title: D. mel DGRP #804 1

first: Jin Billy

last: Li

state: California

address: 300 Pasteur Drive. Alway M303

department: Genetics

institute: Stanford University

data_processing:
Primer sequences were trimmed off paired or single-end sequencing reads before mapping using Tophat.
RNA editing levels were calculated as the fraction of G reads at each site. Only sites covered by 50 reads were used
Genome_build: dm3/droSim1/droYak2/droAna2/dp3/droVir3
Supplementary_files_format_and_content: Processed data files are tab-delineated with a header line and include editing levels of different Drosophila strains and species.

organism: Drosophila melanogaster

source_name: male whole body

growth_protocol: Whole bodies of adult male and female flies aged 5 days old were collected.

extract_protocol:
Total RNA was extracted using the Rneasy Kit (Qiagen). After DNase I treatment, 3 ug of total RNA was used to synthesize the cDNA using iScript Advanced cDNA Synthesis Kit (Bio-Rad). cDNA was purified using the MinElute PCR Purification Kit (Qiagen)
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq) or targeted sequencing

tag: developmental stage

value: 5 day old adult

tag: replicate

tag: library strategy

value: mmPCR-seq

tag: strain


title: WT_0h_2 (ChIP-Seq)

status: Public on Jan 04 2017

type: SRA

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: Negative control for peak calling only (for Samples 11, 13, 15)

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Trimming and filtering of LinDA adapters and low quality sequences was performed using 1) cutadapt  v1.2.1 with options –e 0.2, -n 2 and –m 36 and 2) PRINSEQ lite v0.20.2 with options –trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie v0.12.7 with options –best –m 1
Peak calling was performed for each replicate using the program QuEST v2.4 in transcription factor mode (option “2”) with permissive parameter settings (option “3”) and suppling the corresponding input or mock-treated sample as negative controls in peak calling
Annotation of peak locations with respect to annotated gene features in TAIR10 was performed using the annotatePeaks.pl function from the Homer suite
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files with peak coordinates, enrichment scores, and annnotation information

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 12 day old seedlings

growth_protocol: Seedlings were grown in1x MS medium supplemented with 0.5 % sucrose and 0.1 % claforan for 12 days in a light chamber at long day conditions (16 h light / 8 h dark).

extract_protocol:
For the ChIP experiments, 2 g of seedlings were processed as described earlier (Birkenbihl et al., 2012) following the modified protocol of Grendel et al. (2005). For IP was a rabbit polyclonal anti-HA antibody (Sigma-Aldrich, St. Louis, MA) was used. The precipitated DNA was purified with the Qia quick PCR purification kit (Qiagen, Germany) before library construction.
To prepare the ChIP-seq libraries, the DNA was first amplified by two rounds of linear DNA amplification (LinDA) (Shankaranarayanan et al., 2011) and then libraries were constructed with the NEBNext ChIP-seq Library construction kit (New England Biolabs, Ipswich, MA).
The ChIP-seq libraries were sequenced with an Illumina HiSeq2500, resulting in 7-20 million 100 bp single-end reads per sample.

treatment_protocol: The seedlings were treated with flg22 by replacing the growth medium with medium containing 1 µM flg22 for 2 h.

tag: genotype

value: Col-0 WT

tag: treatment

value: untreated

tag: time-point


title: D. mel DGRP #786 2

city: Stanford

country: USA

library_source: transcriptomic

molecule: total RNA


title: D. mel DGRP #786 1


title: diurnal1A-2800

city: Corvallis

first: Richard

middle: C

last: Cronn

state: Oregon

address: 3200 SW Jefferson Way

department: Pacific Northwest Research Station

institute: USDA Forest Service

description: Douglas-fir diurnal transcriptome analysis

data_processing:
Base-calling and demultiplexing was performed using Casava v1.8 (Illumina Inc.).
Transcript read mapping: To quantify transcript abundance in diurnal and RNA-Seq samples, we mapped reads to the pan-transcriptome reference with bowtie2.2.3 (Langmead and Salzberg, 2012) using the following call:  bowtie2 --end-to-end -D 15 -R 2 -L 22 -i S,1,1.15. This allows 15 consecutive seed extension attempts before the aligner moved on (-D 15), a maximum of 2 attempts to re-seed reads with repetitive seeds (-R 2), and a 22 bp seed (-L 22) with zero allowed mismatches in this seed. The function to determine the interval between seed substrings during multi-seed alignment was set to f(x) = 1 + 1.15 * sqrt(x), where x is the read length (-i S,1,1.15) (based on the 101 bp read lengths this resulted in an interval of 13 bp).  Output from this step is provided as processed data file "filename2.gz"
Transcript filtering and normalization: Since many transcripts showed near-zero counts, we excluded transcripts showing median counts below 5 from analyses because they were essentially indistinguishable from background transcription. For transcripts meeting the median cut-off, counts were normalized using DESeq normalization (Anders and Huber, 2010; Bullard et al., 2010; Dillies et al., 2012).
Genome_build: Douglas-fir pan-transcriptome reference v2.03, TSA submission in progress
Supplementary_files_format_and_content: tab-separated text files were generated using  bowtie 2.2.3; Counts represent the number of reads mapping to each transcript model
Supplementary_files_format_and_content: tab-separated text files were generated using DESeq; Counts represent the number of reads mapping to each transcript model, after the application of a normalization factor to correct for library size

molecule: polyA RNA

organism: Pseudotsuga menziesii

growth_protocol: Trees used for the diurnal transcriptome analysis are a sample from a reciprocal translocation study (Harrington et al., 2010) that includes families from multiple geographic sources in the Pacific Northwestern region of North America. Trees used for diurnal analysis derive from a single source from the reciprocal translocation study (Oregon Siskiyou low elevation; 43.3° N, -123.1° W, 429 m elevation), and were grown in Corvallis, Oregon, USA (42.3° N, -122.9° W, 74 m elevation)(Figure S1). For this study, needles were collected from 6 individual trees (3 half sib families, two sibs per family) that were three years old at the time of the study. Needles from the 2012 cohort were first collected at 2 AM on September 7, 2012, and at 4 hour intervals for a total of 48 hours (12 sample points)

extract_protocol:
Needles (8 – 12 per sample) were collected 2.5 - 5 cm basipetal of dormant branch apical buds from branches representing four cardinal directions. Needles were flash-frozen in liquid N2, followed by homogenization on dry ice (FastPrep-24 mill, matrix A; MP Biomedical, Solon, OH., USA). Ice-cold extraction buffer (1.5 mL of 3M LiCl/8M urea; 1% PVP K-60; 0.1M dithiothreitol; Tai et al., 2004) was added to ground tissue, homogenized, then centrifuged at 200g x 10 min., 4°C. The supernatant was incubated overnight at 4°C, and crude RNA was pelleted (20,000g x 30 min., 4°C) and cleaned using the ZR Plant RNA MiniPrep kit (Zymo Research, Irvine, CA., USA) and DNAse treatment (Turbo DNAse; New England Biolabs, Ipswich, MA., USA). RNA concentration was estimated using a Qubit fluorometer (Invitrogen, Carlsbad, CA., USA), and total RNA yield averaged 0.3 µg/mg tissue.
Indexed Illumina RNA-Seq libraries used 2 µg total RNA and TruSeq chemistry (Illumina Inc., San Diego, CA), modified for strand-specific sampling (Parkhomchuk et al., 2009). In this protocol, the first-strand synthesis reaction was desalted to remove unincorporated dNTPs using Sephadex G-25 (Sigma-Aldrich, St. Louis, MO., USA) filtration. Desalted products were reconstituted in dNTP-free second-strand synthesis buffer, second strand enzyme mix (New England Biolabs, Ipswich, MA., USA), and a dUTP/dNTP mixture (ThermoScientific, Waltham, MA., USA) to incorporate dUTP into the second strand. All other steps follow Illumina protocols, except that uracil-containing strands were degraded using a uracil-specific excision reagent mixture (37°C for 15 minutes; New England Biolabs) prior to PCR. Amplified libraries were quantified by fluorometry and pooled at equimolar 6-plex representation at 10 nM. Sequencing was performed at Oregon State University's Center for Genome Research and Biocomputing (Corvallis, OR., USA) using a HiSeq 2000 (Illumina Inc.) with version 3.0 chemistry.

tag: family-tag

value: Oregon Siskiyou low elevation


title: W40HA_2h_1 (ChIP-Seq)

value: Col-0 WRKY40-HA


title: w18_2h_1 (RNA-Seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 --library-type fr-firststrand
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

extract_protocol:
Total RNA was extracted from 100 mg of untreated or flg22-treated seedlings using the TRI Reagent Solution from Applied Biosystems (AM9738) following the manufacturer´s instructions. The RNA was treated with DNAse I (Roche) and purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany).
RNA-seq libraries were prepared by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq Stranded RNA sample preparation v2 guide (Illumina).

treatment_protocol: The seedlings were treated with flg22 by replacing the growth medium with medium containing 1 µM flg22 for 1 h and 2 h.

value: Col-0 wrky18 mutant


title: W40HA_0h_1 (ChIP-Seq)


title: D. mel DGRP #774 2


title: diurnal1A-2400


title: W18HA_2h_1 (ChIP-Seq)

value: Col-0 WRKY18-HA


title: wt_0h_1 (RNA-Seq)


title: diurnal1A-2000


title: D. mel DGRP #721 2


title: diurnal1A-4400


title: W18HA_0h_1 (ChIP-Seq)


title: D. mel DGRP #721 1


title: D. mel DGRP #804 2


title: WT_2h_2 (ChIP-Seq)

description: Negative control for peak calling only (for Samples 12, 14, 16)


title: D. mel DGRP #441 2


title: W33HA_2h_1 (ChIP-Seq)

value: Col-0 WRKY33-HA


title: D. mel DGRP #441 1


title: diurnal1A-1200


title: diurnal1A-0800


title: diurnal1A-0400


title: W33HA_0h_1 (ChIP-Seq)


title: D. mel DGRP #352 2


title: WT_2h_1 (ChIP-Seq)

description: Negative control for peak calling only (for Samples 4, 6, 8)


title: WT_0h_1 (ChIP-Seq)

description: Negative control for peak calling only (for Samples 3, 5, 7)


title: diurnal1A-0000


title: D. mel DGRP #352 1


title: D. mel DGRP #325 2


title: mouse OB_p30_control_wild type_rep4

city: Shanghai

first: Jiwen

address: NO. 138 Yixueyuan Road

country: China

institute: Fudan University

description: Control (D2)

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Mus musculus

source_name: OB_p30_control_wild type

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The olfactory bulbs from P30 wild type littermate controls and hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox  mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

tag: strain background

value: mixed genetic background of C57BL/6J, 129S6 and CD1

tag: genotype/variation

value: wild type

tag: age

value: postnatal day 30

tag: tissue

value: olfactory bulb


title: Sir3∆wH 2µ (CL1+pCL4)

city: Boston

first: Gloria

last: Jih

state: MA

address: 240 Longwood Ave, LHRRB 517

department: Cell Biology

institute: Harvard Medical School

description: CAGATC

data_processing:
Raw reads were separated by barcode. Barcode sequence were removed from the reads and attached to the identifier. Reads were mapped using bowtie with default configurations. Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV)
Genome_build: GCF_000146045.2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.

organism: Saccharomyces cerevisiae

source_name: Sir3∆wH 2µ (CL1+pCL4)

growth_protocol: Cells were cultured overnight in SC medium, or selective media for cells harboring overexpression plasmids (YEp24 2μ plasmid with Sir3 or Sir3ΔwH expressed from Sir3 endogenous promoter), diluted into fresh media to OD600 = 0.4, and harvested at late log phase (OD600 = 1.5).

extract_protocol:
Cell pellets were resuspended in 600 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 0.1% SDS, 1 mM PMSF, protease inhibitor tablet (Roche)), and disrupted by bead beating (MagNA Lyser, Roche) for 6x30 sec at 4500 rpm with 0.5 mm glass beads. Tubes were punctured and the flow-through was collected in a new tube by centrifugation. After sonication for 3x20 sec at 40% amplitude (Branson Digital Sonifier), the extract was centrifuged (Eppendorf 5415R) for 15 min at 13,000 rpm. The soluble chromatin was then transferred to a fresh tube. Sir3 antibody (Rudner et al., 2005) was preincubated with Dynabeads Protein A, and for each immunoprecipitation, 2 μg antibody bound to 30 μl beads was added to soluble chromatin. Samples were incubated for 2 hours at 4oC with rotation, after which the beads were collected on magnetic stands, and washed 3 times with 1 ml lysis buffer and once with 1 ml TE, and eluted with 100 μl preheated buffer (50 mM Tris.HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65 ˚C for 15 min. The eluate was collected, and 150 μl 1XTE/0.67% SDS was added. Immunoprecipitated samples were incubated overnight at 65 ˚C to reverse crosslink, and treated with 50 μg RNase A at 37oC for 1 h. 5 μl proteinase K (Roche) was added and incubation was continued at 55oC for 1 h. Samples were purified using PCR purification kit (Qiagen).
Libraries for Illumina sequencing were constructed following the protocol detailed in Wong et al, 2013 (Wong, K. H., Jin, Y. and Moqtaderi, Z. 2013. Multiplex Illumina Sequencing Using DNA Barcoding. Current Protocols in Molecular Biology. 101:7.11:7.11.1–7.11.11.), starting with ~5 ng of immunoprecipitated DNA fragments. Each library was generated with custom-made adapters carrying unique 6 nt barcode sequences at the ligating end. Barcoded libraries were mixed and sequenced with Illumina HiSeq 2500.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature (RT), then quenched with 130 mM glycine for 5 min at RT, harvested by centrifugation, washed twice with TBS (50 mM Tris.HCl pH 7.6, 150 mM NaCl), and flash frozen.

tag: media

value: SC-Ura

tag: antibody

value: Sir3 antibody (Rudner et al., 2005)


title: Sir4 I1311N + Sir3 2µ (ADR2973+pJR104)

description: ACTTGA


title: Sir4 I1311N Sir3∆wH + Sir3∆wH 2µ (CL2+pCL4)

description: GATCAG


title: mouse OB_p30_control_wild type_rep3

description: Control (D1)


title: mouse OB_p30_control_wild type_rep1

description: Control (C1)


title: D. mel DGRP #325 1


title: D. mel DGRP #26 2


title: mouse OB_p30_control_wild type_rep2

description: Control (C2)


title: diurnal1A-1600


title: Sir4 I1311N Sir3∆wH (CL2)

description: ACAGTG

source_name: Sir4 I1311N Sir3∆wH (CL2)

value: SC


title: mouse OB_p30_hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox _rep4

description: hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox (B2)

value: hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox


title: D. mel DGRP #26 1

value: 5 day old adult


title: mouse OB_p30_hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox _rep3

description: hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox (B1)


title: D. mel male 2

value: mmPCR-seq


title: D. mel male 1


title: Sir3∆wH (CL1)

description: TTAGGC

source_name: Sir3∆wH (CL1)


title: ∆Sir3 (SF4)

description: CGATGT

source_name: ∆Sir3 (SF4)


title: D. mel female 1

source_name: female whole body


title: Sir3 (SF1)

description: ATCACG

source_name: Sir3 (SF1)


title: D. ana male 4 (targeted seq)

organism: Drosophila ananassae

value: targeted sequencing


title: mouse OB_p30_hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox _rep2

description: hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox (A2)


title: D.vir male 4 (targeted seq)

organism: Drosophila virilis


title: D. pse male 4 (targeted seq)

organism: Drosophila pseudoobscura


title: D. ana male 3 (targeted seq)


title: D. mel DGRP #774 1


title: D.vir male 3 (targeted seq)


title: D. ana female 4 (targeted seq)


title: D. pse female 4 (targeted seq)


title: Sir3 2µ (SF1+pJR104)

description: GCCAAT

source_name: Sir3 2µ (SF1+pJR104)


title: D. ana female 3 (targeted seq)


title: D.vir female 4 (targeted seq)


title: D. pse male 3 (targeted seq)


title: D.vir female 3 (targeted seq)


title: D. pse female 3 (targeted seq)


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and Mek inhibition, replicate 3

status: Public on Jan 03 2017

city: Utrecht

first: Kay

last: Wiebrands

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: *EEC_diff*.csv: Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column names indicate the GeneID and primer number of the sample. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Small intestine

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina HiSeq2500 using 50bp paired end sequencing and Illumina NextSeq500 using 75bp paired end sequencing.

value: Small intestine


title: Sir4 I1311N (ADR2973)

description: TGACCA


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt and Notch inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and EGFR inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and Mek inhibition, replicate 1


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and EGFR inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and EGFR inhibition, replicate 1


title: D. mel female 2


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt and Notch inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt, Notch and Mek inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of Mek inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of Wnt and Notch inhibition, replicate 1


title: Extracted RNA from bulk cells of organoids after 96 hours of Mek inhibition, replicate 1


title: Extracted RNA from bulk cells of organoids after 96 hours of EGFR inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of EGFR inhibition, replicate 1


title: Extracted RNA from bulk cells of organoids after 96 hours, replicate 1


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and Mek inhibition, replicate 3


title: mouse OB_p30_hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox _rep1

description: hGFAP-Cre; Sp8 Flox/Flox; Sp9 Flox/Flox (A1)


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and Mek inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours, replicate 2


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and Mek inhibition, replicate 1


title: co-culture treated with Bic/4AP for 1 h Hs+Ms_Bic-4AP_1h_2

city: Heidelberg

first: Priit

last: Pruunsild

address: INF 364

department: Neurobiology

institute: University of Heidelberg

description:
P0 mouse primary neurons were added to hiPSCd neurons for the last 10 days of differentiation.
polyA purified

data_processing:
Illumina Casava1.7 software used for basecalling.
hiPSCd neuron/mouse primary neuron co-culture sample reads were filtered for human reads as follows. Paired-end reads were aligned independently, without pairing, to the mouse genome assembly GRCm38/mm10 with Bowtie2 version 2.1.0. Unaligned read pairs were joined and split again to eliminate pairs with one aligned read. Then, genome-unaligned paired-end reads were aligned to GRCm38/mm10 transcriptomes (UCSC Genes/knownGene), respectively, with Bowtie2 (2.1.0). The reads not aligned to the mouse genome and transcriptome were handled as reads obtained from hiPSCd neuron-only samples.
Processed mixed-species sample reads and human-cells-only sample reads were aligned to gene model annotations of the human genome assembly GRCh37/hg19 with TopHat version v2.0.9.
Mapped reads per gene were counted strand-specifically with HTSeq-count (HTSeq version 0.6.0 or 0.6.1) in the union overlap resolution mode.
Differentially expressed genes were determined with the DESeq2 package version 1.8.1.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: HTSeq-count read counts per gene.

organism:
Homo sapiens
Mus musculus

source_name: hiPSC-derived neurons

growth_protocol: We differentiated iPSCs to NPCs using a slightly modified spin embryoid body protocol (Kim et al., 2011) with dual SMAD inhibition (Chambers et al., 2009). Differentiation of NPCs was initiated by plating 50,000 cells/cm2 on PO/Lam dishes without EGF and FGF2.  Neuronal differentiation was allowed to proceed for 7 (co-cultures) or 10 (hiPSCd neuron-only cultures) weeks.

extract_protocol:
Total RNA was purified from cultured cells (3.5 cm dish) with RNeasy Mini (hiPSCd neuron/mouse primary neuron co-cultures) or Micro (hiPSCd neuron-only cultures) Kit (Qiagen) along with on-column RNase-Free DNase (Qiagen) digestion of DNA
Poly(A)+ RNA was isolated from total RNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). cDNA libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). NEBNext Multiplex Oligos for Illumina (New England Biolabs) were used.

treatment_protocol: Bicuculline (50 µM) applied together with 4-aminopyridine (250 µM) (Bic/4AP)

tag: cell type

value: forebrain neuron-like, heterogenous

tag: passages

value: from iPSC passages 30-40

tag: iPSc line

value: iPS D1

value: postmitotic


title: co-culture treated with Bic/4AP for 1 h Hs+Ms_Bic-4AP_1h_4

tag: developmental stage


title: H3K27m3 ChIP-seq for wild type flies

city: New Haven

last: Liu

state: CT

address: 10 Amistad st

institute: Yale University

description: ChIP-seq

data_processing:
All the collected sequences from HiSeq2000 are mapped back to Drosophila melanogaster, which is dm3 from USCS genome browser. Up to 3 mismatches are allowed during the mapping process. The sequences that are mappable are subject to the MACS peak calling. Peaks with p-value less than 10-4 are retained for analysis.
Genome_build: dm3
Supplementary_files_format_and_content: text format, in which sequences that were mapped to genome are listed , together with their count number.

source_name: ovary

growth_protocol: 20 degrees C

extract_protocol: Proteins were extracted using 300mM KCl buffer D. Equal amounts of ovarian extract were incubated with antibodies for 2 hours, followed by incubation with Protein A-conjugated Dynabeads (Invitrogen) for 2 hours. Beads were then washed with 0.05% T/PBS, and immunoprecipitates eluted by 2X loading buffer.

treatment_protocol: Dissected ovaries (> 50 pairs) were homogenized in 1.5ml tubes .

value: ovary


title: co-culture treated with Bic/4AP for 1 h Hs+Ms_Bic-4AP_1h_1


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and EGFR inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 96 hours of Mek inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and EGFR inhibition, replicate 1


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt, Notch and EGFR inhibition, replicate 2


title: co-culture untreated control Hs+Ms_CNTR_4


title: co-culture untreated control Hs+Ms_CNTR_3


title: co-culture untreated control Hs+Ms_CNTR_1


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt and Notch inhibition, replicate 1


title: co-culture untreated control Hs+Ms_CNTR_2


title: Extracted RNA from bulk cells of organoids after 6 hours of Mek inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt and Notch inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 6 hours of Wnt and Notch inhibition, replicate 2


title: Extracted RNA from bulk cells of organoids after 96 hours of EGFR inhibition, replicate 3


title: Extracted RNA from bulk cells of organoids after 96 hours, replicate 3


title: H3K27m3 ChIP-seq for piwi mutated flies

description: ChIP-seq


title: RAMPAGE from stomach (ENCLB182WAK)

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR081NTK/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human stomach tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR081NTK
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR296PMS
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB182WAK
size range: >200

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

organism: Homo sapiens

source_name: Homo sapiens stomach tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ff25210b-c3e2-4b96-9ee6-01560fac91f0/@@download/attachment/296877.pdf

value: stomach

value: tissue

tag: description

value: Stomach aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

tag: biosample encode accession

value: 54 year

tag: dev stage

value: adult

tag: Sex

value: male

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS141UOA at ENCODE; https://www.encodeproject.org/ENCBS141UOA/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: co-culture treated with Bic/4AP for 1 h Hs+Ms_Bic-4AP_1h_3


title: Extracted RNA from bulk cells of organoids after 6 hours of Mek inhibition, replicate 1

tag: strain


title: RAMPAGE from upper lobe of left lung (ENCLB492OGZ)

description:
https://www.encodeproject.org/experiments/ENCSR099FOD/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR099FOD
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR425RGZ
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB492OGZ
size range: >200

source_name: Homo sapiens upper lobe of left lung tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/4e080afc-d6df-45c4-9dcb-130cb4a233b0/@@download/attachment/296890.pdf

value: upper lobe of left lung

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: female

value: ENCBS711XVO at ENCODE; https://www.encodeproject.org/ENCBS711XVO/

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


title: Extracted RNA from bulk cells of organoids after 6 hours of EGFR inhibition, replicate 3

value: Small intestine


title: eCLIP from K562 (ENCLB541BNB)

description:
https://www.encodeproject.org/experiments/ENCSR081JYH/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against NSUN2
experiment encode accession: ENCSR081JYH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR595PFU
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB541BNB
size range: 175-300

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/fa2a3246-6039-46ba-b960-17fe06e7876a/@@download/attachment/CLIP_SOP_v1.0.pdf

tag: line

value: immortalized cell line

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

tag: passage number

value: Gene Yeo, UCSD

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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/HB-8065.aspx


title: Extracted RNA from bulk cells of organoids after 6 hours of EGFR inhibition, replicate 2

tag: tissue


title: eCLIP from K562 (ENCLB512BFT)

description:
https://www.encodeproject.org/experiments/ENCSR067UKU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against EWSR1
experiment encode accession: ENCSR067UKU
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2016-04-26
lab: Gene Yeo, UCSD
library encode accession: ENCLB512BFT
size range: 175-300

value: Control

value: adult

tag: age

value: ENCBS489LOC at ENCODE; https://www.encodeproject.org/ENCBS489LOC/


title: RAMPAGE from sigmoid colon (ENCLB306GHY)

description:
https://www.encodeproject.org/experiments/ENCSR035MAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human sigmoid colon tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR035MAJ
assay title: RAMPAGE
assembly: GRCh38, hg19
possible controls: ENCSR827IXS
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB306GHY
size range: >200

source_name: Homo sapiens sigmoid colon tissue female adult (51 year)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/caf3bc92-1754-4bff-aa62-ec7ead801adf/@@download/attachment/296881.pdf

value: sigmoid colon

value: tissue

value: Sigmoid colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: Thomas Gingeras, CSHL

value: ENCBS214FDP at ENCODE; https://www.encodeproject.org/ENCBS214FDP/


title: Extracted RNA from bulk cells of organoids after 6 hours of EGFR inhibition, replicate 1

value: Small intestine


title: Extracted RNA from bulk cells of organoids after 6 hours, replicate 2


title: Extracted RNA from bulk cells of organoids after 6 hours, replicate 3


title: ChIP-IN

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
RNA-seq reads were mapped to the human genome assembly hg38 using STAR aligner v4.1. For mRNA analysis, default parameters were used. For analysis of retrotransposons we used the --outFilterMultimapNmax 1 to only report uniquely mapping reads
ChIP-seq reads were mapped to the human genome assembly hg38 using Bowtie2 with --very-sensitive. All alignments with MAPQ < 10 were discarded.
ChIP-seq peaks were called with MACS2 normalizing against IN. H3K9me3 peaks were called using --broad, TRIM28 peaks were called with default parameters. A cutoff of -q 0.05 was used for both data sets.
mRNA and non-coding RNAs were quantified using the subread package FeatureCounts (--primary) and iGenome NCBI annotation. Retrotransposons were quantified using the RepeatMasker track from UCSC.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-Seq: Matrix of quantification of non-exonic retroelements using featureCounts.
Supplementary_files_format_and_content: ChIP-Seq: Bed files with called peaks.

source_name: hNES cell culture

growth_protocol: AF22 (iPS-derived, hNES) were cultured in DMEM/F12 (Thermo Fisher Scientific) supplemented with Glutamine (2mM, Sigma), Penicillin/Streptomycin (1x, Gibco), N2 supplement (1x, Thermo Fisher Scientific), B27 (0.05x, Invitrogen) , EGF and FGF2 (both 10ng/ml, Thermo Fisher Scientific). Cells were grown on NuncTM T25 or T75 flasks pre-coated with Poly L-Ornithine (15µg/ml, Sigma) and Laminin (2mg/ml, Sigma).  Cells were passaged every 2-3 days using TryplLETM Express enzyme (Life Technologies) and Defined Trypsin Inhibitor (Life Technologies) and plated at a density of 6x104 per cm2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

value: iPS-derived neural progenitor cells

tag: fetal region

tag: embryonic age

tag: antibody


title: ChIP-H3K9me3

tag: cell type

value: H3K9me3 (Active Motif, cat # 39161)


title: Extracted RNA from Lgr5+ cells of EGF inhibited organoids from Lgr5-DTR mice replicate 2

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus. Based on binomial statistics we converted the number of observed unique molecular identifiers into transcript counts.
Genome_build: mm10
Supplementary_files_format_and_content: *.coutt.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: Others (*.csv): Comma separated data file listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the sample type. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.
Supplementary_files_format_and_content: cel-seq_barcodes.csv: Tab separated data file containing all cell specific barcodes. First column contains barcode number and second column contains barcode sequence.

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer’s instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 50bp paired end sequencing.


title: Extracted RNA from Dclk1+ cells of EGF inhibited organoids from Dclk1-GFP mice replicate 1


title: Extracted RNA from Lgr5+ cells of organoids from Lgr5-DTR mice replicate 2


title: Extracted RNA from Lgr5+ cells of EGF inhibited organoids from Lgr5-DTR mice replicate 1


title: ChIP-TRIM28

value: Kap1 (AbCam 10483)


title: Control organoids replicate 2


title: Extracted RNA from bulk cells of organoids after 6 hours, replicate 1


title: Extracted RNA from Dclk1+ cells of organoids from Dclk1-GFP mice replicate 2


title: Control organoids replicate 1


title: Extracted RNA from Lgr5+ cells of organoids from Lgr5-DTR mice replicate 1


title: eCLIP from K562 (ENCLB698TYB)

description:
https://www.encodeproject.org/experiments/ENCSR022BVV/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against LSM11
experiment encode accession: ENCSR022BVV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR952UOL
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB698TYB
size range: 175-300

value: immortalized cell line

value: 53 year

value: female

value: Gene Yeo, UCSD

value: chronic myelogenous leukemia (CML)


title: Extracted RNA from Dclk1+ cells of organoids from Dclk1-GFP mice replicate 1


title: eCLIP from K562 (ENCLB894DQS)

description:
https://www.encodeproject.org/experiments/ENCSR022BVV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against LSM11
experiment encode accession: ENCSR022BVV
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR952UOL
encode release date: 2015-12-16
lab: Gene Yeo, UCSD
library encode accession: ENCLB894DQS
size range: 175-300

value: ENCBS318IMK at ENCODE; https://www.encodeproject.org/ENCBS318IMK/

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/HB-8065.aspx


title: Extracted RNA from Lgr5+ cells of organoids from Lgr5-GFP mice replicate 1


title: Extracted RNA from Lgr5+ cells of organoids from Lgr5-GFP mice replicate 2


title: Extracted RNA from Lgr5+ cells of EGF inhibited organoids from Lgr5-GFP mice replicate 2


title: RAMPAGE from upper lobe of left lung (ENCLB229IGK)

description:
https://www.encodeproject.org/experiments/ENCSR004UBM/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this experiment come from human upper lobe of left lung tissue. They are stranded PE101 Illumina Hi-Seq RAMPAGE libraries from rRNA-depleted Total RNA > 200 nucleotides in size.
experiment encode accession: ENCSR004UBM
assay title: RAMPAGE
assembly: hg19, GRCh38
possible controls: ENCSR839ZDH
encode release date: 2016-10-31
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB229IGK
size range: >200

source_name: Homo sapiens upper lobe of left lung tissue male adult (54 years)

extract_protocol:
file format specification: https://www.encodeproject.org/documents/28a9fcd3-1a6a-4c88-9e30-bd4e43afce42/@@download/attachment/RAMPAGE_Library_Structure_2.pdf
extraction method: see document
general protocol: https://www.encodeproject.org/documents/05dbfc34-c350-482d-8061-2c4337291a4c/@@download/attachment/296876.pdf

value: upper lobe of left lung

value: tissue

value: Lung tissue obtained from GTEx for the Gingeras lab to conduct RNA-Seq assays on.

value: 54 year

value: adult

value: male

value: ENCBS271JIM at ENCODE; https://www.encodeproject.org/ENCBS271JIM/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Extracted RNA from Lgr5+ cells of EGF inhibited organoids from Lgr5-GFP mice replicate 1

value: Small intestine


title: Extracted RNA from single cells of EGF inhibited organoids

description: Ei


title: eCLIP from K562 (ENCLB263TUG)

description:
https://www.encodeproject.org/experiments/ENCSR081JYH/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against NSUN2
experiment encode accession: ENCSR081JYH
assay title: eCLIP
assembly: GRCh38, hg19
possible controls: ENCSR595PFU
encode release date: 2016-09-21
lab: Gene Yeo, UCSD
library encode accession: ENCLB263TUG
size range: 175-300

value: immortalized cell line

value: 53 year

value: ENCBS517UIR at ENCODE; https://www.encodeproject.org/ENCBS517UIR/


title: Extracted RNA from single cells of Mek/WNT/Notch inhibited organoids replicate 2


title: Extracted RNA from single cells of Mek/WNT/Notch inhibited organoids replicate 1


title: Extracted RNA from single cells of EGFR/WNT/Notch inhibited organoids replicate 3


title: Extracted RNA from Dclk1+ cells of EGF inhibited organoids from Dclk1-GFP mice replicate 2


title: Extracted RNA from single cells of EGFR/WNT/Notch inhibited organoids replicate 4


title: Extracted RNA from single cells of EGFR/WNT/Notch inhibited organoids replicate 2


title: Extracted RNA from bulk cells of organoids after 6 hours of Mek inhibition, replicate 2


title: Extracted RNA from single cells of EGFR/WNT/Notch inhibited organoids replicate 1


title: HN rep3

city: New York

first: Man Shan

last: Yu

state: NY

address: 550 First Ave., MSB 258

department: Microbiology

institute: New York University School of Medicine

description: Sample name: HN mESC-3-2-14

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Samples with reads spanning multiple lanes were merged.
The sequencing reads were aligned to the mouse genome (UCSC build mm10) using the STAR aligner.
Likely PCR duplicates were removed with Picard MarkDuplicates tool.
HTSeq was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Counts were normalized and tested for differential expression with the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file contains normalized counts for all genes and samples.

source_name: mouse embryonic stem cells

extract_protocol:
Total RNA was isolated from mESCs using the Direct-zolTM RNA MiniPrep Kit (Zymo Research) according to the manufacturer’s instructions. Bioanalyser was used to determine RNA concentration and quality. 130 ng of total RNA was used to construct RNA-Seq libraries using Illumina TruSeq RNA Library Preparation Kit v2.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Htt-/-

value: mouse embryonic stem cells


title: R1 rep3

description: Sample name: R1 mESC-3-2-14

value: wild type


title: co-culture treated with Bic/4AP for 4 h Hs+Ms_Bic-4AP_4h_3

value: forebrain neuron-like, heterogenous

tag: passages

value: from iPSC passages 30-40

tag: iPSc line

value: iPS D1

tag: developmental stage

value: postmitotic


title: R1 rep2

description: Sample name: R1 mESC-2-20-14


title: R1 rep1

description: Sample name: R1 mESC-2-17-14


title: HN rep2

description: Sample name: HN mESC-2-20-14


title: co-culture treated with Bic/4AP for 4 h Hs+Ms_Bic-4AP_4h_4


title: HN rep1

description: Sample name: HN mESC-2-17-14


title: Striatum-12wks-Rai1-KO-rep1

first: Liqun

last: Luo

address: Herrin Labs, Rooms 152 and 154

department: Department of Biological Sciences

data_processing:
Basecalls performed using  CASAVA v1.8.2
The adaptor sequencing were first scaned and removed for the raw reads by cutadapt (version 1.6 ).
The trimmed sequence were mapped to mouse reference genome (mm9) using Tophat2 with parameters “-I 1000000 --max-coverage-intron 1000000 --max-segment-intron 1000000  --no-coverage-search --b2-very-sensitive   --microexon-search”.
Read pairs, which aligned concordantly to the genome were counted according to the RefGene annotation from UCSC using DEGseq (v0.50.1).
The longest isoform were selected when there are multiple isoforms.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

growth_protocol: Mouse brains from various Rai1 conditional knockouts were used

extract_protocol:
Cortex, stiatum, and hypotahalmus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: Nestin-Cre was used to delete Rai1 from the cortex, Gad2-Cre was used to delete Rai1 from the striatum, and Vglut2-Cre was used to delete Rai1 from the hypothalamus.

tag: generation

value: Striatum

value: 12 weeks

tag: genotype/variation


title: Extracted RNA from single cells of ENR organoids

description: ENR


title: hypothalamus-8wks-WT-rep2

value: hypothalamus

value: 8 weeks


title: hypothalamus-8wks-WT-rep1


title: co-culture treated with Bic/4AP for 4 h Hs+Ms_Bic-4AP_4h_2


title: ChIP-seq from liver (ENCLB004ZPL)

description:
https://www.encodeproject.org/experiments/ENCSR014GMV/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse lung (fragmentation date 08-13-14)
experiment encode accession: ENCSR014GMV
assay title: ChIP-seq
encode release date: 2016-01-09
lab: Richard Myers, HAIB
library encode accession: ENCLB004ZPL

source_name: Mus musculus strain B6NCrl liver tissue postnatal (0 days)

value: Control

value: liver

value: tissue

tag: description

value: pulverized livers pooled from multiple dissections of postnatal 0 day mice

tag: biosample encode accession

tag: dev stage

value: postnatal

value: 0 day

tag: Sex

value: not collected

tag: lab

value: Richard Myers, HAIB

tag: link

value: ENCBS152FNH at ENCODE; https://www.encodeproject.org/ENCBS152FNH/

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


title: Striatum-12wks-Rai1-KO-rep2

tag: strain

tag: tissue

tag: age


title: Striatum-3wks-WT-rep2

value: 3 weeks

value: wild type


title: Striatum-12wks-WT-rep2


title: Cortex-3wks-Rai1-KO-rep2

value: Cortex


title: hypothalamus-8wks-Rai1-KO-rep2


title: Cortex-3wks-WT-rep2


title: Striatum-3wks-Rai1-KO-rep1

value: Striatum


title: Cortex-3wks-Rai1-KO-rep1


title: Striatum-3wks-WT-rep1


title: Cortex-Rai-ChIP-rep1

data_processing:
Basecalls performed using  CASAVA v1.8.2
The paired-end reads were mapped to the mouse reference genome (mm9) using bowtie2 (version 2.2.3),with “—very-sensitive” and default parameters
Read pairs, which aligned concordantly to the genome and had a mapping quality more than 10, were kept for following analysis.
Read pairs mapped to mitochondria DNA were discarded.
Redundancy read pairs from PCR duplication were also removed afterward using Picard tools (version 1.134).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedtools version v2.17.0

source_name: Cortex-Rai-ChIP

growth_protocol: 8-week-old mouse cortex were used

extract_protocol:
Lysates were clarified from sonicated nuclei and Rai1-DNA complexes were isolated with anti-FLAG antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Nextera DNA Library Prep Kit).

treatment_protocol: 8-week-old cortices of male Rai1Tag/+ mice were used for ChIP-seq experiment. Cortical tissues were cross-linked with 1% formaldehyde for 10 minutes at room temperature, followed by quenching with 0.125 M glycine and washed twice with cold PBS containing 0.5 mM PMSF. Chromatin was sonicated to an average size of 0.3–1 kb using Bioruptor (Diagenode). A total of 10 μg of anti-FLAG M2 antibody (Sigma) was added to the sonicated chromatin and incubated overnight at 4°C. Subsequently, 50 μl of protein G Dynal magnetic beads were added to the ChIP reactions and incubated for 6 hours at 4°C. Magnetic beads were washed and chromatin eluted, followed by reversal of crosslinks and DNA purification (ChIP DNA clean & Concentrator kit, ZYMO research).

tag: chip antibody

value: anti-FLAG M2 (Sigma, catalog# F1804)


title: Cortex-Rai-ChIP-rep2


title: Cortex-Input-rep1

source_name: Cortex-Input


title: hypothalamus-8wks-Rai1-KO-rep1

value: hypothalamus


title: Input DNA

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

description: Klf4flox/flox vav-Cre in C57BL/6 background.

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: wig
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks

source_name: Bone Marrow

extract_protocol:
Sorted cells were fixed and then genomic DNA was extracted and sheared. DNA was reverse crosslinked after KLF4 antibody pulldown and was subjected to seuqencing.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.

value: Bone Marrow

value: Normal


title: Striatum-12wks-WT-rep1

value: 12 weeks


title: ChIP-seq from HEK293 (ENCLB011CRM)

description:
https://www.encodeproject.org/experiments/ENCSR103GAK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF175 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR103GAK
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB011CRM
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF175 fusion protein

tag: antibody

tag: line

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF175 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

tag: health state

value: ENCBS558YVE at ENCODE; https://www.encodeproject.org/ENCBS558YVE/

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


title: ChIP-seq from HEK293 (ENCLB692FMX)

description:
https://www.encodeproject.org/experiments/ENCSR103GAK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF175 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR103GAK
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB692FMX
size range: 450-650

value: ENCBS632ODA at ENCODE; https://www.encodeproject.org/ENCBS632ODA/


title: KLF-4 ChIP-Seq

value: KLF-4 KO

value: Klf4flox/flox vav-Cre in C57BL/6 background.


title: ChIP-seq from K562 (ENCLB972VJM)

description:
https://www.encodeproject.org/experiments/ENCSR099NCH/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF24 ChIP-seq on human K562
experiment encode accession: ENCSR099NCH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB972VJM
size range: 450-650

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS831ATS at ENCODE; https://www.encodeproject.org/ENCBS831ATS/

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

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


title: ChIP-seq from K562 (ENCLB081XLD)

description:
https://www.encodeproject.org/experiments/ENCSR099NCH/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF24 ChIP-seq on human K562
experiment encode accession: ENCSR099NCH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB081XLD
size range: 450-650

value: immortalized cell line

value: ENCBS344LIE at ENCODE; https://www.encodeproject.org/ENCBS344LIE/


title: siRNA RNA-seq from K562 (ENCLB357IRB)

description:
https://www.encodeproject.org/experiments/ENCSR100ODO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting NFE2L2.
experiment encode accession: ENCSR100ODO
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR128HAQ, ENCSR109YDL
encode release date: 2016-10-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB357IRB
size range: >200
spikeins used: /references/ENCSR866KGS/

source_name: Homo sapiens K562 immortalized cell line transiently expressing siRNA targeting NFE2L2

value: K562 cells treated with a siRNA knockdown against NFE2L2, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: ENCBS222URM at ENCODE; https://www.encodeproject.org/ENCBS222URM/


title: ChIP-seq from HEK293 (ENCLB138UPY)

description:
https://www.encodeproject.org/experiments/ENCSR098YLE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PRDM1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR098YLE
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB138UPY
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-PRDM1 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS830CXI at ENCODE; https://www.encodeproject.org/ENCBS830CXI/


title: Cortex-Input-rep2

value: Cortex


title: Cortex-3wks-WT-rep1

value: 3 weeks

value: wild type


title: ChIP-seq from K562 (ENCLB664IVC)

description:
https://www.encodeproject.org/experiments/ENCSR097PLG/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ATF1 tagged K562 cell line.
experiment encode accession: ENCSR097PLG
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB664IVC
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ATF1 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF1

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS821FOP at ENCODE; https://www.encodeproject.org/ENCBS821FOP/

value: ENCODE dbxrefs Cellosaurus CVCL_AW13; http://web.expasy.org/cellosaurus/CVCL_AW13


title: eCLIP from HepG2 (ENCLB838EJE)

description:
https://www.encodeproject.org/experiments/ENCSR095SIV/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against LARP7
experiment encode accession: ENCSR095SIV
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-11-09
lab: Gene Yeo, UCSD
library encode accession: ENCLB838EJE
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/dde0b669-0909-4f8b-946d-3cb9f35a6c52/@@download/attachment/eCLIP_analysisSOP_v1.P.pdf
general protocol: https://www.encodeproject.org/documents/842f7424-5396-424a-a1a3-3f18707c3222/@@download/attachment/eCLIP_SOP_v1.P_110915.pdf
extraction method: see document

value: immortalized cell line

value: child

value: 15 year

value: male

tag: passage number

value: Gene Yeo, UCSD

value: hepatocellular carcinoma

value: ENCBS548DJV at ENCODE; https://www.encodeproject.org/ENCBS548DJV/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: eCLIP from K562 (ENCLB143BKD)

description:
https://www.encodeproject.org/experiments/ENCSR096SZE/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against PRPF8
experiment encode accession: ENCSR096SZE
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB143BKD
size range: 175-300

value: Control

value: female

value: ENCBS083CLD at ENCODE; https://www.encodeproject.org/ENCBS083CLD/

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 (ENCLB894ECJ)

description:
https://www.encodeproject.org/experiments/ENCSR093FKD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CREB3 ChIP-seq on human K562
experiment encode accession: ENCSR093FKD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR578SNR
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB894ECJ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-CREB3 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CREB3

value: adult

value: 53 year

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: ENCBS411NIF at ENCODE; https://www.encodeproject.org/ENCBS411NIF/

value: ENCODE dbxrefs Cellosaurus CVCL_AW16; http://web.expasy.org/cellosaurus/CVCL_AW16


title: ChIP-seq from HEK293T (ENCLB983XLW)

description:
https://www.encodeproject.org/experiments/ENCSR094WHO/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXA1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR094WHO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR386FAB
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB983XLW
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: immortalized cell line

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS276VDW at ENCODE; https://www.encodeproject.org/ENCBS276VDW/

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


title: ChIP-seq from MCF-7 (ENCLB364HTU)

description:
https://www.encodeproject.org/experiments/ENCSR096KWU/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF207 ChIP-seq on human MCF-7
experiment encode accession: ENCSR096KWU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB364HTU
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS547AXB at ENCODE; https://www.encodeproject.org/ENCBS547AXB/

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 (ENCLB085HYQ)

description:
https://www.encodeproject.org/experiments/ENCSR093HXE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF16 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR093HXE
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB085HYQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF16 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF16 under the control of a CMV promoter.

value: ENCBS213ZWT at ENCODE; https://www.encodeproject.org/ENCBS213ZWT/


title: ChIP-seq from HEK293T (ENCLB988ZBI)

description:
https://www.encodeproject.org/experiments/ENCSR094WHO/
***************
biological replicate number: 1
technical replicate number: 1
description: FOXA1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR094WHO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR386FAB
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB988ZBI
size range: 450-650

value: ENCBS323RYE at ENCODE; https://www.encodeproject.org/ENCBS323RYE/


title: ChIP-seq from HEK293 (ENCLB211COY)

description:
https://www.encodeproject.org/experiments/ENCSR093HXE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF16 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR093HXE
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB211COY
size range: 450-650

value: ENCBS617FVO at ENCODE; https://www.encodeproject.org/ENCBS617FVO/


title: ChIP-seq from MCF-7 (ENCLB512EHJ)

description:
https://www.encodeproject.org/experiments/ENCSR096KWU/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF207 ChIP-seq on human MCF-7
experiment encode accession: ENCSR096KWU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB512EHJ
size range: 450-650

value: adult

value: ENCBS959SHH at ENCODE; https://www.encodeproject.org/ENCBS959SHH/


title: ChIP-seq from K562 (ENCLB696JWA)

description:
https://www.encodeproject.org/experiments/ENCSR091JXL/
***************
biological replicate number: 2
technical replicate number: 1
description: HES1 ChIP-seq on human K562
experiment encode accession: ENCSR091JXL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB696JWA
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: 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: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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 (ENCLB220ELT)

description:
https://www.encodeproject.org/experiments/ENCSR090JNM/
***************
biological replicate number: 1
technical replicate number: 1
description: HLTF ChIP-seq on human K562
experiment encode accession: ENCSR090JNM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB220ELT
size range: 450-650

value: HLTF

value: female

value: Michael Snyder, Stanford

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


title: ChIP-seq from K562 (ENCLB686JVZ)

description:
https://www.encodeproject.org/experiments/ENCSR086FZL/
***************
biological replicate number: 2
technical replicate number: 1
description: KAT8 ChIP-seq on human K562
experiment encode accession: ENCSR086FZL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB686JVZ
size range: 450-650

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/


title: ChIP-seq from K562 (ENCLB660WJW)

description:
https://www.encodeproject.org/experiments/ENCSR093FKD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CREB3 ChIP-seq on human K562
experiment encode accession: ENCSR093FKD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR578SNR
encode release date: 2016-03-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB660WJW
size range: 450-650

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CREB3

value: Kevin White, UChicago

value: ENCBS312MPK at ENCODE; https://www.encodeproject.org/ENCBS312MPK/

value: ENCODE dbxrefs Cellosaurus CVCL_AW16; http://web.expasy.org/cellosaurus/CVCL_AW16


title: ChIP-seq from HEK293 (ENCLB267TEY)

description:
https://www.encodeproject.org/experiments/ENCSR098YLE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PRDM1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR098YLE
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB267TEY
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM1 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS153AXP at ENCODE; https://www.encodeproject.org/ENCBS153AXP/

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


title: ChIP-seq from K562 (ENCLB827SWV)

description:
https://www.encodeproject.org/experiments/ENCSR091JXL/
***************
biological replicate number: 1
technical replicate number: 1
description: HES1 ChIP-seq on human K562
experiment encode accession: ENCSR091JXL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB827SWV
size range: 450-650

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: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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

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


title: ChIP-seq from K562 (ENCLB608TSI)

description:
https://www.encodeproject.org/experiments/ENCSR091GVJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ATF1 ChIP-seq on human K562
experiment encode accession: ENCSR091GVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR097PLG
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB608TSI
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line derived from K562 stably expressing C-terminal eGFP-ATF1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF1

value: female

value: ENCBS405AAA at ENCODE; https://www.encodeproject.org/ENCBS405AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_AW13; http://web.expasy.org/cellosaurus/CVCL_AW13


title: siRNA RNA-seq from K562 (ENCLB943ODP)

description:
https://www.encodeproject.org/experiments/ENCSR100ODO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA-seq on K562 cells treated with siRNA targeting NFE2L2.
experiment encode accession: ENCSR100ODO
assay title: siRNA RNA-seq
assembly: GRCh38
possible controls: ENCSR128HAQ, ENCSR109YDL
encode release date: 2016-10-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB943ODP
size range: >200
spikeins used: /references/ENCSR866KGS/

value: immortalized cell line

value: K562 cells treated with a siRNA knockdown against NFE2L2, used in RNA-seq experiments.

value: Sherman Weissman, Yale

value: ENCBS707WDQ at ENCODE; https://www.encodeproject.org/ENCBS707WDQ/


title: ChIP-seq from K562 (ENCLB730PMZ)

description:
https://www.encodeproject.org/experiments/ENCSR091GVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ATF1 ChIP-seq on human K562
experiment encode accession: ENCSR091GVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR097PLG
encode release date: 2016-01-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB730PMZ
size range: 450-650

value: Kevin White, UChicago

value: ENCBS377AAA at ENCODE; https://www.encodeproject.org/ENCBS377AAA/

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562


title: ChIP-seq from K562 (ENCLB191LFO)

description:
https://www.encodeproject.org/experiments/ENCSR085DDI/
***************
biological replicate number: 1
technical replicate number: 1
description: NFXL1 ChIP-seq on human K562
experiment encode accession: ENCSR085DDI
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR173USI
encode release date: 2016-12-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB191LFO
size range: 450-650

value: adult

value: Michael Snyder, Stanford

value: ENCBS465MWC at ENCODE; https://www.encodeproject.org/ENCBS465MWC/


title: ChIP-seq from HEK293 (ENCLB227OBL)

description:
https://www.encodeproject.org/experiments/ENCSR080CST/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF639 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR080CST
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB227OBL
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF639 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF639 under the control of a CMV promoter.

value: embryonic

value: unknown

value: ENCBS695IQG at ENCODE; https://www.encodeproject.org/ENCBS695IQG/

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


title: ChIP-seq from K562 (ENCLB340ZRV)

description:
https://www.encodeproject.org/experiments/ENCSR085OAX/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-PTTG1 tagged K562 cell line.
experiment encode accession: ENCSR085OAX
assay title: ChIP-seq
encode release date: 2015-12-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB340ZRV
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-PTTG1 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to PTTG1

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS405IFW at ENCODE; https://www.encodeproject.org/ENCBS405IFW/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW39; http://web.expasy.org/cellosaurus/CVCL_AW39


title: Striatum-3wks-Rai1-KO-rep2

value: Striatum

value: 3 weeks


title: ChIP-seq from K562 (ENCLB261PCM)

description:
https://www.encodeproject.org/experiments/ENCSR090JNM/
***************
biological replicate number: 2
technical replicate number: 1
description: HLTF ChIP-seq on human K562
experiment encode accession: ENCSR090JNM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB261PCM
size range: 450-650

value: HLTF

value: immortalized cell line

value: adult

value: Michael Snyder, Stanford

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

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


title: ChIP-seq from K562 (ENCLB849SFJ)

description:
https://www.encodeproject.org/experiments/ENCSR086FZL/
***************
biological replicate number: 1
technical replicate number: 1
description: KAT8 ChIP-seq on human K562
experiment encode accession: ENCSR086FZL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB849SFJ
size range: 450-650

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

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


title: ChIP-seq from K562 (ENCLB071ZTO)

description:
https://www.encodeproject.org/experiments/ENCSR079WHK/
***************
biological replicate number: 1
technical replicate number: 1
description: MCM5 ChIP-seq on human K562
experiment encode accession: ENCSR079WHK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB071ZTO
size range: 450-650

value: 53 year

value: ENCBS101QRF at ENCODE; https://www.encodeproject.org/ENCBS101QRF/


title: ChIP-seq from HEK293 (ENCLB597LTS)

description:
https://www.encodeproject.org/experiments/ENCSR080CST/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF639 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR080CST
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB597LTS
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF639 under the control of a CMV promoter.

value: embryonic

value: unknown

value: female

value: ENCBS486AZC at ENCODE; https://www.encodeproject.org/ENCBS486AZC/

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


title: ChIP-seq from HepG2 (ENCLB215GBH)

description:
https://www.encodeproject.org/experiments/ENCSR081WLS/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD51 ChIP-seq on human HepG2
experiment encode accession: ENCSR081WLS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB215GBH
size range: 450-650

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS515KFV at ENCODE; https://www.encodeproject.org/ENCBS515KFV/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from K562 (ENCLB142QTG)

description:
https://www.encodeproject.org/experiments/ENCSR079WHK/
***************
biological replicate number: 2
technical replicate number: 1
description: MCM5 ChIP-seq on human K562
experiment encode accession: ENCSR079WHK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB142QTG
size range: 450-650

value: immortalized cell line

value: adult

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS398HUM at ENCODE; https://www.encodeproject.org/ENCBS398HUM/

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


title: ChIP-seq from HepG2 (ENCLB586LIO)

description:
https://www.encodeproject.org/experiments/ENCSR081WLS/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD51 ChIP-seq on human HepG2
experiment encode accession: ENCSR081WLS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2016-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB586LIO
size range: 450-650

value: ENCBS983YXQ at ENCODE; https://www.encodeproject.org/ENCBS983YXQ/


title: eCLIP from HepG2 (ENCLB734PHN)

description:
https://www.encodeproject.org/experiments/ENCSR077KVG/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against IGF2BP3
experiment encode accession: ENCSR077KVG
assay title: eCLIP
assembly: GRCh38, hg19
encode release date: 2015-07-15
lab: Gene Yeo, UCSD
library encode accession: ENCLB734PHN
size range: 175-300

value: Control

value: Gene Yeo, UCSD

value: ENCBS931EXY at ENCODE; https://www.encodeproject.org/ENCBS931EXY/

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from HEK293 (ENCLB786ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR076EZB/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-KLF9 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR076EZB
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB786ZSN
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-KLF9 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-KLF9 under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: ENCBS321GAS at ENCODE; https://www.encodeproject.org/ENCBS321GAS/

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


title: ChIP-seq from HEK293 (ENCLB734LTP)

description:
https://www.encodeproject.org/experiments/ENCSR076EZB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-KLF9 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR076EZB
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB734LTP
size range: 450-650

value: immortalized cell line

value: ENCBS659BWP at ENCODE; https://www.encodeproject.org/ENCBS659BWP/


title: ChIP-seq from K562 (ENCLB619XMM)

description:
https://www.encodeproject.org/experiments/ENCSR085QEV/
***************
biological replicate number: 1
technical replicate number: 1
description: NBN ChIP-seq on human K562
experiment encode accession: ENCSR085QEV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB619XMM
size range: 450-650

value: NBN

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: Michael Snyder, Stanford

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

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 (ENCLB817KEF)

description:
https://www.encodeproject.org/experiments/ENCSR085QEV/
***************
biological replicate number: 2
technical replicate number: 1
description: NBN ChIP-seq on human K562
experiment encode accession: ENCSR085QEV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-06-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB817KEF
size range: 450-650

value: chronic myelogenous leukemia (CML)

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/

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


title: ChIP-seq from K562 (ENCLB902CBU)

description:
https://www.encodeproject.org/experiments/ENCSR080EOT/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR080EOT
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB902CBU
size range: 150-350

value: Control

value: female

value: ENCBS118YJZ at ENCODE; https://www.encodeproject.org/ENCBS118YJZ/


title: ChIP-seq from HepG2 (ENCLB555ADG)

description:
https://www.encodeproject.org/experiments/ENCSR101FJU/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF384 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADG
size range: 150-350

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

value: Hepatocellular carcinoma

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS522AAA at ENCODE; https://www.encodeproject.org/ENCBS522AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from K562 (ENCLB511MDO)

description:
https://www.encodeproject.org/experiments/ENCSR075HTM/
***************
biological replicate number: 1
technical replicate number: 1
description: HDAC2 ChIP-seq on human K562
experiment encode accession: ENCSR075HTM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB511MDO
size range: 450-650

value: 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: Michael Snyder, Stanford

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

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


title: ChIP-seq from HEK293 (ENCLB691XCD)

description:
https://www.encodeproject.org/experiments/ENCSR072LQF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF76 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR072LQF
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB691XCD
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZNF76 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF76 under the control of a CMV promoter.

value: embryonic

value: female

value: unknown

value: ENCBS168VCZ at ENCODE; https://www.encodeproject.org/ENCBS168VCZ/

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


title: ChIP-seq from K562 (ENCLB322GCM)

description:
https://www.encodeproject.org/experiments/ENCSR085DDI/
***************
biological replicate number: 2
technical replicate number: 1
description: NFXL1 ChIP-seq on human K562
experiment encode accession: ENCSR085DDI
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR173USI
encode release date: 2016-12-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB322GCM
size range: 450-650

value: chronic myelogenous leukemia (CML)

value: ENCBS406RFF at ENCODE; https://www.encodeproject.org/ENCBS406RFF/

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


title: ChIP-seq from HepG2 (ENCLB555ADH)

description:
https://www.encodeproject.org/experiments/ENCSR101FJU/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF384 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADH
size range: 150-350

value: Hepatocellular carcinoma

value: child

value: 15 year

value: male

value: hepatocellular carcinoma

value: ENCBS523AAA at ENCODE; https://www.encodeproject.org/ENCBS523AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: ChIP-seq from K562 (ENCLB207AXV)

description:
https://www.encodeproject.org/experiments/ENCSR075HTM/
***************
biological replicate number: 2
technical replicate number: 1
description: HDAC2 ChIP-seq on human K562
experiment encode accession: ENCSR075HTM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB207AXV
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS398HUM at ENCODE; https://www.encodeproject.org/ENCBS398HUM/


title: ChIP-seq from K562 (ENCLB618PJR)

description:
https://www.encodeproject.org/experiments/ENCSR080EOT/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR080EOT
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB618PJR
size range: 150-350

value: Control

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: female

value: chronic myelogenous leukemia (CML)

value: ENCBS684JMW at ENCODE; https://www.encodeproject.org/ENCBS684JMW/

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 HepG2 (ENCLB555ADF)

description:
https://www.encodeproject.org/experiments/ENCSR101FJT/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF143 ChIP-seq on human HepG2
experiment encode accession: ENCSR101FJT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR613TDP
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB555ADF
size range: 150-350

value: Hepatocellular carcinoma

value: child

value: 15 year

value: male

value: hepatocellular carcinoma


title: ChIP-seq from IMR-90 (ENCLB631ERN)

description:
https://www.encodeproject.org/experiments/ENCSR000HPG/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on human IMR90
experiment encode accession: ENCSR000HPG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR970FKL
encode release date: 2016-10-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB631ERN
size range: 150-350

source_name: Homo sapiens IMR-90 primary cell female fetal (16 weeks)

value: primary cell

value: Fetal lung fibroblasts

value: fetal

value: 16 week

value: unknown

value: ENCBS648SCY at ENCODE; https://www.encodeproject.org/ENCBS648SCY/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/

value: ENCODE dbxrefs Cellosaurus CVCL_0347; http://web.expasy.org/cellosaurus/CVCL_0347

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-186.aspx


title: ChIP-seq from MCF-7 (ENCLB457VCC)

description:
https://www.encodeproject.org/experiments/ENCSR066TET/
***************
biological replicate number: 3
technical replicate number: 1
description: RFX1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR066TET
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2016-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB457VCC
size range: 450-650

value: immortalized cell line

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: ENCBS123ZGI at ENCODE; https://www.encodeproject.org/ENCBS123ZGI/

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

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