title: EN_30_d11P.6

description: RawCountsCellPops.txt


title: WT_replicate3

status: Public on Oct 17 2016

type: SRA

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

country: USA

institute: New York University

library_source: genomic

data_processing:
bowtie2 (version 2.2.3) was used to align paired-end fastq files to the S. cerevisiae reference genome
sam files were converted to bam files using samtools. Reads were sorted and filtered to exclude reads with mapq score <30
Remove PCR duplicates: Use MarkDuplicates function in picard tools to mark PCR duplicates in bam file. Used options -Xmx4g , REMOVE_DUPLICATES=false, ASSUME_SORTED=true. Remove reads in bam file marked as PCR duplicates using samtools view using option -F 0x400
Sort bam file by read name using samtools sort using option -n. Convert sorted bam file to a bedpe file using bedtools bamtobed using options -i, -bedpe, - mate1
An in-house python script was used to convert the bedpe file from a zero-based bedpe file to a one-based bedpe. In Bedpe files, starts are zero-based and ends are one-based.
An in-house python script was used to convert the bedpe file to a bed file where it records the 3’ or 5’ ends of the mates depending on whether the first mate is watson or crick. A fragment length limit of 1000 is also imposed.
Linux command sort is used to sort the bed file by chromosome, then base. The options used were -k1n,1 -k2n,2 -t $'\t'
Two sgr files for watson and crick fragments are created from the bed file using bedtools genomecov. The options used are -i, -g with a genome size file containing the sizes of each chromosome, -d, -strand with either ‘+’ or ‘-‘.
Percent Watson and percent Crick strand files were calculated from the sgr files, adding 1 to all values to avoid zeros
Genome_build: Genome_build: Yeast S288C, build R64-1-1, released Feb 2011
Supplementary_files_format_and_content: [.sgr] Percent Watson strand hit files calculated per chromosome and per base.  Three columns: chromosome, base,Percent Watson strand hits

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: WT

growth_protocol: YPD, 30˚C

extract_protocol:
Okazaki fragments were enriched and purified as described previously (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)
Libraries were generated as previously described (Smith, D. J., and Whitehouse, I. (2012). Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 483, 434-438)

treatment_protocol: All cells were treated with doxycycline for 2.5h to deplete DNA ligase. For HU-treated cultures, HU was added to 25 mM 1h before the addition of doxycycline.

tag: strain background

tag: genotype/variation

value: WT

tag: construct

value: Doxycycline-repressible CDC9 allele

tag: molecule subtype

value: DNA; Okazaki Fragments

tag: treatment

value: doxycycline for 2.5h


title: UMI_3

city: Stockholm

first: Ilgar

last: Abdullayev

address: Nobels väg 3

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Processing raw reads: The sequence in FastQ file corresponding to UMIs were removed from sequence reads and appended to the read name (for later analyses). Adapter and polyA sequences were removed from reads using cutadapt v1.8.1, with minimum overlap between adapter and the 3’ of the read set to 1 nt. Reads shorter than 18 nt after adaptor trimming were discarded.
Alignment: Trimmed reads were aligned to the human genome (hg38) using STAR v2.4.0 with parameters --outSAMstrandField intronMotif --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 18 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1. We did not allow any mismatches within the first 25 nucleotides and allowed only 1 mismatch in the remaining part of the sequence reads (25 – 41 nts). Spliced alignments were disabled and hard/soft-clipping was disabled for the 5’ of the read. Soft-clipping of up to 3 nts were allowed at the 3’ end of the read in order to account for RNA editing and 3’ tRNA modifications such as addition of CCA. Reads mapping with insertions or deletions were removed.
Counting unqiue molecules: We collapsed PCR amplicons and counted RNA molecules using the adjacency network approach (dedup_umi.py at https://github.com/CGATOxford/UMI-tools), where reads with UMIs having a single Hamming distance from another UMI were collapsed. We separated RNA molecule counts into two categories based on the extent of the alignment of our sequenced read with the human genome. Reads aligning over the full sequence (41 nts) were assigned as precursor molecules, whereas reads aligning with 40 or less nts were assigned as a potential small RNA. Potential small RNAs were further scrutinized to find instances were trimmed 3’ ends matched the genomic sequence after the alignment (cases where actual RNA sequence matched adapter sequence, false positive adapter trimming). Consequently, these molecules were instead assigned to the precursor RNA.
Annotating molecules: We estimated expression for annotation transcripts in the following databases (Gencode V22, Mirbase V21 and GtRNAdb).  During the quantification procedure, molecules were hierarchical assigned to annotated biotypes in the following order: Mirbase miRNAs, tRNAs from GtRNAdb, small RNA biotypes from Gencode (such as snoRNAs, snRNAs, rRNAs etc.), and lastly the remaining of Gencode transcripts such as protein coding and lincRNAs. We counted molecules from both intronic and exonic regions of the protein coding and lincRNAs in an attempt to capture small RNAs transcribed from these regions. We used a weighing approach to assign molecules of sequences mapping to multiple genomic location, by divided by number of annotated location the sequence aligned to. Finally, for miRNAs we collapsed molecules supporting the same miRNA that were expressed from different genomic loci (i.e. where the microRNAs gene was present in multiple genomic locations).
Filtering samples: We excluded libraries with fewer than one million reads (before alignment) and if the number of expressed transcripts were more than two standard deviations of the median number of expressed transcripts obtained within the cell population (to filter out potential doublets and low-quality libraries). All analyses in the manuscript was carried out on small RNA molecule counts (i.e. amplicon corrected values), except otherwise noted.
Genome_build: hg38
Supplementary_files_format_and_content: Tabular expression matrix

molecule: total RNA

organism: synthetic construct

source_name: Artificial

growth_protocol: HEK293T and glioblastoma cells (U87, KS4, JM3, JM4) were mycoplasma tested. Naïve Stem Cell Culture: Human ESC line WA09 (female) (WiCell, Madison, WI) was transitioned from conventional primed conditions to 5iAF naïve state by closely following the conversion protocol described in Theunissen et al., 2014. Naïve hESCs were maintained and expanded in a medium containing 50:50 N2B27/Neurobasal (GIBCO) with 1mM glutamine (Invitrogen), 1% NEAA (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), and freshly supplemented with 10 µM Y-27632 ROCKi (Stemgent), 1 µM PD0325901 MEKi (Sigma), 1 µM IM-12 GSK3i (Sigma), SB590885 BRAFi (Sigma), 1 µM WH-4-023 SRCi (Sigma), 20 ng/ml Activin A (R&D), 0.5 % KOSR (Invitrogen), 8 ng/ml bFGF (R&D), 50 ug/ml BSA (Sigma), and 20 ng/ml hLIF (Millipore) (Theunissen et al. 2014). Cells were propagated on irradiated E12.5 MEFs (GIBCO) seeded at 250 k cells/well of a 6 well (9.5 cm2), and once colonies reached confluence they were dissociated and expanded by single cell using Accutase (GIBCO). WA09 (H9) has been mycoplasma tested and validated for pluripotency by teratoma assay (in primed state) as well as immunocytochemistry (for both naive and primed). Based on our Smart-seq2 data, our cells exhibit a transcriptional profile that are indicative of the previously reported works that we aimed to reproduce. This cell line was obtained from WiCell Research Institute, Inc. from which we hold the MTA (license). Primed Stem Cell Culture: Conventional primed human hESC line WA09 (WiCell, Madison, WI) was maintained on a layer of mouse embryonic fibroblasts (MEF), in media consisting of: DMEM: F12 (Invitrogen), 20 % KSR (Invitrogen), 4 ng/ml bFGF (R&D), 2 mM glutamine (GIBCO), 0.1 mM non-essential amino acids (Invitrogen), 0.1 mM ß-Mercaptoethanol (Sigma). Once colonies reached confluence they were mechanically passaged through dissociation using a 26-gauge needle (VWR).

extract_protocol:
Cells were lysed directly into the reaction tube. No RNA extraction was performed.
Plates were pre-deposited with 3 µl of lysis buffer (0.13 % Triton-X-100, 4 u recombinant RNase Inhibitor, Takara). After single cell sorting, the plates were transferred to -80 °C for long storage. After thawing the plate, 1 µl of 5.8 S rRNA masking oligo (5 pmol) was added and the whole plate was incubated at 72 °C for 20 minutes.  Then, 2 µl of 3’ adaptor ligation reaction was added (20 pmol 3’ adaptor oligo, 8.33 % PEG 8000, 50 u T4 RNA Ligase 2, truncated KQ, NEB, 0.83 X T4 RNA ligase buffer, NEB, 4 u recombinant RNase Inhibitor, Takara) and reaction was incubated at 30 °C for 6 h followed by 4 °C for 10 hours.  Next, 3 µl of RT primer and free adaptor removal enzymes were added (200 pmol RT primer, 2.5 u Lambda exonuclease, NEB, 10 u 5’ deadenylase, NEB) and the reaction was incubated at 30 °C for 15 minutes followed by 37 °C for 15 minutes. Next, 2 µl of 5’ adaptor ligation reaction was added (45 pmol 5’ adaptor oligo, 0.68 mM Tris-buffered ATP, Thermo Fisher, 4 u T4 RNA ligase, Thermo Fisher,  0.23 X T4 RNA ligase buffer, NEB ) and the mix was incubated at 37 °C for 1 hour. Reverse transcription reaction was performed by adding 7 µl of RT reaction (1.28 X Taq DNA Polymerase PCR Buffer, Thermo Fisher, 8.33 mM DTT, 0.42 mM/each dNTP, 4 u recombinant RNase Inhibitor, 150 u Superscript II reverse transcriptase, Thermo Fisher). The PCR amplification is carried out by adding 35 µl of the reagents (0.94 X Phusion HF buffer, 1 u Phusion Hot Start II DNA Polymerase, Thermo Fisher, 0.12 mM/each dNTP,  1.89 µM RP1 primer) and incubating at 98 °C for 30 seconds followed by 13 cycles of 98 °C for 10 seconds, 60 °C for 30 seconds and 72 °C for 30 seconds and a final incubation at 72 °C for 5 minutes. At last, 1 µl of the amplified product is transferred to a fresh tube and the second PCR reaction is added (2 µM indexed primers, 0.2 µM RP1 primer, 1 X Phusion HF buffer, 0.5 u Phusion Hot Start II DNA Polymerase, Thermo Fisher,  0.2 mM/each dNTP) and incubating at 98 °C for 30 seconds followed by 13 cycles of 98 °C for 10 seconds, 67 °C for 30 seconds and 72 °C for 30 seconds and a final incubation at 72 °C for 5 minutes. The amplified libraries of single cells are then pooled and purified with DNA Clean & Concentrator™-5, Zymo research. All samples have been sequenced 1x 43 bp or 1x 51 bp using Illumina HiSeq 2500 instrument.

tag: sample type

value: Artificial


title: EN_30_d11P.5

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: WEHI

description: RawCountsCellPops.txt

data_processing:
Illumina CASAVA pipeline version 1.8.2 used for basecalling.
The raw reads were mapped to the human genome (hg19) using the STAR aligner version 2.4.0h1 in the two pass mapping mode
The mapped reads were quantified at the gene level using featureCounts version 1.4.6 using GENCODE Release 19 comprehensive annotation
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with Gene symbol and Gene length in the first two columns, followed by 26 columns containing counts for each sample

organism: Homo sapiens

source_name: day 11 differentiated SOX17 mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

value: d2 SB & CHIR plus BVSAF

tag: culture medium

value: APEL cell culture medium


title: EN_30_d11P.4

description: RawCountsCellPops.txt

value: BMP4, VEGF,SCF,ACTIVIN A, FGF (BVSAF)


title: UMI_8


title: WT_replicate2


title: UMI_2


title: EN_39_d10.1

description: RawCountsCellPops.txt

source_name: day 10 differentiated SOX17 mCHERRY/w RUNX1C GFP/w H9 human embryonic stem cells


title: EN_30_d11P.3

description: RawCountsCellPops.txt


title: WT_replicate1


title: UMI_1


title: EN_30_d11P.1

description: RawCountsCellPops.txt


title: Schwann 1

status: Public on Oct 16 2016

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

data_processing:
Sequence quality control and alignment to the Rn5 reference genome were performed with TopHat 2.1.0 (Trapnell et al. 2009).
Estimates of gene expression levels were calculated with the GeneProf Quantitate Gene Expression module.
Differential gene expression was performed with DESeq v2.6 (Anders & Huber 2010).
Statistical analysis was performed with SPSS Statistics (IBM) software and GENE-E (Broad Institute) web-based application.
Functional enrichment analysis was performed with FunRich (Pathan et al. 2015).
Genome_build: Rn5
Supplementary_files_format_and_content: BAM alignment were converted to wig files with the GeneProf web-based software (Halbritter et al. 2012; Halbritter et al. 2014).

organism: Rattus norvegicus

source_name: Primary Schwann cells

extract_protocol:
RNA isolation was performed with the RNeasy Mini Kit (QIAGEN).
Libraries were prepared with the TruSeq RNA Library Preparation Kit v2 (Illumina) and sequenced with the Genome Analyzer IIx (Illumina).

tag: cell type

value: Primary Schwann cells


title: Schwann 3


title: iSchwann 1

source_name: Fibroblast-derived Schwann cells

value: Fibroblast-derived Schwann cells


title: Fibroblast 2

source_name: Primary fetal fibroblasts

value: Primary fetal fibroblasts


title: Fibroblast 1


title: Fibroblast 3


title: Schwann 2


title: MW2 RPMI liquid 37C Bioreplicate1 mRNA-seq

status: Public on Oct 15 2016

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description: Ribopedletion followed by stranded RNAseq preparation

data_processing:
FASTQ files for each EMOTE sample is obtained by demultiplexing the original FASTQ file according to the EMOTE-barcode detected in the reads. Demultiplexing is performed by EMOTEconv program, allowing for 1 mismatch in the EMOTE recognition sequence.
EMOTE reads are parsed from the FASTQ files to extract the UMI sequence, and the mapping sequence. This step is performed by EMOTEconv program.
The mapping sequence of each read is aligned to the corresponding bacterial genome using Bowtie. Reads aligning to multiple position on the genome are ignored to keep only unambiguously mapped reads.
For each position on the genome, Emoteconv quantify the number of read whose first base align at this position (N value). In a second it corrects for potential PCR bias by removing duplicated reads (that have the same UMI sequence), and quantify again (Q value).
Supplementary_files_format_and_content: EMOTE_Saureus_unambiguous.tsv.gz: abundance measurements across S. aureus genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Eaerogenes_unambiguous.tsv.gz: abundance measurements across E. aerogenes genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Sepidermidis_unambiguous.tsv.gz: abundance measurements across S. epidermidis genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Abaumannii_unambiguous.tsv.gz: abundance measurements across A. baumannii genome (tab separated text file)

organism: Staphylococcus aureus

source_name: exponentially growing culture

extract_protocol: RNA extraction protocol not provided.

tag: growth conditions

value: 37°C, RPMI liquid

tag: strain


title: MW2 RPMI liquid 37C Bioreplicate2 mRNA-seq


title: MW2 MH agar 37C Bioreplicate2 without RppH

description: processed data file: EMOTE_Saureus_unambiguous.tsv.gz

data_processing:
Library strategy: TSS-EMOTE
FASTQ files for each EMOTE sample is obtained by demultiplexing the original FASTQ file according to the EMOTE-barcode detected in the reads. Demultiplexing is performed by EMOTEconv program, allowing for 1 mismatch in the EMOTE recognition sequence.
EMOTE reads are parsed from the FASTQ files to extract the UMI sequence, and the mapping sequence. This step is performed by EMOTEconv program.
The mapping sequence of each read is aligned to the corresponding bacterial genome using Bowtie. Reads aligning to multiple position on the genome are ignored to keep only unambiguously mapped reads.
For each position on the genome, Emoteconv quantify the number of read whose first base align at this position (N value). In a second it corrects for potential PCR bias by removing duplicated reads (that have the same UMI sequence), and quantify again (Q value).
Supplementary_files_format_and_content: EMOTE_Saureus_unambiguous.tsv.gz: abundance measurements across S. aureus genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Eaerogenes_unambiguous.tsv.gz: abundance measurements across E. aerogenes genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Sepidermidis_unambiguous.tsv.gz: abundance measurements across S. epidermidis genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Abaumannii_unambiguous.tsv.gz: abundance measurements across A. baumannii genome (tab separated text file)

extract_protocol:
RNA extraction protocol not provided.
EMOTE, as described in associated paper

value: 37°C, MH agar

value: without RppH

tag: emote library

tag: emote barcode

value: TCGG


title: iSchwann 3


title: MW2 MH agar 37C Bioreplicate2 with RppH

value: with RppH

value: CAAG


title: MW2 RPMI liquid 37C Bioreplicate2 without RppH

value: CGTC


title: MW2 RPMI liquid 37C Bioreplicate2 with RppH

value: AAGT


title: MW2 MH agar 37C Bioreplicate1 without RppH

value: CCGA


title: MW2 MH liquid 30C Bioreplicate1 with RppH

value: 30°C, MH liquid

value: GGTA


title: MW2 MH liquid 30C Bioreplicate2 with RppH

value: GTAT


title: MW2 MH liquid 30C Bioreplicate2 without RppH

value: TACA


title: MW2 MH liquid 37C Bioreplicate2 with RppH

value: 37°C, MH liquid


title: MW2 MH agar 37C Bioreplicate1 with RppH

value: CTCG


title: MW2 RPMI liquid 37C Bioreplicate1 with RppH


title: MW2 RPMI liquid 37C Bioreplicate1 without RppH


title: AD+SB+LDN_rep1

city: Shanghai

first: Xiaoqing

last: Zhang

address: 1239 Siping Road

country: China

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.14
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v2.0.2. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: embryonic stem cell_AD treated with SB431542 and LDN193189

extract_protocol:
Cells were cultured at different conditions and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: tissue

value: inner cell mass

tag: age

value: culture for 4 days

tag: genotype

value: wild type

tag: culture condition

value: AD with SB431542 and LDN193189


title: MW2 MH liquid 37C Bioreplicate1 with RppH


title: CNOT7KD high temp 1

city: Worcester

first: Rhonda

middle: Leah

last: McFleder

state: MA

address: 373 Plantation st, Biotech II, S204

department: Molecular Medicine

institute: University of Massachussets Medical School

description:
mRNAs with long poly(A) tails (>50) from cells infected with CNOT7 shRNA replicate 1
DESeq_WT75xK75_sig.csv
all.rsem.gene.summary.tpm.txt

data_processing:
Illumina RTA CASAVA program was used for base calling.
Sequencing reads were trimmed for the adaptor sequences and low-quality sequence, before being mapped to the mm10 genome using Tophat2. Sequences were then mapped to the transriptome using RSEM.
Differential expression was compared between the CNOT7KD and Scrambled total RNA samples, and between the CNOT7KD and Scrambled long-tailed samples using DESeq2 in R.
Genome_build: mm10
Supplementary_files_format_and_content: Output from RSEM and DESeq

molecule: polyA RNA

organism: Mus musculus

source_name: CNOT7KD high temp, cultured hippocampal neurons

growth_protocol: Primary cultured hippocampal neurons were isolated from mice embryos (E19) and cultured using standard procedures.

extract_protocol:
Total RNA was extracted using Trizol, RNA was then incubated with poly(U) agarose to isolate polyadenylated mRNA. Total polyadenylated mRNA was extracted using 75˚C extraction buffer to remove all polyadenylated mRNAs from the agarose. To isolate only mRNAs with long poly(A) tails, agarose was washed with 50˚C wash buffer to remove all mRNAs with short poly(A) tails (<50) long poly(A) tails were then extracted with 75˚C extraction buffer (high-temp samples).
Libraries were prepared using the Nextflex qRNA-Seq Kit v2

treatment_protocol: At DIV13-15, cultured hippocampal neurons were infected with a lentivirus expressing either a scrambled or CNOT7 targeting shRNA.

value: cultured hippocampal neurons

tag: genotype/variation

value: CNOT7 knockdown

tag: days in vitro (div)

tag: poly(a) tail size

value: long poly(A) (>50)


title: CNOT7KD high temp 2

description:
mRNAs with long poly(A) tails (>50) from cells infected with CNOT7 shRNA replicate 2
DESeq_WT75xK75_sig.csv
all.rsem.gene.summary.tpm.txt


title: EB+SB+LDN_rep2

source_name: embryonic stem cell_EB treated with SB431542 and LDN193189

value: EB with SB431542 and LDN193189


title: Scrambled high-temp 2

description:
mRNAs with long poly(A) tails (>50) from cells infected with Scrambled shRNA replicate 2
DESeq_WT75xK75_sig.csv
all.rsem.gene.summary.tpm.txt

source_name: Scrambled high-temp, cultured hippocampal neurons

value: control


title: EB+SB+LDN_rep1


title: pglp1_LC_01

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.8 software used for basecalling.
Illumina reads were mapped to the TAIR9 release of the Arabidopsis thaliana genome using the CLC Genomics Workbench with default parameters.
The resulting raw read counts were used for downstream analyses.
RNAseq data were statistically evaluated using edgeR on raw read counts as implemented in Bioconductor. Genes were called significantly differentially expressed if the FDR (q) value was below 0.01.
Reads Per Kilobase per Million mapped reads (RPKM) were reported for all transcripts. RPKM values were averaged for the replicates of each condition and the log2 fold-changes between LC and HC values (= LC/HC-fold changes) were calculated by formally adding one read to all RPKM values to account for transcripts with no expression detected in one or more samples before fold-change calculation and logarithmic transformation.
Supplementary_files_format_and_content: Excel sheet (Supplemental Table 4.xls) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw counts, RPKM for each sample and mean RPKM for biological replicates, log2 fold-changes between LC and HC values (log2FC), and edgeR results of differential gene expression comparing LC against HC transcript abundances of each plant line.

organism: Arabidopsis thaliana

source_name: pglp1-1, T-DNA insertion line, LC

growth_protocol: Plants were grown in controlled environmental chambers (Percival; 10/14-h day/night cycle, 20/18 °C, ~120 µmol photons m-2 s-1, 10000 mL L-1 CO2, and 70% relative humidity) on a 4:1 mixture of soil and vermiculite and regularly watered with 0.2% Wuxal liquid fertilizer.

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Nucleospin RNA plant kit (Macherey-Nagel). Residues of DNA were removed with DNase (Fermentas). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed  and sequenced in single-end mode (100 bp read length) on an Illumina HiSeq 2000 platform and in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform, respectively.

treatment_protocol: At growth stage 5.1 (Boyes et al., 2001) the HC-to-LC transition was carried out at the end of the dark period with reducing the CO2 concentration from high CO2 (HC; 1%) to low CO2 (LC; 0.038%) while all other growth parameters were kept constant. Samples were taken under HC conditions and after the HC-to- LC transition, 8 h after onset of light.

value: leaf

value: pglp1-1, T-DNA insertion line

tag: co2 condition

value: LC


title: Scrambled high-temp 1

description:
mRNAs with long poly(A) tails (>50) from cells infected with Scrambled shRNA replicate 1
DESeq_WT75xK75_sig.csv
all.rsem.gene.summary.tpm.txt


title: AD+SB+LDN_rep2


title: iSchwann 2

value: Fibroblast-derived Schwann cells


title: Scrambled 2

description:
Total mRNA from cells infected with Scrambled shRNA replicate 2
DESeq_WTxK_sig.csv
all.rsem.gene.summary.tpm.txt

source_name: Scrambled, cultured hippocampal neurons

value: total poly(A)


title: MW2 MH liquid 37C Bioreplicate2 without RppH

tag: treatment

value: without RppH

value: ACAC


title: CNOT7KD 2

description:
Total mRNA from cells infected with CNOT7 shRNA replicate 2
DESeq_WTxK_sig.csv
all.rsem.gene.summary.tpm.txt

source_name: CNOT7KD, cultured hippocampal neurons


title: EB_rep2

source_name: embryonic stem cell_EB

value: EB


title: EB_rep3

value: inner cell mass


title: Scrambled 1

description:
Total mRNA from cells infected with Scrambled shRNA replicate 1
DESeq_WTxK_sig.csv
all.rsem.gene.summary.tpm.txt


title: mutant rep1

city: Jerusalem

first: Sharona

last: Tornovsky Babaey

address: Jerusalem 91120, Israel

department: Endocrinology and Metabolism

country: Israel

institute: Hebrew University-Hadassah Medical Center

description: processed data file column: F0_ZM

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse mm9 genome and Refseq transcriptome, as well as for transcript quantitation .
Differential expression analysis was carried out using a custom script implementing EdgeR software
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited file of raw read counts

source_name: pancreatic islets

growth_protocol: mice were kept in SPF facility

extract_protocol:
Pancreatic islets were isolated from transgenic GCK mutant (GCK Y214C) and control littermates. RNA was extracted using Qiagen RNA extraction Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment prior to RNA extraction

value: Pancreatic islets

value: 5-6 weeks


title: glyk1_LC_02

source_name: glyk1-1, T-DNA insertion line, LC

value: glyk1-1, T-DNA insertion line


title: control rep3

description: processed data file column: M0_control

value: wild type


title: MW2 MH liquid 30C Bioreplicate1 without RppH

value: 30°C, MH liquid


title: AD+SB+LDN_rep3

value: culture for 4 days

value: AD with SB431542 and LDN193189


title: mutant rep2

description: processed data file column: F1_ZM


title: glyk1_LC_01


title: CNOT7KD 1

description:
Total mRNA from cells infected with CNOT7 shRNA replicate 1
DESeq_WTxK_sig.csv
all.rsem.gene.summary.tpm.txt

value: cultured hippocampal neurons

value: CNOT7 knockdown


title: EB+SB+LDN_rep3

value: EB with SB431542 and LDN193189


title: shm1_LC_02

source_name: shm1-2, T-DNA insertion line, LC

value: leaf

value: shm1-2, T-DNA insertion line

value: LC


title: EB_rep1


title: hpr1_LC_02

source_name: hpr1-1, T-DNA insertion line, LC

value: hpr1-1, T-DNA insertion line


title: control rep1

description: processed data file column: F3_control


title: hpr1_LC_01


title: pglp1_LC_02

value: pglp1-1, T-DNA insertion line


title: control rep2

description: processed data file column: F4_control


title: mutant rep3

description: processed data file column: F2_ZM


title: upper leaf - plant 3

city: Tainan

first: Yao-Cheng

last: Lin

address: No. 59, Siraya Blvd., SinShih Dist.

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description:
BR3A
Maize leaf with minimal infection by C. zeina

data_processing:
Data were then filtered to remove adapters and trimmed for quality using Trimmomatic (v0.30; (Bolger et al., 2014); settings TruSeq3-PE-2.fa:2:30:10 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 ).
Filtered reads were aligned to v5b.60 of the Zea mays genome (retrieved from the Phytozome v9.1 resource,  Schaeffer et al., 2013) using GSNAP (Wu and Nacu 2010 ) with following setting: -n 3 -A sam --quality-protocol illumina -B 5 -k 15 --maxsearch 50  -t 16  -N 1 --split-output output_file--no-sam-headers --force-xs-dir.
The longest transcript gene structure  in the Z. mays annotation GFF3 file (retrieved from the Phytozome v9.1 resource) was used to estimate the transcript abundance in each locus by HTseq
Count Per Million of library size (CPM) were calculated using a protocol from  edgeR. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the gene of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: v5b.60
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...

organism: Zea mays

source_name: leaf

growth_protocol: Maize B73 grown in the field in Greytown, Kwazulu-Natal, South Africa with natural infection of Cercospora zeina.  Planted in December 2012.

extract_protocol:
Total RNA was extracted using Qiazol, treated with DNAse, and purified with RNeasy Plant Mini kit according to manufacturer’s instructions (Qiagen, Hilden, Germany).  Total RNA was shown to be of good quality using an Agilent Bioanalyser (average RIN number = 7.7).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Maize B73

tag: infection


title: lower leaf - plant 3

description:
BR3B
Maize leaf with severe infection by C. zeina


title: WT_LC_02

source_name: Wildtype, LC

value: Wildtype


title: upper leaf - plant 2

description:
BR2A
Maize leaf with minimal infection by C. zeina


title: WT_LC_01


title: shm1_LC_01


title: lower leaf - plant 1

description:
BR1B
Maize leaf with severe infection by C. zeina


title: lower leaf - plant 2

description:
BR2B
Maize leaf with severe infection by C. zeina


title: upper leaf - plant 1

description:
BR1A
Maize leaf with minimal infection by C. zeina


title: S. epidermidis Bioreplicate2 with RppH

description: processed data file: EMOTE_Sepidermidis_unambiguous.tsv.gz

organism: Staphylococcus epidermidis

value: 37°C, MH liquid

value: with RppH

value: GCTG


title: E. aerogenes Bioreplicate2 without RppH

description: processed data file: EMOTE_Eaerogenes_unambiguous.tsv.gz

organism: Klebsiella aerogenes

value: 37°C, LB medium

value: without RppH

value: CGTC


title: shm1_HC_01

source_name: shm1-2, T-DNA insertion line, HC

value: HC


title: S. epidermidis Bioreplicate2 without RppH

value: TTGA


title: shm1_HC_02


title: E. aerogenes Bioreplicate2 with RppH

value: AAGT


title: glyk1_HC_02

source_name: glyk1-1, T-DNA insertion line, HC

value: glyk1-1, T-DNA insertion line


title: hpr1_HC_01

source_name: hpr1-1, T-DNA insertion line, HC

value: leaf


title: A. baumannii Bioreplicate2 with RppH

description: processed data file: EMOTE_Abaumannii_unambiguous.tsv.gz

organism: Acinetobacter baumannii

source_name: exponentially growing culture

value: CTCG


title: WT_HC_01

source_name: Wildtype, HC


title: pglp1_HC_01

source_name: pglp1-1, T-DNA insertion line, HC


title: A. baumannii Bioreplicate1 without RppH

value: TCGG


title: WT_LC_03

value: LC


title: S. epidermidis Bioreplicate1 with RppH

value: GGTA


title: glyk1_HC_01


title: WT_HC_02


title: S. epidermidis Bioreplicate1 without RppH

value: ACAC


title: E. aerogenes Bioreplicate1 without RppH

value: AGGA


title: WT_HC_03

value: Wildtype


title: A. baumannii Bioreplicate2 without RppH

value: CCGA


title: E. aerogenes Bioreplicate1 with RppH

value: with RppH

value: ATTG


title: A. baumannii Bioreplicate1 with RppH

value: 37°C, LB medium

value: CAAG


title: ChIP-seq from forebrain (ENCLB476ARX)

status: Public on Oct 14 2016

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR992SHK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR992SHK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB476ARX
size range: 300-500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (10.5 days)

tag: antibody

value: forebrain

value: tissue

tag: description

value: Forebrain from 51 embryonic 10.5 day mice

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: pglp1_HC_02

tag: tissue

value: leaf

tag: genotype

value: pglp1-1, T-DNA insertion line

value: HC


title: hpr1_HC_02

value: hpr1-1, T-DNA insertion line


title: ChIP-seq from midbrain (ENCLB054RSL)

description:
https://www.encodeproject.org/experiments/ENCSR989LUY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR989LUY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB054RSL
size range: 300-500

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (10.5 days)

value: midbrain

value: Midbrain from 69 embryonic 10.5 day mice

tag: age

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: ChIP-seq from forebrain (ENCLB900RYV)

description:
https://www.encodeproject.org/experiments/ENCSR992SHK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR992SHK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB900RYV
size range: 300-500

value: Forebrain from 69 embryonic 10.5 day mice

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/


title: ChIP-seq from hindbrain (ENCLB418QBA)

description:
https://www.encodeproject.org/experiments/ENCSR984OHL/
***************
biological replicate number: 1
technical replicate number: 2,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR984OHL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB418QBA
size range: 300-500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (10.5 days)

value: hindbrain

value: tissue

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/


title: ChIP-seq from midbrain (ENCLB742CFZ)

description:
https://www.encodeproject.org/experiments/ENCSR966TCN/
***************
biological replicate number: 2
technical replicate number: 2,3,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR966TCN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB742CFZ
size range: 300-500

value: Midbrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: ChIP-seq from midbrain (ENCLB618BWK)

description:
https://www.encodeproject.org/experiments/ENCSR989LUY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR989LUY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB618BWK
size range: 300-500

value: Len Pennacchio, LBNL

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from embryonic facial prominence (ENCLB228CEE)

description:
https://www.encodeproject.org/experiments/ENCSR914QGB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR914QGB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB228CEE
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: ChIP-seq from embryonic facial prominence (ENCLB140ZQH)

description:
https://www.encodeproject.org/experiments/ENCSR914QGB/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR914QGB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB140ZQH
size range: 300-500

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: ChIP-seq from hindbrain (ENCLB008HIY)

description:
https://www.encodeproject.org/experiments/ENCSR984OHL/
***************
biological replicate number: 2
technical replicate number: 1,2,3
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR984OHL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB008HIY
size range: 300-500

value: Hindbrain from 51 embryonic 10.5 day mice

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: ChIP-seq from hindbrain (ENCLB399PHG)

description:
https://www.encodeproject.org/experiments/ENCSR962MBB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR962MBB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB399PHG
size range: 300-500

value: hindbrain

value: tissue


title: ChIP-seq from limb (ENCLB412JWR)

description:
https://www.encodeproject.org/experiments/ENCSR906RTN/
***************
biological replicate number: 1
technical replicate number: 1,2,3
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR906RTN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB412JWR
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (10.5 days)

value: limb

value: Limb from 69 embryonic 10.5 day mice

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: ChIP-seq from midbrain (ENCLB841FLB)

description:
https://www.encodeproject.org/experiments/ENCSR842LMA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR842LMA
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB841FLB
size range: 300-500

value: Control

value: midbrain

value: Midbrain from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: ChIP-seq from midbrain (ENCLB735ZEL)

description:
https://www.encodeproject.org/experiments/ENCSR842LMA/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR842LMA
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB735ZEL
size range: 300-500

value: Midbrain from 51 embryonic 10.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from fibroblast of arm (ENCLB091KWS)

description:
https://www.encodeproject.org/experiments/ENCSR440MLE/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing Fibroblast of Arm
experiment encode accession: ENCSR440MLE
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB091KWS

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: WGBS from mammary epithelial cell (ENCLB522AUR)

description:
https://www.encodeproject.org/experiments/ENCSR656TQD/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HMEC
experiment encode accession: ENCSR656TQD
assay title: WGBS
assembly: GRCh38
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB522AUR

source_name: Homo sapiens mammary epithelial primary cell female (50 years)

value: mammary epithelial cell

value: mammary epithelial cells

value: 50 year

value: unknown

value: female

value: Bradley Bernstein, Broad

value: ENCBS091ENC at ENCODE; https://www.encodeproject.org/ENCBS091ENC/

value: Derived from ENCODE donor ENCDO830BUW; https://www.encodeproject.org/ENCDO830BUW/

value: ENCODE dbxrefs HMEC; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HMEC


title: ChIP-seq from heart (ENCLB035WYN)

description:
https://www.encodeproject.org/experiments/ENCSR782DGO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR782DGO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB035WYN
size range: 300-500

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (10.5 days)

value: heart

value: tissue

value: Heart from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from heart (ENCLB907BUA)

description:
https://www.encodeproject.org/experiments/ENCSR782DGO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR782DGO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB907BUA
size range: 300-500

value: Heart from 51 embryonic 10.5 day mice

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: ChIP-seq from heart (ENCLB929JTX)

description:
https://www.encodeproject.org/experiments/ENCSR782DEA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR782DEA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB929JTX
size range: 300-500


title: ChIP-seq from midbrain (ENCLB614JTQ)

description:
https://www.encodeproject.org/experiments/ENCSR769ITO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR769ITO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB614JTQ
size range: 300-500

value: midbrain

value: Midbrain from 51 embryonic 10.5 day mice

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: ChIP-seq from hindbrain (ENCLB023MMM)

description:
https://www.encodeproject.org/experiments/ENCSR962MBB/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR962MBB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB023MMM
size range: 300-500

value: hindbrain

value: Hindbrain from 51 embryonic 10.5 day mice

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: ChIP-seq from embryonic facial prominence (ENCLB248BCY)

description:
https://www.encodeproject.org/experiments/ENCSR765JWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR765JWZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB248BCY
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: ChIP-seq from midbrain (ENCLB400FEJ)

description:
https://www.encodeproject.org/experiments/ENCSR747ZXL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR747ZXL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB400FEJ
size range: 300-500

value: tissue

value: Midbrain from 69 embryonic 10.5 day mice

value: embryonic

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: ChIP-seq from forebrain (ENCLB845UZM)

description:
https://www.encodeproject.org/experiments/ENCSR825ZJV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR825ZJV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB845UZM
size range: 300-500

value: forebrain

value: Forebrain from 51 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/


title: ChIP-seq from forebrain (ENCLB013VEF)

description:
https://www.encodeproject.org/experiments/ENCSR825ZJV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR825ZJV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB013VEF
size range: 300-500

value: Forebrain from 69 embryonic 10.5 day mice

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from midbrain (ENCLB310AWZ)

description:
https://www.encodeproject.org/experiments/ENCSR747ZXL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR747ZXL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB310AWZ
size range: 300-500

value: midbrain

value: Midbrain from 51 embryonic 10.5 day mice

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: ChIP-seq from limb (ENCLB527PYJ)

description:
https://www.encodeproject.org/experiments/ENCSR863VHE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR863VHE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB527PYJ
size range: 300-500

value: limb

value: Limb from 69 embryonic 10.5 day mice

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: ChIP-seq from limb (ENCLB271BAA)

description:
https://www.encodeproject.org/experiments/ENCSR863VHE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR863VHE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB271BAA
size range: 300-500

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: WGBS from mammary epithelial cell (ENCLB975DHQ)

description:
https://www.encodeproject.org/experiments/ENCSR656TQD/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HMEC
experiment encode accession: ENCSR656TQD
assay title: WGBS
assembly: GRCh38
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB975DHQ

source_name: Homo sapiens mammary epithelial primary cell female

value: mammary epithelial cell

value: primary cell

value: unknown

value: female

value: Richard Myers, HAIB

value: ENCBS225LHC at ENCODE; https://www.encodeproject.org/ENCBS225LHC/

value: Derived from ENCODE donor ENCDO344AAA; https://www.encodeproject.org/ENCDO344AAA/


title: ChIP-seq from forebrain (ENCLB629XAA)

description:
https://www.encodeproject.org/experiments/ENCSR737JHU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR737JHU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB629XAA
size range: 300-500

value: forebrain

value: Forebrain from 69 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from heart (ENCLB839PRX)

description:
https://www.encodeproject.org/experiments/ENCSR782DEA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR782DEA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB839PRX
size range: 300-500

value: heart

value: tissue

value: Heart from 51 embryonic 10.5 day mice

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: ChIP-seq from forebrain (ENCLB101IFI)

description:
https://www.encodeproject.org/experiments/ENCSR737JHU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR737JHU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB101IFI
size range: 300-500

value: Forebrain from 51 embryonic 10.5 day mice

value: embryonic

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/


title: ChIP-seq from hindbrain (ENCLB734NRG)

description:
https://www.encodeproject.org/experiments/ENCSR731KRE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR731KRE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB734NRG
size range: 300-500

value: hindbrain

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/


title: ChIP-seq from forebrain (ENCLB234LTZ)

description:
https://www.encodeproject.org/experiments/ENCSR735VEJ/
***************
biological replicate number: 2
technical replicate number: 3,2,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR735VEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB234LTZ
size range: 300-500

value: forebrain


title: ChIP-seq from forebrain (ENCLB474BOT)

description:
https://www.encodeproject.org/experiments/ENCSR776WPN/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR776WPN
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB474BOT
size range: 300-500

value: Control


title: ChIP-seq from forebrain (ENCLB743EUA)

description:
https://www.encodeproject.org/experiments/ENCSR776WPN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR776WPN
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB743EUA
size range: 300-500

value: Forebrain from 69 embryonic 10.5 day mice

value: pooled male and female


title: ChIP-seq from limb (ENCLB410VVO)

description:
https://www.encodeproject.org/experiments/ENCSR687ALB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR687ALB
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB410VVO
size range: 300-500

value: limb

value: Limb from 51 embryonic 10.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: ChIP-seq from limb (ENCLB304SBJ)

description:
https://www.encodeproject.org/experiments/ENCSR687ALB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR687ALB
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB304SBJ
size range: 300-500

value: tissue

value: Limb from 69 embryonic 10.5 day mice

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from heart (ENCLB480FUQ)

description:
https://www.encodeproject.org/experiments/ENCSR681NQF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR681NQF
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB480FUQ
size range: 300-500

value: heart

value: Heart from 69 embryonic 10.5 day mice

value: embryonic

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: ChIP-seq from hindbrain (ENCLB437CQW)

description:
https://www.encodeproject.org/experiments/ENCSR703TBR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR703TBR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB437CQW
size range: 300-500

value: hindbrain

value: Hindbrain from 51 embryonic 10.5 day mice

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: ChIP-seq from midbrain (ENCLB146JCJ)

description:
https://www.encodeproject.org/experiments/ENCSR966TCN/
***************
biological replicate number: 1
technical replicate number: 2,3,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR966TCN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB146JCJ
size range: 300-500

value: midbrain

value: Midbrain from 69 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: ChIP-seq from midbrain (ENCLB050TQJ)

description:
https://www.encodeproject.org/experiments/ENCSR769ITO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR769ITO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB050TQJ
size range: 300-500

value: healthy

value: Len Pennacchio, LBNL


title: ChIP-seq from limb (ENCLB088JQZ)

description:
https://www.encodeproject.org/experiments/ENCSR906RTN/
***************
biological replicate number: 2
technical replicate number: 1,3,2
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR906RTN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB088JQZ
size range: 300-500

value: limb

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: ChIP-seq from hindbrain (ENCLB150WCY)

description:
https://www.encodeproject.org/experiments/ENCSR608QBO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR608QBO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB150WCY
size range: 300-500

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from embryonic facial prominence (ENCLB880QXA)

description:
https://www.encodeproject.org/experiments/ENCSR765JWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR765JWZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB880QXA
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: embryonic

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: ChIP-seq from forebrain (ENCLB786YNB)

description:
https://www.encodeproject.org/experiments/ENCSR735VEJ/
***************
biological replicate number: 1
technical replicate number: 2,1,3
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR735VEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB786YNB
size range: 300-500

value: forebrain

value: Forebrain from 69 embryonic 10.5 day mice

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/


title: ChIP-seq from hindbrain (ENCLB001DTM)

description:
https://www.encodeproject.org/experiments/ENCSR731KRE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR731KRE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB001DTM
size range: 300-500

value: hindbrain

value: Hindbrain from 51 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/


title: ChIP-seq from hindbrain (ENCLB732YVL)

description:
https://www.encodeproject.org/experiments/ENCSR594JGI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR594JGI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB732YVL
size range: 300-500

value: tissue

value: healthy

value: Len Pennacchio, LBNL


title: WGBS from fibroblast of arm (ENCLB373TCH)

description:
https://www.encodeproject.org/experiments/ENCSR440MLE/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing Fibroblast of Arm
experiment encode accession: ENCSR440MLE
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB373TCH

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from hindbrain (ENCLB402NEG)

description:
https://www.encodeproject.org/experiments/ENCSR703TBR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR703TBR
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB402NEG
size range: 300-500

value: hindbrain

value: Hindbrain from 69 embryonic 10.5 day mice

value: embryonic

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Patient 10 Tumor

city: Aurora

first: Peter

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

data_processing:
Library strategy: PAS-Seq
Bases were called on raw CIF image files using AYB (http://www.ebi.ac.uk/goldman-srv/AYB/), which simultaneously removed the 14 nt poly(A) tail in bases 7-20, leaving the 6 bp UMI followed by the remainder of the read.
Reads were demultiplexed with fastq-multx (https://github.com/brwnj/fastq-multx) and the demultiplexed reads were processed with cutadapt (https://code.google.com/p/cutadapt/) to remove 3’ adaptor sequences and 3’ bases with QUAL < 10.
Trimmed reads were aligned to the genome using NovoAlign (http://www.novocraft.com/products/novoalign/), and UMIs were collapsed using umitools (https://github.com/brwnj/umitools).
Strand-specific peaks were called on alignments using MACS2 (https://github.com/taoliu/MACS).
Called peaks from all samples were merged to create a master list of breast poly(A) sites. All sites with more than 6 adenosine residues in the 10 bases immediately downstream of the called poly(A) site were excluded from further analysis due to likelihood of priming on genomically encoded poly(A) tracts, and all sites within 5 nt of each other were merged into one site.
Genome_build: hg19
Supplementary_files_format_and_content: BED file containins consensus peak calls (sites of polyadenylation) for all 24 samples.

source_name: Breast tumor

extract_protocol:
Total RNA was isolated using the miRNeasy Kit (Qiagen) according to manufacturer instructions.
We performed PAS-seq with extensive modifications. Total RNA was fragmented and DNase treated by incubating with 1.5X First Strand Buffer (ThermoFisher Scientific) and 50U/mL RQ1 RNase-free DNase (Promega) for 30 minutes at 37C, followed by 3 minutes at 95C. The RNA was then concentrated using the RNeasy minElute kit (Qiagen), and the concentrated, fragmented RNA was reverse transcribed using SuperScript II (ThermoFisher Scientific) as follows: First, 1µg of RNA was mixed with 1µL each of primers 1320 UMI-DT2 (TVN primer with UMI) and 1290 SMART-TRUSEQ (template switching primer) in 12.5µL total volume and incubated at 65C for 5 minutes, followed by a hold at 42C. Next, 4 µL 5X First-strand buffer, 2 µL 100 mM DTT, 0.5 µL RNasin Plus (Promega), and 1 µL SuperScript II were added to the RNA+primers (all pre-warmed to 42C). The reaction was held at 42C for 50 minutes, followed by 15 minutes at 70C. The resulting cDNA was then amplified using Phusion Hot Start II (ThermoFisher Scientific) as follows: 4µL of cDNA and 1µL of TRU-SEQ barcoded primer mix (Illumina) were used in a standard 25µL reaction with the following program: [1. 98C 2:00,  2. 98C 0:10, 3. 60C 0:30, 4. 72C 0:30, 5. repeat steps 2-4 2x, 6. 98C 0:10, 7. 72C 1:00, 8. repeat steps 6-7 24x, 9. 72C 10:00]. Resulting PCR products were then run on a 2% SeaPlaque agarose (Lonza) gel. The region between 250 and 380bp was excised and the DNA purified using the minElute Gel Kit (QIagen). The resulting libraries were then sequenced on an Illumina Hiseq 2000 (50bp, single end).

value: Breast tumor

tag: tumor/normal

value: tumor

tag: er status

value: Positive

tag: pr status

tag: her2 status


title: ChIP-seq from heart (ENCLB493JHQ)

description:
https://www.encodeproject.org/experiments/ENCSR582SPN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR582SPN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB493JHQ
size range: 300-500

value: heart

value: tissue

value: Heart from 51 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: Patient 09 Normal

source_name: Adjacent normal breast tissue

value: Adjacent normal breast tissue

value: normal


title: ChIP-seq from embryonic facial prominence (ENCLB294FWI)

description:
https://www.encodeproject.org/experiments/ENCSR682UEM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR682UEM
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB294FWI
size range: 300-500

value: Control

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/


title: ChIP-seq from embryonic facial prominence (ENCLB909DSC)

description:
https://www.encodeproject.org/experiments/ENCSR682UEM/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR682UEM
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB909DSC
size range: 300-500

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: embryonic

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from midbrain (ENCLB330GHT)

description:
https://www.encodeproject.org/experiments/ENCSR581EJK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR581EJK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB330GHT
size range: 300-500

value: midbrain

value: Midbrain from 69 embryonic 10.5 day mice

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: ChIP-seq from forebrain (ENCLB789URI)

description:
https://www.encodeproject.org/experiments/ENCSR558NWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR558NWQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB789URI
size range: 300-500

value: forebrain

value: tissue

value: Forebrain from 69 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/


title: Patient 11 Tumor

value: Breast tumor

value: tumor

value: Positive

value: Undefined


title: Patient 12 Normal

value: Adjacent normal breast tissue

value: normal


title: ChIP-seq from heart (ENCLB211QML)

description:
https://www.encodeproject.org/experiments/ENCSR681NQF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR681NQF
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB211QML
size range: 300-500

value: Control

value: heart

value: Heart from 51 embryonic 10.5 day mice

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: Patient 12 Tumor

value: Negative


title: Patient 11 Normal


title: ChIP-seq from hindbrain (ENCLB771JVZ)

description:
https://www.encodeproject.org/experiments/ENCSR608QBO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR608QBO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB771JVZ
size range: 300-500

value: hindbrain

value: tissue

value: Hindbrain from 51 embryonic 10.5 day mice

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from hindbrain (ENCLB936VTO)

description:
https://www.encodeproject.org/experiments/ENCSR594JGI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR594JGI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR191XBS
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB936VTO
size range: 300-500

value: Hindbrain from 69 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/


title: Patient 07 Normal

value: Adjacent normal breast tissue

value: normal


title: Patient 10 Normal


title: ChIP-seq from heart (ENCLB690UDD)

description:
https://www.encodeproject.org/experiments/ENCSR455REA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR455REA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB690UDD
size range: 300-500

value: heart


title: ChIP-seq from embryonic facial prominence (ENCLB234QYJ)

description:
https://www.encodeproject.org/experiments/ENCSR538DPG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR538DPG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB234QYJ
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: Patient 06 Tumor

value: Breast tumor

value: tumor


title: Patient 06 Normal


title: Patient 08 Normal


title: Patient 08 Tumor

value: Positive

value: Undefined


title: Patient 09 Tumor


title: ChIP-seq from midbrain (ENCLB908NFO)

description:
https://www.encodeproject.org/experiments/ENCSR581EJK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR581EJK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB908NFO
size range: 300-500

value: midbrain

value: tissue

value: Midbrain from 51 embryonic 10.5 day mice

value: embryonic

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/


title: ChIP-seq from forebrain (ENCLB334LJO)

description:
https://www.encodeproject.org/experiments/ENCSR558NWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR558NWQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB334LJO
size range: 300-500

value: forebrain

value: Forebrain from 51 embryonic 10.5 day mice

value: pooled male and female

value: ENCBS790BBA at ENCODE; https://www.encodeproject.org/ENCBS790BBA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Patient 04 Normal

value: Adjacent normal breast tissue

value: normal


title: Patient 03 Normal


title: ChIP-seq from forebrain (ENCLB692UAN)

description:
https://www.encodeproject.org/experiments/ENCSR368RJD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR368RJD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB692UAN
size range: 300-500


title: ChIP-seq from forebrain (ENCLB503ABN)

description:
https://www.encodeproject.org/experiments/ENCSR368RJD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse forebrain
experiment encode accession: ENCSR368RJD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR776WPN
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB503ABN
size range: 300-500

value: Forebrain from 69 embryonic 10.5 day mice

value: ENCBS152ONW at ENCODE; https://www.encodeproject.org/ENCBS152ONW/


title: Patient 07 Tumor

value: Breast tumor

value: tumor

value: Positive

value: Undefined


title: ChIP-seq from limb (ENCLB316IZZ)

description:
https://www.encodeproject.org/experiments/ENCSR318QFY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR318QFY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB316IZZ
size range: 300-500

value: limb

value: tissue

value: Limb from 51 embryonic 10.5 day mice

value: embryonic

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: ChIP-seq from limb (ENCLB359KXC)

description:
https://www.encodeproject.org/experiments/ENCSR318QFY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR318QFY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB359KXC
size range: 300-500

value: Limb from 69 embryonic 10.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/


title: ChIP-seq from embryonic facial prominence (ENCLB404QJP)

description:
https://www.encodeproject.org/experiments/ENCSR538DPG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR538DPG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB404QJP
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: pooled male and female

value: healthy

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Patient 02 Tumor

value: Breast tumor

value: tumor

value: Negative


title: ChIP-seq from heart (ENCLB104MIA)

description:
https://www.encodeproject.org/experiments/ENCSR582SPN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR582SPN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB104MIA
size range: 300-500

value: heart

value: Heart from 69 embryonic 10.5 day mice

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: ChIP-seq from embryonic facial prominence (ENCLB039NTY)

description:
https://www.encodeproject.org/experiments/ENCSR285IQN/
***************
biological replicate number: 2
technical replicate number: 2,3,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR285IQN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB039NTY
size range: 300-500

value: tissue

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: embryonic

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: ChIP-seq from Karpas-422 (ENCLB054TSL)

description:
https://www.encodeproject.org/experiments/ENCSR963HAR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR963HAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054TSL
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens Karpas-422 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

tag: line

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: adult

value: female

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: ChIP-seq from Karpas-422 (ENCLB500NGD)

description:
https://www.encodeproject.org/experiments/ENCSR963HAR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR963HAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB500NGD
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

value: ENCBS171YVY at ENCODE; https://www.encodeproject.org/ENCBS171YVY/


title: ChIP-seq from Karpas-422 (ENCLB477KVN)

description:
https://www.encodeproject.org/experiments/ENCSR978BQI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR978BQI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB477KVN
size range: 300-700
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf


title: Patient 05 Normal

value: Adjacent normal breast tissue

value: normal


title: Patient 05 Tumor

value: Breast tumor

value: tumor

value: Negative


title: ChIP-seq from heart (ENCLB427SIX)

description:
https://www.encodeproject.org/experiments/ENCSR328WMV/
***************
biological replicate number: 1
technical replicate number: 2,1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR328WMV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB427SIX
size range: 300-500

value: heart

value: tissue

value: Heart from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from fibroblast of arm (ENCLB839TOH)

description:
https://www.encodeproject.org/experiments/ENCSR914AWT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR914AWT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB839TOH
size range: 200-600
nucleic acid starting quantity: 156.75
nucleic acid starting quantity units: ng

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: Patient 04 Tumor

value: Breast tumor

value: tumor

value: Negative

value: Positive


title: ChIP-seq from heart (ENCLB318HWH)

description:
https://www.encodeproject.org/experiments/ENCSR266JQW/
***************
biological replicate number: 2
technical replicate number: 1,3,2
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR266JQW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB318HWH
size range: 300-500

value: heart

value: tissue

value: Heart from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS510GHM at ENCODE; https://www.encodeproject.org/ENCBS510GHM/


title: ChIP-seq from limb (ENCLB831RUI)

description:
https://www.encodeproject.org/experiments/ENCSR238SGC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR238SGC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB831RUI
size range: 300-500

value: limb

value: Limb from 51 embryonic 10.5 day mice

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from heart (ENCLB970TUS)

description:
https://www.encodeproject.org/experiments/ENCSR455REA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR455REA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB970TUS
size range: 300-500

value: Heart from 69 embryonic 10.5 day mice

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: ChIP-seq from heart (ENCLB440EWV)

description:
https://www.encodeproject.org/experiments/ENCSR328WMV/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR328WMV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB440EWV
size range: 300-500


title: Patient 03 Tumor

value: Breast tumor

value: tumor


title: ChIP-seq from OCI-LY1 (ENCLB128JVY)

description:
https://www.encodeproject.org/experiments/ENCSR859JNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859JNA
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB128JVY
size range: 200-600
nucleic acid starting quantity: 35.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY1 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b4b48e6e-d14b-4359-96de-5e8c782c7bcf/@@download/attachment/TF_ChIP_Protocol_from_Shawn.pdf

value: immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: adult

value: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from Karpas-422 (ENCLB045WMI)

description:
https://www.encodeproject.org/experiments/ENCSR867UKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR867UKC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB045WMI
size range: 200-600

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: Patient 02 Normal

value: Adjacent normal breast tissue

value: normal


title: ChIP-seq from embryonic facial prominence (ENCLB098LTB)

description:
https://www.encodeproject.org/experiments/ENCSR285IQN/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR285IQN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB098LTB
size range: 300-500

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from HCT116 (ENCLB700WXT)

description:
https://www.encodeproject.org/experiments/ENCSR810BDB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR810BDB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB700WXT
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: Patient 01 Normal

value: Adjacent normal breast tissue

value: normal


title: ChIP-seq from embryonic facial prominence (ENCLB090LLC)

description:
https://www.encodeproject.org/experiments/ENCSR151APL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR151APL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB090LLC
size range: 300-500

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS199YOQ at ENCODE; https://www.encodeproject.org/ENCBS199YOQ/


title: ChIP-seq from midbrain (ENCLB785CNN)

description:
https://www.encodeproject.org/experiments/ENCSR272GNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR272GNQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB785CNN
size range: 300-500

value: midbrain

value: Midbrain from 51 embryonic 10.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS613YYL at ENCODE; https://www.encodeproject.org/ENCBS613YYL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Patient 01 Tumor

value: Breast tumor

value: tumor

value: Negative


title: ChIP-seq from heart (ENCLB189AXN)

description:
https://www.encodeproject.org/experiments/ENCSR266JQW/
***************
biological replicate number: 1
technical replicate number: 2,1
description: H3K27me3 ChIP-seq on embryonic 10.5 day mouse heart
experiment encode accession: ENCSR266JQW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR681NQF
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB189AXN
size range: 300-500

value: heart

value: Heart from 69 embryonic 10.5 day mice

value: ENCBS366XOW at ENCODE; https://www.encodeproject.org/ENCBS366XOW/


title: ChIP-seq from midbrain (ENCLB140BPV)

description:
https://www.encodeproject.org/experiments/ENCSR272GNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse midbrain
experiment encode accession: ENCSR272GNQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR842LMA
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB140BPV
size range: 300-500

value: tissue

value: Midbrain from 69 embryonic 10.5 day mice

value: ENCBS491CAX at ENCODE; https://www.encodeproject.org/ENCBS491CAX/


title: R1_input

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing:
library strategy: m6A-seq
Base calling was performed using CASAVA 1.3
Alignment was done by TopHat v2.0.14
Peak calling was done by customized algorithm
Genome_build: hg38; panTro4; rheMac2(Mmul_051212)
Supplementary_files_format_and_content: Peaks were generated by customized algorithm, enrichment score of each peak file represented the ratio of reads between m6A-enriched mRNA and intact mRNA.

organism: Macaca mulatta

source_name: LCL

growth_protocol: LCLs were cultured in RPMI1640 media with 15% FBS and Penicillin-Streptomycin

extract_protocol:
Regular RNA isolation
Illumina TruSeq stranded total RNA protocol

treatment_protocol: mRNA was fragmented to ~100nt, and enriched by m6A specific antibody

tag: cell line

value: lymphoblastoid cell line (LCL)

tag: ip antibody

value: none (input)


title: R1_IP

value: m6A specific antibody (SYSY, CAT#202003, LOT#42)