligos were precipitated. 3' ends of oligos were tailed with ribo GTP using terminal deoxynucleotidyl transferase (TdT), tailed oligos were ligated to double-stranded linker with dC overhang using T4 RNA ligase 2, complementary strands of Spo11 oligos were synthesized with Klenow DNA polymerase. Oligo:linker cassettes were gel-extracted from a 10% denaturing polyacrylamide gel and ethanol-precipitated. The complementary strands of Spo11 oligo:linker cassettes were subjected to another round of rG tailing, ligation to another linker and strand synthesis. 454 sequencing primers were added to the resulting adaptor-Spo11 oligo cassettes by low cycle numbers of PCR. PCR products (~100-140 bp) were gel-purified from a 10% neutral polyacrylamide gel. Purified amplicons were sequenced on 454 platform in the Genomics Core Laboratory at Memorial Sloan-Kettering Cancer Center.


title: dataset 1B

description: PCR amplification was carried out from adaptor-ligated Spo11 oligos, prepared for 1A.


title: dataset 2

description: Spo11 oligos were purified from an independent culture, and adaptor ligation and PCR amplification was carried out.


title: dataset 1A

description: Spo11 oligos were purified from the same culture with datasets 1B and 1C. Adaptor ligation and PCR amplification was carried out.


title: DatasetN2_0hr

data_processing: For mapping of the Illumina reads (1–9 million reads per dataset) to both the SGD and SK1 genomes, the rmapper-ls program from SHRiMP was used with more stringent “gapless” parameters:  -s 111101111 -o 10001 -n 1 -m 1 -i -6 -g -5000 -e -5000 -h 24.   The match score was 1, mismatches were -6 and gap openings and extensions were 5,000 which effectively make them infinite on this scale. The Smith-Waterman cutoff was 24; so a read would need at least 24 matches (with zero mismatches) to pass. We recorded 10,001 optimal hits. This number was chosen to insure that all multiple mappings were enumerated and we checked the mapping results to verify that the most degenerate multiple mapping read was below this threshold.  The mapping data were then post-processed following previously described methods (Kaplan et al., Nature 2009). We first looked across all datasets to identify regions containing reads that mapped to other locations as well. These regions, extended by 150 bp on each side are denoted as MASK (a 0 in the MASK field means not masked). We next computed a histogram of distances by taking for each read the distances to all other reads that were downstream and on the opposite strand. The first mode of this distribution of distances was defined as the mononucleosome DNA length (Lnuc). Each read was extended to length Lnuc, then an occupancy table was computed by summing at each base pair the number of extended reads that overlapped that base pair.

source_name: Synchronized meiotic culture

growth_protocol: Synchronized meiotic diploid cultures of S. cerevisiae of strain background SK1 (NKY611: MATα/MATa, ho::LYS2/”, lys2/“, ura3/”, leu2::hisG/”) were set up as follows: A saturated YPD culture was used to inoculate 200 ml liquid YPA medium (1% yeast extract, 2% Bacto peptone, 1% potassium acetate) to OD600 = 0.2 and grown in 2-liter unbaffled Erlenmeyer flasks at 250 rpm at 30°C for 14 hrs. Cells were harvested, washed once in sterile water, resuspended in sporulation medium to OD600 ~1.9 (in 0.3% potassium acetate for Dataset N1) or to OD600 ~6.5 (in 2% potassium acetate at for Dataset N2) and incubated in 2-liter unbaffled Erlenmeyer flasks at 250 rpm at 30°C.

extract_protocol: Samples of 50 ml were harvested at 0, 1, 2, 3 or 4 hr after transfer to sporulation conditions, and immediately crosslinked by addition of formaldehyde to 1% and incubation for 15 min at room temperature. Glycine was then added to a final concentration of 125 mM, cells were pelleted and resuspended in 18.5 ml Buffer Z (0.5 M sorbitol, 50 mM Tris-HCl, pH 7.4, 10 mM β-mercaptoethanol) containing 5 mg zymolyase 100T (US Biological) and incubated at 30°C for 30 min. Spheroplasted cells were pelleted, supernatants removed, and treated with a dilution series of micrococcal nuclease (MNase) from 5 to 80 Units (Worthington Biochemical, Corp.) in NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 0.5 mM spermidine, 1 mM β-mercaptoethanol, 0.075% NP-40) and incubated at 37°C for 20 min. Digestions were stopped by the addition of 5% SDS and 50 mM EDTA followed by the addition of 100 μg proteinase K (Fisher Scientific) and incubated at 65°C for 18 hr. DNA was then extracted with 1.5 M ammonium acetate, pH 5.5 and 500 μl of phenol-chloroform-isoamyl alcohol (25:24:1), washed with 100% isopropanol and then 70% ethanol, and treated with RNase. Mononucleosome-sized DNA generated by treatment with 20 (Dataset N1) or 40 (Dataset N2) units MNase was then purified by size fractionation on agarose gels and prepared for sequencing using the Genomic DNA Sample Prep Kit (Illumina, Inc.) and sequenced using the Illumina Genome Analyzer Systems at the MIT Biopolymers Facility (Dataset N1) or at the Genomics Resource Center at The Rockefeller University (Dataset N2).

tag: time in meiosis (hr)


title: DatasetN1_1hr


title: DatasetN2_4hr


title: SuHw-p1a..p1b

status: Public on Mar 04 2011

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description:
Pair end
The mapped read file was generated using single-end library data. The pair-end data was used for different purposes such as to see how different read length affects mappability etc, but not mapped at a fixed read length.

data_processing: Reads were aligned to the UCSC D. melanogaster reference genome (dm3) using ELAND

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: Cells (S2) were grown as described by the DGRC and the Cherbas Lab.

extract_protocol:
White lab: After chromatin immuno-precipitation, the DNA was purified in 30ul of water.  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.
Lieb lab: Libraries were prepared according to Illumina's recommendations. 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 adaptor ligation, fractions 150-500bps were band isolated from 2% agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles. 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.
Average pair-end library size: ~300bp

treatment_protocol: After the expansion of S2 cell line, cells were transfered into a plate. Once confluent, 1.8% formaldehyde was added to the cell culture. Cells were harvested in presence of the formaldehyde with the help of a cell scrapper. After 15 minutes of incubation at room temperature, the cross-linking reaction was quenched with glycine for 5 minutes. Cells pellet were then washed 3 times with lysis buffer. Regular chromatin extraction before sonication was then performed. Sonicated chromatin was then used for ChIP experiments or directly for DNA extraction for the Input samples. ChIP was performed as previously described (Negre et al. PLoS Genetic 2010). H3K36me3 antibody is from Abcam. Su(Hw) antibody is from Pamela K. Geyer's lab. Both are rabbit polyclonals.

tag: antibody name

value: anti-SuHw

tag: manufacturer

value: Pamela K. Geyer's lab

tag: lot/batch#

tag: catalog #


title: gDNA-p1a..p1b

description:
Pair end
Lieb lab
The mapped read file was generated using single-end library data. The pair-end data was used for different purposes such as to see how different read length affects mappability etc, but not mapped at a fixed read length.


title: SuHw-s1..s7

description:
Single end
White lab and Lieb lab
The mapped read file was generated using single-end library data. The pair-end data was used for different purposes such as to see how different read length affects mappability etc, but not mapped at a fixed read length.


title: H3K36me3-s1..s7

value: Abcam


title: gDNA-s1..s5


title: Input-p1a..p1b


title: H3K36me3-p1a..p1b


title: DatasetN1_2hr

tag: strain


title: Input-s1..s7


title: DatasetN1_0hr


title: gDNA-p2a..p2b


title: brain_RNAseq_Tdp43-oligo_rep3.1

status: Public on Mar 03 2011

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: strand-specific RNAseq

data_processing: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata

source_name: Striatum

extract_protocol: The RNA-seq libraries were constructed as described previously (Parkhomchuk, 2009) with slight modifications. Briefly, 7mg of total RNA was used for polyadenylated RNA selection using oligo-dT paramagnetic beads (Invitrogen). First-strand synthesis was prepared using a combination of oligodT primers and random hexamers with SuperScript III reverse transcriptase (Invitrogen), using gradually increasing temperature.  dNTPs were then removed from the reaction by gel filtration through Sephadex G-50 (GE-health care) spin columns equilibrated with 1mM TrisHCl, pH 7.0. Second strand was then synthesized by a 2hr-incubation for 16oC with a dUTP-containing nucleotide mixture, 100mM MgCl2, 0.1M DTT, and a combination of ligase (NEB), DNA polymerase I (NEB) and RNase H (Invitrogen) in second strand synthesis buffer (Invitrogen). Double-stranded cDNA was then purified through spin columns (QIAGEN) and fragmented by ultrasonic digestion (Bioruptor, Diagenode) with continuous cooling at 1oC, using repeated cycles of 30 sec sonication with 100% amplitude and 30 sec breaks for 2-3 hrs. 1-2 mL of the material was used to check the level of fragmentation on a FlashGel DNA Cassette 1.2% (LONZA). End repair, A-tailing and adaptor ligation were all performed according to the Illumina protocol and libraries were subjected to electrophoresis on a 2% Low Range Ultra Agarose gel (BioRad). Fragments with a size range of 150-200 bp were cut out of the gel and libraries were gel purified on spin columns (QIAGEN) according to the manufacturer’s instructions. Prior to amplification, libraries were incubated with Uracil N-Glycosylase (Applied Biosystems) to digest the dUTP-containing strand, thereby ensuring a single orientation of our RNA-seq libraries. 8 pM of amplified libraries was used for sequencing on the Illumina GA2 for 72 cycles.

treatment_protocol: 8-10 week old female C57Bl/6 mice were anesthetized with 2.5-3% isofluorane, and a midline incision of approximately 1cm was made on their heads. Using stereotaxic guides, 3 mL of antisense oligonucleotide (ASO) solution targeting Tdp-43 or a control – corresponding to a total of 75 mg or 100 mg ASOs – or saline buffer was injected using a Hamilton syringe directly into their striatum. The incision was closed with sutures and the mice were allowed to recover in their cages. They were monitored for any adverse effects for the next two weeks until they were sacrificed. The striatum and adjacent cortex area were dissected, placed in separate tubes containing 1 mL Trizol (Invitrogen) and were frozen at -80oC until use.

tag: age

value: 8-10 weeks

tag: treatment

value: Tdp-43 anti-sense oligo


title: brain_RNAseq_control-oligo_rep3.3

description: strand-specific RNAseq

value: control anti-sense oligo


title: brain_RNAseq_control-oligo_rep3.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep4.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep1.3

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep2.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep1.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep4.1

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep1.1

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep1.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep2.1

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep4.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep2.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep3.2

description: strand-specific RNAseq


title: brain_RNAseq_Tdp43-oligo_rep2.3

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep4.3

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep4.1

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep3.1

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep2.1

description: strand-specific RNAseq


title: brain_RNAseq_control-oligo_rep1.1

description: strand-specific RNAseq


title: msl_repII_lane02

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate II, lane2

data_processing: Reads were mapped to the D. melanogaster genome (dm3) using Bowtie alignment software (bowtie-bio.sourceforge.net), allowing at most one base mismatch and discarding all non-uniquely mapping reads

source_name: SL2 Cells

growth_protocol: Drosophila SL2 cells were grown in Schneider's medium with 10% FBS

extract_protocol: GRO-Seq Nuclei extraction and nascent RNA purification protocol is detailed in Larschan et al., Submitted

treatment_protocol: RNAi treatment was conducted for 6 days after bathing

tag: biological replicate

value: Replicate II

tag: RNAi treatment

value: MSL2 RNAi


title: CLIPseq_Tdp43_low-Mnase

description: Cross-linking IP against Tdp-43

source_name: Whole brain

extract_protocol: Cells from whole brain of ten mice were pooled; cell suspension was distributed in 10 cm cell culture dishes and irradiated three times at 400 mJ/cm2 on ice with short breaks between each exposure. Irradiated brain cells were precipitated by brief centrifugation at 4oC, resuspended in PBS and distributed in ten 1.6 mL tubes, each containing cells corresponding to one mouse brain. Cells were disrupted on ice using PBS containing 0.1% SDS, 0.5% deoxycholate (Na), 0.5% NP-40, DNase treated and cleared from cell debris. Cell extracts were then incubated with protein G paramagnetic beads (Invitrogen) coupled to a custom-made mouse monoclonal anti-TDP-43 antibody (Ling, 2010) (40mg of antibody per 400 mL of beads per sample).  After 4hrs, beads were washed and associated RNAs were treated with three different concentrations (100U, 0.2U and 0.02U per sample) of micrococcal nuclease (MNase, Roche), while attached on the beads. Samples were then treated with alkaline phosphatase (NEB) and an RNA-linker (5¢P-UCGUAUGCCGUCUUCUGCUUG-Pmm, Thermo Scientific) was attached to the 3¢ end of RNAs. At this step we saved 40ul of each sample for immunoblot analysis before radiolabelling. The remaining samples were then labeled with P32-g-ATP using T4 polynucleotide kinase (NEB). Unlabelled and radiolabeled RNA-protein complexes were then released from the beads by incubating at 70oC in NuPAGE LDS sample buffer without reducing agent (Invitrogen). Samples were then migrated on 10% Bis-Tris NuPAGE gels using MES buffer (Invitrogen) and transferred to nitrocellulose membranes (0.45 mm pore size, Invitrogen). The membrane with unlabelled samples was subjected to immunobloting using a primary antibody rabbit anti-TDP-43 (Aviva system biology; Cat #ARP38942_T100; 1:2,000) (see below for the immunoblot protocol). The membrane with the radiolabelled samples was rinsed with PBS, put in a clean plastic wrap and exposed to an autoradiography film. Using the autoradiogram as a guide, membrane pieces containing complexes with higher molecular weight than the expected protein size were excised. Isolated membrane pieces were then incubated with 4mg/mL Proteinase K (Takara Bio Inc.) at 37oC for 20 min with shaking at 1200 rpm. The reaction was stopped with the addition of 7 M Urea and incubation at 37oC for 20 min with shaking at 1000 rpm. The released RNA were then extracted with phenol:chloroform.  To precipitate the RNA, the aqueous phase was transferred in a separate tube where sodium acetate, linear acrylamide, ethanol and isopropanol were added and the samples were incubated at -20oC overnight. The next day, samples were centrifuged for 10 mins at maximum speed in a microcentrifuge at 4oC. RNA pellets were washed twice with 75% ethanol and dried at room temperature. RNAs were resuspended in an RNA ligation buffer and an RNA-linker (Bi-AAUGAUACGGCGACCACCGA, Thermo Scientific) was attached to their 5¢ end. Samples were treated once more with DNase I and precipitated with Phenol Chloroform as described above. RNAs were then reverse transcribed using SuperScript III (Invitrogen) and amplified by PCR using high fidelity Phusion polymerase (NEB) with the following primers: CAAGCAGAAGACGGCATACGA (P3) and AATGATACGACCACCGA (P5). Amplified libraries were then migrated in a 12% acrylamide gel and 75-200bp DNA fragments were excised and frozen at -20oC overnight. Acrylamide pieces were crushed into smaller pieces and DNA fragments were eluted by incubating overnight at 4oC in 50mM NaCl, 10mM TrisHCl, pH=8.0. Supernatants containing the DNA libraries were incubated with 3M sodium acetate and 100% ethanol with glycogen to facilitate DNA precipitation overnight at -80oC. DNA fragments were precipitated and pellets were resuspended in water and filtered through Spin X Centrifuge tube filter (Costar) to remove acrylamide contaminants. DNA libraries were precipitated and then resuspended in 12-20mL of DEPC-treated water. Libraries were quantified by the Qubit Quantitation Platform (Invitrogen) before loading on an Illumina Genome Analyzer 2 (GA2) flow-cell in a concentration of 8 pM per lane. Sequencing was carried out on the Illumina GA2 according to the manufacturer’s instructions for 36 cycles using the “P5” primer.

value: 8 weeks

tag: antibody

tag: vendor

value: Aviva system biology


title: CLIPseq_Tdp43_high-Mnase

description: Cross-linking IP against Tdp-43


title: msl_repII_lane01

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate II, lane1


title: brain_RNAseq_control-oligo_rep2.3

description: strand-specific RNAseq


title: msl_repI_lane04

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate I, lane4

value: Replicate I


title: msl_repI_lane02

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate I, lane2


title: msl_repI_lane01

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate I, lane1


title: gfp_repII_lane02

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate II, lane2

value: control GFP RNAi


title: gfp_repI_lane01

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate I, lane1

tag: rnai treatment


title: gfp_repI_lane03

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate I, lane3


title: gfp_repII_lane01

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate II, lane1


title: Myers_BC_Stomach_01-11002_1_None_BioChain

status: Public on Mar 01 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description: Reduced Representation

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

tag: cell

tag: cell organism

value: Human

tag: cell description

value: Donor 01-11002; Age 83; Caucasian; DNA Extract

tag: cell karyotype

value: Normal

tag: cell lineage

value: Stomach

tag: cell sex

value: F

tag: replicate

tag: obtainedby

value: BioChain


title: Myers_HSMMtube_1_None_Duke

description: Reduced Representation

source_name: HSMMtube

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMMtube_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMMtube

value: Normal Human Skeletal Muscle Myotubes

value: normal

value: B

value: Duke


title: gfp_repI_lane02

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate I, lane2


title: Myers_LNCaP_1_androgen_Duke

description: Reduced Representation

source_name: LNCaP

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:LNCaP_Crawford_protocol.pdf Yale_TFBS(Farnham):LNCaP_protocol.pdf UW_Stam:LNCaP_Stam_protocol.pdf

value: LNCaP

value: prostate adenocarcinoma

value: cancer

value: "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old Caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC

value: M

value: androgen

tag: treatment description

value: 12hrs, 1nM Methyltrienolone (R1881) (Crawford)


title: Mef2a [ChIP-seq]

status: Public on Mar 02 2011

first: Sek Won

last: Kong

address: 300 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description: Mef2a fbio ChIP

data_processing: Alignments was done against build mm9 using bowtie, and peaks detection by Sole-Search ( http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi ).  Sole-Search Analysis Summary is available as Series GSE21529 supplementary file.

source_name: HL-1 cells

growth_protocol: HL-1 cells were cultured routinely, and split 1:3 every 3-4 days until full confluence.

extract_protocol: Libraries were generated according to Illumina single-end ChIP-seq library preparation ( Cat# IP-102-1001)

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression, and TRE promoter driving transcription factor Mef2a for 48 hrs before cells harvest for chromatin preparation

tag: strain

tag: cell line

value: HL-1 cardiac muscle cell line

tag: protocol

value: Mef2a fbio ChIP

tag: chip antibody


title: Gata4 [ChIP-seq]

description: Gata4 fbio ChIP

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression, and TRE promoter driving transcription factor Gata4 for 48 hrs before cells harvest for chromatin preparation

value: Gata4 fbio ChIP


title: Myers_HIPEpiC_2_None_UW

description: Reduced Representation

source_name: HIPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HIPEpiC_Stam_protocol.pdf

value: HIPEpiC

value: Human

value: Human Iris Pigment Epithelial Cells

value: U

tag: treatment

value: UW


title: Nkx2-5 [ChIP-seq]

description: Nkx2-5 fbio ChIP

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression, and TRE promoter driving transcription factor Nkx2-5 for 48 hrs before cells harvest for chromatin preparation

value: Nkx2-5 fbio ChIP


title: Srf [ChIP-seq]

description: Srf fbio ChIP

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression, and TRE promoter driving transcription factor Srf for 48 hrs before cells harvest for chromatin preparation

value: Srf fbio ChIP


title: msl_repI_lane03

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq MSL2 RNAi, Replicate I, lane3

tag: biological replicate

value: Replicate I

tag: RNAi treatment

value: MSL2 RNAi


title: Tbx5 [ChIP-seq]

description: Tbx5 fbio ChIP

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression, and TRE promoter driving transcription factor Tbx5 for 48 hrs before cells harvest for chromatin preparation

value: Tbx5 fbio ChIP


title: Myers_HMEC_1_None_UW

description: Reduced Representation

source_name: HMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HMEC_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf

value: HMEC

value: Human Mammary Epithelial Cells

value: F


title: Myers_HSMM_3_None_Duke

description: Reduced Representation

source_name: HSMM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMM_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMM

value: Normal Human Skeletal Muscle Myoblasts

value: normal

value: B

value: Duke


title: Input control [ChIP-seq]

description: input DNA

treatment_protocol: Control input DNA

value: HL-1 cardiac muscle cell line

value: input DNA control


title: BirA control [ChIP-seq]

description: BirA control

treatment_protocol: Confluent HL-1 cells were infected with adenovirus expressing cardiac troponin T promoter driving rtTA and BirA expression.

value: BirA control


title: Myers_HRE_2_None_UW

description: Reduced Representation

source_name: HRE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

value: HRE

value: Human

value: Human Renal Epithelial cells (normal)

value: U

value: UW


title: Myers_HTR8svn_1_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:HTR8svn_Crawford_protocol.pdf

value: Trophoblast (HTR-8/SVneo) cell line. A thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo.

value: Blastula


title: Myers_GM19240_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM19240_Crawford_protocol.pdf

value: B-Lymphocyte

value: YORUBA, Epstein-Barr Virus, Female


title: Myers_HCPEpiC_1_None_UW

description: Reduced Representation

source_name: HCPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells


title: Myers_T-47D_1_DMSO_0.02pct_24hr_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:T47D_Myers_protocol.pdf

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: hypotriploid

value: F

value: 24h,0.02% DMSO (Myers)

value: HudsonAlpha


title: gfp_repI_lane04

description:
RNA-Seq of nascent RNA transcripts.
GRO-Seq Control RNAi, Replicate I, lane4

value: Replicate I

value: control GFP RNAi


title: Myers_Melano_3_None_Duke

description: Reduced Representation

source_name: Melano

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Melano_Crawford_protocol.pdf

value: Melano

value: Human

value: melanocytes

value: Duke


title: P300 [ChIP-seq]

description: ChIP against P300

treatment_protocol: ChIP against P300

value: HL-1 cardiac muscle cell line

value: ChIP against P300

value: P300 antibody (Santa Cruz, catalog# sc-585x, lot# c0509)


title: Myers_BC_Lung_01-11002_2_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Normal

value: Lung

value: BioChain


title: Myers_PanIslets_2_None_Duke

description: Reduced Representation

source_name: PanIslets

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:PanIslets_Crawford_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin(Lieb):PanIslets_Lieb_protocol.pdf

value: PanIslets

value: human pancreatic islets

value: M


title: Myers_CMK_2_None_UW

description: Reduced Representation

source_name: CMK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:CMK_Stam_protocol.pdf

value: CMK

value: Human Acute Megakaryocytic Leukemia Cells

value: UW


title: Myers_BC_Skeletal_Muscle_H12817N_1_None_BioChain

description: Reduced Representation

value: Donor H12817N; Age 71; Caucasian; DNA and RNA Extract

value: Skeletal muscle


title: Myers_MCF10A-Er-Src_3_TAM_1uM_36hr_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS(Struhl):MCF-10A_Struhl_protocol.pdf

value: Human

value: mammary gland, non-tumorigenic epithelial, inducible cell line

value: stable and near-diploid

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: F

value: 36h, 1uM tamoxifen (Myers)

value: Stanford


title: Myers_NT2-D1_2_None_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NT2-D1_protocol.pdf

value: malignant pluripotent embryonal carcinoma (Ntera2)

value: cancer

value: "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC


title: Myers_NH-A_2_None_UW

description: Reduced Representation

source_name: NH-A

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad:NH-A_Bernstein_protocol.pdf UW_Stam: NH-A_Stam_protocol.pdf

value: primary cell

value: astrocyte

value: NH-A

value: normal human astrocytes

value: U


title: Myers_LNCaP_2_None_Duke

description: Reduced Representation

value: LNCaP

value: prostate adenocarcinoma

value: "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old Caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC

value: M

value: Duke


title: Myers_HCM_2_None_UW

description: Reduced Representation

source_name: HCM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCM_Stam_protocol.pdf

value: HCM

value: Human

value: Human Cardiac Myocytes

value: UW


title: Myers_HeLa-S3_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf

value: immortalized cell line

tag: line

value: cervical carcinoma

value: ectoderm

value: F

value: HudsonAlpha


title: Myers_Osteobl_1_None_Duke

description: Reduced Representation

source_name: Osteobl

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Osteoblast_Crawford_protocol.pdf Broad_Histone:Osteoblast_Bernstein_protocol.pdf

tag: cell

value: Osteobl

value: Normal human osteoblasts (NHOst)

value: normal


title: Myers_HPAEpiC_2_None_UW

description: Reduced Representation

source_name: HPAEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAEpiC_Stam_protocol.pdf

value: HPAEpiC

tag: cell organism

value: Human Pulmonay Alevolar Epithelial Cells

value: U


title: Myers_ECC-1_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:ECC1_Myers_protocol.pdf

tag: cell description

value: ECC-1 is a human epithelial cell line derived from an endometrium adenocarcinoma.

value: unknown


title: Myers_BC_Liver_01-11002_1_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

tag: cell karyotype

value: Normal

value: Liver

value: BioChain


title: Myers_SAEC_1_None_UW

description: Reduced Representation

source_name: SAEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SAEC_Stam_protocol.pdf

value: SAEC

value: Human

value: Small Airway Epithelial Cells

value: UW


title: Myers_GM12878_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

value: lymphoblastoid

value: relatively normal

tag: cell lineage

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus

value: F

value: HudsonAlpha


title: Myers_U87_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:U-87_Myers_protocol.pdf

value: human glioblastoma; astrocytoma

value: hypodiploid female with a modal chromosome number of 44 in 48% of cells and a 5.9% rate of higher ploidy

tag: cell sex


title: Myers_SK-N-MC_2_None_HudsonAlpha

description: Reduced Representation

source_name: SK-N-MC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:SK-N-MC_protocol.pdf

value: immortalized cell line

value: SK-N-MC

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor

value: cancer

value: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC

tag: replicate


title: Myers_AG09319_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: Adult human gum tissue fibroblasts

tag: obtainedby


title: Myers_GM12891_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM12891_Crawford_protocol.pdf

value: B-Lymphocyte

value: CEPH/UTAH PEDIGREE 1463, Epstein-Barr Virus, Male

value: M


title: Myers_AoSMC_2_None_Duke

description: Reduced Representation

source_name: AoSMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:AoSMC_Crawford_protocol.pdf

value: AoSMC

value: Human

value: aortic smooth muscle cells

value: U

value: Duke


title: Myers_PFSK-1_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:PFSK-1_protocol.pdf

value: neuroectodermal cell line derived from a human cerebral brain tumor

value: ectoderm

value: HudsonAlpha


title: Myers_SK-N-SH_RA_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: neuroblastoma cell line differentiated w/ retinoic acid

value: F

value: UW


title: Myers_PANC-1_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:PANC-1_Myers_protocol.pdf UW_Stam:PANC-1_Stam_protocol.pdf

value: immortalized cell line

value: pancreatic carcinoma

value: cancer, male


title: Myers_BC_Brain_H11058N_1_None_BioChain

description: Reduced Representation

value: Donor H11058N; Age 66; Asian; DNA Extract

value: Normal

value: Brain

value: BioChain


title: Myers_GM12878_1_None_HudsonAlpha

description: Reduced Representation

value: Human

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus


title: Myers_BC_Uterus_BN0765_2_None_BioChain

description: Reduced Representation

value: Donor BN0765; Age 44; Asian; DNA Extract

value: Uterus


title: Myers_HSMM_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMM_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMM

value: Normal Human Skeletal Muscle Myoblasts

value: normal

value: B

value: Duke


title: Myers_HRPEpiC_2_None_UW

description: Reduced Representation

source_name: HRPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRPEpiC_Stam_protocol.pdf

value: HRPEpiC

value: Human Retinal Pigment Epithelial Cells

value: U

value: UW


title: Myers_AG10803_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: Adult human abdominal skin fibroblasts

value: M


title: Myers_T-47D_1_Estradiol_10nM_24hr_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:T47D_Myers_protocol.pdf

value: Human

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: hypotriploid

value: F

tag: treatment description

value: 24,10nM Estradiol  (Myers)

value: HudsonAlpha


title: Myers_HRCEpiC_1_None_UW

description: Reduced Representation

source_name: HRCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRCEpiC_Stam_protocol.pdf

value: HRCEpiC

value: Human Renal Cortical Epithelial cells (normal)


title: Myers_GM12892_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM12892_Crawford_protocol.pdf

value: B-Lymphocyte

value: CEPH/UTAH PEDIGREE 1463, Epstein-Barr Virus, Female


title: Myers_GM19239_1_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM19239_Crawford_protocol.pdf

value: YORUBA, Epstein-Barr Virus, Male

value: Duke


title: testes_lysate_beta_eliminated

status: Public on Mar 05 2011

city: Grenoble

first: Philipp

last: Berninger

address: 6, rue Jules Horowitz

country: France

institute: EMBL Grenoble

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using oligomap. All reads with only one genomic mapping with zero errors were retained and used for analysis. The phb_testes_lysate_beta_processed_lib.txt data file contains the obtained sequences in the first column and their copynumber in the second column. All those reads mapped uniquely (1 match) and perfectly (no mismatch/error) to the Mus musculus mm9 genome. The genomic coordinates are in columns 3-6.

source_name: total testes

growth_protocol: Total testis RNA from 6 months old C57/BL6 mice

extract_protocol: Total testis RNA was isolated using TRIzol. Sodium periodate treatment and β-elimination were performed.

tag: strain

tag: tissue

value: testes


title: Myers_HCT-116_2_None_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:HCT-116_protocol.pdf UW_Stam:HCT116_Stam_protocol.pdf

value: immortalized cell line

value: colorectal carcinoma

value: cancer

value: endoderm

value: Stanford


title: Myers_BC_Left_Ventricle_N41_2_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Human

value: Donor N41; Age 26; Asian; DNA Extract

value: Normal

value: Left ventrible

value: M

value: BioChain


title: Myers_SKMC_1_None_UW

description: Reduced Representation

source_name: SKMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SkMC_Stam_protocol.pdf

value: SKMC

value: Human Skeletal Muscle Cells

value: U

value: UW


title: Myers_MCF10A-Er-Src_1_None_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS(Struhl):MCF-10A_Struhl_protocol.pdf

value: mammary gland, non-tumorigenic epithelial, inducible cell line

value: stable and near-diploid

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: F


title: Myers_AG04449_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04449_Stam_protocol.pdf

value: Fetal buttock/thigh fibroblast


title: Myers_Myometr_1_None_Duke

description: Reduced Representation

source_name: Myometr

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Myometr_Crawford_protocol.pdf

value: Myometr

value: Myometrial cells

value: Duke


title: Myers_U87_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:U-87_Myers_protocol.pdf

value: Human

value: human glioblastoma; astrocytoma

value: hypodiploid female with a modal chromosome number of 44 in 48% of cells and a 5.9% rate of higher ploidy

value: HudsonAlpha


title: Myers_BC_Placenta_UHN00189_2_None_BioChain

description: Reduced Representation

value: Donor UHN00189; Age 29; Native Indian; DNA Extract

value: Normal

value: Placenta

value: BioChain


title: Myers_HTB-11_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:HTB-11_Myers_protocol.pdf

value: Human neuroblastoma


title: Myers_Astrocy_2_None_Duke

description: Reduced Representation

source_name: Astrocy

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Astrocytes_Crawford_protocol.pdf

value: Astrocy

value: Normal human astrocytes

value: normal

value: U


title: Myers_BC_Adrenal_Gland_H12803N_2_None_BioChain

description: Reduced Representation

value: Donor H12803N; Age 88; Caucasian; DNA Extract

value: Adrenal gland

value: F


title: Myers_AG09309_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: Adult human toe fibroblast

value: UW


title: Myers_BE2_C_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:BE2-C_Myers_protocol.pdf

value: Human

value: M


title: Myers_Osteobl_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Osteoblast_Crawford_protocol.pdf Broad_Histone:Osteoblast_Bernstein_protocol.pdf

value: Osteobl

value: Normal human osteoblasts (NHOst)

value: Duke


title: Myers_SK-N-MC_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:SK-N-MC_protocol.pdf

value: SK-N-MC

value: neuroepithelioma cell line derived from a metastatic supra-orbital human brain tumor

value: cancer

value: "SK-N-MC was isolated in September of l971 and was found to have moderate dopamine - beta - hydroxylase activity as well as formaldehyde induced fluorescence indicative of intracellular catecholamines." - ATCC

value: HudsonAlpha


title: Myers_AG04450_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: primary cell

value: fibroblast of lung

value: Fetal lung fibroblast


title: Myers_BC_Leukocyte_UHN00204_1_None_BioChain

description: Reduced Representation

value: Donor UHN00204; Age 54; Caucasian; DNA Extract

value: Normal

value: Peripheral blood mononuclear cell

value: BioChain


title: Myers_BC_Kidney_01-11002_2_None_BioChain

description: Reduced Representation

value: Human

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Kidney

value: F


title: Myers_GM12892_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM12892_Crawford_protocol.pdf

value: B-Lymphocyte

value: CEPH/UTAH PEDIGREE 1463, Epstein-Barr Virus, Female


title: Myers_BC_Stomach_01-11002_2_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA Extract

value: Stomach


title: Myers_H1-hESC_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/H1_ES_protocol.pdf

value: Human Embryonic Stem Cells

value: normal

value: embryonic stem cells

value: M


title: Myers_ProgFib_1_None_Duke

description: Reduced Representation

source_name: ProgFib

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:progeria_Crawford_protocol.pdf

value: ProgFib

value: HGPS (HGADFN167, progeria research foundation)

value: progeria

value: U

value: Duke


title: Myers_PanIslets_1_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:PanIslets_Crawford_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin(Lieb):PanIslets_Lieb_protocol.pdf

value: PanIslets

value: Human

value: human pancreatic islets


title: Myers_BC_Pericardium_H12529N_1_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor H12529N; Age 70; Caucasian; DNA Extract

value: Normal

value: Pericardium

value: F

value: BioChain


title: Myers_BC_Kidney_01-11002_1_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Kidney


title: Myers_Hepatocytes_2_None_Duke

description: Reduced Representation

source_name: Hepatocytes

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Hepatocytes_Crawford_protocol.pdf

value: Hepatocytes

value: Primary Human Hepatocytes

value: normal

value: Liver perfused by enzymes to generate single cell suspension

value: B


title: Myers_BC_Skin_01-11002_2_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA Extract

value: Skin


title: Myers_NH-A_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad:NH-A_Bernstein_protocol.pdf UW_Stam: NH-A_Stam_protocol.pdf

value: NH-A

value: normal human astrocytes

value: U

value: UW


title: Myers_BE2_C_2_None_HudsonAlpha

description: Reduced Representation

value: Human

value: Human neuroblastoma

value: M

value: HudsonAlpha


title: Myers_PanIslets_4_None_Duke

description: Reduced Representation

source_name: PanIslets

value: PanIslets

value: human pancreatic islets

value: Duke


title: Myers_BC_Skeletal_Muscle_H12817N_2_None_BioChain

description: Reduced Representation

value: Donor H12817N; Age 71; Caucasian; DNA and RNA Extract

value: Normal

value: Skeletal muscle

value: BioChain


title: Myers_HTR8svn_3_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:HTR8svn_Crawford_protocol.pdf

value: Trophoblast (HTR-8/SVneo) cell line. A thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo.

value: normal

value: Blastula

value: F


title: Myers_AG09319_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: Adult human gum tissue fibroblasts


title: Myers_BC_Skin_01-11002_1_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA Extract

value: Skin


title: Myers_LNCaP_1_None_UW

description: Reduced Representation

source_name: LNCaP

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:LNCaP_Crawford_protocol.pdf Yale_TFBS(Farnham):LNCaP_protocol.pdf UW_Stam:LNCaP_Stam_protocol.pdf

value: LNCaP

value: Human

value: prostate adenocarcinoma

value: cancer

value: "LNCaP clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy of the left supraclavicular lymph node of a 50-year-old Caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." - ATCC

value: UW


title: Myers_NHDF-neo_2_None_UW

description: Reduced Representation

source_name: NHDF-neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-neo_Stam_protocol.pdf

value: NHDF-neo

value: Neonatal Human Dermal Fibroblasts

value: U


title: Myers_Melano_1_None_Duke

description: Reduced Representation

source_name: Melano

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Melano_Crawford_protocol.pdf

value: Melano

value: melanocytes

value: Duke


title: Myers_LNCaP_1_None_Duke

description: Reduced Representation

value: M


title: Myers_NHBE_1_None_UW

description: Reduced Representation

source_name: NHBE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:NHBE_Crawford_protocol.pdf

value: NHBE

value: normal human bronchial epithelial cells

value: F


title: Myers_NB4_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NB4_protocol.pdf UW_Stam:NB4_Stam_protocol.pdf

value: acute promyelocytic leukemia cell line


title: Myers_MCF10A-Er-Src_1_TAM_1uM_36hr_Stanford

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS(Struhl):MCF-10A_Struhl_protocol.pdf

value: mammary gland, non-tumorigenic epithelial, inducible cell line

value: stable and near-diploid

value: derived from the MCF-10A parental cells and contain ER-Src, a derivative of the Src kinase oncoprotein (v-Src) that is fused to the ligand-binding domain of the estrogen receptor (ER)

value: 36h, 1uM tamoxifen (Myers)

value: Stanford


title: Myers_HMEC_2_None_UW

description: Reduced Representation

source_name: HMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HMEC_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf

value: HMEC

value: Human

value: Human Mammary Epithelial Cells

value: UW


title: Myers_HepG2_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: liver carcinoma

value: cancer

value: endoderm


title: Myers_HAEpiC_2_None_UW

description: Reduced Representation

source_name: HAEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAEpiC_Stam_protocol.pdf

value: HAEpiC

value: Human Amniotic Epithelial Cells

value: U


title: Myers_K562_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: leukemia

value: "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: F

value: HudsonAlpha


title: Myers_HCM_1_None_UW

description: Reduced Representation

source_name: HCM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCM_Stam_protocol.pdf

value: HCM

value: Human Cardiac Myocytes


title: Myers_HRCEpiC_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRCEpiC_Stam_protocol.pdf

value: HRCEpiC

value: Human Renal Cortical Epithelial cells (normal)

value: normal


title: Myers_PANC-1_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:PANC-1_Myers_protocol.pdf UW_Stam:PANC-1_Stam_protocol.pdf

value: Human

value: pancreatic carcinoma

value: cancer, male

value: M


title: Myers_HEEpiC_1_None_UW

description: Reduced Representation

source_name: HEEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

value: Human Esophageal Epithelial Cells

value: UW


title: Myers_GM12878-XiMat_2_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:GM12878-XiMat_Myers_protocol.pdf

value: lymphoblastoid

value: relatively normal

value: International HapMap Project - CEPH/Utah - European Caucasion; Epstein-Barr Virus;Cloned for maternal X inactivation


title: Myers_ECC-1_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:ECC1_Myers_protocol.pdf

value: ECC-1 is a human epithelial cell line derived from an endometrium adenocarcinoma.

value: unknown

value: F


title: Myers_Fibrobl_2_None_Duke

description: Reduced Representation

source_name: Fibrobl

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:fibroblast_Crawford_protocol.pdf

value: Fibrobl

value: Normal child fibroblast; donor sex:female

value: Duke


title: Myers_BC_Left_Ventricle_N41_1_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor N41; Age 26; Asian; DNA Extract

value: Normal

value: Left ventrible

value: BioChain


title: Myers_BC_Pancreas_H12817N_1_None_BioChain

description: Reduced Representation

value: Human

value: Donor H12817N; Age 71; Caucasian; DNA and RNA Extract

value: Pancreas

value: M


title: Myers_T-47D_2_Estradiol_10nM_24hr_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:T47D_Myers_protocol.pdf

value: T-47D is a human epithelial cell line derived from an mammary ductal carcinoma.

value: hypotriploid

value: 24,10nM Estradiol  (Myers)

value: HudsonAlpha


title: Myers_GM19239_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM19239_Crawford_protocol.pdf

value: B-Lymphocyte

value: YORUBA, Epstein-Barr Virus, Male


title: Myers_BC_Testis_N30_2_None_BioChain

description: Reduced Representation

value: Donor N30; Age 41; Asian; DNA Extract

value: Testis


title: Myers_HNPCEpiC_1_None_UW

description: Reduced Representation

source_name: HNPCEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HNPCEpiC_Stam_protocol.pdf

value: HNPCEpiC

value: Human Non-Pigment Ciliary Epithelial Cells

value: U

value: UW


title: Myers_HCF_1_None_UW

description: Reduced Representation

source_name: HCF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCF_Stam_protocol.pdf

value: HCF

value: Human Cardiac Fibroblasts


title: Myers_PrEC_1_None_UW

description: Reduced Representation

source_name: PrEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:PrEC_Stam_protocol.pdf

value: PrEC

value: Human

value: Human Prostate Epithelial Cell line

value: Normal

value: Epithelial


title: Myers_BC_Breast_02-03015_1_None_BioChain

description: Reduced Representation

value: Donor 02-03015; Age 21; Caucasian; DNA Extract

value: Breast

value: F

value: BioChain


title: Myers_SAEC_2_None_UW

description: Reduced Representation

source_name: SAEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SAEC_Stam_protocol.pdf

value: SAEC

value: Small Airway Epithelial Cells

value: normal


title: Myers_HCPEpiC_2_None_UW

description: Reduced Representation

source_name: HCPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells


title: Myers_AG04449_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04449_Stam_protocol.pdf

value: Fetal buttock/thigh fibroblast

value: M

value: UW


title: Myers_NT2-D1_1_None_Uw

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NT2-D1_protocol.pdf

value: malignant pluripotent embryonal carcinoma (Ntera2)

value: cancer

value: "The NTERA-2 cl.D1 cell line is a pluripotent human testicular embryonal carcinoma cell line derived by cloning the NTERA-2 cell line." - ATCC

value: Uw


title: Myers_HRE_1_None_UW

description: Reduced Representation

source_name: HRE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

value: HRE

value: Human

value: Human Renal Epithelial cells (normal)

value: U


title: Myers_BC_Lung_01-11002_1_None_BioChain

description: Reduced Representation

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Normal

value: Lung

value: F

value: BioChain


title: Myers_HCF_2_None_UW

description: Reduced Representation

value: HCF

value: Human Cardiac Fibroblasts


title: Myers_NB4_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NB4_protocol.pdf UW_Stam:NB4_Stam_protocol.pdf

value: acute promyelocytic leukemia cell line


title: Myers_HAEpiC_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HAEpiC_Stam_protocol.pdf

value: HAEpiC

value: Human Amniotic Epithelial Cells

value: UW


title: Myers_IMR90_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:IMR90_Stam_protocol.pdf

value: Normal Human Lung Fibroblasts


title: Myers_HEK293_1_None_Uw

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: embryonic kidney

value: cancer

value: endoderm

value: Uw


title: Myers_BC_Pericardium_H12529N_2_None_BioChain

description: Reduced Representation

value: Human

value: Donor H12529N; Age 70; Caucasian; DNA Extract

value: Pericardium


title: Myers_Melano_2_None_Duke

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:Melano_Crawford_protocol.pdf

value: Melano

value: melanocytes

value: U

value: Duke


title: Myers_BC_Pancreas_H12817N_2_None_BioChain

description: Reduced Representation

value: Donor H12817N; Age 71; Caucasian; DNA and RNA Extract

value: Normal

value: Pancreas

value: M

value: BioChain


title: Myers_GM12891_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:GM12891_Crawford_protocol.pdf

value: B-Lymphocyte

value: CEPH/UTAH PEDIGREE 1463, Epstein-Barr Virus, Male

value: HudsonAlpha


title: Myers_AG04450_1_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: Fetal lung fibroblast

value: UW


title: Myers_HIPEpiC_1_None_UW

description: Reduced Representation

source_name: HIPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HIPEpiC_Stam_protocol.pdf

value: HIPEpiC

value: Human

value: Human Iris Pigment Epithelial Cells


title: Myers_BC_Skeletal_Muscle_01-11002_2_None_BioChain

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Myers_BioChain_protocol.pdf

value: Donor 01-11002; Age 83; Caucasian; DNA and RNA Extract

value: Skeletal muscle

value: F


title: Myers_HEEpiC_2_None_UW

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

value: Human Esophageal Epithelial Cells

value: U


title: Myers_AoSMC_1_None_Duke

description: Reduced Representation

source_name: AoSMC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:AoSMC_Crawford_protocol.pdf

value: AoSMC

value: aortic smooth muscle cells

value: Duke


title: Myers_IMR90_2_None_UW

description: Reduced Representation

value: Normal Human Lung Fibroblasts


title: Myers_HSMM_1_None_Duke

description: Reduced Representation

source_name: HSMM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HSMM_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HSMM_HSMMtube_Crawford_protocol.pdf

value: HSMM

value: Normal Human Skeletal Muscle Myoblasts

value: normal

value: B


title: Myers_Jurkat_2_None_UW

description: Reduced Representation

source_name: Jurkat

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Jurkat_protocol.pdf UW_Stam:Jurkat_Stam_protocol.pdf

value: Jurkat

value: T lymphoblastoid cell line derived from an acute T cell leukemia

value: cancer

value: "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC

value: M

value: UW


title: Myers_PanIslets_5_None_Duke

description: Reduced Representation

source_name: PanIslets

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:PanIslets_Crawford_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin(Lieb):PanIslets_Lieb_protocol.pdf

value: PanIslets

value: Human

value: human pancreatic islets


title: Myers_PFSK-1_1_None_HudsonAlpha

description: Reduced Representation

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:PFSK-1_protocol.pdf

value: neuroectodermal cell line derived from a human cerebral brain tumor

value: ectoderm

value: HudsonAlpha