title: Lib4_Rods_Rep4

description:
RNA Barcodes in Rods
processed data file: Lib4Results.tab

extract_protocol:
RNA was isolated from sorted cells using Qiagen RNeasy® Mini Kit with on-column DNase digestion. After reverse transcription using Takara PrimeScript RT Reagent Kit (#RR047A) barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers (Primers #3-11).
barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers (Primers #3-11)

value: Rods

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007913


title: Triptolide-treated sample 1

status: Public on Oct 25 2017

type: SRA

city: New York City

first: Jason

middle: Gardiner

last: Dumelie

state: NY

address: 1300 York Ave

department: Phamacology

country: USA

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
Base calling was perfomed using CASAVA version 1.8.2
Data filtering was performed using Flexbar version 2.5 with the following settings: quality format i1.8, phred minimum of 30, 10 nt removed from 5' end of reads
Alignment was performed using Bismark version 0.14.3 with the following settings: paired-end reads were analysed with the distance between reads limited to 1000 nt, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Alignment was repeated on reads that were not successfully aligned in the first alignment. This second round of alignment used Bismark version 0.14.3 with the following settings: single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Data filtering was performed on reads that did not align in the first two alignment steps using Flexbar version 2.5 with the following settings: all nucleotides 55 nt or further 3' of the start of the read were removed
Alignment was repeated on trimmed reads that were not successfully aligned in the first two alignments. This third round of alignment used Bismark version 0.14.3 with the following settings: trimmed single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Duplicate reads were removed using the deduplicate_bismark tool from the Bismark version 0.14.3 library
The cytosine conversion status of each cytosine in each read was determined using the bismark_methylation_extractor from Bismark version 0.14.3
BisDRIP-seq scores were calculated for each read using custom scripts.  To do this, we first created an estimate of the frequency at which conversions would be seen in a read by chance using a sample-specific estimate of the stochastic rate of conversion.  This frequency was then used to calculate the expected number of reads with a given number of conversions assuming conversions are stochastic and assuming a binomial distribution.  A read bisDRIP-seq score was then calculated based on the ratio of the observed number of reads with a specific cytosine-conversion frequency to the expected number of reads with that cytosine-conversion frequency.  Thus a pair of reads that contained the same number of cytosines and the same number of conversions would be given the same bisDRIP-seq score.
BisDRIP-seq scores for each ten nucleotide region in the genome were calculated by multiplying the bisDRIP-seq score of any reads that aligned to that ten nucleotide region with the fraction of the read that interesected with the ten nucleotide region.
For *bed.txt files: 'bisDRIP-seq scores' were calculated for each read. bisDRIP-seq scores were calculated based on the number of cytosines converted in the read, relative to the likelihood of observing that number of conversions by stochastic noise using a binomial distribution (see Methods from Dumelie and Jaffrey, 2017 for full details).
bisDRIP-seq score were normalized so that the sum of bisDRIP-seq scores within each sample was 1,000,000.
Genome_build: GRCh38
Supplementary_files_format_and_content:
Tab-delimitted files containing the: chromosome, position of a cytosine, number of conversions observed at that cytosine, fraction of reads where that cytosine was converted, number of reads that aligned to that cytosine.
bedGraph files containing: chromosome, start and stop of ten nucleotide region, bisDRIP-seq score of that region
*bed.txt files contain the chromosome, start, stop, read name, bisDRIP-seq score and strand in tab-seperated columns for each read with a bisDRIP-seq score above zero

molecule: genomic DNA

organism: Homo sapiens

source_name: triptolide treatment

growth_protocol: MCF-7 cells (10 million per 15 cm plate) were cultured for three days at 37oC in 50 ml of Gibco's phenol red-free Dulbecco's Modified Eagle's Medium (Thermo Fisher Scientific, Waltham, Massachusetts) containing 5% charcoal-stripped fetal bovine serum (Thermo Fisher Scientific, Waltham, Massachusetts).  Media was replaced after two days.

extract_protocol:
Cells were lysed using SDS in the presense of bisulfite. Bisulfite was dialysed out of the sample. Samples were treated with SDS and proteinase K to remove proteins. Nucleic acids were then extracted with phenol/chloroform. DNA was then digested with restriction enzymes and RNA-DNA hybrids were immunoprecipitated using S9.6 enzymes.
DNA was sonicated using a covaris S-2 into 300 bp fragments. A Pico-Methyl Seq Library Prep Kit (Zymo Research, Irvine, California) was used to create the DNA sequencing library.  This kit is primarily designed for mapping 5-methylcytosine in small quantities of genomic DNA.  We omitted the bisulfite-treatment steps included in this kit.  Instead, only the library preparation steps were followed. These steps were followed for each sample as instructed by the manufacturer.  These steps amplified the DNA and used random priming to add indexes to the DNA library that are compatible with Illumina's TruSeq technology. As described in the Pico-Methyl Seq Library Prep Kit instructions, these indexes contain one of six barcodes that we used to differentiate samples added to the same lane during sequencing.

treatment_protocol: Triptolide was added to the media covering the MCF-7 cells at a concentration of 1 µM.  The plates containing the cells were gently swirled to evenly distribute the triptolide.  The plates were then incubated for 2 hr at 37C.

tag: cell line

value: MCF-7 cells


title: WT 3hr IL6SB  3

city: Chapel Hill

first: Yisong

last: Wan

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill

description: Smad4_Featurecount_STAR_DESeq_exp_log2_normalized.xlsx

library_source: transcriptomic

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
RNA-SEQ reads (~40M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from featureCounts  were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

molecule: total RNA

organism: Mus musculus

source_name: peripheral lymph-nodes and spleens

extract_protocol:
Cells were collected after treatment and RNA extracted with Trizol and purified with with Qiagen Rneasy Kit
Libraries were constructed with the use of the Illumina TruSeq library construction kit V2 (Cat #RS-122-2001) according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina HiSeq 2000 sequencer

treatment_protocol: CD4+ T cells were activated and cultured under Th0 or IL6+TGFbR inhibitor condition

tag: background

tag: gender

value: Female

tag: tissue

value: Spleen+Lymph nodes

tag: cell type

value: CD4+T cell

tag: timepoint

value: 3 hour post treatment

tag: treatment

value: IL6+TGFbR inhibitor

tag: genotype

value: WT


title: Control-treated sample 11

source_name: control

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample received a 40 min 100 µM estrogen treatment.


title: Control-treated sample 12

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample received a 160 min 100 µM estrogen treatment.


title: Triptolide-treated sample 2


title: WT 3hr IL6SB  2


title: Lib4_Rods_Rep2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Barcode sequences were extracted from 50bp reads by taking only reads starting with the expected backbone sequence: “TCCTGCTGGAGTTCGTGACCTGCATGCGCCGAA”. From these reads the sequence at position 34-48 was extracted. The frequency of each barcode sequence was calculated to get counts for each sample. Counts of barcodes were normalized to library size. Enrichment of barcodes in the RNA sample was calculated over their representation in the AAV input. Barcodes not sufficiently covered in the AAV sequencing were discarded (depending on sequencing depth 2-16 reads). The median activity of all barcodes per CRE was calculated. Only CREs that were covered in at least 2 out of 3 biological replicates with at least three barcodes were used for downstream analysis.
processed data: Tab delimited, summary table of the expression values for each tested seqeunce in the tested cell types
Genome_build: mm9

source_name: Rods

tag: mouse strain


title: KO 3hr IL6SB  1


title: Lib4_Rods_Rep3


title: Control-treated sample 13

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes.


title: RNaseHtreatedsample

source_name: MCF-7 cells

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. In this sample, no 100 µM estrogen was added prior to cell lysis.

value: RNase H treated sample. RNase H was added to this sample prior to immunoprecipitation and during the final two wash steps. 0.1U/ul RNase I was added to both samples and two additional washes were performed to the immunoprecipitation. 0.1mM DTT was added as vehicle instead of RNase H.


title: Control-treated sample 10


title: RNAseq_Rods_Rep1

data_processing:
Raw sequence files were aligned using QuasR (using Bowtie as an aligner against the Mus Musculus genome (BSgenome.Mmusculus.UCSC.mm9).Reads in genes were collected using QuasR based on UCSC transcript annotation for mm9 and RPKM per gene were calculated.
processed data: Tab delimited, average RPKM for UCSC transcripts across four cell types
Genome_build: mm9

extract_protocol: After retina dissection and dissociation, cells were FACS-sorted directly in lysis buffer of the RNA-easy mini kit (Qiagen) that was used for RNA extraction. RNA-seq libraries for were prepared using the Norgen single cell RNA-seq preparation kit (51800).


title: Lib3_wholeRetina_Rep3

description:
RNA Barcodes in whole retina
processed data file: Lib3Results.tab

source_name: whole Retina

extract_protocol:
RNA was isolated from sorted cells using Qiagen RNeasy® Mini Kit with on-column DNase digestion followed by reverse transcription using Takara PrimeScript RT Reagent Kit (#RR047A).
barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers (Primers #3-11)

value: whole Retina

value: B6Cf1-Tg(Gja10-Cre, #14)BR x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007917


title: Control-treated sample 7

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample received a 10 min 100 µM estrogen treatment.


title: Control-treated sample 9

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample received a 25 min 100 µM estrogen treatment.


title: Control-treated sample 8


title: KO 3hr IL6SB  2


title: ChIP-seq Cbx7

city: Boston

first: Michael

last: Rosenberg

state: MA - Massachusetts

address: 185 Cambridge street

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

description: ChIP-seq library

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
Adaptor sequences were trimmed from libraries with either Trim Galore! v0.3.3 (for dCLIP-seq and RNA-seq; stringency 15 for dCLIP Control rep 2, dCLIP Cbx7 rep 2 and 3 ; stringency 12 for rest of the experiments; allowed error rate 0.2) or Cutadapt v1.2.1 (for ChIP-seq; allowed error rate 0.2). PCR duplicates were removed by custom programs prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of the ES cell lines, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm9 genome. RNA was aligned with Tophat (v2.0.8 or greater), while DNA was aligned using Novoalign (3.00.03). Post-processing of mm9 alignments was performed with custom C and Perl programs and bash shell scripts, SAMtools v0.1.18, and BEDtools v2.17.0. These included accounting, alignment file-type conversion, extracting and sorting uniquely/paired-end reads (SAMtools), and obtaining wig coverage files (DNA: BEDtools genomecov; RNA: SAMtools depth).
For dCLIP, Fragment per million (fpm) wig files were then created by scaling uniquely aligned wig files to total number of fragments per million in each library (determined by SAMtools flagstat combining reads “with itself and mate mapped” and “singletons”).
dCLIP-seq enriched tag density wig files were viewed in UCSC genome browser (7) or Integrated Genome Browser (IGB) (8). Then consecutive wig entries of equal coverage were merged forming bed files that were used for peak calling. The peak caller software PeakRanger (v.1.16)  was used. The software requires an even distribution of watson/crick entries, thus, prior to peak calling, strand specific bed file entries were randomized per each strand. PeakRanger was called with arguments ranger –p 0.01 –-format bed –gene_annot_file (mm9), –d experiment and –c mock-transfected control, to identify narrow peaks with p-value 0.01 or less. To assemble RNA transcripts from RNA-seq data, Cufflinks (v2.1.1) was used on composite alignments with upper-quartiles-norm normalization, and guided (-g) with mm9 Ensembl transcripts. The resulting transcripts were purged of entries with FPKM=0, converted to bed format, and merged using BEDtools merge with options –nms, -scores mean, -s.
ChIP-seq coverage of uniquely aligned neutral/cas/mus (comp) reads were obtained and normalized to input libraries using in-house software (smoothing parameters: window size 500 and step size 100). To obtain highly significant ChIP peaks, we used the software macs2 (version 2.1.0.20150603) with highly stringent constraints (p 0.01) to identify ChIP peaks versus input for the IP.  Additionally, we compared the IP versus a control IP using PeakSeq (version 1.3) with stringent constraints (Enrichment_fragment_length 200, Enrichment_mapped_fragment_length 200, Background_model Simulated, max_Qvalue 0.1,target_FDR 0.05, N_Simulations 10, Minimum_interpeak_distance 200).  Then we constrained the macs called ChIP peaks to only those that were also called against the control experiment.  Finally, we limited the resulting peaks to those that intersect with IP enriched regions six-fold over the input. IP and input regions are obtained using smoothed coverage data using a 500 nucleotide window with 100 nucleotide steps.
Genome_build: mm9
Supplementary_files_format_and_content:
BigWig files (.bw extension) are coverage files for dCLIP-seq, RNA-seq and ChIP-seq data. I have placed both scaled and unscaled BigWig files. Scaled files have <fpm> added to the file name.
Bed files contain peaks called for dCLIP-seq and ChIP-seq experiments.
dCLIP and RNA-seq BigWig files were arranged strand-specifically. cwig - means CRICK strand. Wwig - Watson strand.
Peakranger bed files were also arranged strand-specifically. Positive strand - Watson strand. Negative - Crick strand.

source_name: ESCs_ChIP-seq Cbx7

growth_protocol: Undifferentiated EL 16.7 Day 0 mouse ES cells were cultured in the presence of LIF under adherent conditions on mouse embryonic fibroblasts feeder layer.

extract_protocol:
Cells were crosslinked with 1.1% formaldeyde for 20 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of 100-500bp. Cleared lysates were incubated overnight with anti-HA tag antibody, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked on 650C and treated with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were constructed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB). Multiplexed library, Ilumina barcode#10, TAGCTT.Paired-end 50bp reads

treatment_protocol: Formaldehyde cross-linking

tag: strain background

value: CAST/Ei x 129/Sv/Jae

tag: Sex

value: female

value: undifferentiated embryonic stem cells

tag: genotype/variation

value: stable expression of HA-tagged Cbx7, clone 12D

tag: chip antibody

value: anti HA tag antibody (Sigma,H6908)

tag: molecule subtype

value: Genomic DNA


title: ChIP-seq Cbx7 Input

description: ChIP-seq library

source_name: ESCs_ChIP-seq Cbx7 Input

extract_protocol:
Cells were crosslinked with 1.1% formaldeyde for 20 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of 100-500bp. Cleared lysates were incubated overnight with anti-HA tag antibody, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked on 650C and treated with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were constructed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB). Multiplexed library, Ilumina barcode#11, GGCTAC.Paired-end 50bp reads


title: Lib3_wholeRetina_Rep1


title: Lib3_wholeRetina_Rep2


title: ChIP-seq Control Input

description: ChIP-seq library

source_name: ESCs_ChIP-seq Control Input

extract_protocol:
Cells were crosslinked with 1.1% formaldeyde for 20 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of 100-500bp. Cleared lysates were incubated overnight with anti-HA tag antibody, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked on 650C and treated with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were constructed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB). Multiplexed library, Ilumina barcode#3, TTAGGC. Paired-end 50bp reads

value: stable expression of  control vector, clone 2D


title: Lib3_HC_Rep3

description:
RNA Barcodes in horizontal cells
processed data file: Lib3Results.tab

source_name: Horizontal Cells

value: Horizontal Cells


title: Lib3_HC_Rep2


title: Control-treated sample 5

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample received a 150 sec 100 µM estrogen treatment.

value: MCF-7 cells


title: ChIP-seq Control

description: ChIP-seq library

source_name: ESCs_ChIP-seq Control

extract_protocol:
Cells were crosslinked with 1.1% formaldeyde for 20 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of 100-500bp. Cleared lysates were incubated overnight with anti-HA tag antibody, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked on 650C and treated with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
ChIP-seq libraries were constructed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB). Multiplexed library, Ilumina barcode#1, ATCACG. Paired-end 50bp reads


title: RNA-seq Cbx7 rep 2

description: RNA-seq library

source_name: ESCs_RNA-seq Cbx7

extract_protocol:
Total RNA was Trizol-extracted from cells used for dCLIP experiments.
Extracted RNA was depleted of ribosomal RNA using Ribominus kit (Life technologies). Strand-specific cDNA libraries were constructed using Superscript III reverse-transcriptase for first-strand synthesis, NEBNext mRNA Second Strand Synthesis Module supplemented with dUTP (NEB) for second-strand synthesis, and NEBNext ChIP-Seq Library Prep Master Mix Set for library preparation.Multiplexed library, Ilumina barcode#12, CTTGTA. Single-end 50bp reads

treatment_protocol: No treatment

value: stable expression of BirA biotinylase and Biotin-tagged Cbx7, clone 6F

value: Total RNA


title: Lib3_HC_Rep1


title: Lib3_SBAC_Rep3

description:
RNA Barcodes in SBAC
processed data file: Lib3Results.tab

source_name: Starbust amacrine cells

value: Starbust amacrine cells

value: 129S6-Chat_tm1(cre)Lowl/J x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007921


title: Lib3_SBAC_Rep2


title: Lib4_Rods_Rep1

value: Rods

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007913


title: RNA-seq Control rep 1

description: RNA-seq library

source_name: ESCs_RNA-seq Control

extract_protocol:
Total RNA was Trizol-extracted from cells used for dCLIP experiments.
Extracted RNA was depleted of ribosomal RNA using Ribominus kit (Life technologies). Strand-specific cDNA libraries were constructed using Superscript III reverse-transcriptase for first-strand synthesis, NEBNext mRNA Second Strand Synthesis Module supplemented with dUTP (NEB) for second-strand synthesis, and NEBNext ChIP-Seq Library Prep Master Mix Set for library preparation.Multiplexed library, Ilumina barcode#2, CGATGT. Single-end 50bp reads

value: stable expression of BirA biotinylase and control vector, clone 1D


title: Control-treated sample 1

data_processing:
Base calling was perfomed using CASAVA version 1.8.2
Data filtering was performed using Flexbar version 2.5 with the following settings: quality format i1.8, phred minimum of 30, 10 nt removed from 5' end of reads
Alignment was performed using Bismark version 0.14.3 with the following settings: paired-end reads were analysed with the distance between reads limited to 1000 nt, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Alignment was repeated on reads that were not successfully aligned in the first alignment. This second round of alignment used Bismark version 0.14.3 with the following settings: single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Data filtering was performed on reads that did not align in the first two alignment steps using Flexbar version 2.5 with the following settings: all nucleotides 55 nt or further 3' of the start of the read were removed
Alignment was repeated on trimmed reads that were not successfully aligned in the first two alignments. This third round of alignment used Bismark version 0.14.3 with the following settings: trimmed single-end reads were analysed, alignments steps used Bowtie2 alignment tool version 2.2.5, post-bisulfite adapter tagging was selected, no mismatched nucleotides were allowed.
Duplicate reads were removed using the deduplicate_bismark tool from the Bismark version 0.14.3 library
The cytosine conversion status of each cytosine in each read was determined using the bismark_methylation_extractor from Bismark version 0.14.3
BisDRIP-seq scores were calculated for each read using custom scripts.  To do this, we first created an estimate of the frequency at which conversions would be seen in a read by chance using a sample-specific estimate of the stochastic rate of conversion.  This frequency was then used to calculate the expected number of reads with a given number of conversions assuming conversions are stochastic and assuming a binomial distribution.  A read bisDRIP-seq score was then calculated based on the ratio of the observed number of reads with a specific cytosine-conversion frequency to the expected number of reads with that cytosine-conversion frequency.  Thus a pair of reads that contained the same number of cytosines and the same number of conversions would be given the same bisDRIP-seq score.
BisDRIP-seq scores for each ten nucleotide region in the genome were calculated by multiplying the bisDRIP-seq score of any reads that aligned to that ten nucleotide region with the fraction of the read that interesected with the ten nucleotide region.
For *bed.txt files: 'bisDRIP-seq scores' were calculated for each read. bisDRIP-seq scores were calculated based on the number of cytosines converted in the read, relative to the likelihood of observing that number of conversions by stochastic noise using a binomial distribution (see Methods from Dumelie and Jaffrey, 2017 for full details).
bisDRIP-seq score were normalized so that the sum of bisDRIP-seq scores within each sample was 1,000,000.
Genome_build: GRCh38
Supplementary_files_format_and_content:
Tab-delimitted files containing the chromosome, position of a cytosine, number of conversions observed at that cytosine, fraction of reads where that cytosine was converted, number of reads that aligned to that cytosine.
bedGraph files containing: chromosome, start and stop of ten nucleotide region, bisDRIP-seq score of that region
*bed.txt files contain the chromosome, start, stop, read name, bisDRIP-seq score and strand in tab-seperated columns for each read with a bisDRIP-seq score above zero

treatment_protocol: In these experiments, we included MCF-7 cells that were treated with 100 µM estrogen (Sigma-Aldrich, Saint Louis, Missouri) prior to lysis to ensure transcriptional activation at a broad set of genes. This control sample did not receive 100 µM estrogen treatment.


title: RNA-seq Cbx7 rep 1

description: RNA-seq library

extract_protocol:
Total RNA was Trizol-extracted from cells used for dCLIP experiments.
Extracted RNA was depleted of ribosomal RNA using Ribominus kit (Life technologies). Strand-specific cDNA libraries were constructed using Superscript III reverse-transcriptase for first-strand synthesis, NEBNext mRNA Second Strand Synthesis Module supplemented with dUTP (NEB) for second-strand synthesis, and NEBNext ChIP-Seq Library Prep Master Mix Set for library preparation.Multiplexed library, Ilumina barcode#6, GCCAAT. Single-end 50bp reads

value: stable expression of BirA biotinylase and Biotin-tagged Cbx7, clone 3E


title: Control-treated sample 2


title: Lib3_SBAC_Rep1


title: RNA-seq control rep 2

description: RNA-seq library

source_name: ESCs_RNA-seq control

extract_protocol:
Total RNA was Trizol-extracted from cells used for dCLIP experiments.
Extracted RNA was depleted of ribosomal RNA using Ribominus kit (Life technologies). Strand-specific cDNA libraries were constructed using Superscript III reverse-transcriptase for first-strand synthesis, NEBNext mRNA Second Strand Synthesis Module supplemented with dUTP (NEB) for second-strand synthesis, and NEBNext ChIP-Seq Library Prep Master Mix Set for library preparation.Multiplexed library, Ilumina barcode#4, TGACCA.Single-end 50bp reads

value: CAST/Ei x 129/Sv/Jae

value: stable expression of BirA biotinylase and control vector, clone 2F


title: dCLIP Cbx7 rep 3

description: dCLIP-seq Library

source_name: ESCs_dCLIP Cbx7

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #12, CTTGTA. Paired-end 50bp reads

treatment_protocol: UV cross-linking

value: female

value: undifferentiated embryonic stem cells

value: RNA extracted from membrane


title: WT 3hr IL6SB  1

value: Female

value: Spleen+Lymph nodes

value: CD4+T cell

value: 3 hour post treatment

value: IL6+TGFbR inhibitor

value: WT


title: Lib2_Rods_Rep3

description:
RNA Barcodes in Rods
processed data file: Lib2Results.tab


title: dCLIP Cbx7 rep 2

description: dCLIP-seq Library

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #6, GCCAAT. Paired-end 50bp reads


title: Control-treated sample 6

value: MCF-7 cells


title: Lib2_Rods_Rep2


title: dCLIP Control rep 2

description: dCLIP-seq Library

source_name: ESCs_dCLIP Control

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #4, TGACCA. Paired-end 50bp reads


title: Lib2_Rods_Rep1


title: Lib2_Cones_Rep3

description:
RNA Barcodes in Cones
processed data file: Lib2Results.tab

source_name: Cones

value: Cones

value: d4-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007911


title: dCLIP Control rep 1

description: dCLIP-seq Library

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #3, TTAGGC. Paired-end 50bp reads


title: Input for ChIP-seq, lin-35(n745) extract rep 3

city: Santa Cruz

first: Paul

last: Goetsch

state: CA

address: 1156 High Street

department: MCD Biology

institute: UCSC

data_processing:
bowtie 1.1.2 was run with the -m 2 -S options to map the Illumina reads to the genome version ws220/ce10
SPP v1.10.1 peak caller (from phantompeakqualtools) was run on the bowtie output for each subunit for each replicate (rep 1-3), pseudoreplicates (rep1.pr1,rep1.pr2,etc), pooled replicates (rep 0), and pooled psuedoreplicates (rep0.pr1,rep0.pr2) against pooled input with the following parameters: -npeak=40000, -savn, -savp, -rf
IDR v2.0.2 was run on SPP peak outputs for each subunit on replicates (rep1v2, rep1v3, rep2v3) defining N1-2, N1-3, and N2-3 (threshold IDR < 0.01), selfPseudoReplicates (rep1.pr1vpr2) defining N1, N2, and N3 (threshold IDR < 0.02), and pooledPseudoReplicates (rep0.pr1vpr2) defining Np (threshold IDR  < 0.005). N1-2, N1-3, and N2-3 were averaged to define Nt for each factor, which was selected as the final number of peaks passing the 1% IDR threshold. The Rescue Ratio (Np/Nt) and Self-consistency ratio (Max(N1,N2,N3)/Min(N1,N2,N3)) were calculated to check for low consistency between replicates (low consistency is defined as ratio >> 2).
The deepTools v2.0 tool bamCompare was used to normalize to input and create bigwig signal track files for visualization. Pooled replicates were normalized to pooled input using the Signal Extraction Scaling (SES) method using the following parameters: --scaleFactorsMethod SES--numberOfSamples=100000 --ratio ratio  --binSize 10 --pseudocount=1 --extendReads x (x was calculated from SPP analysis for each factor)
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bigwig signal track files of combined replicates (rep0) for each ChIP normalized to pooled input using the SES method (Diaz et al. 2012) and narrowPeak files containing peak regions for each ChIP (IDR < 0.01)

organism: Caenorhabditis elegans

growth_protocol: Synchronized N2 or lin-35(n745) L1s were grown in standard S-basal media liquid culture for 72 or 96 hours, respectively. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated for up to 3.5 hours then frozen in liquid nitrogen

extract_protocol:
Crosslinked samples were resuspended in FA buffer, and sonicated in a Diagenode Bioruptor (60 pulses of 30 seconds at full power with 1 minute rest in between). Extracts were clarified, protein concentrations determined using a Qubit fluorometer, and precleared with Protein A Dynabeads before proceeding to ChIP. DRM subunits were individually IPed using 1-5 μg appropriate antibodies on prepared lysates. ChIPs were performed with 1-2 mg of extract, and 2% of the extract was set aside for an input reference control. ChIPs were incubated overnight at 4°C with 1% sarkosyl. Protein A Dynabeads equilibrated in 20 μL FA buffer were added and incubated for 2 hours at 4°C. ChIPs were washed with the following buffers: once with FA buffer containing 1 M NaCl, once with FA buffer containing 0.5 M NaCl, once with TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). 2 elutions of 50 μL elution buffer containing TE plus 1% SDS and 250 mM NaCl were incubated at 55°C. Eluted ChIP and input samples were incubated with proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified by phenol-chloroform extraction and ethanol precipitation using glycogen as a carrier.
Libraries from wild-type late embryos, extracts rep 1a, 1b, 2a, and 2b: Both ChIP and input DNA samples have their ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3?-dA overhangs are then added with Klenow Fragment (3? to 5?exo minus), and Illumina adapters are subsequently ligated to the ends. Next, PCRamplification is performed using Illumina 1.1 and 2.1 primers, for a total of 18 cycles. AmplifiedDNA libraries are size-selected on a 2% agarose gel so that fragments sized between 250-350bp are obtained; gel extraction is carried out at room temperature. Libaries from wild-type late embryo extract rep 3 and lin-35(n745) late embryo extracts rep 1-3 were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). Amplifed libraries were size selected to obtain 200-500 base pair fragments using Agencourt AMPure XP beads (Beckman Coulter).

treatment_protocol: Frozen late embryos were ground using a mortar and pestle and crosslinked for 10 minutes in 1% formaldehyde.

value: late embryo


title: dCLIP Cbx7 rep 1

description: dCLIP-seq Library

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB).  Illumina barcode #4, TGACCA. Paired-end 50bp reads

value: stable expression of BirA biotinylase and Biotin-tagged Cbx7, clone 6F


title: Lib2_Cones_Rep2


title: Input for ChIP-seq, wildtype extract rep 3

source_name: Input for ChIP-seq, wildtype extract

value: wild-type


title: Control-treated sample 4

source_name: control

extract_protocol:
Cells were lysed using SDS in the presense of bisulfite. Bisulfite was dialysed out of the sample. Samples were treated with SDS and proteinase K to remove proteins. Nucleic acids were then extracted with phenol/chloroform. DNA was then digested with restriction enzymes and RNA-DNA hybrids were immunoprecipitated using S9.6 enzymes.
DNA was sonicated using a covaris S-2 into 300 bp fragments. A Pico-Methyl Seq Library Prep Kit (Zymo Research, Irvine, California) was used to create the DNA sequencing library.  This kit is primarily designed for mapping 5-methylcytosine in small quantities of genomic DNA.  We omitted the bisulfite-treatment steps included in this kit.  Instead, only the library preparation steps were followed. These steps were followed for each sample as instructed by the manufacturer.  These steps amplified the DNA and used random priming to add indexes to the DNA library that are compatible with Illumina's TruSeq technology. As described in the Pico-Methyl Seq Library Prep Kit instructions, these indexes contain one of six barcodes that we used to differentiate samples added to the same lane during sequencing.


title: Control-treated sample 3


title: Lib2_Cones_Rep1


title: Input KO 2

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
ChIP-Seq reads (~60M per sample) were aligned to the UCSC mm10 reference genome using Bowtie1. Duplicate reads are removed.
FindPeaks from Homer (Version 4.8.3) was used to call all reported ChIP-seq peaks with  default parameters and “-F 2 -L 0 -C 1.5 -fdr 0.005"; Peak calling for all samples used pooled input sample as noise control.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: Activated CD4+ T cell under IL6+TGFbR inhibitor condition

extract_protocol:
Cells were harvested and fixed with FA for 20min at 37C. And then performed ChIP.
Libraries were constructed with the use of the Illumina TruSeq DNA library construction kit V2 according to manufacturer's protocol. Libaries were pooled and sequenced on the Illumina NextSeq500 sequencer

treatment_protocol: CD4+ T cells were activated and cultured under IL6+TGFbR inhibitor condition

value: Male

value: 12 hour post treatment

tag: antibody


title: LIN-54 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
LIN-54.BH00004.N2.rep0.vsInputRep0.SES.bw
LIN-54.BH00004.N2.IDR.0.01.narrowPeak

tag: chip-antibody

value: Horvitz lab BH0004 (Harrison et al. 2006)

tag: input control

value: wild-type extract rep 3


title: Input KO 1

value: pooled male and female


title: Input WT 2

value: Female


title: Input WT 1

value: Spleen+Lymph nodes


title: LIN-37 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
LIN-37.SDQ3166.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-37.SDQ3166.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3166

value: lin-35(n745) extract rep 3


title: LIN-52 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
LIN-52.BH00001.N2.rep0.vsInputRep0.SES.bw
LIN-52.BH00001.N2.IDR.0.01.narrowPeak

value: Horvitz lab BH0001 (Harrison et al. 2006)


title: MZnanog 6 hpf

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

address: 1390 Presidents Circle, Crocker Science Center Receiving, Crocker Science Center Receiving

department: Biological Sciences

institute: University of Utah

description: processed data file: 6hr_gene_exp.diff

data_processing:
Reads were aligned for each sample using TopHat v2.0.13 (Trapnell et al., 2009) with the following command “tophat -o <output directory> -p 16 --no-novel-juncs -G <gene table> <Bowtie2 genome index> <fastq reads>”
Transcript abundance and differential expression were determined using Cufflinks v2.2.1 (Trapnell et al., 2012) with the following command for each developmental stage “cuffdiff -p 16 -b <genome.fa -u -L <labels> -o <output directory> <gene table> <wild type aligned reads .bam file> <mutant aligned reads .bam file>”
Genome_build: zv9
Supplementary_files_format_and_content: tab delimited text files containing FPKMs from cuffdiff output

organism: Danio rerio

source_name: Whole embryos (n=40)

growth_protocol: Embryos were grown at 28.5C until point of collection

extract_protocol:
Total RNA was extracted using Trizol protocol
Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2

tag: developmental stage

value: 6.5 hpf

value: MZnanog

value: whole embryo


title: KO 2

tag: background

value: CD4+T cell

value: IL6+TGFbR inhibitor


title: LIN-9 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
LIN-9.BH00005.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-9.BH00005.lin-35.n745.IDR.0.01.narrowPeak

value: late embryo

value: Horvitz lab BH0005 (Harrison et al. 2006)


title: LIN-37 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
LIN-37.SDQ3166.N2.rep0.vsInputRep0.SES.bw
LIN-37.SDQ3166.N2.IDR.0.01.narrowPeak

value: wild-type


title: WT 2

tag: gender

value: 12 hour post treatment

value: WT


title: MZnanog 4 hpf

description: processed data file: 4hr_gene_exp.diff

value: 4 hpf

tag: tissue


title: LIN-9 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
LIN-9.BH00005.N2.rep0.vsInputRep0.SES.bw
LIN-9.BH00005.N2.IDR.0.01.narrowPeak

value: wild-type extract rep 3


title: WT 1

value: Female

tag: cell type


title: EFL-1 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
EFL-1.SDQ3590.lin-35.n745.rep0.vsInputRep0.SES.bw
EFL-1.SDQ3590.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3590


title: EFL-1 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
EFL-1.SDQ3590.N2.rep0.vsInputRep0.SES.bw
EFL-1.SDQ3590.N2.IDR.0.01.narrowPeak


title: Lib3_AAV

description:
DNA Barcodes in AAV
processed data file: Lib3Results.tab

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Barcode sequences were extracted from 50bp reads by taking only reads starting with the expected backbone sequence: “TCCTGCTGGAGTTCGTGACCTGCATGCGCCGAA”. From these reads the sequence at position 34-48 was extracted. The frequency of each barcode sequence was calculated to get counts for each sample. Counts of barcodes were normalized to library size. Enrichment of barcodes in the RNA sample was calculated over their representation in the AAV input. Barcodes not sufficiently covered in the AAV sequencing were discarded (depending on sequencing depth 2-16 reads). The median activity of all barcodes per CRE was calculated. Only CREs that were covered in at least 2 out of 3 biological replicates with at least three barcodes were used for downstream analysis.
Genome_build: mm9

molecule: other

organism: Adeno-associated virus

source_name: AAV

extract_protocol:
Phenol-Chloroform
AAV barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers

value: AAV


title: Wild type 4 hpf replicate 2

description: processed data file: 4hr_gene_exp.diff

value: wild type


title: Lib2_AAV

description: DNA Barcodes in AAV


title: Lib1_AAV

description: DNA Barcodes in AAV


title: Wild type 4 hpf replicate 1

description: processed data file: 4hr_gene_exp.diff


title: DPL-1 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
DPL-1.SDQ3599.lin-35.n745.rep0.vsInputRep0.SES.bw
DPL-1.SDQ3599.lin-35.n745.IDR.0.01.narrowPeak

value: SDIX/Novus Biologicals Q3599

value: lin-35(n745) extract rep 3


title: KO 1

value: pooled male and female

value: Spleen+Lymph nodes

tag: timepoint


title: LIN-52 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
LIN-52.BH00001.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-52.BH00001.lin-35.n745.IDR.0.01.narrowPeak

value: Horvitz lab BH0001 (Harrison et al. 2006)


title: Wild type 6 hpf replicate 2

description: processed data file: 6hr_gene_exp.diff

value: 6.5 hpf

value: whole embryo


title: MZnanog 2 hpf

description: processed data file: 2hr_gene_exp.diff

value: 2 hpf

value: MZnanog


title: DPL-1 ChIP-seq in wild-type late embryos, rep 3

description:
processed data file:
DPL-1.SDQ3599.N2.rep0.vsInputRep0.SES.bw
DPL-1.SDQ3599.N2.IDR.0.01.narrowPeak

value: wild-type

value: late embryo


title: Wild type 6 hpf replicate 1

description: processed data file: 6hr_gene_exp.diff


title: Wild type 2 hpf replicate 1

description: processed data file: 2hr_gene_exp.diff


title: Wild type 2 hpf replicate 2

description: processed data file: 2hr_gene_exp.diff


title: LD Li

city: DELHI

first: AAKANSHA

last: SHARMA

state: DELHI

address: CHATTRA MARG

department: ZOOLOGY

country: India

institute: UNIVERSITY OF DELHI

data_processing:
454 pyrosequencing were de-multiplexed using python based QIIME packag
Adapter trimming was done using Roche 454 MID Y adaptor sequences
The HQ reads so obtained were further processed as per new-tuxedo protocol (Pertea et al., 2016)
Genome_build: FicAlb_1.4; https://www.ncbi.nlm.nih.gov/assembly/GCA_000247815.1/
Supplementary_files_format_and_content: gtf file

organism: Emberiza melanocephala

source_name: Liver

extract_protocol:
The tissues were homogenized to powder form in the liquid Nitrogen with the help of mortar and pestle and total RNA extraction was done using Tri reagent (AM7020; Ambion, Austin, TX, USA).
RNA libraries were prepared for sequencing using standard 454 pyrosequencing protocols

value: Caught from wild

tag: seasonal state

value: long day

value: Liver


title: SD Li

tag: genotype


title: LD Hy

source_name: Hypothalamus

value: short day

value: Hypothalamus


title: SD Hy


title: SBR5_PRIM

city: Bielefeld

first: Volker

last: F. Wendisch

state: NRW

address: Universitätsstr. 25

department: Genetics of Prokaryotes

country: Germany

institute: Bielefeld University

description: Protocol for 5'end enriched library preparation

data_processing:
Sequencing was performed in single-read mode with 50 nt read length for the enriched 5’‑ends cDNA library and in paired-end mode with 20 nt read length for the whole transcriptome cDNA library. The base calling was realized with the Illumina instrument software.
The last bases of all sequence reads from the enriched 5’‑ends approach were trimmed to a final length of 20 nt. Next, these trimmed reads were mapped to the P. riograndensis SBR5 reference sequences using the exact mapping algorithm BOWTIE (Langmead et al. 2009, Genome Biology) and allowing a single mismatch to occur in the alignment of each read. In case of the reads belonging to the whole transcriptome RNA-seq data set, the forward and reverse read were combined to one read, containing the reference sequence as an insert, if both reads were present and in inverse orientation in a maximal distance of 1 kb to each other. Sequence reads not fulfilling this criterion were retained as single mapping reads. Paired mappings with a distance larger than 1 kb were discarded from subsequent analyses.
For the visualization of the mapped short reads, the Java software ReadXplorer (Hilker et al. 2014, Bioinformatics) was used.
The identification of putative transcription start sites was performed based on the method described previously (Irla et al. 2015, BMC Genomics), but with a recently developed transcriptome analysis module which will be integrated into the software ReadXplorer in the near future (Hilker et al. 2014, Bioinformatics)
Genome_build: EMBL/GenBank accession no. LN831776
Supplementary_files_format_and_content: Excel files include TSS and RPKM values.

organism: Paenibacillus riograndensis

source_name: cell culture

growth_protocol: Cells were cultivated in 16 different conditions.

extract_protocol:
For the extraction of total RNA the NucleoSpin RNA isolation kit (MACHEREY-NAGEL, Düren, Germany) and the RNase-free DNase set (QIAGEN, Hilden, Germany) were used according to the manufacturer’s instructions. The total RNA was isolated individually for each cultivation condition. The quality and quantity of the isolated RNA was assessed by PCR with gene-specific primers and with capillary gel electrophoresis (Agilent Bioanalyzer 2100 system using the Agilent RNA 6000 Pico kit; Agilent Technologies, Böblingen, Germany). The extracted RNA samples were pooled in equal parts and the pool of total RNA was subsequently used for the preparation of two different cDNA libraries.
The cDNA libraries ofP. riograndensis SBR5 were prepared according to two different protocols. One approach focused on the enrichment of 5’‑ends of primary transcripts, while the other method allowed the analysis of the whole transcriptome. Both cDNA library preparation protocols have been previously described in detail  (Irla et al. 2015, BMC Genomics). In the present study, the experimental workflow was changed at two steps. The first difference is that the amplification of cDNA fragments was customized by adding the PCR additive betaine to a final concentration of 2.7 M in each PCR reaction. Secondly, after cDNA amplification the two libraries were purified and size-selected via gel electrophoresis for fragment sizes between 100 and 800 bp.

tag: strain


title: WT4 CD4+YFP+

status: Public on Oct 24 2017

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were processed using fastx toolkit to trim for adapter and quality and filter for low quality.
Processed reads were mapped to the Mus musculus genome using Hisat2.
Reads mapping to genes were counted using htseq-count.
Gene normalization and differential expression analysis was performed using Deseq2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited text file containing deseq2 normalized values in a single matrix format.

source_name: Treg cells

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA kit with an additional on-column Dnase 1 treatment.
Each sample was processed using Truseq Stranded mRNA Sample Preparation, October 2013, Rev. E., with one modification at the end of the protocol on pg.41; post-amplification the libraries were purified with Ampure XP beads twice. The libraries were individually barcoded and multiplexed into a single sample. This multiplexed sample was clustered on a Paired-end, RAPID, 2-lane flowcell and sequenced on a Hiseq 2500 DNA sequencer for 100 cycles in each read direction, for a total of 200 cycles, plus an additional 7 cycles to sequence the barcodes.

value: Foxp3 YFP-Cre Wildtype

tag: infection

value: LCMV Armstrong

value: Treg cells


title: KO4 CD4+YFP+

value: IFNAR flox Foxp3 YFP-Cre Knockout


title: KO3 CD4+YFP+


title: WT2 CD4+YFP+


title: KO1 CD4+YFP+


title: KO2 CD4+YFP+


title: WT3 CD4+YFP+


title: WT5

value: wild type


title: SBR5_WT

description: Protocol for whole transcriptome library preparation


title: KO4

value: IFNAR deficient


title: KO5


title: WT1 CD4+YFP+


title: KO2


title: KO3


title: KO1


title: WT1


title: WT4


title: LIN-54 ChIP-seq in lin-35(n745) late embryos, rep 3

description:
processed data file:
LIN-54.BH00004.lin-35.n745.rep0.vsInputRep0.SES.bw
LIN-54.BH00004.lin-35.n745.IDR.0.01.narrowPeak

value: Horvitz lab BH0004 (Harrison et al. 2006)

value: lin-35(n745) extract rep 3


title: 0.7M_rGAL4_w1118_2

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

institute: Binghamton University

description: VDRC's w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.7 M sucrose food until fat body harvest

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE MB8 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: MB8
Supplementary_files_format_and_content: Excel worksheet "GEO upload processed data" containing normalized RPKM for each raw dataset, indexed by Ensembl and Flybase gene Accession (Fbgn number)

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Males (Vienna Drosophila Resource Center #60000 or #992 stocks) were crossed to UAS-Dcr2; r4-GAL4 driver line virgin females to produce offspring that chronically express dsRNA to elicit RNA interference against the InR gene in the larval fat body.

extract_protocol:
Fat bodies were homogenized in Trizol and total RNA isolated after DNAse digestion.
RiboZero subtraction was used to remove rRNA and then reverse transcription, size exclusion, amplification, and bar coding produced the final library.
Reads using bar-coded cDNA were generated by Illumina Hi-Seq analyzer.

treatment_protocol: Larvae were reared until reaching wandering third instar stage, then fat bodies were isolated by shearing and separation by centrifugation before freezing in Trizol.

value: wandering third instar larva

value: fat body

tag: Sex

value: female

tag: treatment


title: 0.7M_rGAL4_w1118_3

tag: genotype/variation

value: VDRC's w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock

value: reared at 25 deg C on 0.7 M sucrose food until fat body harvest


title: 0.7M_rGAL4_InRi_1

description: VDRC's UAS-InRi (#992) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.7 M sucrose food until fat body harvest


title: 0.15M_rGAL4_InRi_3

description: VDRC's UAS-InRi (#992) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.15 M sucrose food until fat body harvest


title: 0.7M_rGAL4_w1118_1


title: 0.15M_rGAL4_InRi_1

value: VDRC's UAS-InRi (#992) stock crossed with a UAS-Dcr2; r4-GAL4 stock

value: reared at 25 deg C on 0.15 M sucrose food until fat body harvest


title: 0.15M_rGAL4_w1118_2

description: VDRC's w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.15 M sucrose food until fat body harvest


title: 0.15M_rGAL4_w1118_1


title: hsGAL4_yw_withHS_2

description:
Bloomington's y1w1118 (#6598) stock crossed with a hs-GAL4 stock, heat shocked 6 hours prior to harvest
ctrl_w_hs2

data_processing:
To produce bed alignments, sequenced reads were aligned to the D. melanogaster UCSC dm3 assembly using Tophat (v1.3.2) and Bowtie (v0.12.7). Default Tophat settings were used.
Gene expression was quantified by processing the Tophat produced bam alignments with Cufflinks (v1.1.0) and the modENCODE dm3 annotation.
Expression was normalized by applying upper-quartile normalization as defined in "Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments", Bullard et al. BMC Bioinformatics. 2010; 11: 94
Genome_build: dm3
Supplementary_files_format_and_content: Excel worksheet "GEO processed data for InRCA" containing normalized RPKM for each raw dataset, indexed by gene Accession (CG number)

growth_protocol: Males (Bloomington's 6598 or 8263 stocks) were crossed to hs-GAL4 driver line virgin females to produce offspring that could express constitutively active InR in a heat-dependent manner.

treatment_protocol: Larvae were reared on control lab food until reaching mid-third instar stage, then heat shocked or mock heat shocked (transfer to a new vial but no heat) at 37C for 30 minutes. Fat bodies were isolated after a 6 hour recovery by shearing and separation by centrifugation.

value: feeding mid-third instar larva


title: hsGAL4_yw_withHS_1

description:
Bloomington's y1w1118 (#6598) stock crossed with a hs-GAL4 stock, heat shocked 6 hours prior to harvest
ctrl_w_hs1


title: WT3


title: hsGAL4_yw_withHS_3

description:
Bloomington's y1w1118 (#6598) stock crossed with a hs-GAL4 stock, heat shocked 6 hours prior to harvest
ctrl_w_hs3


title: WT2


title: hsGAL4_UAS-InRCA_noHS_1

description:
Bloomington's  UAS-InR.A1325D (#8263) stock crossed with a hs-GAL4 stock, then reared at 25 deg C until fat body harvest
InRCA_no_hs1


title: 0.7M_rGAL4_InRi_2


title: ChIP-seq from HEK293 (ENCLB200QRC)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR897RVP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF514 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR897RVP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB200QRC
size range: 450-650

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

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF514 fusion protein

extract_protocol: not provided

tag: line

value: immortalized cell line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF514 under the control of a CMV promoter.

tag: biosample encode accession

tag: lab

value: Michael Snyder, Stanford

tag: health state

value: unknown

tag: age

tag: dev stage

value: embryonic

tag: link

value: ENCBS984ZDJ at ENCODE; https://www.encodeproject.org/ENCBS984ZDJ/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from adrenal gland (ENCLB777JGU)

description:
https://www.encodeproject.org/experiments/ENCSR899JSO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human adrenal gland
experiment encode accession: ENCSR899JSO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR091EBM
encode release date: 2016-11-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB777JGU
size range: 450-650

source_name: Homo sapiens adrenal gland tissue male adult (37 years)

tag: antibody

value: CTCF

value: adrenal gland

value: tissue

value: male

value: 37 year

value: adult

value: ENCBS693ETI at ENCODE; https://www.encodeproject.org/ENCBS693ETI/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: 0.15M_rGAL4_w1118_3

tag: developmental stage

value: wandering third instar larva

tag: tissue

value: fat body

value: female

value: VDRC's w1118 (#60000) stock crossed with a UAS-Dcr2; r4-GAL4 stock

value: reared at 25 deg C on 0.15 M sucrose food until fat body harvest


title: ChIP-seq from HEK293 (ENCLB610BWI)

description:
https://www.encodeproject.org/experiments/ENCSR897RVP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF514 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR897RVP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB610BWI
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF514 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: ENCBS899PRO at ENCODE; https://www.encodeproject.org/ENCBS899PRO/


title: ChIP-seq from HEK293 (ENCLB229VFX)

description:
https://www.encodeproject.org/experiments/ENCSR897JCM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF491 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR897JCM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB229VFX
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF491 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF491 under the control of a CMV promoter.

value: embryonic

value: ENCBS671DPO at ENCODE; https://www.encodeproject.org/ENCBS671DPO/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: hsGAL4_UAS-InRCA_withHS_2

description:
Bloomington's UAS-InR.A1325D (#8263) stock crossed with a hs-GAL4 stock, heat shocked 6 hours prior to harvest
InRCA_w_hs2

value: feeding mid-third instar larva


title: ChIP-seq from MCF-7 (ENCLB295WCE)

description:
https://www.encodeproject.org/experiments/ENCSR897JAS/
***************
biological replicate number: 2
technical replicate number: 1
description: CREB1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR897JAS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB295WCE
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: adult

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS488MMM at ENCODE; https://www.encodeproject.org/ENCBS488MMM/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from liver (ENCLB085OZB)

description:
https://www.encodeproject.org/experiments/ENCSR893QWP/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on REST-human
experiment encode accession: ENCSR893QWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB085OZB

source_name: Homo sapiens liver tissue female child (4 years)

value: REST

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: female

value: healthy

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from HEK293 (ENCLB516FCM)

description:
https://www.encodeproject.org/experiments/ENCSR897JCM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF491 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR897JCM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB516FCM
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF491 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS323PSJ at ENCODE; https://www.encodeproject.org/ENCBS323PSJ/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: hsGAL4_UAS-InRCA_withHS_3

description:
Bloomington's UAS-InR.A1325D (#8263) stock crossed with a hs-GAL4 stock, heat shocked 6 hours prior to harvest
InRCA_w_hs3

value: feeding mid-third instar larva

value: fat body


title: hsGAL4_UAS-InRCA_noHS_2

description:
Bloomington's  UAS-InR.A1325D (#8263) stock crossed with a hs-GAL4 stock, then reared at 25 deg C until fat body harvest
InRCA_no_hs2


title: ChIP-seq from HEK293 (ENCLB988HVS)

description:
https://www.encodeproject.org/experiments/ENCSR892ZTO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF548 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR892ZTO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB988HVS
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF548 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF548 under the control of a CMV promoter.

value: ENCBS302IJW at ENCODE; https://www.encodeproject.org/ENCBS302IJW/


title: hsGAL4_UAS-InRCA_noHS_3

description:
Bloomington's  UAS-InR.A1325D (#8263) stock crossed with a hs-GAL4 stock, then reared at 25 deg C until fat body harvest
InRCA_no_hs3


title: ChIP-seq from HepG2 (ENCLB182SDO)

description:
https://www.encodeproject.org/experiments/ENCSR784FYS/
***************
biological replicate number: 2
technical replicate number: 1
description: RBFOX2 ChIP-seq in HepG2
experiment encode accession: ENCSR784FYS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB182SDO
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

value: RBFOX2 ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: ENCBS994RVB at ENCODE; https://www.encodeproject.org/ENCBS994RVB/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: 0.7M_rGAL4_InRi_3

description: VDRC's UAS-InRi (#992) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.7 M sucrose food until fat body harvest

value: wandering third instar larva

value: female


title: ChIP-seq from HEK293 (ENCLB739OBC)

description:
https://www.encodeproject.org/experiments/ENCSR892QHR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PRDM6 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR892QHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB739OBC
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-PRDM6 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM6 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: ENCBS568BLW at ENCODE; https://www.encodeproject.org/ENCBS568BLW/


title: ChIP-seq from HepG2 (ENCLB411RCQ)

description:
https://www.encodeproject.org/experiments/ENCSR872EVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PCBP1 ChIP-seq in HepG2
experiment encode accession: ENCSR872EVQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB411RCQ
size range: 200-400

value: PCBP1 ChIP-seq in HepG2

value: child

value: ENCBS034PYO at ENCODE; https://www.encodeproject.org/ENCBS034PYO/


title: ChIP-seq from HepG2 (ENCLB242HHG)

description:
https://www.encodeproject.org/experiments/ENCSR872EVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PCBP1 ChIP-seq in HepG2
experiment encode accession: ENCSR872EVQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB242HHG
size range: 200-400

value: ENCBS025AAW at ENCODE; https://www.encodeproject.org/ENCBS025AAW/


title: ChIP-seq from subcutaneous adipose tissue (ENCLB411JNA)

description:
https://www.encodeproject.org/experiments/ENCSR790VEV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human adipose tissue
experiment encode accession: ENCSR790VEV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR496OMO
encode release date: 2016-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB411JNA
size range: 450-650

source_name: Homo sapiens subcutaneous adipose tissue female adult (51 year)

value: CTCF

value: subcutaneous adipose tissue

value: tissue

value: 51 year

value: adult

value: ENCBS644JJL at ENCODE; https://www.encodeproject.org/ENCBS644JJL/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: ChIP-seq from stomach (ENCLB830ZJO)

description:
https://www.encodeproject.org/experiments/ENCSR890ONE/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR890ONE
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB830ZJO

source_name: Homo sapiens stomach tissue male adult (37 years)

extract_protocol: extraction method: see document

value: Control

value: stomach

value: male

value: Richard Myers, HAIB

value: 37 year

value: ENCBS555DNU at ENCODE; https://www.encodeproject.org/ENCBS555DNU/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ChIP-seq from esophagus muscularis mucosa (ENCLB811GNK)

description:
https://www.encodeproject.org/experiments/ENCSR891WPD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on muscle layer of esophagus
experiment encode accession: ENCSR891WPD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR662VAE
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB811GNK

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (51 year)

value: esophagus muscularis mucosa

value: female

value: ENCBS256BDN at ENCODE; https://www.encodeproject.org/ENCBS256BDN/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/ff8c38b8-9743-4b9d-92df-11776af354c5/@@download/attachment/84275.svs


title: ChIP-seq from liver (ENCLB478LYF)

description:
https://www.encodeproject.org/experiments/ENCSR893QWP/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on REST-human
experiment encode accession: ENCSR893QWP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB478LYF

value: REST

value: liver

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from tibial nerve (ENCLB044VRK)

description:
https://www.encodeproject.org/experiments/ENCSR889VXP/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Nov 08 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR889VXP
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB044VRK

source_name: Homo sapiens tibial nerve tissue female adult (51 year)

value: Control

value: tibial nerve

value: tissue

value: Richard Myers, HAIB

value: 51 year

value: adult

value: ENCBS842RPA at ENCODE; https://www.encodeproject.org/ENCBS842RPA/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/2bf62bc0-22fd-41ea-89c9-a84c756bcc30/@@download/attachment/84263.svs


title: ChIP-seq from HepG2 (ENCLB699EGM)

description:
https://www.encodeproject.org/experiments/ENCSR868JLS/
***************
biological replicate number: 1
technical replicate number: 1
description: U2AF1 ChIP-seq in HepG2
experiment encode accession: ENCSR868JLS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB699EGM
size range: 200-400

value: immortalized cell line

value: U2AF1 ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: ENCBS717MSF at ENCODE; https://www.encodeproject.org/ENCBS717MSF/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: Hi-C from SJCRH30 (ENCLB379VAF)

description:
https://www.encodeproject.org/experiments/ENCSR998ZSP/
***************
biological replicate number: 1
technical replicate number: 1
description: HiC experiment done on SJCRH30
experiment encode accession: ENCSR998ZSP
assay title: Hi-C
assembly: hg19
encode release date: 2016-05-13
lab: Job Dekker, UMass
library encode accession: ENCLB379VAF

source_name: Homo sapiens SJCRH30 immortalized cell line

value: This immortalized cell line was established from cells from the metastatic site of the bone marrow of a child with rhabdomyosarcoma.

value: unknown

value: 17 year

value: John Stamatoyannopoulos, UW

value: ENCBS504BIZ at ENCODE; https://www.encodeproject.org/ENCBS504BIZ/

value: Derived from ENCODE donor ENCDO339AAA; https://www.encodeproject.org/ENCDO339AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0041; http://web.expasy.org/cellosaurus/CVCL_0041


title: ChIP-seq from HEK293 (ENCLB710IXD)

description:
https://www.encodeproject.org/experiments/ENCSR892QHR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PRDM6 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR892QHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB710IXD
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM6 under the control of a CMV promoter.

value: female

value: Michael Snyder, Stanford

value: embryonic

value: ENCBS913UOH at ENCODE; https://www.encodeproject.org/ENCBS913UOH/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HepG2 (ENCLB297BUH)

description:
https://www.encodeproject.org/experiments/ENCSR991ADX/
***************
biological replicate number: 1
technical replicate number: 1
description: U2AF2 ChIP-seq in HepG2
experiment encode accession: ENCSR991ADX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB297BUH
size range: 200-400

value: immortalized cell line

value: U2AF2 ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: child

value: ENCBS030GWA at ENCODE; https://www.encodeproject.org/ENCBS030GWA/


title: ChIP-seq from HepG2 (ENCLB447UUR)

description:
https://www.encodeproject.org/experiments/ENCSR991ADX/
***************
biological replicate number: 2
technical replicate number: 1
description: U2AF2 ChIP-seq in HepG2
experiment encode accession: ENCSR991ADX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB447UUR
size range: 200-400

value: 15 year

value: ENCBS808XDL at ENCODE; https://www.encodeproject.org/ENCBS808XDL/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: ChIP-seq from K562 (ENCLB134QRS)

description:
https://www.encodeproject.org/experiments/ENCSR788RSW/
***************
biological replicate number: 2
technical replicate number: 1
description: SOX6 ChIP-seq on human K562
experiment encode accession: ENCSR788RSW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB134QRS
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

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

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS543YEP at ENCODE; https://www.encodeproject.org/ENCBS543YEP/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB788HDH)

description:
https://www.encodeproject.org/experiments/ENCSR788RSW/
***************
biological replicate number: 1
technical replicate number: 1
description: SOX6 ChIP-seq on human K562
experiment encode accession: ENCSR788RSW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB788HDH
size range: 450-650

value: immortalized cell line

value: female

value: Michael Snyder, Stanford

value: ENCBS603CUX at ENCODE; https://www.encodeproject.org/ENCBS603CUX/


title: ChIP-seq from K562 (ENCLB902XHD)

description:
https://www.encodeproject.org/experiments/ENCSR786OQY/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB5 ChIP-seq on human K562
experiment encode accession: ENCSR786OQY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB902XHD
size range: 450-650

value: ENCBS320BUL at ENCODE; https://www.encodeproject.org/ENCBS320BUL/


title: ChIP-seq from K562 (ENCLB506CVR)

description:
https://www.encodeproject.org/experiments/ENCSR849DZW/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZKSCAN8 tagged K562 cell line.
experiment encode accession: ENCSR849DZW
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB506CVR
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZKSCAN8 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF192

value: Kevin White, UChicago

tag: passage number

value: ENCBS539IPB at ENCODE; https://www.encodeproject.org/ENCBS539IPB/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ98; http://web.expasy.org/cellosaurus/CVCL_GZ98


title: ChIP-seq from K562 (ENCLB567SCE)

description:
https://www.encodeproject.org/experiments/ENCSR786OQY/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBTB5 ChIP-seq on human K562
experiment encode accession: ENCSR786OQY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB567SCE
size range: 450-650

value: adult

value: 53 year

value: ENCBS906KIP at ENCODE; https://www.encodeproject.org/ENCBS906KIP/


title: ChIP-seq from K562 (ENCLB483RRD)

description:
https://www.encodeproject.org/experiments/ENCSR750LYM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NR2C2 ChIP-seq on human K562
experiment encode accession: ENCSR750LYM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR017CYU
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB483RRD
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NR2C2 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2C2

value: chronic myelogenous leukemia (CML)

value: ENCBS168GXP at ENCODE; https://www.encodeproject.org/ENCBS168GXP/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ91; http://web.expasy.org/cellosaurus/CVCL_GZ91


title: ChIP-seq from K562 (ENCLB980RBC)

description:
https://www.encodeproject.org/experiments/ENCSR754ZHU/
***************
biological replicate number: 1
technical replicate number: 1
description: SNRNP70 ChIP-seq in K562
experiment encode accession: ENCSR754ZHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB980RBC
size range: 200-400

value: immortalized cell line

value: SNRNP70 ChIP-seq in K562

value: female

value: Xiang-Dong Fu, UCSD

value: ENCBS910CTC at ENCODE; https://www.encodeproject.org/ENCBS910CTC/


title: ChIP-seq from GM12878 (ENCLB524SVT)

description:
https://www.encodeproject.org/experiments/ENCSR785OKZ/
***************
biological replicate number: 3
technical replicate number: 1
description: RB1 ChIP-seq on human GM12878
experiment encode accession: ENCSR785OKZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB524SVT
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: Michael Snyder, Stanford

value: ENCBS965YSG at ENCODE; https://www.encodeproject.org/ENCBS965YSG/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from K562 (ENCLB304GIX)

description:
https://www.encodeproject.org/experiments/ENCSR750LYM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NR2C2 ChIP-seq on human K562
experiment encode accession: ENCSR750LYM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR017CYU
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB304GIX
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: Kevin White, UChicago

value: 53 year

value: adult

value: ENCBS250NTO at ENCODE; https://www.encodeproject.org/ENCBS250NTO/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from GM12878 (ENCLB369DMO)

description:
https://www.encodeproject.org/experiments/ENCSR785OKZ/
***************
biological replicate number: 4
technical replicate number: 1
description: RB1 ChIP-seq on human GM12878
experiment encode accession: ENCSR785OKZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB369DMO
size range: 450-650

value: immortalized cell line

value: ENCBS607NAA at ENCODE; https://www.encodeproject.org/ENCBS607NAA/


title: ChIP-seq from MCF-7 (ENCLB830CNH)

description:
https://www.encodeproject.org/experiments/ENCSR897JAS/
***************
biological replicate number: 1
technical replicate number: 1
description: CREB1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR897JAS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB830CNH
size range: 450-650

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS670IYV at ENCODE; https://www.encodeproject.org/ENCBS670IYV/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031


title: ChIP-seq from HEK293 (ENCLB967WER)

description:
https://www.encodeproject.org/experiments/ENCSR878DES/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF624 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR878DES
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB967WER
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF624 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF624 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS381KVD at ENCODE; https://www.encodeproject.org/ENCBS381KVD/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HEK293 (ENCLB051TDS)

description:
https://www.encodeproject.org/experiments/ENCSR878DES/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF624 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR878DES
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB051TDS
size range: 450-650

value: ENCBS333EUU at ENCODE; https://www.encodeproject.org/ENCBS333EUU/


title: ChIP-seq from K562 (ENCLB691FNS)

description:
https://www.encodeproject.org/experiments/ENCSR969FPP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-BACH1 tagged K562 cell line.
experiment encode accession: ENCSR969FPP
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB691FNS
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-BACH1 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to BACH1

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS706JJD at ENCODE; https://www.encodeproject.org/ENCBS706JJD/

value: ENCODE dbxrefs Cellosaurus CVCL_AW14; http://web.expasy.org/cellosaurus/CVCL_AW14


title: ChIP-seq from HEK293 (ENCLB422XEO)

description:
https://www.encodeproject.org/experiments/ENCSR781EQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB48 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR781EQJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB422XEO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZBTB48 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB48 under the control of a CMV promoter.

value: female

value: ENCBS608CNR at ENCODE; https://www.encodeproject.org/ENCBS608CNR/


title: 0.15M_rGAL4_InRi_2

description: VDRC's UAS-InRi (#992) stock crossed with a UAS-Dcr2; r4-GAL4 stock, then reared at 25 deg C on 0.15 M sucrose food until fat body harvest

source_name: fat body

value: wandering third instar larva

value: fat body


title: ChIP-seq from HEK293 (ENCLB629UUD)

description:
https://www.encodeproject.org/experiments/ENCSR892ZTO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF548 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR892ZTO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB629UUD
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF548 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS867ZTE at ENCODE; https://www.encodeproject.org/ENCBS867ZTE/


title: ChIP-seq from K562 (ENCLB071EPQ)

description:
https://www.encodeproject.org/experiments/ENCSR975SSR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ELF1 ChIP-seq on human K562
experiment encode accession: ENCSR975SSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR675JUK
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB071EPQ
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ELF1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF1

value: Kevin White, UChicago

value: ENCBS872CIK at ENCODE; https://www.encodeproject.org/ENCBS872CIK/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ81; http://web.expasy.org/cellosaurus/CVCL_GZ81


title: ChIP-seq from K562 (ENCLB771QPO)

description:
https://www.encodeproject.org/experiments/ENCSR847LBF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-FOXJ2 ChIP-seq on human K562
experiment encode accession: ENCSR847LBF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR765SXU
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB771QPO
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-FOXJ2 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOXJ2

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS039TGQ at ENCODE; https://www.encodeproject.org/ENCBS039TGQ/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ85; http://web.expasy.org/cellosaurus/CVCL_GZ85


title: ChIP-seq from HEK293 (ENCLB053CLF)

description:
https://www.encodeproject.org/experiments/ENCSR781EQJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB48 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR781EQJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB053CLF
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB48 under the control of a CMV promoter.

value: female

value: ENCBS634DCB at ENCODE; https://www.encodeproject.org/ENCBS634DCB/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from K562 (ENCLB034SSH)

description:
https://www.encodeproject.org/experiments/ENCSR845MXF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ADNP tagged K562 cell line.
experiment encode accession: ENCSR845MXF
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB034SSH
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ADNP fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ADNP

value: ENCBS559UBQ at ENCODE; https://www.encodeproject.org/ENCBS559UBQ/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ75; http://web.expasy.org/cellosaurus/CVCL_GZ75


title: ChIP-seq from K562 (ENCLB346TCP)

description:
https://www.encodeproject.org/experiments/ENCSR975SSR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ELF1 ChIP-seq on human K562
experiment encode accession: ENCSR975SSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR675JUK
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB346TCP
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF1

value: Kevin White, UChicago

value: ENCBS861JYZ at ENCODE; https://www.encodeproject.org/ENCBS861JYZ/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/