title: OEP01_N704_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: OEP01_N704_S501

status: Public on Apr 14 2017

type: SRA

city: Berkeley

first: Diya

last: Das

state: California

address: 265 Life Sciences Addition #3200

department: Molecular & Cell Biology

country: USA

institute: University of California, Berkeley

description:
oeHBCdiff_Cufflinks_eSet_counts_table.txt
oeHBCdiff_Cufflinks_eSet_fpkm_table.txt
oeHBCdiff_Cufflinks_eSet_tpm_table.txt
oeHBCdiff_RSEM_eSet_expectedCounts_table.txt
oeHBCdiff_RSEM_eSet_fpkm_table.txt
oeHBCdiff_RSEM_eSet_tpm_table.txt
oeHBCdiff_kallisto_eSet_estimatedCounts_table.txt
oeHBCdiff_kallisto_eSet_tpm_table.txt
oeHBCdiff_Cufflinks_eSet.Rda
oeHBCdiff_RSEM_eSet.Rda
oeHBCdiff_kallisto_eSet.Rda
oeHBCdiff_countsMatrix.txt

library_source: transcriptomic

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3). TPMs were derived from Cufflinks (Version 2.2.1) FPKMs.
As a second strategy for getting gene level counts, we used RSEM (Version 1.2.31) to get expected counts.
As a third stategy for getting gene level counts, we used kallisto (Version 0.43.0) to obtain estimated counts and RPKMs.
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content: tab-delimited text files include gene level count, FPKM, and TPM values for each sample derived from Cufflinks and featureCounts
Supplementary_files_format_and_content: tab-delimited text files include gene level expected count, FPKM, and TPM values for each sample derived from RSEM
Supplementary_files_format_and_content: tab-delimited text files include gene level estimated count and TPM values for each sample derived from kallisto
Supplementary_files_format_and_content: ExpressionSets that include all metadata and the appropriate count data for each of our three alignment and gene level count procedures (oeHBCdiff_Cufflnks_eSet, oeHBCdiff_RSEM_eSet, oeHBCdiff_kallisto_eSet)
Supplementary_files_format_and_content: oeHBCdiff_phenoData.txt: metadata on samples including experimental condition and batch
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_counts_table.txt: abundance measurements (featureCounts), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_fpkm_table.txt: abundance measurements (Cufflinks), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_tpm_table.txt: abundance measurements (derived from Cufflinks fpkms), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_expectedCounts_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_fpkm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_tpm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_estimatedCounts_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_tpm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_countsMatrix.txt: normalized counts matrix, text file

molecule: polyA RNA

organism: Mus musculus

source_name: olfactory epithelium

extract_protocol:
Olfactory epithelium was dissected from transgenic animals; the dorsal region corresponding to the sensory olfactory epithelium was isolated and dissociated with papain for 25 minutes.  Labeled cells were collected by FACS.
The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single-cell RNA-sequencing.  scRNA-Seq was performed on Illumina HISEQ 2500 sequencer; up to 192 samples were sequenced per lane, often in Rapid Run mode.

value: M

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

value: medium

value: Frodo

tag: ercc spike-in dilution

tag: experimental condition

value: Krt5-Rosa-eYFP, 96 hours post tamoxifen


title: OEP01_N703_S505

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: OEP01_N703_S506

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate


title: OEP01_N706_S506

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date


title: OEP01_N703_S507

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N703_S501

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: OEP01_N703_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEP01_N703_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: OEP01_N702_S507

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N702_S508

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEP01_N702_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: OEP01_N702_S505

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: OEP01_N705_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N702_S504

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: OEP01_N702_S502

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: OEP01_N702_S501

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEP01_N702_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N701_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: OEP01_N701_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEP01_N701_S504

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: OEP01_N701_S506

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N701_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEP01_N701_S507

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: OEP01_N701_S503

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: OEP01_N701_S501

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEP01_N703_S504

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N728_S505

value: F

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

value: B

tag: lane

tag: cdna concentration (ng/μl)

value: Smeagol


title: GBCP05_N728_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N728_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N727_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N728_S503

tag: dilution plate coordinate

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tag: lane

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title: GBCP05_N727_S507

tag: age

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title: GBCP05_N727_S510

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N727_S508

tag: dilution plate coordinate

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tag: c1 machine id


title: GBCP05_N727_S506

tag: age

tag: expt condition

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tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N727_S502

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N726_S510

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N726_S506

tag: age

tag: expt condition

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tag: c1 chip size

tag: c1 machine id


title: GBCP05_N726_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N726_S507

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N727_S505

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N726_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N726_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N727_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCP05_N726_S502

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N726_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N724_S507

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N724_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N724_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N724_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N724_S510

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N724_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N724_S502

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N723_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N723_S508

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N723_S507

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCP05_N723_S506

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N723_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N723_S510

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N722_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N723_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N723_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N722_S510

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N722_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N721_S510

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N721_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N722_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N721_S507

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCP05_N721_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N721_S506

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N721_S505

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N724_S511

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N721_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N720_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N721_S502

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N720_S511

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N719_S511

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N719_S507

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N719_S508

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N720_S510

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCP05_N720_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N722_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N719_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N719_S510

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N720_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N719_S502

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N719_S503

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N720_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N718_S511

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N718_S508

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N718_S510

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N718_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCP05_N718_S507

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N719_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N718_S503

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N720_S507

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCP05_N718_S505

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N716_S511

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N716_S507

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N716_S508

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCP05_N716_S506

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N716_S510

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCP05_N720_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N716_S505

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N714_S518

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

value: C

value: small

tag: ercc spike-in dilution

tag: experimental condition


title: GBCP05_N716_S503

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N714_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N716_S502

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N714_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N714_S513

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N712_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCP05_N718_S502

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N712_S521

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N712_S520

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N712_S518

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N712_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N711_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N712_S513

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N712_S515

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N711_S521

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N711_S520

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N711_S513

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N711_S518

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N711_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N714_S520

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N711_S517

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N711_S516

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N710_S518

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N710_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N710_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N710_S517

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N710_S520

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N707_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N710_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N710_S513

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N714_S522

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N707_S522

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N712_S517

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N714_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N707_S517

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N707_S520

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N707_S516

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N714_S517

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N710_S515

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N706_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N706_S520

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N707_S513

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N706_S518

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N706_S522

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N706_S515

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N706_S517

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N706_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N705_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N706_S513

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N705_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N705_S518

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N705_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N707_S518

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N704_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N705_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N704_S521

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N705_S513

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N703_S520

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N704_S520

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N703_S522

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N707_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N704_S517

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N705_S520

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N705_S517

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N704_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N704_S513

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N704_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N703_S518

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N702_S521

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N703_S517

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N704_S518

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N702_S520

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N703_S513

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N702_S522

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N703_S515

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dob

tag: facs & c1 date


title: GBCO04_N703_S521

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N703_S516

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N702_S517

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N702_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: GBCO04_N701_S522

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N702_S513

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: c1 chip size

tag: c1 machine id


title: GBCO04_N701_S517

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: GBCO04_N701_S518

tag: age

tag: expt condition

tag: sex type

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: GBCO04_N701_S516

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: ercc spike-in dilution

tag: experimental condition


title: GBCO04_N701_S515

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: RNA_CKO_luc_P25_rep2

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC mm9 genome assembly using STAR (v2.5.2a) with default settings.
Only the reads with no more than  4% (2 bp) mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Differentially expressed genes are analyzed using featureCounts (v1.5.0-p2) and DESeq2 (v1.12.3).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using deepTools

molecule: total RNA

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Peking University and Boston Children’s Hospital.

extract_protocol:
mRNA was isolated from total RNA using Dynabeads Oligo(dT), followed by first and second strands synthesis. RNA-seq libraries were prepared from fragmented double-stranded cDNA using ScriptSeq v2 (Epicenter)
RNA-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 independent RNA-seq samples were used for one single RNA-seq library preparation

treatment_protocol: mice were injected with AAV9 by intraperitoneal or intravascular injection where indicated as described previously (Lin, et al. Circ Res. 2015)

tag: cell type

value: isolated adult ventricular cardiomyocytes

tag: strain background

tag: genotype/variation

value: EED CKO


title: RNA_CKO_luc_P25_rep1


title: RNA_CKO_HDAC_rep1

value: HDAC rescue in EED CKO


title: RNA_CKO_EED_P25_rep2

value: EED rescue in EED CKO


title: RNA_CKO_EED_P25_rep1


title: GBCO04_N702_S518

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date


title: RNA_Het_rep1

value: wild type


title: RNA_CKO_rep2

extract_protocol:
mRNA was isolated from total RNA using Dynabeads Oligo(dT), followed by first and second strands synthesis. RNA-seq libraries were prepared from fragmented double-stranded cDNA using ScriptSeq v2 (Epicenter)
RNA-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit. 2 independent RNA-seq samples were used for one single RNA-seq library preparation.

tag: tissue

value: Heart


title: RNA_Het_rep2


title: RNA_CKO_rep1


title: RNA_WT_rep1

value: WT


title: RNA_WT_rep2


title: GBCO04_N702_S516

value: M

tag: visual qc

value: Yes

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: H3K27me3_heto_rep2

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.7.12 with default settings.
Only the reads with no more than  4% (2 bp) mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Peaks were called using MACS2 (version 2.1.0) with the following setting:  –keep-dup=1, --broad .
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using deepTools

molecule: genomic DNA

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit. 1 or 2 independent ChIP samples were used for one single ChIP-seq library preparation.

tag: cell type

tag: strain background

tag: chip antibody

tag: genotype/variation

tag: injected with

value: Not injected


title: HDAC2_CKO

tag: tissue

value: HDAC2 (Abcam, ab7029)


title: H3K27me3_heto_rep1


title: HDAC2_heto


title: GBCO04_N701_S521

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: medium

tag: c1 machine id

value: Frodo


title: GBCO04_N701_S520

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: H3K27me3_CKO_luc_rep2

tag: tissue

tag: cell type

tag: strain background

tag: chip antibody

tag: genotype/variation

tag: injected with

value: AAV-luciferase


title: GBCO04_N701_S513

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: H3K27me3_CKO_luc_rep1

tag: tissue

tag: cell type

tag: strain background


title: input_rescue

description:
Total_DNA
Input for both H3K27ac and H3K27me3 rescue

tag: chip antibody

value: none (input)

tag: genotype/variation

tag: injected with


title: H3K27me3_CKO_HDAC1/2_rep2


title: H3K27ac_heto_rep1

value: H3K27ac ( Abcam, ab4729)


title: H3K27ac_heto_rep2


title: H3K27ac_CKO_HDAC1/2_rep2


title: H3K27ac_CKO_luc_rep2


title: H3K27ac_CKO_luc_rep1


title: RNA_CKO_HDAC_rep2


title: H3K27ac_CKO_HDAC1/2_rep1


title: input_EED_ChIP


title: input_HDAC2


title: EED_ChIP_rep1


title: EED_ChIP_rep2


title: H3K27me3_CKO_HDAC1/2_rep1


title: input_H3K27me3_WT_CKO

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.7.12 with default settings
Only the reads with no more than  4% (2 bp) mismatches and uniquely mapped to reference genome were kept by using Bash Shell.
Peaks were called using MACS2 (version 2.1.0) with the following setting:  –keep-dup=1, --broad .
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using deepTools

source_name: genomic DNA from mixed samples of WT and CKO

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 independent ChIP samples were used for one single ChIP-seq library preparation

value: wild type; CKO


title: H3K27me3_Heto_P25_rep1

description: input sample used: input_H3K27me3_H3K27ac_P25

value: Myh6-Cre+ ; Eed fl/+  (Heto:phenotype is the same as WT)

value: isolated adult ventricular cardiomyocytes

value: H3K27me3 (Millipore, 17-622)


title: input_H3K27ac_WT_CKO


title: input_H3K27me3_H3K27ac_P14

source_name: input for all P14 samples

value: Myh6-Cre+ ; Eed fl/fl  (EED Knockout; CKO)


title: input_H3K27me3_H3K27ac_P5

source_name: input for all P5 samples


title: H3K27me3_CKO_rep1

description: input sample used: input_H3K27me3_WT_CKO


title: H3K27me3_WT_rep1

value: wild type


title: H3K27me3_WT_rep2

value: Heart


title: H3K27me3_CKO_rep2


title: H3K27me3_CKO_EED_P5_rep2

description: input sample used: input_H3K27me3_H3K27ac_P5

value: AAV9 expressing EED at P5

value: H3K27me3 (Millipore, 07-449)


title: H3K27me3_CKO_EED_P5_rep1


title: H3K27me3_CKO_luc_P5_rep2

value: AAV9 expressing luciferase at P5


title: H3K27me3_CKO_luc_P5_rep1


title: H3K27ac_WT_rep1

description: input sample used: input_H3K27ac_WT_CKO

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_WT_rep2

description: input sample used: input_H3K27ac_WT_CKO


title: H3K27ac_CKO_rep2

description: input sample used: input_H3K27ac_WT_CKO


title: H3K27ac_CKO_luc_P5_rep2

value: H3K27ac (Active Motif, 39133)


title: input_H3K27me3_H3K27ac_P25

source_name: input for all P25 samples


title: H3K27me3_CKO_luc_P25_rep1

value: AAV9 expressing luciferase at P25


title: H3K27me3_WT_rep3


title: H3K27ac_CKO_rep1

description: input sample used: input_H3K27ac_WT_CKO


title: H3K27ac_CKO_luc_P25_rep1


title: H3K27me3_CKO_EED_P25_rep2

value: AAV9 expressing EED at P25


title: H3K27me3_CKO_EED_P25_rep1


title: H3K27ac_CKO_luc_P5_rep1


title: H3K27ac_Heto_P25_rep1


title: H3K27ac_CKO_EED_P5_rep2


title: H3K27me3_CKO_EED_P14_rep2

description: input sample used: input_H3K27me3_H3K27ac_P14

value: AAV9 expressing EED at P14


title: H3K27me3_CKO_EED_P14_rep1


title: H3K27ac_CKO_EED_P5_rep1


title: Patchd1_138_ko

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

country: Spain

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9
Supplementary_files_format_and_content: Table_S3.xlsx: Gene read counts and DEseq2 pvalues  Table_S4.xlsx: Cell types enrichments  Table_S5.txt: GO enrichments summary for DOWN-regulated genes  Table_S6.txt: GO enrichments summary for UP-regulated genes  Table_S7.xlsx: GO enrichments detailed for DOWN-regulated genes  Table_S8.xlsx: GO enrichments detailed for UP-regulated genes Table_S9.xlsx: Cistrome and MotifMap enrichments

source_name: whole hippocampus

extract_protocol:
Total RNA was Trizol extracted. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

tag: age

value: brain

tag: tissue compartment

value: hippocampus

tag: strain

tag: genotype

value: PTCHD1 mutant


title: H3K27ac_CKO_EED_P25_rep2


title: H3K27ac_CKO_EED_P25_rep1


title: Patchd1_136_wt


title: Patchd1_137_wt


title: Patchd1_140_ko


title: Kansl1_4wt_k4me3

data_processing:
alignment was done with BWA 0.6.2
read counting was performed with custom C++ script
Genome_build: mm9
Supplementary_files_format_and_content: kansl1.xlsx: Peak calls, reads counts and pvalues for Kansl1 +/-. GEO only.
qdel.xlsx: Peak calls, reads counts and pvalues for Del/+. GEO only.
Table_S5.txt: cluster1 GO enrichments
Table_S6.txt: cluster2 GO enrichments
Table_S7.txt: cluster3 GO enrichments
Table_S8.txt: cluster4 GO enrichments
Table_S9.txt: Kansl1+/- DOWN-reg GO enrichments
Table_S10.txt: Kansl1+/- UP-reg GO enrichments
Table_S11.txt: Del/+ DOWN-reg GO enrichments
Table_S12.txt: Del/+ UP-reg GO enrichments
Table_S13.txt: cluster1 other enrichments (cell-types, chromosomes, gene features..)
Table_S14.txt: cluster2 other enrichments (cell-types, chromosomes, gene features..)
Table_S15.txt: cluster3 other enrichments (cell-types, chromosomes, gene features..)
Table_S16.txt: cluster4 other enrichments (cell-types, chromosomes, gene features..)
Table_S17.txt: Kansl1+/- DOWN-reg other enrichments (cell-types, chromosomes, gene features..)
Table_S18.txt: Kansl1+/- UP-reg other enrichments (cell-types, chromosomes, gene features..)
Table_S19.txt: Del/+ DOWN-reg other enrichments (cell-types, chromosomes, gene features..)
Table_S20.txt: Del/+ UP-reg other enrichments (cell-types, chromosomes, gene features..)

extract_protocol:
Chipping for H3k4me3 (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.

value: Kansl1 wt control


title: H3K27ac_CKO_EED_P14_rep2

value: isolated adult ventricular cardiomyocytes


title: Patchd1_135_ko


title: Kansl1_37ko_k4me3

value: Kansl1 +/- mutant


title: 17qDel_1ko_k4me3

value: Del/+ mutant


title: siMalat1_RNA-seq

city: Shenzhen

first: Kun

last: Sun

address: Rm B505, No. 9 Duxue Road, Nanshan District

department: Cancer Research

country: China

institute: Shenzhen Bay Laboratory

description: siMalat1 knockdown

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were first aligned to the mm9 genome using TopHat (v2.0.9). Then expression quantification was conducted using Cufflinks (v2.1.1).
Differentially expression between siNC and siMalat1 was conducted using Cuffdiff (v2.1.1) against RefSeq genes.
Genome_build: mm9
Supplementary_files_format_and_content: Differentially expressed genes analysis result in EXCEL XLSX format.

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were growed in gowth medium containing DMEM, 10% FBS and 1% pen/srep.

extract_protocol:
Purified RNA was fragmented and the cDNA was synthesized by reverse transcription. The resulting double-stranded DNA fragments were en-repaired and A-nucleotide overhangs were added.
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)

tag: cell line

value: myoblasts


title: Kansl1_40_WT_k4me3


title: 17qDel_14_KO_k4me3


title: siNC_RNA-seq

description: negative control


title: 17qDel_4wt_k4me3

value: Del wt control


title: Kansl1_13_KO_k4me3


title: Kansl1_52_KO_k4me3


title: 17qDel_6_WT_k4me3


title: 17qDel_2_KO_k4me3


title: 17qDel_15_WT_k4me3


title: Kansl1_31_WT_k4me3


title: Patchd1_131_wt

value: wild type


title: B4-drug

status: Public on Apr 13 2017

city: Philadelphia

first: Sydney

middle: M

last: Shaffer

state: PA

address: BRB II/III, Room 445, 421 Curie Blvd

institute: University of Pennsylvania

description:
B4-drug
processed data file: meltedData_wm983b_run4.tsv

data_processing:
Aligned reads to hg19 using STAR.
Quantified reads per gene using HTSeq.
Performed differential expression analysis using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain a melted table of raw counts for every gene in each sample.

organism: Homo sapiens

growth_protocol: We grew melanoma cell lines (WM989 and WM983B) from the lab of Meenhard Herlyn in Tu2% media containing 78% MCDB, 20% Leibovitz’s L-15 media, 2% FBS, and 1.68mM CaCl2.

extract_protocol:
We extracted RNA using Qiagen miRNAeasy extraction kit.
We selected polyadenylated RNA and prepared barcoded RNA sequencing libraries using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: We treated cells with 1uM vemurafenib.

tag: subclone

tag: condition

value: Drug


title: G6-no-drug

description:
G6-no-drug
processed data file: meltedData_wm983b_run4.tsv

value: NoDrug


title: plusQ_MYC

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illumina's CASAVA software.
Fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1 with default parameters and normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with the genomeCoverageBed function from BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph format as described in the UCSC file format guide (https://genome.ucsc.edu/goldenpath/help/bedgraph.html)

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% FBS (Biochrom) and 1% penicillin/streptomycin. Experiments were performed using DMEM reconstituted with 2 mM glutamine, 2.5 g/l glucose, 0.015 g/l phenol red, 10% dialyzed FBS and 1% penicillin/streptomycin, without sodium pyruvate . For starvation experiments, cells were washed twice with PBS and cultured in reconstituted DMEM without glutamine.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay.

treatment_protocol: Cells were treated with 100 nM 4-Hydroxytamoxifen for 15 hours, then glutamine starved for 5 hours in presence of  4-Hydroxytamoxifen

tag: treatment1(myc-er+oht or empty vector)

tag: treatment2(glutamine(q) concentration)

tag: antibody

value: MYC N262 (sc-764, Santa Cruz)


title: plusQ_input


title: B3-no-drug

description:
B3-no-drug
processed data file: meltedData_wm983b_run4.tsv


title: E10-1-A2

description:
E10-1-A2
processed data file: meltedData_wm983b_run4.tsv


title: B10-2-A4

description:
B10-2-A4
processed data file: meltedData_wm983b_run4.tsv


title: E2-1-A3

description:
E2-1-A3
processed data file: meltedData_wm983b_run4.tsv


title: E10-2-C2

description:
E10-2-C2
processed data file: meltedData_wm983b_run4.tsv


title: H3K27ac_CKO_EED_P14_rep1

value: Myh6-Cre+ ; Eed fl/fl  (EED Knockout; CKO)

value: Heart

value: H3K27ac (Active Motif, 39133)


title: E2-drug

description:
E2-drug
processed data file: meltedData_wm983b_run4.tsv


title: B4-no-drug

description:
B4-no-drug
processed data file: meltedData_wm983b_run4.tsv


title: G6-drug

description:
G6-drug
processed data file: meltedData_wm983b_run4.tsv


title: D5-drug

description:
D5-drug
processed data file: meltedData_wm983b_run3.tsv


title: E3.5_MethylC-Seq

city: Beijing

first: Lu

last: Wang

email: share.luwang@gmail.com, liuj@big.ac.cn

address: No.1 Beichen West Road

institute: Beijing Institute of Genomics

data_processing:
Illumina Casava 1.82 software was used for basecalling.
Once the sequencing data was obtained from Hiseq-2000, the raw data will be analyzed by the standard combined pipeline in the lab including five steps: 1) finding reads hit by adaptor sequence with a custom pair-wise alignment script, 2) low-quality base trimming by Trimmomatic with default parameters, 3) mapping paired-end methylC-seq reads by Bismark (version 0.7.8) with stringent parameters: -N 1 –X 600, 4) removing duplicates by using Picard program, 5) trimming the overlapped part of paired-end reads from one end.
Quantification of methylation levels of CpGs: For CpG i, define mi as the number of reads showing methylation over position i (both strands). Define ui as the number of reads showing lack of methylation over CpG i. The methylation level is estimated as mi/(mi + ui), which is an estimate of the probability that CpG i is methylated in a molecule sampled randomly from the cell population. Because CpG methylation is symmetric, mi and ui include observations associated with the cytosines on both strands for the i-thCpG.
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Format: bed; content: Methylation level for each CpG site plus 2 columns representing the numbers of Cs and Ts. For strand-specific files, the position of each CpG site is displayed as the C position in Watson strand.

source_name: E3.5 embryos

extract_protocol: MethylC-Seq: Purified DNA spiked in with 0.1% unmethylated cl857 Sam7 lambda DNA (Promega) was sonicated using the microtube protocol-300 of Covaris S2 (Applied Biosystems). End-repair, dA-tailing and ligation were performed using the NEBNext End Repair Module, dA-Tailing Module and NEB T4 ligase. The adaptor-ligated DNA with insert size larger than 200 bp was selected by gel electrophoresis. Bisulfite conversion was performed using the EZ DNA methylation Gold Kit (Zymo Research) according to the manufacturer’s instructions. The time of 64°C incubation was 2 hr for some libraries. Bisulfite- treated DNA was amplified using ZymoTaq DNA Polymerase or KAPA HiFi HotStart Uracil+ ReadyMix with 14-15 cycles.  Mouse gametes and embryos were collected at minimal volume and frozen. DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) and RNA was isolated using RNeasy Micro Kit (QIAGEN).

value: E3.5 embryo


title: B3-drug

description:
B3-drug
processed data file: meltedData_wm983b_run4.tsv


title: E7-2-B1

description:
E7-2-B1
processed data file: meltedData_wm983b_run4.tsv


title: E10-no-drug

description:
E10-no-drug
processed data file: meltedData_wm983b_run4.tsv


title: E10-drug

description:
E10-drug
processed data file: meltedData_wm983b_run4.tsv


title: G6-1-C4

description:
G6-1-C4
processed data file: meltedData_wm983b_run4.tsv


title: C3-1-B1

description:
C3-1-B1
processed data file: meltedData_wm983b_run3.tsv


title: B2-2-C2

description:
B2-2-C2
processed data file: meltedData_wm983b_run3.tsv


title: E3-1-B4

description:
E3-1-B4
processed data file: meltedData_wm983b_run3.tsv


title: C10-1-A2

description:
C10-1-A2
processed data file: meltedData_wm983b_run3.tsv


title: E7-1-C3

description:
E7-1-C3
processed data file: meltedData_wm983b_run3.tsv


title: E2-no-drug

description:
E2-no-drug
processed data file: meltedData_wm983b_run4.tsv


title: G7-2-A4

description:
G7-2-A4
processed data file: meltedData_wm983b_run3.tsv


title: E7-1-A3

description:
E7-1-A3
processed data file: meltedData_wm983b_run4.tsv


title: G8-2-B3

description:
G8-2-B3
processed data file: meltedData_wm983b_run3.tsv


title: G6-1-C2

description:
G6-1-C2
processed data file: meltedData_wm983b_run4.tsv


title: F9-2-B1

description:
F9-2-B1
processed data file: meltedData_wm983b_run3.tsv


title: G7-1-B3

description:
G7-1-B3
processed data file: meltedData_wm983b_run3.tsv


title: D2-2-A1

description:
D2-2-A1
processed data file: meltedData_wm983b_run3.tsv


title: D5-no-drug

description:
D5-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: D5-1-B3

description:
D5-1-B3
processed data file: meltedData_wm983b_run3.tsv


title: E3-drug

description:
E3-drug
processed data file: meltedData_wm983b_run3.tsv


title: E3-no-drug

description:
E3-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: D2-no-drug

description:
D2-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: E7-drug

description:
E7-drug
processed data file: meltedData_wm983b_run3.tsv


title: D3-drug

description:
D3-drug
processed data file: meltedData_wm983b_run3.tsv


title: E7-no-drug

description:
E7-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: G5-Plate1-C2-Week1

description:
G5-Plate1-C2-Week1
processed data file: meltedwm983bLdB_run2.tsv


title: G5-Plate1-A1

description:
G5-Plate1-A1
processed data file: meltedwm983bLdB_run2.tsv


title: G5-Plate1-C2-DrugOn

description:
G5-Plate1-C2-DrugOn
processed data file: meltedwm983bLdB_run2.tsv


title: D3-no-drug

description:
D3-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: F9-Plate1-C1

description:
F9-Plate1-C1
processed data file: meltedwm983bLdB_run2.tsv


title: D2-drug

description:
D2-drug
processed data file: meltedData_wm983b_run3.tsv


title: F9-Plate1-B3

description:
F9-Plate1-B3
processed data file: meltedwm983bLdB_run2.tsv


title: F9-NoDrug

description:
F9-NoDrug
processed data file: meltedwm983bLdB_run2.tsv


title: C10-Plate1-B4

description:
C10-Plate1-B4
processed data file: meltedwm983bLdB_run2.tsv


title: G5-Plate1-C2-Week5

description:
G5-Plate1-C2-Week5
processed data file: meltedwm983bLdB_run2.tsv


title: G5-Plate1-C2-Week3

description:
G5-Plate1-C2-Week3
processed data file: meltedwm983bLdB_run2.tsv


title: F9-PLX48hrs

description:
F9-PLX48hrs
processed data file: meltedwm983bLdB_run2.tsv


title: G7-2-A2

description:
G7-2-A2
processed data file: meltedData_wm983b_run3.tsv


title: G5-Plate1-C2-48hrsOff

description:
G5-Plate1-C2-48hrsOff
processed data file: meltedwm983bLdB_run2.tsv


title: B10-drug

description:
B10-drug
processed data file: meltedData_wm983b_run3.tsv


title: B7-Plate2-A1-Week5

description:
B7-Plate2-A1-Week5
processed data file: meltedwm983bLdB_run2.tsv


title: B7-Plate2-A1-Week3

description:
B7-Plate2-A1-Week3
processed data file: meltedwm983bLdB_run2.tsv


title: C6-NoDrug

description:
C6-NoDrug
processed data file: meltedwm983bLdB_run2.tsv


title: C10-Plate2-C4

description:
C10-Plate2-C4
processed data file: meltedwm983bLdB_run2.tsv


title: B7-NoDrug

description:
B7-NoDrug
processed data file: meltedwm983bLdB_run2.tsv


title: B10-no-drug

description:
B10-no-drug
processed data file: meltedData_wm983b_run3.tsv


title: C10-NoDrug

description:
C10-NoDrug
processed data file: meltedwm983bLdB_run2.tsv


title: C6-PLX48hrs

description:
C6-PLX48hrs
processed data file: meltedwm983bLdB_run2.tsv


title: B7-PLX48hrs

description:
B7-PLX48hrs
processed data file: meltedwm983bLdB_run2.tsv


title: B7-Plate2-A1-DrugOn

description:
B7-Plate2-A1-DrugOn
processed data file: meltedwm983bLdB_run2.tsv


title: C6-Plate2-A2

description:
C6-Plate2-A2
processed data file: meltedwm983bLdB_run2.tsv


title: SubcloneG8-NoDrug-1

description:
SubcloneG8-NoDrug-1
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: B7-Plate2-A1-Week1

description:
B7-Plate2-A1-Week1
processed data file: meltedwm983bLdB_run2.tsv


title: SubcloneG7-Plate1-ColonyA3

description:
SubcloneG7-Plate1-ColonyA3
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: C10-PLX48hrs

description:
C10-PLX48hrs
processed data file: meltedwm983bLdB_run2.tsv


title: SubcloneG7-Plate2-ColonyB1

description:
SubcloneG7-Plate2-ColonyB1
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG7-Drug-10

description:
SubcloneG7-Drug-10
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG8-Drug-2

description:
SubcloneG8-Drug-2
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG8-Plate2-ColonyA4

description:
SubcloneG8-Plate2-ColonyA4
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG7-NoDrug

description:
SubcloneG7-NoDrug
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG5-Drug-4

description:
SubcloneG5-Drug-4
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG8-Plate1-ColonyC3

description:
SubcloneG8-Plate1-ColonyC3
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG5-NoDrug-3

description:
SubcloneG5-NoDrug-3
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneG5-Plate2-ColonyB1

description:
SubcloneG5-Plate2-ColonyB1
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneF4-NoDrug-7

description:
SubcloneF4-NoDrug-7
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneF4-Drug-8

description:
SubcloneF4-Drug-8
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneF4-Plate1-ColonyB1

description:
SubcloneF4-Plate1-ColonyB1
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneF4-Plate2-ColonyC3

description:
SubcloneF4-Plate2-ColonyC3
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: B7-Plate2-A1-48hrsOff

description:
B7-Plate2-A1-48hrsOff
processed data file: meltedwm983bLdB_run2.tsv


title: SubcloneE9-Plate1-ColonyB4

description:
SubcloneE9-Plate1-ColonyB4
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneE9-NoDrug-5

description:
SubcloneE9-NoDrug-5
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: SubcloneE9-Plate1-ColonyB3

description:
SubcloneE9-Plate1-ColonyB3
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: ColonyH1-WellD5-48hrholiday

description:
ColonyH1-WellD5-48hrholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellD5-7dayholiday

description:
ColonyH1-WellD5-7dayholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellA3-drug

description:
ColonyH1-WellA3-drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellA3-7dayholiday

description:
ColonyH1-WellA3-7dayholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellA3-48hrholiday

description:
ColonyH1-WellA3-48hrholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellC5

description:
ColonyH1-WellC5
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: SubcloneE9-Drug-6

description:
SubcloneE9-Drug-6
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: ColonyH1-WellD5-drug

description:
ColonyH1-WellD5-drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellC6-7dayholiday

description:
ColonyG3-WellC6-7dayholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyH1-WellC2

description:
ColonyH1-WellC2
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellC6

description:
ColonyE3-WellC6
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellC6-48hrholiday

description:
ColonyG3-WellC6-48hrholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellB6-drug

description:
ColonyG3-WellB6-drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellC3

description:
ColonyE3-WellC3
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellA4-drug

description:
ColonyE3-WellA4-drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellB6-7dayholiday

description:
ColonyG3-WellB6-7dayholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellA4-48hrholiday

description:
ColonyE3-WellA4-48hrholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellA4-7dayholiday

description:
ColonyE3-WellA4-7dayholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyH3_Drug

description:
A6_ColonyH3_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyH1_NoDrug

description:
A6_ColonyH1_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyH1_Drug

description:
A6_ColonyH1_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellC6-drug

description:
ColonyG3-WellC6-drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyH3_NoDrug

description:
A6_ColonyH3_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: SubcloneG5-Plate2-ColonyB2

description:
SubcloneG5-Plate2-ColonyB2
processed data file: wm983bLdB_star_HTSeqCounts.tsv


title: A6_ColonyF2_Drug

description:
A6_ColonyF2_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyG3_NoDrug

description:
A6_ColonyG3_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyG3_Drug

description:
A6_ColonyG3_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyG3-WellB6-48hrholiday

description:
ColonyG3-WellB6-48hrholiday
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyC2_NoDrug

description:
A6_ColonyC2_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyE2_NoDrug

description:
A6_ColonyE2_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyE2_Drug

description:
A6_ColonyE2_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyC3_Drug

description:
A6_ColonyC3_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: neg-week5-v2_ATAC-seq

description: ATAC-sequencing

data_processing:
We aligned our reads to hg19 with bowtie2
HOMER package for peak calling, differential peak calling, motif analysis, and gene ontology analysis
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format

source_name: WM989 cell line

extract_protocol: We performed ATAC sequencing on WM989-A6 melanoma cells according to Buenrostro et al. Briefly, we lysed the cells and set up the transposition reaction with the Tn5 Transposes (Illumina Catalog #FC121-1030) at 37℃ for 30 minutes. We cleaned the reaction with a Qiagen MinElute Kit and then amplified the libraries using custom Nextera PCR primers.

tag: drug tx

value: week 5

tag: population

value: EGFR-negative

value: melanoma


title: neg-p14-week4-v2_ATAC-seq

description: ATAC-sequencing

value: week 4

tag: cell type


title: A6_ColonyE3_NoDrug

description:
A6_ColonyE3_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyE3_Drug

description:
A6_ColonyE3_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: A6_ColonyC3_NoDrug

description:
A6_ColonyC3_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: neg-p9-week4_ATAC-seq

description: ATAC-sequencing


title: mix-week5-v2_ATAC-seq

description: ATAC-sequencing

value: mix


title: A6_ColonyC2_Drug

description:
A6_ColonyC2_Drug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: mix-p14-week4-v2_ATAC-seq

description: ATAC-sequencing


title: A6_ColonyF2_NoDrug

description:
A6_ColonyF2_NoDrug
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: ColonyE3-WellA1

description:
ColonyE3-WellA1
processed data file: wm9LdB_star_HTSeqCounts_full.tsv


title: mix-p14-noDrug-v2_ATAC-seq

description: ATAC-sequencing

value: no drug


title: mix-p9-noDrug_ATAC-seq

description: ATAC-sequencing


title: mix-p14-week1-v2_ATAC-seq

description: ATAC-sequencing

value: week 1


title: mix-p9-week1_ATAC-seq

description: ATAC-sequencing


title: EGFR-p14-week4-v2_ATAC-seq

description: ATAC-sequencing

value: EGFR-high


title: EGFR-week5-v2_ATAC-seq

description: ATAC-sequencing


title: mix-p9-week4_ATAC-seq

description: ATAC-sequencing


title: EGFR-p14-week1-v2_ATAC-seq

description: ATAC-sequencing


title: EGFR-p9-week4_ATAC-seq

description: ATAC-sequencing


title: nodrug_EGFR_02

description:
SortNoDrugEGFR1
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv

data_processing:
Aligned reads to hg19 using STAR.
Quantified reads per gene using HTSeq.
Performed differential expression analysis using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file contains a melted table of raw counts for every gene in each sample.

source_name: WM989 melanoma cells

tag: time in drug

tag: sorting condition

value: EGFR


title: EGFR-p9-week1_ATAC-seq

description: ATAC-sequencing


title: EGFR-p9-noDrug_ATAC-seq

description: ATAC-sequencing


title: nodrug_EGFR_09

description:
SortNoDrugEGFR2
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: 1week_EGFR_10

description:
week1-EGFRpos-2
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv

value: 1 week


title: nodrug_EGFR_10

description:
SortNoDrugEGFR3
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: nodrug_mix_10

description:
SortNoDrugMix3
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: 1week_mix_09

description:
Sort1WeekDrugMix1
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: EGFR-p14-noDrug-v2_ATAC-seq

description: ATAC-sequencing


title: 1week_EGFR_09

description:
week1-EGFRpos-1
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: nodrug_mix_02

description:
SortNoDrugMix1
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: nodrug_mix_09

description:
SortNoDrugMix2
processed data file: meltedData_20150722_EGFRsortRNArun1.tsv


title: 4weeks_mix_09

description:
week4-mix-1
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv

value: 4 weeks


title: 4weeks_neg_10

description:
week4-EGFRneg-2
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv

value: neg


title: 4weeks_neg_09

description:
week4-EGFRneg-1
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: K562 dCas9-KRAB, 10 sgRNAs targeting TAD2 SE2 enhancers, high MOI, batch 1

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description:
RX141A-mix
sgRNAs and barcodes: listed in supplementary document

data_processing:
Basecalls performed by Illumina bcl2fastq.
Drop-Seq data were mapped using Drop-Seq Tools to the human genome augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome build: hg19
processed_data_files_format_and_content: read counts for all genes

source_name: K562 cells

growth_protocol: K562 were cultured in IMDM plus 10% FBS and pen/strep at 37C and 5% CO2.

extract_protocol: Single cell RNA sequencing was performed using the Drop-Seq method. Briefly, single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (NanoShift). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by Tn5-mediated tagmentation of cDNA, and amplified by PCR (Kapa) and purified by SPRI beads.

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Titrated virus aliquot(s) were thawed to room temperature, combined as a pool, and added to the plates. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection.


title: K562 dCas9-KRAB, 10 sgRNAs targeting TAD2 SE2 enhancers, low MOI, batch 4

description:
RX140-D
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, 10 sgRNAs targeting TAD2 SE2 enhancers, low MOI, batch 3

description:
RX140-C
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, 10 sgRNAs targeting TAD2 SE2 enhancers, low MOI, batch 1

description:
RX140-A
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 8

description:
RX134-8
sgRNAs and barcodes: listed in supplementary document

data_processing:
Basecalls performed by Illumina bcl2fastq v2.17.1.14 .
Drop-Seq data were mapped using Drop-Seq Tools to the human genome augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome build: hg19
Supplementary_files_format_and_content: read counts for all genes


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 9

description:
RX134-9
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, biorep 2, batch 1

description:
RX135-1
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 7

description:
RX134-7
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, biorep 2, batch 2

description:
RX135-mix
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 6

description:
RX134-6
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 12

description:
RX134-mix
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, biorep 2, batch 1

description:
RX136-1
sgRNAs and barcodes: listed in supplementary document


title: 4weeks_EGFR_09

description:
week4-EGFRpos-1
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: 1week_mix_10

description:
week1-mix-2
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 5

description:
RX134-5
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 3

description:
RX134-3
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 4

description:
RX134-4
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 2

description:
RX134-2
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 1

description:
RX134-1
sgRNAs and barcodes: listed in supplementary document


title: 4weeks_mix_10

description:
week4-mix-2
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 5

description:
RX133-2
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 10

description:
RX134-10
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 6

description:
RX133
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 2, batch 11

description:
RX134-13
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 4

description:
RX132-4
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 2

description:
RX132-2
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 3

description:
RX132-3
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, 10 sgRNAs targeting TAD2 SE2 enhancers, low MOI, batch 2

description:
RX140-B
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, biorep 2, batch 2

description:
RX136-mix
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, biorep 3, batch 1

description:
RX132-1
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 16

description:
JD130-6
sgRNAs and barcodes: listed in supplementary document

data_processing:
Basecalls performed by Picard ExtractIlluminaBarcodes v1.117.
Drop-Seq data were mapped using Drop-Seq Tools to the human genome augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome build: hg19
Supplementary_files_format_and_content: read counts for all genes

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Titrated virus aliquot(s) were thawed to room temperature and one virus was added to each well. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection. One batch of cells were treated with TNF-alpha for 1 hour. Immediately prior to library construction, the TNF-alpha treated cells (labeled with sgRNA64) and mock treated cells (labeled with sgRNA63) were combined to a single tube in PBS/BSA.


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 15

description:
JD130-5
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 14

description:
JD130-4
sgRNAs and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 13

description:
JD130-3
sgRNAs and barcodes: listed in supplementary document


title: K562, dCas9-KRAB, infected with sgRNA64 (rep4); treated with TNFalpha for 1h

description:
PZ310
sgRNA ID: sgRNA64
sgRNA barcode ID:

data_processing:
Basecalls performed bcl2fastq v2.17.1.14.
RNA-seq reads were aligned using the STAR aligner v2.4.2a with default parameters to the hg19 genome assembly augmented with a sequence representing the sgRNA-containing plasmid with a fully degenerate 12-bp barcode sequence.
Mapped reads were filtered for mapping quality >= 10, and PCR duplicates were removed with Picard v1.117.
Read counts were tabulated with featureCounts v1.5.0.
Genome build: hg19
Supplementary_files_format_and_content: read counts for all genes

extract_protocol:
total RNA was extracted from cells using Trizol Reagent (Thermo), and were subjected to enrichment of polyA+ RNA using the NEBNext Poly(A) kit (NEB).
Strand-specific polyA+ RNA-Seq was performed using the LM-Seq method, as described previously. Briefly, PolyA+ RNA was fragmented at 85°C in SmartScribe first-strand buffer (CloneTech) supplemented with a 3’ sequencing adapter containing a random hexamer sequence.  The fragmented RNA were subjected to first strand cDNA synthesis, followed by RNase A/H treatment.  The remaining single-stranded DNA were ligated to a 5’ sequencing adapter.  The libraries were then amplified by PCR using Illumina TruSeq-compatible primers and purified using SPRI purification beads.

treatment_protocol: HEK293T cells were cultured in DMEM with 10% FBS and pen/strep. For lentiviral packaging, 3X106 293T cells were seeded in a 6 cm dish one day before transfection. The indicated viral plasmid(s) were co-transfected with lentivirus packaging plasmids pMD2.G and psPAX2 (Addgene ID 12259 and 12260) with 4:2:3 ratio by using Lipofectamine 3000 (Thermo Fisher) according to the manufacturer's protocol. Twelve hours after transfection, media was changed to fresh DMEM with 10% FBS plus Pen/Strep. Seventy-two hours after transfection, virus-containing media was collected, passed through a 45 um filter, and aliquoted into 1.5ml tubes. Viruses were stored in -80°C before infection or titration. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. Virus aliquot(s) were thawed to room temperature and added to the plates. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection.


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 12

description:
JD130-2
sgRNAs and barcodes: listed in supplementary document


title: K562, dCas9-KRAB, infected with sgRNA64 (rep3); treated with TNFalpha for 1h

description:
PZ309
sgRNA ID: sgRNA64
sgRNA barcode ID:


title: K562 dCas9-KRAB, WT vs TNFA treatment, biorep1, batch 11

description:
JD130-1
sgRNAs and barcodes: listed in supplementary document


title: K562, dCas9-KRAB, infected with sgRNA64 (rep1); treated with TNFalpha for 1h

description:
PZ307
sgRNA ID: sgRNA64
sgRNA barcode ID:


title: K562, dCas9-KRAB, infected with sgRNA63 (rep5)

description:
PZ306
sgRNA ID: sgRNA63
sgRNA barcode ID:


title: K562, dCas9-KRAB, infected with sgRNA63 (rep4)

description:
PZ305
sgRNA ID: sgRNA63
sgRNA barcode ID:


title: K562, dCas9-KRAB, infected with sgRNA63 (rep1)

description:
PZ302
sgRNA ID: sgRNA63
sgRNA barcode ID:


title: K562, dCas9-KRAB, infected with sgRNA63 (rep2)

description:
PZ303
sgRNA ID: sgRNA63
sgRNA barcode ID:


title: K562, dCas9-KRAB, infected with sgRNA63 (rep3)

description:
PZ304
sgRNA ID: sgRNA63
sgRNA barcode ID:


title: MYCER_minusQ_Pol2pSer2

data_processing:
Fastq files were generated using Illumina's CASAVA software.
Reads were mapped to the human genome (hg19) using Bowtie v1.1.1 with default parameters and normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with the genomeCoverageBed function from BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph format as described in the UCSC file format guide (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

treatment_protocol: Cells were treated with 100 nM 4-Hydroxytamoxifen for 15 hours, then glutamine starved for 5 hours in presence of 4-Hydroxytamoxifen.

tag: treatment1(myc-er+oht or empty vector +oht)

value: MYC-ER+OHT

value: RNAPII pSer2 (ab5095 , Abcam)


title: MYCER_minusQ_Pol2

value: RNAPII (sc-899, Santa Cruz)


title: EV_minusQ_Pol2

value: vector+OHT


title: EV_plusQ_Pol2pSer2


title: EV_plusQ_Pol2


title: 4weeks_EGFR_10

description:
week4-EGFRpos-2
processed data file: meltedData_20150831_EGFRsortRNArun2.tsv


title: EV_minusQ_Pol2pSer2


title: EV_plusQ_input


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 4

description: sgrnas and barcodes: listed in supplementary document


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 3


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 4


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 6


title: K562, dCas9-KRAB, infected with sgRNA64 (rep2); treated with TNFalpha for 1h

description:
PZ308
sgRNA ID: sgRNA64
sgRNA barcode ID:


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 5


title: K562, dCas9-KRAB, infected with sgRNA64 (rep5); treated with TNFalpha for 1h

description:
PZ311
sgRNA ID: sgRNA64
sgRNA barcode ID:


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 3


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 5


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 6


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 3


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 2


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 2


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 4


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 1


title: ZTF cells

city: Oklahoma

first: Christopher

middle: Lee

last: Sansam

state: OK

address: 825 NE 13th Street

department: Cell Cycle and Cancer Biology Program

institute: Oklahoma Medical Research Foundation

description:
ZTF_cells_S_G1
Paired-end G1 ans S samples

data_processing:
Basecalls performed using bcl2fastq
Sequencing reads were aligned to the GRCz10 genome build using BWA-mem with standard parameters, and PCR duplicates were marked with PiCard
Data were filtered to removed 100bp regions with greater than 5 standard deviations from the genome median (chromosome 4 excluded).
200 read count G1 windows of varying sizes were defined and S-phase reads counted in the same windows
Data was normalized by setting the genome mean (excluding chromosome 4) replication timing value to 0, and standard deviation to 1.
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: txt files were generated using Matlab and contain a genomic coordinate (chromosome number in column 1 and chromosomal location in column 2), and replication timing value in column 3.  Timing value represents S-phase copy number relative to G1 sample, normalized to a genome mean of 0 and standard deviation of 1 (excluding chromosome 4)

organism: Danio rerio

source_name: ZTF cells

growth_protocol: For whole embryos, timed matings were performed between dozens of adults and hundres of embryos were collected in 10 minute intervals.  Embryos were allowed to develop in a 28.5C incubator until appropriate developmental stage was reached.  Developmental stage was visually assessed, embryos were dechorionated, deyolked, and cells were fixed in 70% ethanol and stored at -20C.  Primary ZTF cells were generated from adult zebrafish tailfin clip.  Tail clips were washed extensively with PBS/pen/strep then grown in Amniomax-II complete medium, with twice weekly media changes, in a 96-well coated tissue culture plate, at 28.5C and 5%CO2.  As fibroblasts migrated out of the tissue and filled the well, cells were trypsinized to remove from plate and transferred to progressively larger coated cell culture plates.  Once cells filled a 6 cell plate, they were transferred to 6cm coated cell culture plates and the medium was changed to DMEM with 15% serum and added L-glutamine.

extract_protocol:
FACS purified cell pellets were removed from -20C and briefly thawed on ice.  Cells were resuspended in SDS buffer and then proteinase K was added.  Solution was quickly vortexed and incubated at 56C for 2hrs with periodic vortexing.  After 2 hours of cell lysis, DNA was isolated by phenol-chloroform extraction and ethanol precipitation.  Briefly, a 1:1 ratio of phenol-chloroform was added to cell lysate, vortexed vigorously for 15sec, centrifuged at 14,000g and 4C for 10 minutes, and top aqueous layer containing DNA was transferred to a new tube.  A 1/10 volume of sodium acetate and 2.5x volume of ethanol was added to precipitate DNA, along with glycogen as a carrier.   Solution was placed at -80C for 20 minutes, centrifuged at 14,000g for 15 minutes, pellet was washed with 70% ethanol and centrifuged as before, pellet was resuspended in water.  Solution was RNAse treated by adding 4ul of 2mg/ml DNAse-free RNAse A (Genelink) and placing at 37C for 1hr.  DNA was then purified by phenol-choloroform extraction and ethanol precipitation as before, quantified using a Qubit dsDNA High Sensitivity assay, and solution stored at -20C.
Purified DNA solution was thawed and 1ug of DNA was sheared on a Covaris S220 Focused-ultrasonicator optimized to produce 300bp fragments.  Quality of sheared DNA was analyzed using an Agilent TapeStation 2200 with High Sensitivity D1000 ScreenTape.  Libraries were prepared using NEBNext DNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina according to manufacturer’s instructions.  Briefly, DNA fragment ends are prepared for adapter ligation, adapters are ligated onto DNA, adapter-ligated DNA is size-selected and cleaned up,  5 cycles of PCR amplification of adapter-ligated DNA was performed with different multiplex primers for each sample, and PCR was cleaned up.  Quality of library prep was analyzed on Agilent 2200 TapeStation and quantified using Qubit.  DNA libraries were pooled and sequenced at a depth of 300 million total reads per lane in 100bp paired-end read fragments on Illumina HiSeq 2500.

treatment_protocol: Ethanol-fixed 28hpf embryos and ZTF cells were removed from -20C, centrifuged at 1400g and 4C, and placed on ice.  The supernatant was removed and cell pellet was resuspended in PBS with 1%BSA to wash cells.  Cells were centrifuged as before and cells were resuspended in cold propidium iodide solution to stain DNA and incubated on ice for 5 minutes.  The cells were then filtered through a 40um mesh then sorted on a FACSAria at a flowrate of 1.0ml/min.  Cells are first gated by FCS/SSC to removed cell debris, then by FSC/PI to removed cell doublets.  Cells are then sorted based on DNA content, sorting the left side of a G1 peak of 2N DNA content to prevent S-phase contamination, and cells in S-phase between the 2N and 4N DNA content peaks were sorted.  More than 500,000 total cells were sorted for all G1 and S-phase samples and cells were kept at 4C or on ice during sorting.  Sorted cells were then centrifuged at 1400g, washed in PBS-BSA, centrifuged again as before, and the dry pellet was frozen at -20C.

tag: developmental stage

value: Primary adult tailfin fibroblast culture

tag: tissue


title: Shield rep2

description:
Exp1_Shield_2
Paired-end S sample
processed data file: Shield_average.txt (processed from two repeats)

source_name: whole embryos_Shield

value: Shield stage embryos

value: Whole embryos


title: Bud rep1

description:
Exp1_Bud
Paired-end S sample
processed data file: Bud_average.txt (processed from two repeats)

source_name: whole embryos_Bud

value: Bud stage embryos


title: Bud rep2

description:
Exp1_Bud_3
Paired-end S sample
processed data file: Bud_average.txt (processed from two repeats)


title: Dome rep2

description:
Exp1_Dome_3
Paired-end S sample
processed data file: Dome_average.txt (processed from two repeats)

source_name: whole embryos_Dome

value: Dome stage embryos


title: K562 dCas9-KRAB, Lenti-sgRNA set B pooled infection, batch 11


title: K562 dCas9-KRAB, Lenti-sgRNA set A pooled infection, batch 1


title: K562 dCas9-KRAB, Lenti-sgRNA set C pooled infection, batch 7


title: Dome rep1

description:
Exp1_Dome
Paired-end S sample
processed data file: Dome_average.txt (processed from two repeats)