title: OEL07_N721_S502

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N721_S505

status: Public on Oct 30 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:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_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
tab-delimited text files include gene level expected count, FPKM, and TPM values for each sample derived from RSEM
tab-delimited text files include gene level estimated count and TPM values for each sample derived from kallisto
ExpressionSets that include all metadata and the appropriate count data for each of our three alignment and gene level count procedures (oeHBC_Cufflinks_eSet, oeHBC_RSEM_eSet, oeHBC_Kallisto_eSet)
oeHBC_phenoData.txt: metadata on samples including experimental condition and batch; includes samples from GSE95601
oeHBC_Cufflinks_eSet_counts_table.txt: abundance measurements (featureCounts), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_fpkm_table.txt: abundance measurements (Cufflinks), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_tpm_table.txt: abundance measurements (derived from Cufflinks fpkms), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_featureData.txt: information about the genes
oeHBC_Cufflinks_eSet_protocolData.txt: QC metrics, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_expectedCounts_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_fpkm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_tpm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_featureData.txt: information about the genes
oeHBC_RSEM_eSet_protocolData.txt: QC metrics, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_estimatedCounts_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_tpm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_featureData.txt: information about the genes
oeHBC_Cufflinks_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_RSEM_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_kallisto_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_WTregen_countsMatrix.txt: normalized counts matrix (log2), text file
oeHBC_WTKOregen_countsMatrix.txt: normalized counts matrix (log2), text file
oeHBC_diffregen_countsMatrix.txt: normalized counts matrix (log2), text file; includes samples from GSE95601

molecule: polyA RNA

organism: Mus musculus

source_name: Krt5-Rosa-eYFP_Sox2 cKO_96 hrs post injury

extract_protocol:
dissociation 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.
single cell isolation, lysis, RT, amplification: 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.
sequencing library synthesis: 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 sequencers; up to 192 samples were sequenced per lane, often in Rapid Run mode.

tag: strain background

tag: sex type

value: F

tag: age

tag: tissue

value: olfactory epithelium

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

value: B

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: SMALL

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: OEL07_N721_S511

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

value: SMEAGOL


title: OEL07_N721_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N720_S511

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N721_S508

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N720_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N720_S508

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N720_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N720_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N720_S503

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N720_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N719_S511

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N719_S510

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N719_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N719_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N719_S505

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N719_S502

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N718_S511

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N722_S503

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N718_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N718_S508

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N718_S507

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N718_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N718_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N718_S505

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N716_S511

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N716_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N716_S508

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N716_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N716_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N718_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N716_S503

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N716_S502

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N715_S522

tag: facs selection

value: C

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N720_S502

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL07_N719_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N715_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N715_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N715_S518

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N715_S517

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N715_S516

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N715_S513

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N715_S515

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N714_S522

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N714_S520

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N714_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N714_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N714_S516

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N714_S513

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL07_N716_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N712_S522

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N712_S520

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N712_S518

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N712_S521

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N712_S513

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N712_S516

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N714_S518

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N711_S522

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N711_S521

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N711_S517

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N711_S518

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N711_S516

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N710_S518

description:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTregen_countsMatrix.txt
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_countsMatrix.txt

source_name: Krt5-Rosa-eYFP_24 hrs post injury

tag: strain background

tag: sex type

value: M

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N712_S515

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N710_S516

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N710_S517

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N710_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N707_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N714_S515

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N707_S518

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N710_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N710_S520

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N707_S522

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N707_S521

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N710_S513

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL07_N719_S508

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N712_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N711_S520

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N707_S517

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N707_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N707_S513

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N707_S516

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N706_S518

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N706_S522

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N706_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N706_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N706_S516

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N706_S513

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N706_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N705_S522

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N705_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N705_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N705_S518

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N705_S517

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N705_S513

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N705_S515

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N704_S520

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N704_S518

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N704_S522

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N704_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N704_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N704_S516

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N704_S513

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N704_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N703_S520

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N703_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N706_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N703_S518

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N703_S522

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N703_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N703_S515

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N703_S516

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N703_S513

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N702_S522

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N702_S516

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N702_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N702_S517

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N702_S513

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N702_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N705_S516

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N702_S518

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N701_S520

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N701_S518

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N701_S521

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N701_S517

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N701_S513

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL06_N701_S516

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N729_S511

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N729_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N729_S510

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N701_S515

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N729_S508

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N728_S511

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N728_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL06_N702_S521

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N729_S506

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N728_S508

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N728_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N728_S507

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N728_S503

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N727_S511

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N728_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL06_N701_S522

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N727_S510

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N727_S506

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N727_S505

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N727_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N727_S507

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N727_S508

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N726_S511

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N727_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N726_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N726_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N726_S507

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N726_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N728_S506

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N726_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N724_S511

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N726_S508

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N724_S508

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N724_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N724_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N724_S505

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N724_S506

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N724_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N724_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N723_S508

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N723_S510

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N723_S511

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N723_S507

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N723_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N723_S502

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N722_S510

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N723_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N722_S511

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N722_S508

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N726_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N722_S507

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N722_S503

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N722_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEL05_N721_S510

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N721_S507

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEL05_N722_S506

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: pDAB448-022-12

city: Indianapolis

first: Lyudmila

middle: V

last: Sidorenko

state: Indiana

address: 9330 Zionsville Rd

institute: DOW AgroSciences

description:
sRNA
111448-1-022-AJ001-Sx020-Sx001-12_S19

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 14 nt and 35 nt nucleotides (for HiSeq 2000) and 14 nt and 75 nt (for Nextseq 500).
Sequence data processing was conducted using in-house Perl scriptsand Unix shell scripts developed by Genomics group at DOW AgroSciences.
Genome_build: Maize B73 AGPv2_5b
Supplementary_files_format_and_content: tag count file

molecule: total RNA

organism: Zea mays

source_name: Maize leaves, V5/V6

growth_protocol: Greenhouse grown plants

extract_protocol:
Total RNA extraction
small RNA library preparation

value: leaf

tag: transgene construct

value: pDAB

tag: copy number of transgene

value: single copy

tag: multigene construct design

value: cry1Ab, Zm


title: pDAB449-008-01

description:
sRNA
111449-1-008-AJ001-Sx012-Sx004-1_S20

value: cry1Ab, ZmMod


title: pDAB448-022-03

description:
sRNA
111448-1-022-AJ001-Sx020-Sx001-03_S17


title: OEL05_N721_S506

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: pDAB449-008-11

description:
sRNA
111449-1-008-AJ001-Sx012-Sx004-11_S22

tag: tissue


title: OEL05_N721_S508

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: pDAB447-002-09

description:
sRNA
111447-1-002-AJ001-Sx023-Sx029-09_S16

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design

value: cry1Ab, ZmHiGC


title: pDAB449-008-05

description:
sRNA
111449-1-008-AJ001-Sx012-Sx004-5_S21


title: pDAB447-002-08

description:
sRNA
111447-1-002-AJ001-Sx023-Sx029-08_S15


title: pDAB448-022-05

description:
sRNA
111448-1-022-AJ001-Sx020-Sx001-05_S18


title: OEL05_N723_S506

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: OEL05_N721_S503

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: ercc spike-in dilution


title: pDAB447-002-03

description:
sRNA
111447-1-002-AJ001-Sx023-Sx029-03_S12

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: pDAB447-002-05

description:
sRNA
111447-1-002-AJ001-Sx023-Sx029-05_S13


title: pDAB443-016-12

description:
sRNA
111443-3-016-001AJ-Sx023-Sx024-12_S11

value: cry1Fa, Zm


title: pDAB447-002-06

description:
sRNA
111447-1-002-AJ001-Sx023-Sx029-06_S14


title: OEL05_N722_S502

value: olfactory epithelium

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date


title: pDAB443-016-08

description:
sRNA
111443-3-016-001AJ-Sx023-Sx024-08_S10

tag: tissue


title: OEL05_N721_S505

tag: strain background

tag: sex type

tag: age

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: c1 chip size

tag: c1 machine id


title: pDAB443-016-05

description:
sRNA
111443-3-016-001AJ-Sx023-Sx024-05_S9

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: OEL05_N720_S511

tag: visual qc

value: Yes

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: ercc spike-in dilution


title: OEL05_N721_S502

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

value: YFP+

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: facs & c1 date


title: pDAB441-016-12

description:
sRNA
111441-3-016-001AJ-Sx014-Sx024-12_S8

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design

value: cry1Fa, ZmMod


title: OEL05_N720_S510

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: index set

value: B

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 chip size

value: SMALL

tag: c1 machine id


title: OEL05_N720_S508

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: dob

value: FRODO

tag: ercc spike-in dilution


title: OEL05_N720_S507

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate coordinate

tag: index set

tag: facs & c1 date


title: OEL05_N718_S510

source_name: Krt5-Rosa-eYFP_96 hrs post injury

tag: strain background

tag: sex type

tag: age

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 chip size

tag: c1 machine id


title: OEL05_N718_S508

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: dob

tag: ercc spike-in dilution


title: pDAB441-016-02

description:
sRNA
111441-3-016-001AJ-Sx014-Sx024-02_S6

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: OEL05_N718_S506

description:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTregen_countsMatrix.txt
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_countsMatrix.txt

tag: strain background

tag: sex type

tag: age

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate coordinate

tag: index set

tag: facs & c1 date


title: OEL05_N718_S507

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: library plate id

tag: barcode

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 chip size

tag: c1 machine id


title: OEL05_N718_S503

tag: strain background

tag: sex type

tag: age

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dob

tag: ercc spike-in dilution


title: pDAB435-003-05

description:
sRNA
111435-1-003-AJ001-Sx019-Sx012-05_S4

tag: tissue

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: pDAB435-003-12

description:
sRNA
111435-1-003-AJ001-Sx019-Sx012-12_S5


title: OEL05_N718_S505

tag: cell type

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: facs & c1 date


title: OEL05_N718_S502

tag: strain background

tag: sex type

tag: age

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: c1 chip size

tag: c1 machine id


title: pDAB435-003-04

description:
sRNA
111435-1-003-AJ001-Sx019-Sx012-04_S3

tag: tissue

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: pDAB435-003-03

description:
sRNA
111435-1-003-AJ001-Sx019-Sx012-03_S2


title: pDAB435-003-01

description:
sRNA
111435-1-003-AJ001-Sx019-Sx012-01_S1


title: JNRF04_N724_S515

tag: cell type

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: D

tag: sequencing run id

tag: ercc spike-in dilution


title: JNRF04_N724_S517

tag: strain background

tag: sex type

value: M

tag: age

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: W3A-2

city: Madrid

first: Nuria

last: Niell

address: C/Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas Alberto Sols

data_processing:
Sample were sequenced on an Illumina HiSeq 2000 platform
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13).
Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
Alignment of fastq reads was performed using TopHat version 2.0.14 against hg19/GRCh37.75 assembly of the human reference genome using standard parameters.
Quantification of feature alignments was performed using HTSeq-counts from HTSeq framework version 0.6.0  using GRCh37.75 GTF gene model.
Normalization of the count data and statistical analysis for the differential expression was performed with edgeR package version 3.12.1 for R statistical computing software.
Genome_build: GRCh37.75/hg19
Supplementary_files_format_and_content: Normalised counts: RPKM (Reads Per Kilobase per Million of mapped reads)=(raw counts that map to the feature x read length)/(feature length x total number of mapped reads from the sample in millions)

organism: Homo sapiens

source_name: CCD-18Co colon fibroblasts

growth_protocol: CCD-18Co cells were cultured in MEM medium supplemented with 10% FBS, L-glutamine and sodium pyruvate.

extract_protocol:
After the treatment we obtained total RNA from three independent biological replicates using the RNeasymini kit (Qiagen).
1 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 9.2 to 9.6 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fractions were purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by 9 cycles of PCR with Illumina PE primers. The resulting purified cDNA library of template molecules of known strand origin was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Cells were treated with vehicle or Wnt3A (recombinant human factor, stock 200 µg/ml) to a final concentration of 100 ng/ml for 24 h.

tag: strain

tag: treatment

value: Recombinant Wnt3A (human)


title: W3A-3


title: pDAB441-016-04

description:
sRNA
111441-3-016-001AJ-Sx014-Sx024-04_S7

tag: tissue

value: leaf

tag: transgene construct

value: pDAB

tag: copy number of transgene

tag: multigene construct design


title: JNRF04_N724_S513

tag: strain background

tag: cell type

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: OEL05_N718_S511

tag: sex type

tag: age

tag: tissue

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: JNRF04_N723_S522

tag: strain background

tag: cell type

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode


title: JNRF04_N723_S521

tag: sex type

tag: age

tag: tissue

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 machine id

tag: ercc spike-in dilution


title: W3A-1

tag: strain

tag: treatment


title: JNRF04_N723_S520

tag: strain background

tag: cell type

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: Ctrl-3

value: Vehicle


title: JNRF04_N723_S516

tag: sex type

tag: age

tag: tissue

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate


title: KO-I+L

city: shanghai

first: wei

last: zhang

address: 800 Dongchuan Road. Minhang

country: China

institute: shanghai jiaotong university

data_processing:
Illumina HiSeq 2000 used for basecalling.
The reads were alighed to mm10 assembly
The quality of the raw sequencing reads were checked using FastQC(v0.10.1) and RSeQC
The count of gene reads was calculated by HTSeq (v0.6.0)
Genome_build: mm10
Supplementary_files_format_and_content: The DEGs were analyzed by DEGseq (v1.24.0) in R software with a cutoff of p<=0.001, false discovery rate (FDR) <=0.1%

source_name: BMDCs

extract_protocol:
Total RNA were isolated using the RNeasy Kit (Qiagen), Illumina TruSeq strand-specific mRNA sample preparation system were used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and GOLPH2 KO BMDCs were primed with IFN-gamma for 16h, then were stimulated with LPS for 4h.

tag: strain

tag: genotype


title: JNRF04_N723_S518

tag: strain background

tag: cell type

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: index set

tag: sequencing run id

tag: lane

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N723_S513

tag: sex type

tag: age

tag: tissue

tag: expt condition

tag: number of animals

tag: dilution plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: WT_Liver_Male_CHDI-00340246_10mg/kg_rep5 [328127_135_Liver_Male_WT_L5.D710_clipped]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.B38, gene models version Ensembl.R75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: background

tag: genotype

value: Wild Type

value: Liver

tag: Sex

value: Male

value: 12 weeks

tag: treatment

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

value: Oral

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: Ctrl-2

tag: strain


title: WT_Liver_Male_CHDI-00340246_10mg/kg_rep4 [328130_127_Liver_Male_WT_L6.D701_clipped]

tag: tissue

tag: age


title: JNRF04_N722_S522

tag: strain background

tag: sex type

value: olfactory epithelium

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: c1 batch id

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N724_S516

tag: strain background

value: M

tag: age

tag: tissue

tag: dilution plate coordinate

value: D

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: SMALL

value: FRODO


title: WT-I+L

tag: strain

tag: genotype

value: wide type


title: JNRF04_N722_S521

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: c1 plate coordinate

tag: library plate id

tag: barcode


title: KO-con

tag: age


title: JNRF04_N723_S517

tag: strain background

tag: tissue

tag: dilution plate coordinate

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Male_CHDI-00340246_10mg/kg_rep2 [328090_155_Liver_Male_WT_L7.D709_clipped]

tag: background

tag: genotype

value: Wild Type

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Liver_Male_CHDI-00340246_10mg/kg_rep3 [328197_147_Liver_Male_WT_L5.D709_clipped]

tag: tissue

value: Liver

tag: age


title: JNRF04_N722_S520

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: JNRF04_N722_S518

tag: age

tag: tissue

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Male_CHDI-00340246_10mg/kg_rep1 [328094_139_Liver_Male_WT_L8.D701_clipped]

tag: background

tag: genotype

tag: Sex

value: Male

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF04_N722_S517

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: JNRF04_N722_S516

tag: age

tag: tissue

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 machine id

tag: ercc spike-in dilution


title: Ctrl-1

tag: strain

tag: treatment

value: Vehicle


title: WT_Liver_Female_CHDI-00340246_10mg/kg_rep3 [328179_143_Liver_Female_WT_L2.D703_clipped]

tag: background

tag: genotype

tag: Sex

value: Female

value: 12 weeks

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT-con

tag: age


title: JNRF04_N722_S513

tag: strain background

tag: sex type

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: WT_Liver_Female_CHDI-00340246_10mg/kg_rep1 [328112_131_Liver_Female_WT_L1.D705_clipped]

tag: background

tag: genotype

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: WT_Liver_Female_CHDI-00340246_10mg/kg_rep2 [328103_159_Liver_Female_WT_L1.D710_clipped]

tag: tissue


title: JNRF04_N721_S522

tag: strain background

tag: sex type

value: olfactory epithelium

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Female_CHDI-00340246_10mg/kg_rep4 [328121_123_Liver_Female_WT_L4.D704_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF04_N721_S521

tag: strain background

tag: sex type

value: M

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

value: D

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: WT_Liver_Male_Vehicle_rep4 [328091_148_Liver_Male_WT_L7.D710_clipped]

source_name: Liver, Vehicle

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Liver_Male_Vehicle_rep2 [328061_140_Liver_Male_WT_L1.D704_clipped]


title: JNRF04_N721_S516

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

value: SMALL

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: JNRF04_N721_S518

tag: age

tag: tissue

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date

tag: c1 chip size


title: JNRF04_N723_S515

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: WT_Liver_Male_Vehicle_rep1 [328093_156_Liver_Male_WT_L7.D712_clipped]

tag: background

tag: genotype

value: Wild Type

value: Liver

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Liver_Male_Vehicle_rep3 [328134_136_Liver_Male_WT_L7.D705_clipped]

tag: tissue

value: Male

value: Vehicle


title: JNRF04_N721_S517

tag: strain background

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Male_Vehicle_rep5 [328073_128_Liver_Male_WT_L3.D704_clipped]

tag: background

tag: genotype

tag: Sex

tag: age

value: 12 weeks

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF04_N721_S513

tag: strain background

tag: sex type

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set


title: OEL05_N721_S511

tag: age

value: B

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Female_CHDI-00340246_10mg/kg_rep5 [328158_151_Liver_Female_WT_L1.D704_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: Female

tag: treatment

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: JNRF04_N720_S522

tag: strain background

tag: sex type

tag: age

value: olfactory epithelium

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: WT_Liver_Female_Vehicle_rep3 [328111_144_Liver_Female_WT_L2.D706_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: treatment

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: WT_Liver_Female_Vehicle_rep5 [328203_152_Liver_Female_WT_L6.D703_clipped]

tag: age


title: JNRF04_N720_S521

tag: strain background

tag: sex type

value: M

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N722_S515

tag: tissue

value: YFP+

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: D

tag: sequencing run id

value: SMALL


title: JNRF04_N720_S520

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

value: FRODO


title: WT_Liver_Female_Vehicle_rep2 [328068_124_Liver_Female_WT_L2.D711_clipped]

tag: background

tag: genotype

value: Wild Type

value: Liver

tag: Sex

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF04_N721_S520

tag: tissue

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Liver_Female_Vehicle_rep1 [328065_132_Liver_Female_WT_L2.D708_clipped]

tag: background

tag: genotype

tag: Sex

tag: age

value: 12 weeks

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency


title: R6/2_HD_Liver_Male_CHDI-00340246_10mg/kg_rep5 [328126_137_Liver_Male_Tg_L5.D709_clipped]

tag: tissue

value: Male

tag: treatment dose

tag: treatment duration


title: R6/2_HD_Liver_Male_CHDI-00340246_10mg/kg_rep4 [328082_133_Liver_Male_Tg_L5.D701_clipped]

value: 10 mg/kg


title: JNRF04_N720_S518

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF04_N720_S515

tag: age

tag: tissue

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N721_S515

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: R6/2_HD_Liver_Male_CHDI-00340246_10mg/kg_rep2 [328140_153_Liver_Male_Tg_L8.D711_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Liver_Male_CHDI-00340246_10mg/kg_rep3 [328081_145_Liver_Male_Tg_L5.D712_clipped]

tag: tissue

tag: age


title: WT_Liver_Female_Vehicle_rep4 [328106_160_Liver_Female_WT_L1.D703_clipped]

value: Female


title: JNRF04_N720_S516

tag: strain background

tag: sex type

value: olfactory epithelium

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N720_S513

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: JNRF04_N719_S522

tag: strain background

tag: sex type

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set


title: JNRF04_N719_S520

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Liver_Male_CHDI-00340246_10mg/kg_rep1 [328069_125_Liver_Male_Tg_L3.D712_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: JNRF04_N719_S518

tag: strain background

tag: sex type

value: M

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: R6/2_HD_Liver_Female_CHDI-00340246_10mg/kg_rep2 [328159_121_Liver_Female_Tg_L6.D707_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Liver_Female_CHDI-00340246_10mg/kg_rep4 [328107_129_Liver_Female_Tg_L2.D702_clipped]


title: JNRF04_N719_S517

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N719_S515

tag: age

tag: tissue

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: D

tag: sequencing run id

tag: lane

value: SMALL


title: JNRF04_N719_S513

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

value: FRODO


title: JNRF04_N719_S516

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N720_S517

tag: age

tag: tissue

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: R6/2_HD_Liver_Male_Vehicle_rep4 [328213_126_Liver_Male_Tg_L1.D701_clipped]

tag: background

tag: genotype

value: Liver

tag: Sex

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Liver_Female_CHDI-00340246_10mg/kg_rep5 [328150_149_Liver_Female_Tg_L4.D709_clipped]

value: 12 weeks

tag: treatment dose


title: R6/2_HD_Liver_Female_CHDI-00340246_10mg/kg_rep1 [328145_157_Liver_Female_Tg_L3.D704_clipped]


title: JNRF04_N718_S522

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Liver_Male_Vehicle_rep3 [328186_138_Liver_Male_Tg_L3.D710_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Liver_Male_Vehicle_rep2 [328071_154_Liver_Male_Tg_L3.D702_clipped]

value: Male


title: JNRF04_N718_S521

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF04_N719_S521

tag: age

tag: tissue

tag: c1 plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N718_S520

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: R6/2_HD_Liver_Male_Vehicle_rep5 [328189_134_Liver_Male_Tg_L4.D701_clipped]

tag: background

tag: genotype

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Liver_Male_Vehicle_rep1 [328120_146_Liver_Male_Tg_L4.D703_clipped]

tag: tissue


title: R6/2_HD_Liver_Female_CHDI-00340246_10mg/kg_rep3 [328124_141_Liver_Female_Tg_L5.D707_clipped]

tag: treatment dose

value: 10 mg/kg


title: R6/2_HD_Liver_Female_Vehicle_rep4 [328101_130_Liver_Female_Tg_L1.D708_clipped]

value: Oral


title: R6/2_HD_Liver_Female_Vehicle_rep5 [328209_150_Liver_Female_Tg_L2.D709_clipped]

value: Female


title: JNRF04_N718_S517

tag: strain background

tag: sex type

value: olfactory epithelium

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Liver_Female_Vehicle_rep3 [328181_158_Liver_Female_Tg_L2.D705_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration


title: JNRF04_N718_S518

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: R6/2_HD_Liver_Female_Vehicle_rep2 [328084_122_Liver_Female_Tg_L6.D703_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

value: 6 hours


title: JNRF04_N718_S515

tag: strain background

tag: sex type

value: M

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF04_N718_S516

tag: age

tag: tissue

value: Horizontal basal cell (HBC) stem cell

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: R6/2_HD_Liver_Female_Vehicle_rep1 [328167_142_Liver_Female_Tg_L7.D703_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF04_N718_S513

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Male_CHDI-00340246_10mg/kg_rep5 [328198_7_Left_Striatum_Male_WT_L5.D710_clipped]

source_name: Striatum, CHDI-00340246, 10mg/kg

tag: background

tag: genotype

value: Wild Type

tag: tissue

value: Striatum

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency


title: JNRF04_N716_S521

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: D

tag: sequencing run id

value: SMALL


title: JNRF04_N716_S520

tag: tissue

tag: facs selection

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: JNRF04_N716_S518

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: c1 batch id


title: WT_Striatum_Male_CHDI-00340246_10mg/kg_rep3 [328067_15_Left_Striatum_Male_WT_L2.D710_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: 12 weeks

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Striatum_Male_CHDI-00340246_10mg/kg_rep1 [328215_35_Left_Striatum_Male_WT_L8.D703_clipped]

value: Male


title: JNRF04_N716_S517

tag: strain background

tag: facs selection

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Male_CHDI-00340246_10mg/kg_rep4 [328199_19_Left_Striatum_Male_WT_L6.D711_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Striatum_Female_CHDI-00340246_10mg/kg_rep5 [328207_3_Left_Striatum_Female_WT_L7.D707_clipped]

value: Oral


title: WT_Striatum_Female_CHDI-00340246_10mg/kg_rep3 [328164_39_Left_Striatum_Female_WT_L7.D712_clipped]

value: Female


title: JNRF04_N716_S516

tag: strain background

tag: sex type

value: olfactory epithelium

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF04_N716_S515

tag: age

tag: tissue

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Female_CHDI-00340246_10mg/kg_rep4 [328087_31_Left_Striatum_Female_WT_L6.D706_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration


title: WT_Striatum_Female_CHDI-00340246_10mg/kg_rep2 [328210_23_Left_Striatum_Female_WT_L1.D710_clipped]

value: 6 hours


title: JNRF04_N716_S513

tag: strain background

tag: sex type

value: M

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF03_N710_S507

description:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_countsMatrix.txt

value: FFF

tag: age

tag: tissue

value: Horizontal basal cell (HBC) stem cell

value: A

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Male_Vehicle_rep5 [328075_8_Left_Striatum_Male_WT_L4.D706_clipped]

source_name: Striatum, Vehicle

tag: background

tag: genotype

value: Wild Type

value: Striatum

tag: Sex

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N710_S503

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

value: FRODO


title: JNRF03_N710_S505

tag: age

tag: tissue

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF03_N710_S506

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: JNRF04_N716_S522

tag: age

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: D

tag: sequencing run id

value: SMALL


title: JNRF03_N710_S502

tag: tissue

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Male_CHDI-00340246_10mg/kg_rep2 [328202_27_Left_Striatum_Male_WT_L6.D702_clipped]

tag: background

tag: genotype

tag: Sex

value: Male

value: 12 weeks

tag: treatment

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: JNRF03_N707_S511

tag: strain background

tag: sex type

tag: age

value: olfactory epithelium

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: JNRF03_N707_S510

value: FFF

tag: tissue

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF03_N707_S508

tag: strain background

tag: sex type

tag: age

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection


title: WT_Striatum_Female_CHDI-00340246_10mg/kg_rep1 [328201_11_Left_Striatum_Female_WT_L6.D701_clipped]

tag: background

tag: genotype

tag: Sex

value: Female

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: WT_Striatum_Female_Vehicle_rep3 [328060_40_Left_Striatum_Female_WT_L1.D703_clipped]

value: Wild Type

tag: tissue

value: Striatum


title: WT_Striatum_Male_Vehicle_rep1 [328066_36_Left_Striatum_Male_WT_L2.D709_clipped]

value: Vehicle


title: WT_Striatum_Male_Vehicle_rep3 [328155_16_Left_Striatum_Male_WT_L5.D703_clipped]


title: WT_Striatum_Female_Vehicle_rep1 [328108_12_Left_Striatum_Female_WT_L1.D702_clipped]


title: JNRF03_N707_S506

tag: strain background

value: Yes

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: A

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Female_Vehicle_rep4 [328089_4_Left_Striatum_Female_WT_L7.D708_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Striatum_Male_Vehicle_rep2 [328123_20_Left_Striatum_Male_WT_L4.D706_clipped]

value: Male


title: WT_Striatum_Female_Vehicle_rep5 [328196_32_Left_Striatum_Female_WT_L5.D708_clipped]

value: 12 weeks


title: JNRF03_N707_S505

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

value: FRODO


title: JNRF03_N707_S503

tag: age

tag: tissue

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Female_Vehicle_rep2 [328102_24_Left_Striatum_Female_WT_L1.D709_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Striatum_Male_CHDI-00340246_10mg/kg_rep5 [328217_33_Left_Striatum_Male_Tg_L8.D705_clipped]

tag: treatment dose

value: 10 mg/kg


title: JNRF03_N707_S507

tag: strain background

tag: sex type

value: FFF

tag: age

value: olfactory epithelium

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: R6/2_HD_Striatum_Male_CHDI-00340246_10mg/kg_rep3 [328122_5_Left_Striatum_Male_Tg_L4.D705_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N707_S502

tag: strain background

tag: sex type

tag: age

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Striatum_Male_Vehicle_rep4 [328177_28_Left_Striatum_Male_WT_L1.D701_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: treatment

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration


title: R6/2_HD_Striatum_Male_CHDI-00340246_10mg/kg_rep4 [328132_25_Left_Striatum_Male_Tg_L6.D703_clipped]

tag: age

tag: treatment dose

value: 6 hours


title: JNRF03_N706_S511

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF03_N706_S507

tag: age

tag: tissue

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF03_N706_S508

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: R6/2_HD_Striatum_Female_CHDI-00340246_10mg/kg_rep5 [328147_37_Left_Striatum_Female_Tg_L3.D706_clipped]

tag: background

tag: genotype

tag: Sex

value: Female

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Striatum_Male_CHDI-00340246_10mg/kg_rep1 [328138_13_Left_Striatum_Male_Tg_L7.D709_clipped]

tag: tissue

value: Striatum

tag: age


title: JNRF03_N706_S506

tag: strain background

tag: sex type

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Striatum_Female_CHDI-00340246_10mg/kg_rep4 [328165_29_Left_Striatum_Female_Tg_L7.D701_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N706_S505

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: R6/2_HD_Striatum_Female_CHDI-00340246_10mg/kg_rep3 [328117_1_Left_Striatum_Female_Tg_L3.D712_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N706_S503

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Striatum_Female_CHDI-00340246_10mg/kg_rep2 [328153_21_Left_Striatum_Female_Tg_L4.D712_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N706_S502

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: JNRF03_N706_S510

tag: age

tag: tissue

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Striatum_Male_Vehicle_rep1 [328156_34_Left_Striatum_Male_Tg_L5.D704_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N705_S511

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: R6/2_HD_Striatum_Male_Vehicle_rep5 [328059_18_Left_Striatum_Male_Tg_L1.D702_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency


title: R6/2_HD_Striatum_Female_CHDI-00340246_10mg/kg_rep1 [328208_9_Left_Striatum_Female_Tg_L7.D708_clipped]

tag: treatment dose

tag: treatment duration


title: R6/2_HD_Striatum_Male_Vehicle_rep2 [328175_6_Left_Striatum_Male_Tg_L1.D711_clipped]


title: JNRF03_N705_S503

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: R6/2_HD_Striatum_Male_Vehicle_rep4 [328100_26_Left_Striatum_Male_Tg_L1.D707_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N705_S505

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: A

tag: sequencing run id


title: R6/2_HD_Striatum_Female_Vehicle_rep4 [328113_2_Left_Striatum_Female_Tg_L2.D708_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency


title: R6/2_HD_Striatum_Female_Vehicle_rep3 [328080_10_Left_Striatum_Female_Tg_L5.D711_clipped]

tag: treatment duration


title: R6/2_HD_Striatum_Male_Vehicle_rep3 [328144_14_Left_Striatum_Male_Tg_L3.D703_clipped]


title: JNRF03_N705_S510

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF03_N705_S502

tag: age

tag: tissue

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: JNRF03_N705_S506

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: R6/2_HD_Striatum_Female_Vehicle_rep1 [328096_22_Left_Striatum_Female_Tg_L8.D703_clipped]

tag: background

tag: genotype

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Striatum_Female_Vehicle_rep2 [328172_30_Left_Striatum_Female_Tg_L1_clipped]

tag: tissue


title: WT_Cortex_Male_CHDI-00340246_10mg/kg_rep5 [328062_95_Left_Cortex_Male_WT_L1.D705_clipped]

source_name: Cortex, CHDI-00340246, 10mg/kg

value: Wild Type

value: Cortex

value: Male

tag: treatment dose


title: WT_Cortex_Male_CHDI-00340246_10mg/kg_rep4 [328205_107_Left_Cortex_Male_WT_L7.D705_clipped]

value: 12 weeks

value: Oral


title: JNRF03_N704_S506

source_name: Krt5-Rosa-eYFP_Sox2 cKO_72 hrs post tamoxifen_uninjured

tag: strain background

tag: sex type

value: M

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: JNRF03_N704_S505

tag: age

tag: tissue

value: olfactory epithelium

tag: cell type

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: JNRF03_N704_S507

tag: strain background

tag: sex type

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set


title: R6/2_HD_Striatum_Male_CHDI-00340246_10mg/kg_rep2 [328072_17_Left_Striatum_Male_Tg_L3.D703_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment dose

value: 10 mg/kg

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration

value: 6 hours


title: R6/2_HD_Striatum_Female_Vehicle_rep5 [328110_38_Left_Striatum_Female_Tg_L2.D705_clipped]

tag: tissue

value: Striatum

value: Female

tag: age

value: Vehicle


title: JNRF03_N704_S503

tag: strain background

tag: sex type

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: c1 batch id

value: A

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: JNRF03_N704_S502

tag: age

tag: tissue

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: MEDIUM


title: JNRF03_N705_S508

tag: strain background

tag: sex type

value: FFF

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: JNRF03_N705_S507

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: WT_Cortex_Male_CHDI-00340246_10mg/kg_rep3 [328078_99_Left_Cortex_Male_WT_L4.D709_clipped]

tag: background

tag: genotype

value: Wild Type

tag: tissue

value: Cortex

tag: Sex

value: Male

tag: age

value: 12 weeks

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration