title: JNRF03_N703_S511

tag: strain background

tag: sex type

value: M

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

value: FRODO


title: WT_Cortex_Male_CHDI-00340246_10mg/kg_rep2 [328141_115_Left_Cortex_Male_WT_L8.D712_clipped]

status: Public on Oct 30 2017

type: SRA

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

country: USA

institute: CHDI

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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

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

tag: tissue

value: Cortex

tag: Sex

value: Male

tag: age

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: JNRF03_N703_S510

city: Berkeley

first: Diya

last: Das

state: California

address: 265 Life Sciences Addition #3200

department: Molecular & Cell Biology

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

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

source_name: Krt5-Rosa-eYFP_Sox2 cKO_72 hrs post tamoxifen_uninjured

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

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: dilution plate coordinate

tag: c1 plate coordinate

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_Cortex_Male_CHDI-00340246_10mg/kg_rep1 [328116_87_Left_Cortex_Male_WT_L3.D711_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_N703_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

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: WT_Cortex_Female_CHDI-00340246_10mg/kg_rep5 [328097_119_Left_Cortex_Female_WT_L8.D704_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: Female

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Cortex_Female_CHDI-00340246_10mg/kg_rep4 [328157_83_Left_Cortex_Female_WT_L5.D705_clipped]


title: WT_Cortex_Female_CHDI-00340246_10mg/kg_rep3 [328160_91_Left_Cortex_Female_WT_L1.D709_clipped]


title: JNRF03_N703_S506

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: 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_Vehicle_rep1 [328166_116_Left_Cortex_Male_WT_L7.D702_clipped]

source_name: Cortex, Vehicle

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: JNRF03_N703_S503

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: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

value: FRODO


title: WT_Cortex_Female_CHDI-00340246_10mg/kg_rep2 [328188_111_Left_Cortex_Female_WT_L3.D712_clipped]

tag: background

tag: genotype

value: Wild Type

tag: tissue

value: Cortex

tag: Sex

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency


title: WT_Cortex_Male_Vehicle_rep3 [328162_100_Left_Cortex_Male_WT_L6.D710_clipped]

value: Male

value: 12 weeks

tag: treatment duration


title: WT_Cortex_Female_Vehicle_rep4 [328136_84_Left_Cortex_Female_WT_L7.D707_clipped]

value: Oral


title: WT_Cortex_Male_Vehicle_rep5 [328193_96_Left_Cortex_Male_WT_L4.D705_clipped]

value: once


title: WT_Cortex_Female_CHDI-00340246_10mg/kg_rep1 [328194_103_Left_Cortex_Female_WT_L5.D706_clipped]

value: 10 mg/kg

value: 6 hours


title: JNRF03_N703_S505

tag: strain background

tag: sex type

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: 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_Vehicle_rep2 [328143_88_Left_Cortex_Male_WT_L1.D710_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_Cortex_Male_Vehicle_rep4 [328173_108_Left_Cortex_Male_WT_L2_clipped]


title: JNRF03_N702_S510

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: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: A

tag: sequencing run id

tag: lane


title: JNRF03_N703_S502

tag: age

tag: tissue

tag: c1 plate coordinate

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_Cortex_Female_Vehicle_rep2 [328161_120_Left_Cortex_Female_WT_L6.D709_clipped]

tag: background

tag: genotype

tag: Sex

value: Female

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N702_S508

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: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane


title: WT_Cortex_Female_Vehicle_rep1 [328216_112_Left_Cortex_Female_WT_L8.D704_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency


title: WT_Cortex_Female_Vehicle_rep3 [328137_92_Left_Cortex_Female_WT_L7.D708_clipped]

tag: treatment duration


title: R6/2_HD_Cortex_Male_CHDI-00340246_10mg/kg_rep4 [328104_93_Left_Cortex_Male_Tg_L2.D711_clipped]

tag: treatment dose


title: R6/2_HD_Cortex_Male_CHDI-00340246_10mg/kg_rep5 [328176_97_Left_Cortex_Male_Tg_L1.D712_clipped]


title: DAS454_047m

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Inflorescences from pDAB454 transgenic plants, "event.plant": 068.047

library_source: genomic

data_processing:
Library strategy: methylC-Seq
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: AT_TAIR10_genome
Supplementary_files_format_and_content: tag count file

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: developing inflorescence

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by method described in BMC Research Notes 1, p.93-9 (2008). Genomic DNA was extracted by method described in Nucl. Acids Res. 8, p.4321-25 (1980).
Small RNA libraries were constructed using Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNAseq libraries were constructed using  Illumina Truseq RNA library Preparation kit v2 (RS-122-2001). Methyl C-seq libraries were constructed using method described in Nat. Prot. 10, 475-83 (2015).

value: developing inflorescence

tag: transgene construct

tag: copy number of transgene

value: single copy

tag: multigene construct design

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: DAS525_015m

description: Inflorescences from pDAB525 transgenic plants, "event.plant": 149.015

value: canola-biased coding sequences for HetI gene; microalgal coding sequences for PFA1, PFA2, and PFA3 gene


title: DAS454_008m

description: Inflorescences from pDAB454 transgenic plants, "event.plant": 039.008


title: JNRF03_N702_S507

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: 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: DAS525_019m

description: Inflorescences from pDAB525 transgenic plants, "event.plant": 020.019

tag: tissue

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: JNRF03_N703_S507

tag: strain background

tag: sex type

tag: age

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: index set

tag: sequencing run id

tag: lane


title: DAS588_008m

description: Inflorescences from pDAB588 transgenic plants, "event.plant": 009.008


title: DAS588_002m

description: Inflorescences from pDAB588 transgenic plants, "event.plant": 009.002


title: DAS588_020m

description: Inflorescences from pDAB588 transgenic plants, "event.plant": 042.020


title: JNRF03_N702_S511

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: DAS588_018r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 042.018

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 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: AT_TAIR10_genome
Supplementary_files_format_and_content: tag count file

source_name: developing green siliques

tag: tissue

value: developing green siliques

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: WT_Cortex_Female_Vehicle_rep5 [328206_104_Left_Cortex_Female_WT_L1.D708_clipped]

tag: background

tag: genotype

value: Wild Type

value: Cortex

tag: Sex

tag: age

value: 12 weeks

tag: treatment

tag: treatment administration route

value: Oral

tag: treatment frequency

value: once

tag: treatment duration


title: R6/2_HD_Cortex_Male_CHDI-00340246_10mg/kg_rep3 [328151_105_Left_Cortex_Male_Tg_L4.D710_clipped]

value: Male

tag: treatment dose

value: 10 mg/kg

value: 6 hours


title: DAS588_024r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 042.024


title: R6/2_HD_Cortex_Male_CHDI-00340246_10mg/kg_rep1 [328169_85_Left_Cortex_Male_Tg_L8.D705_clipped]


title: JNRF03_N702_S505

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

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

value: MEDIUM

tag: ercc spike-in dilution


title: R6/2_HD_Cortex_Female_CHDI-00340246_10mg/kg_rep5 [328152_109_Left_Cortex_Female_Tg_L1.D707_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: Female

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: JNRF03_N702_S506

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: facs & c1 date

tag: c1 chip size

tag: c1 machine id

value: FRODO


title: JNRF03_N702_S503

tag: age

tag: tissue

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: ercc spike-in dilution


title: R6/2_HD_Cortex_Male_CHDI-00340246_10mg/kg_rep2 [328105_113_Left_Cortex_Male_Tg_L2.D712_clipped]

tag: background

tag: genotype

tag: Sex

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Cortex_Female_CHDI-00340246_10mg/kg_rep1 [328171_81_Left_Cortex_Female_Tg_L1.D712_clipped]


title: R6/2_HD_Cortex_Female_CHDI-00340246_10mg/kg_rep2 [328195_117_Left_Cortex_Female_Tg_L5.D707_clipped]


title: JNRF03_N702_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: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: DAS588_014r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 009.014

tag: tissue

value: developing green siliques

tag: transgene construct

tag: copy number of transgene

value: single copy

tag: multigene construct design

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: R6/2_HD_Cortex_Female_CHDI-00340246_10mg/kg_rep3 [328185_101_Left_Cortex_Female_Tg_L3.D709_clipped]

tag: background

tag: genotype

value: Cortex

tag: Sex

tag: age

value: 12 weeks

tag: treatment

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: DAS588_008r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 009.008


title: JNRF03_N701_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

tag: cdna concentration (ng/μl)

tag: dob

tag: ercc spike-in dilution


title: R6/2_HD_Cortex_Male_Vehicle_rep4 [328211_114_Left_Cortex_Male_Tg_L1.D711_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: Male

tag: age

tag: treatment

value: Vehicle

tag: treatment administration route

tag: treatment frequency

value: once

tag: treatment duration


title: JNRF03_N701_S510

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: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: R6/2_HD_Cortex_Male_Vehicle_rep5 [328074_86_Left_Cortex_Male_Tg_L4.D705_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

value: 6 hours


title: DAS588_002r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 009.002

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: JNRF03_N701_S508

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 coordinate

tag: index set

value: A

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: ercc spike-in dilution


title: R6/2_HD_Cortex_Female_Vehicle_rep4 [328131_82_Left_Cortex_Female_Tg_L1.D701_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

value: Female

tag: age

tag: treatment

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: DAS525_019r

description: T4 seeds from pDAB525 transgenic plants, "event.plant": 020.019

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design

value: canola-biased coding sequences for HetI gene; microalgal coding sequences for PFA1, PFA2, and PFA3 gene


title: R6/2_HD_Cortex_Female_Vehicle_rep5 [328142_90_Left_Cortex_Female_Tg_L1.D702_clipped]


title: DAS525_015r

description: T4 seeds from pDAB525 transgenic plants, "event.plant": 149.015

value: developing green siliques


title: R6/2_HD_Cortex_Male_Vehicle_rep2 [328115_98_Left_Cortex_Male_Tg_L3.D710_clipped]


title: R6/2_HD_Cortex_Male_Vehicle_rep3 [328135_94_Left_Cortex_Male_Tg_L7.D706_clipped]


title: R6/2_HD_Cortex_Male_Vehicle_rep1 [328182_106_Left_Cortex_Male_Tg_L2.D706_clipped]


title: R6/2_HD_Cortex_Female_Vehicle_rep3 [328109_118_Left_Cortex_Female_Tg_L2.D704_clipped]


title: JNRF03_N701_S507

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: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

value: FRODO


title: DAS588_020r

description: T4 seeds from pDAB588 transgenic plants, "event.plant": 042.020

tag: tissue

tag: transgene construct

tag: copy number of transgene

value: single copy

tag: multigene construct design

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: R6/2_HD_Cortex_Female_Vehicle_rep2 [328184_110_Left_Cortex_Female_Tg_L3.D708_clipped]

tag: background

tag: genotype

value: Cortex

tag: Sex

tag: age

value: 12 weeks

tag: treatment

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: R6/2_HD_Cortex_Female_Vehicle_rep1 [328214_102_Left_Cortex_Female_Tg_L8.D702_clipped]

value: Vehicle

value: once


title: R6/2_HD_Cortex_Female_CHDI-00340246_10mg/kg_rep4 [328133_89_Left_Cortex_Female_Tg_L6.D704_clipped]

tag: treatment dose

value: 10 mg/kg

value: 6 hours


title: JNRF03_N701_S506

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

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

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: ercc spike-in dilution


title: JNRF03_N701_S505

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

value: A

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: WT_Cerebellum_Male_CHDI-00340246_10mg/kg_rep4 [328178_75_Left_Cerebellum_Male_WT_L1.D702_clipped]

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

tag: background

tag: genotype

value: Wild Type

value: Cerebellum

tag: Sex

value: Male

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: DAS454_017r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 068.017

value: developing green siliques

tag: transgene construct

tag: copy number of transgene

value: single copy

tag: multigene construct design


title: WT_Cerebellum_Male_CHDI-00340246_10mg/kg_rep3 [328064_59_Left_Cerebellum_Male_WT_L2.D707_clipped]

tag: age


title: JNRF03_N701_S503

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

tag: strain background

tag: sex type

tag: tissue

value: olfactory epithelium

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

tag: cdna concentration (ng/μl)

tag: dob

value: MEDIUM

value: FRODO

tag: ercc spike-in dilution


title: WT_Cerebellum_Male_CHDI-00340246_10mg/kg_rep5 [328148_67_Left_Cerebellum_Male_WT_L3.D707_clipped]

tag: background

tag: genotype

tag: tissue

tag: Sex

tag: age

value: 12 weeks

tag: treatment

tag: treatment dose

tag: treatment administration route

value: Oral

tag: treatment frequency

tag: treatment duration


title: WT_Cerebellum_Male_CHDI-00340246_10mg/kg_rep2 [328099_47_Left_Cerebellum_Male_WT_L1.D706_clipped]

value: 10 mg/kg

value: once


title: WT_Cerebellum_Male_CHDI-00340246_10mg/kg_rep1 [328163_55_Left_Cerebellum_Male_WT_L6.D711_clipped]

value: 6 hours


title: DAS454_008r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 039.008

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: JNRF03_N701_S502

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: 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: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: DAS454_005r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 039.005

tag: tissue

tag: transgene construct

tag: copy number of transgene

tag: multigene construct design


title: DAS454_047r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 068.047


title: WT_Cerebellum_Female_CHDI-00340246_10mg/kg_rep2 [328070_63_Left_Cerebellum_Female_WT_L3.D701_clipped]

tag: background

tag: genotype

value: Wild Type

tag: Sex

value: Female

tag: age

tag: treatment

tag: treatment dose

tag: treatment administration route

tag: treatment frequency

tag: treatment duration


title: WT_Cerebellum_Female_CHDI-00340246_10mg/kg_rep1 [328192_79_Left_Cerebellum_Female_WT_L4.D704_clipped]

value: Cerebellum


title: DAS496_038r

description: T3 seeds from pDAB496 transgenic plants, event 038

value: developing green siliques

value: canola-biased coding sequences for PFA1, PFA2, and HetI genes; microalgal coding sequences for PFA3 gene


title: WT_Cerebellum_Male_Vehicle_rep5 [328212_48_Left_Cerebellum_Male_WT_L1.D712_clipped]

source_name: Cerebellum, Vehicle

value: Male

value: Vehicle


title: WT_Cerebellum_Female_CHDI-00340246_10mg/kg_rep4 [328083_43_Left_Cerebellum_Female_WT_L5.D702_clipped]


title: DAS454_003r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 039.003

value: single copy


title: DAS496_023r

description: T3 seeds from pDAB496 transgenic plants, event 023


title: WT_Cerebellum_Female_Vehicle_rep5 [328076_52_Left_Cerebellum_Female_WT_L4.D707_clipped]

value: 12 weeks


title: WT_Cerebellum_Male_Vehicle_rep1 [328088_76_Left_Cerebellum_Male_WT_L6.D707_clipped]

value: Oral


title: DAS454_042r

description: T4 seeds from pDAB454 transgenic plants, "event.plant": 068.042


title: WT_Cerebellum_Female_CHDI-00340246_10mg/kg_rep3 [328119_71_Left_Cerebellum_Female_WT_L3_clipped]

value: 10 mg/kg


title: WT_Cerebellum_Female_Vehicle_rep4 [328098_64_Left_Cerebellum_Female_WT_L8.D705_clipped]

value: once


title: WT_Cerebellum_Male_Vehicle_rep2 [328146_68_Left_Cerebellum_Male_WT_L3.D705_clipped]

value: 6 hours


title: WT_Cerebellum_Male_Vehicle_rep3 [328114_60_Left_Cerebellum_Male_WT_L3.D709_clipped]


title: WT_Cerebellum_Female_Vehicle_rep1 [328118_72_Left_Cerebellum_Female_WT_L1.D706_clipped]


title: DAS496_T2r

description: T2 seeds from pDAB496 transgenic plants


title: DAS454_068r

description: T3 seeds from pDAB454 transgenic plants, event 068

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: DAS454_039r

description: T3 seeds from pDAB454 transgenic plants, event 039


title: DAS496_019r

description: T3 seeds from pDAB496 transgenic plants, event 019


title: WT_Cerebellum_Female_Vehicle_rep2 [328129_44_Left_Cerebellum_Female_WT_L1.D711_clipped]


title: WT_Cerebellum_Female_CHDI-00340246_10mg/kg_rep5 [328085_51_Left_Cerebellum_Female_WT_L6.D704_clipped]


title: WT_Cerebellum_Female_Vehicle_rep3 [328187_80_Left_Cerebellum_Female_WT_L3.D711_clipped]


title: R6/2_HD_Cerebellum_Male_CHDI-00340246_10mg/kg_rep5 [328154_57_Left_Cerebellum_Male_Tg_L5.D702_clipped]


title: WT_Cerebellum_Male_Vehicle_rep4 [328183_56_Left_Cerebellum_Male_WT_L2.D707_clipped]


title: R6/2_HD_Cerebellum_Male_CHDI-00340246_10mg/kg_rep3 [328128_65_Left_Cerebellum_Male_Tg_L5.D711_clipped]


title: R6/2_HD_Cerebellum_Male_CHDI-00340246_10mg/kg_rep4 [328174_45_Left_Cerebellum_Male_Tg_L1.D710_clipped]


title: DAS454_T2r

description: T2 seeds from pDAB454 transgenic plants


title: DAS588_024s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 042.024


title: R6/2_HD_Cerebellum_Female_CHDI-00340246_10mg/kg_rep5 [328092_41_Left_Cerebellum_Female_Tg_L7.D711_clipped]


title: R6/2_HD_Cerebellum_Female_CHDI-00340246_10mg/kg_rep4 [328125_61_Left_Cerebellum_Female_Tg_L5.D708_clipped]


title: R6/2_HD_Cerebellum_Male_CHDI-00340246_10mg/kg_rep1 [328190_53_Left_Cerebellum_Male_Tg_L4.D702_clipped]


title: R6/2_HD_Cerebellum_Female_CHDI-00340246_10mg/kg_rep3 [328063_77_Left_Cerebellum_Female_Tg_L1.D706_clipped]


title: R6/2_HD_Cerebellum_Male_Vehicle_rep5 [328086_58_Left_Cerebellum_Male_Tg_L6.D705_clipped]


title: DAS588_018s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 042.018


title: R6/2_HD_Cerebellum_Male_Vehicle_rep4 [328218_46_Left_Cerebellum_Male_Tg_L8.D706_clipped]


title: R6/2_HD_Cerebellum_Male_Vehicle_rep3 [328079_66_Left_Cerebellum_Male_Tg_L5.D710_clipped]


title: R6/2_HD_Cerebellum_Female_CHDI-00340246_10mg/kg_rep1 [328168_49_Left_Cerebellum_Female_Tg_L7.D704_clipped]


title: DAS588_020s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 042.020


title: R6/2_HD_Cerebellum_Male_Vehicle_rep1 [328170_74_Left_Cerebellum_Male_Tg_L8.D706_clipped]


title: R6/2_HD_Cerebellum_Female_CHDI-00340246_10mg/kg_rep2 [328149_69_Left_Cerebellum_Female_Tg_L4.D708_clipped]


title: DAS588_014s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 009.014


title: DAS588_002s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 009.002


title: DAS588_008s

description:
small RNA
T4 seeds from pDAB588 transgenic plants, "event.plant": 009.008


title: DAS525_015s

description:
small RNA
T4 seeds from pDAB525 transgenic plants, "event.plant": 149.015

value: canola-biased coding sequences for HetI gene; microalgal coding sequences for PFA1, PFA2, and PFA3 gene


title: R6/2_HD_Cerebellum_Female_Vehicle_rep4 [328180_42_Left_Cerebellum_Female_Tg_L2.D704_clipped]


title: DAS525_019s

description:
small RNA
T4 seeds from pDAB525 transgenic plants, "event.plant": 020.019


title: R6/2_HD_Cerebellum_Female_Vehicle_rep3 [328095_70_Left_Cerebellum_Female_Tg_L8.D702_clipped]


title: R6/2_HD_Cerebellum_Female_Vehicle_rep1 [328191_50_Left_Cerebellum_Female_Tg_L4.D703_clipped]


title: R6/2_HD_Cerebellum_Female_Vehicle_rep2 [328200_62_Left_Cerebellum_Female_Tg_L6.D712_clipped]


title: R6/2_HD_Cerebellum_Male_Vehicle_rep2 [328204_54_Left_Cerebellum_Male_Tg_L7.D704_clipped]


title: R6/2_HD_Cerebellum_Female_Vehicle_rep5 [328139_78_Left_Cerebellum_Female_Tg_L8.D710_clipped]


title: R6/2_HD_Cerebellum_Male_CHDI-00340246_10mg/kg_rep2 [328077_73_Left_Cerebellum_Male_Tg_L4.D708_clipped]


title: DAS454_047s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 068.047


title: DAS454_042s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 068.042


title: R6/2_HD_Cortex_Male_Vehicle_replicate3

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.mm10, gene models version Ensembl.R78
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: R6/2, Cortex, Vehicle

value: Cortex

value: Twice-Daily (b.i.d)

value: from 4 to 12 weeks


title: WT_Cortex_Female_Vehicle_replicate4

source_name: WT, Cortex, Vehicle

value: Wild Type

value: Female


title: WT_Cortex_Female_Vehicle_replicate3


title: R6/2_HD_Cortex_Female_Vehicle_replicate4


title: DAS454_017s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 068.017

value: developing green siliques


title: R6/2_HD_Cortex_Male_Vehicle_replicate2


title: WT_Cortex_Male_Vehicle_replicate3


title: R6/2_HD_Cortex_Female_Vehicle_replicate3


title: WT_Cortex_Male_Vehicle_replicate2


title: DAS454_003s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 039.003


title: DAS454_005s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 039.005


title: WT_Cortex_Female_Vehicle_replicate2


title: R6/2_HD_Cortex_Female_CHDI-00340246_30mg/kg_replicate3

value: 30 mg/kg


title: R6/2_HD_Cortex_Male_Vehicle_replicate1

value: Male


title: DAS496_038s

description:
small RNA
T3 seeds from pDAB496 transgenic plants, event 038

value: canola-biased coding sequences for PFA1, PFA2, and HetI genes; microalgal coding sequences for PFA3 gene


title: R6/2_HD_Cortex_Female_Vehicle_replicate2

value: Vehicle


title: DAS496_023s

description:
small RNA
T3 seeds from pDAB496 transgenic plants, event 023

value: single copy


title: R6/2_HD_Cortex_Male_CHDI-00340246_30mg/kg_replicate2

value: 12 weeks

value: Oral


title: WT_Cortex_Male_Vehicle_replicate4


title: DAS496_019s

description:
small RNA
T3 seeds from pDAB496 transgenic plants, event 019


title: DAS496_T2s

description:
small RNA
T2 seeds from pDAB496 transgenic plants


title: R6/2_HD_Cortex_Male_CHDI-00340246_30mg/kg_replicate4


title: R6/2_HD_Cortex_Female_Vehicle_replicate1


title: DAS454_039s

description:
small RNA
T3 seeds from pDAB454 transgenic plants, event 039


title: R6/2_HD_Cortex_Female_CHDI-00340246_30mg/kg_replicate2


title: R6/2_HD_Cortex_Female_CHDI-00340246_30mg/kg_replicate1


title: DAS454_068s

description:
small RNA
T3 seeds from pDAB454 transgenic plants, event 068


title: DAS454_008s

description:
small RNA
T4 seeds from pDAB454 transgenic plants, "event.plant": 039.008


title: R6/2_HD_Cortex_Male_CHDI-00340246_30mg/kg_replicate1


title: WT_Cortex_Male_Vehicle_replicate1


title: R6/2_HD_Striatum_Female_CHDI-00340246_30mg/kg_replicate4

description: 409941_R62J3179_07_Right_Striatum_L4.D704

value: Striatum


title: WT_Striatum_Female_Vehicle_replicate4

description: 409944_R62J3170_06_Right_Striatum_L4.D707

source_name: WT, Striatum, Vehicle


title: R6/2_HD_Striatum_Male_CHDI-00340246_30mg/kg_replicate2

description: 409942_R62J3178_03_Right_Striatum_L4.D705


title: WT_Cortex_Female_Vehicle_replicate1


title: R6/2_HD_Striatum_Male_CHDI-00340246_30mg/kg_replicate4

description: 409945_R62J3173_01_Right_Striatum_L5.D708


title: R6/2_HD_Striatum_Male_CHDI-00340246_30mg/kg_replicate3

description: 409943_R62J3168_02_Right_Striatum_L4.D706


title: EKVX-1735-3

city: Los Angeles

first: Tanyalak

last: Parimon

state: CA

address: 127 San Vicente

department: Medicine

institute: Cedars-Sinai Medical Center

description: EKVX KO-3

data_processing:
miRNA sequencing short reads were aligned to human reference genome (GRCh38) using Bowtie2 (v2.2.3) ;
Aligned sequences were mapped to mature miRNAs with annotation from miRBase (v.21);
The relative expression abundances of miRNAs were calculated as Count-Per-Million (CPM).
Genome_build: GRCh38
Supplementary_files_format_and_content: CPM

organism: Homo sapiens

source_name: Lung epithelial cells

growth_protocol: EKVX-cells were plated in T-25 flask at 2x106 density and cultivated in Dulbecco's minimal essential medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 mg/mL streptomycin at 37°C in 5% CO2 overnight. Then, cells were washed 3 times with PBS and cultured in DMEM media supplemented with 10% exosome-depleted FBS (System Biosciences, Inc. (SBI), Palo Alto, CA) for 48 hours

extract_protocol:
Exosomes were isolated from cell culture media using using ExoQuick-TCTM (SBI), and microRNA was purified using QIAGEN miRNeasy micro kit (QIAGEN, Valencia, CA) per the manufacture’s protocols
Libraries were prepared according to standard Ilumina's instructions

tag: cell type

value: Carcinoma cells

tag: cellular portion

value: Exosomes

tag: genotype/variation

value: syndecan-1 knock-down

tag: passages


title: DAS454_T2s

description:
small RNA
T2 seeds from pDAB454 transgenic plants

tag: tissue

value: canola-biased coding sequences for PFA1, PFA2, PFA3, and HetI genes


title: R6/2_HD_Cortex_Female_CHDI-00340246_30mg/kg_replicate4

value: Cortex

value: Twice-Daily (b.i.d)


title: R6/2_HD_Cortex_Male_CHDI-00340246_30mg/kg_replicate3

value: from 4 to 12 weeks


title: EKVX-1735-2

description: EKVX KO-2


title: WT_Striatum_Female_Vehicle_replicate3

description: 409939_R62J3175_06_Right_Striatum_L4.D702

value: Wild Type

value: Female


title: R6/2_HD_Striatum_Female_Vehicle_replicate4

description: 409937_R62J3174_03_Right_Striatum_L3.D712

source_name: R6/2, Striatum, Vehicle


title: WT_Striatum_Female_Vehicle_replicate2

description: 409936_R62J3180_06_Right_Striatum_L3.D711


title: WT_Striatum_Female_Vehicle_replicate1

description: 409935_R62J3169_03_Right_Striatum_L3.D710


title: EKVX-Scrb-3

description: EKVX Cntl-3

value: wild-type


title: R6/2_HD_Striatum_Female_CHDI-00340246_30mg/kg_replicate3

description: 409934_R62J3174_04_Right_Striatum_L3.D709

value: 30 mg/kg


title: EKVX-Scrb-2

description: EKVX Cntl-2


title: EKVX-Scrb-1

description: EKVX Cntl-1


title: WT_Striatum_Male_Vehicle_replicate3

description: 409931_R62J3180_02_Right_Striatum_L2.D706

value: Male


title: WT_Striatum_Male_Vehicle_replicate2

description: 409930_R62J3170_01_Right_Striatum_L2.D705

value: Vehicle


title: Person 8 hyperthyroid

city: Rotterdam

first: Selmar

last: Leeuwenburgh

state: Zuid-Holland

address: Wytemaweg 80

department: Internal medicine

country: Netherlands

institute: Erasmus MC

data_processing:
Basecalling: Illumina RTA and Demultiplexing Illumina CASAVA
Alignment: tophat-2.0.13 with Bowtie version 2.2.4.0
ReadCounting with htseq
Differential expression analysis with DESeq2 R bioconductor package
Genome_build: GRCh38
Supplementary_files_format_and_content: Output of DESeq2 with gene name,baseMean, log2FoldChange, lfcSE, stat, pvalue, padj columns

source_name: Whole blood

extract_protocol:
Whole blood samples were collected in PAXgene tubes(PreAnalytiX, Hombrechtikon, Switzerland,catalog number 762165 ). RNA was isolated using PAXgene blood miRNA kits (PreAnalytiX, Hombrechtikon, Switzerland, catalog number 763134 ). For RNAseq analysis ribosomal RNA and globin mRNAs were first removed from an aliquot of the RNA samples using the Globin-Zero Gold rRNA Removal Kit (Illumina, San Diego, USA).
Kapa Stranded RNA library was prepared (Kapa Stranded RNA kit, Kapabiosystems), followed by sequencing on a HiSeq2500 system, for single end reads, 50 bp in length (Illumina, USA).

treatment_protocol: Peripheral blood samples were obtained from all participants when overt biochemical hypothyroidism was achieved by withdrawal of LT4 substitution in thyroidectomized patients as well as when TSH suppression was achieved after restarting LT4 replacement therapy.

tag: condition

value: hyperthyroid

value: Whole blood


title: R6/2_HD_Striatum_Male_CHDI-00340246_30mg/kg_replicate1

description: 409929_R62J3172_02_Right_Striatum_L2.D704

value: 12 weeks

value: Oral


title: Person 7 hyperthyroid


title: R6/2_HD_Striatum_Male_Vehicle_replicate2

description: 409928_R62J3182_03_Right_Striatum_L2.D703

value: Striatum


title: WT_Striatum_Male_Vehicle_replicate4

description: 409940_R62J3182_01_Right_Striatum_L4.D703


title: R6/2_HD_Striatum_Female_Vehicle_replicate1

description: 409927_R62J3173_04_Right_Striatum_L2.D702


title: EKVX-1735-1

description: EKVX KO-1

value: Carcinoma cells

value: Exosomes


title: WT_Striatum_Male_Vehicle_replicate1

description: 409926_R62J3187_03_Right_Striatum_L1.D701


title: R6/2_HD_Striatum_Male_Vehicle_replicate1

description: 409925_R62J3184_02_Right_Striatum_L1.D712


title: R6/2_HD_Striatum_Female_CHDI-00340246_30mg/kg_replicate1

description: 409923_R62J3181_02_Right_Striatum_L1.D710


title: R6/2_HD_Striatum_Male_Vehicle_replicate3

description: 409938_R62J3171_03_Right_Striatum_L3.D701


title: Person 5 hyperthyroid


title: Person 4 hyperthyroid


title: Person 6 hyperthyroid


title: CD1dKOxE7onC5728dpg_1

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

country: Australia

institute: The University of Queensland

data_processing:
Libraries were sequenced on Illumina HiSeq2000 machine with a PE 2 x 100 tag format.
Raw read counts from sequenced libraries were quality checked with the FastQC tool, trimmed using the Trimmomatic tool.
Read pairs were mapped to the mouse reference genome (mm10) using the Rsubread tool in R.
Reads were also mapped to HPV16 E7 gene sequence to obtain expression level of E7 oncogene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw counts of sequencing reads for each Sample

source_name: CD1dKOxE7onC5728dpg_ear skin

extract_protocol:
Whole ear samples and grafts were collected from mice euthanized with 5% CO2. Samples were collected into Eppendorf tubes and immediately snap frozen on dry ice. Samples were kept in the -80°C freezer until used for RNA extraction. All RNA extractions were performed using Trizol and Qiagen RNeasy mini kit (catalogue #74106, Qiagen, Clifton Hill, VIC, Australia)) following manufacturer’s protocol.
cDNA library preparation from RNA samples was performed using Low Throughput Sample Protocol (suitable for 48 samples or less) from Illumina TruSeq RNA Sample Preparation Kit v2 (catalogue #15027387, #15025063 and #15027084 obtained from Illumina, San Diego, CA, USA).

tag: recipient strain

value: grafted ear skin

tag: donor genotype


title: Person 1 hyperthyroid


title: R6/2_HD_Striatum_Female_Vehicle_replicate3

description: 409933_R62J3186_02_Right_Striatum_L3.D708

tag: background


title: Person 3 hyperthyroid


title: CD1dKOxE7onC5728dpg_3


title: CD1dKOxE7onC5714dpg_2

source_name: CD1dKOxE7onC5714dpg_ear skin


title: CD1dKOxE7onC5714dpg_3


title: R6/2_HD_Striatum_Female_Vehicle_replicate2

description: 409932_R62J3168_03_Right_Striatum_L2.D707

tag: genotype


title: CD1dKOxE7onC5728dpg_2


title: CD1dKOxE7onC5714dpg_1


title: Person 2 hyperthyroid


title: E7onC5728dpg_1

source_name: E7onC5728dpg_ear skin


title: Person 8 hypothyroid

value: hypothyroid


title: Person 7 hypothyroid


title: E7onC5728dpg_3


title: E7onC5728dpg_2


title: E7onC5714dpg_3

source_name: E7onC5714dpg_ear skin


title: E7onC5714dpg_2


title: E7onC5714dpg_1


title: R6/2_HD_Striatum_Female_CHDI-00340246_30mg/kg_replicate2

description: 409924_R62J3177_04_Right_Striatum_L1.D711

tag: Sex

value: Twice-Daily (b.i.d)


title: Person 6 hypothyroid


title: C57onC5728dpg_2

source_name: C57onC5728dpg_ear skin


title: C57onC5728dpg_3


title: C57onC5728dpg_1


title: Person 4 hypothyroid


title: C57onC5714dpg_3

source_name: C57onC5714dpg_ear skin


title: C57onC5714dpg_1


title: C57onC5714dpg_2


title: Person 1 hypothyroid


title: Person 3 hypothyroid


title: FOXO1_ChIPSeq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: FOXO1_ ChIPseq_in_pre-leukemia_cells

growth_protocol: IMDM media , 20% BIT, 2% Glutamine, 1% pen/Strep, cytokines: IL-6, Flt3-L, SCF, TPO, IL-3 (10 ng/mL

extract_protocol:
ChIP-Seq assays in AE cells ,were performed essentially as previously described (Ptasinska et al., 2014). Antibodies for HA (Sigma, H6908) and  FOXO1 (Abcam ab39670) were used.Cells were first washed with PBS and then cross-linked with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG) (Sigma) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS with 1% formaldehyde (~0.34 M) for 10 minutes at room temperature. All crosslinking reactions were quenched by adding 4 volumes of PBS and 0.125 M glycine, cells were washed twice in PBS and incubated with Buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK) and 0.1 mM PMSF), incubated for 10 min at 4°C with rotation, and centrifuged 5 min at 500 x g at 4 °C. The pellet was resuspended in 10 ml of ice–cold Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, protease inhibitor cocktail and 0.1 mM PMSF), incubated for 10 min at 4 °C with rotation and centrifuged for 5 min at 500 x g at 4 °C. Cells were resuspended in 600 μl of ice-cold ChIP lysis buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.25% SDS, protease inhibitor cocktail and 0.1 mM PMSF), incubated 10 min on ice and sonicated at 5 °C using a Bioruptor™ (Diagenode) to generate fragments an average length of 500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high). The lysates were centrifuged for 5 min at 16,000 x g at 4 °C and the supernatants were diluted with two volumes of ice-cold ChIP dilution buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 7.5% glycerol, protease inhibitor cocktail and 0.1 mM PMSF). For each IP, 15 μl of Dynabeads® protein G (Dynal) were pre–incubated with 50 μg BSA and 1-2 μg antibody for 2 h at 4 °C with rotation. The blocked antibody-bound protein G mix was added to 20–25 μg chromatin in a total volume of 500 μl diluted ChIP lysis buffer and incubated for 2 h at 4°C with rotation. After magnetic separation the beads were washed once with 1 ml wash buffer 1 (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with 1 ml wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 1 ml LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate) and twice with 1 ml TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). For each wash the beads were mixed with ice-cold washing buffers for 10 min at 4 °C. The immunoprecipitated DNA was eluted two times with 50 μl ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 15 min at RT with shaking. At this step the input control (1% of the starting material) was included in the experimental procedure after first adjusting the final volume to 100 μl with ChIP elution buffer. The eluted DNA was incubated overnight at 65 °C in the presence of 50 μg proteinase K. The DNA was finally purified using Agencourt AMPure (Beckman Coulter) magnetic beads according to the manufacturer’s instructions, eluted with 50 μl x TE and analysed by qPCR using SYBR Green reagents.
KAPA Hyper Prep Kit, Kapa biosystems

treatment_protocol: untreated cells

tag: cell population

value: CD34+ human cord blood cells

value: pre-leukemia stem cells


title: Person 2 hypothyroid


title: AE_ChIPSeq

source_name: AE_ ChIPseq_in_pre-leukemia_cells


title: ME_JH_112315_1109-ATACSlice03-03-1plus2

first: Jenna

middle: E

last: Haines

address: 151 Koshland Hall

department: Molecular and Cellular Biology

institute: University of California Berkeley

description:
Insert Size - 50-400
011617_081817_RemDUP_041217_Bowtie2_ME_JH_112315_1109-ATACSlice03-03-1plus2_shifted_lessthan130_1MNorm.wig

data_processing:
Sequencing reads were aligned to the D. melanogaster genome (Flybase Release 5) using Bowtie2 with options set as -5 5 -3 5 -N 1 -X 2000 --local --very-sensitive-local.
Sam files were then sorted and converted to Bam files using Samtools, only keeping uniquely mapped reads with a MAPQ score of 30 or higher using  -q 30. Duplicates were removed with Picard. Bams were then converted to bed files with bedtools and shifted using a custom shell script to reflect a 4bp increase on the plus strand and a 5bp decrease on the minus strand
Replicate bed files were merged. Finally shifted bed files were converted into wig files using custom scripts
Merged wig files were normalized to reflect 10 million mapped Drosophila melanogaster reads. Anterior, posterior and combined samples were additionally normalized by linear regression to the whole embryo sample (not including the y-intercept).
Replicates were merged and peaks were called on the merged bed file using MACS2 with the following parameters  --nomodel --nolambda --keep-dup all --call-summits
Genome_build: The sequencing reads were aligned to the D. melanogaster genome (Flybase Release 5).
Supplementary_files_format_and_content: Normalized wig files contain a wig score across 10bp windows that is normalized to 10 million mapped reads and by the slope of the linear regression against whole embryo samples.

organism: Drosophila melanogaster

source_name: Stage 5 D.mel embryos

growth_protocol: Drosophila melanogaster OregonR embryos were collected for 2 hours and aged for 90 minutes on molasses agar plates. Embryos were then dechorionated with 30%-50% bleach solution for three minutes. Embryos were hand staged at 20x magnification at 14°C to be mitotic  cycle 14 (NC14).

extract_protocol:
Transposed DNA was purified using Qiagen Minelute kit.  Libraries were then amplified using Phusion (NEB cat no. F531S) and Illumina Nextera index kit (cat no. FC-121-1011). Libraries were then purified with Ampure Beads at a 1.2 : 1 beads to sample ratio
Libraries were constructed using a modified Illumina Nextera DNA protocol and sequenced on the Hiseq4000 using 100bp paired end reads. Fragments over 500bp were removed from libraries using a Pippen prep to reduce sequencing bias with the Hiseq4000.

treatment_protocol: NC14 embryos were placed in a custom freezing buffer consisting of ATAC-seq lysis buffer [25] without detergent, 5% glycerol, and 1ul of bromoblue dye. Embryos were then taken out of the freezing buffer and placed onto a glass slide which was then put on dry ice for 2-5 minutes. Once embryos were completely frozen, the glass slide was removed and embryos were sliced with a chilled razorblade. Sliced embryo halves were moved to tubes containing ATAC-seq lysis buffer with 0.15mM spermine added to help stabilize chromatin. Embryo halves were then homogenized using Kimble Kontes Pellet Pestle (cat no. K749521-1590). IGEPal CA-630 was added to a final concentration of 0.1%. After a 10 minute incubation nuclei were spun down and resuspended in water. Twenty halves were added to the transposition reaction containing 25ul of 2x TD buffer (Illumina), and 7.5ul of Tn5 enzyme (Illumina). The reaction was incubated at 37°C for 30 minutes.

tag: line

value: Oregon R

value: 1/3 of sample 4 and 1/3 of sample 5 or 13.33 embryo halves equivalents

tag: developmental stage

value: Embryonic Stage 5


title: ME_JH_112315_1109-ATACSlice03-01-20Ant

description:
Insert Size - 50-400
011718_MERGED_2reps_081817_RemDUP_041217_Bowtie2_ME_JH_112315_20Ant_shifted_lessthan130_10MNorm_linregwhole.wig

value: 20 embryo halves


title: tDNA2334_rep1

first: Xavier

last: Darzacq

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

data_processing:
Library strategy: Micro-C
OLB 1.9/CASAVA_v1.8.2 were used for base calling.
Barcoded libraries were demultiplexed autmatically by Illumina Basespace platform.
Paired reads were mapped to reference genome separately by Bowtie2.
Parse SAM files and remove duplicate reads.
Mate unique paired reads and generate BED file for all valid interactions.
Triplet sparse conact matrix with various resolutions (e.g., 100bp, 200bp, 1kb, and 5kb) were generated, in which the first two columns are bin numbers and the third colum is interaction count.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: BED (Chr1, Pos1, Strand1, Chr2, Pos2, Strand2), contact matrix

organism: Saccharomyces cerevisiae

growth_protocol: The 100mL yeast cultures were grown to midlog phase ~OD 0.55 in indicated media at 30 C.

extract_protocol:
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~10-12 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina Nextseq 500 paired end sequencing with 42 x 42 bp reads.

treatment_protocol: Yeast cells were fixed with 3% formaldehyde for 10 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted and spheroplasted with Zymolyase. The spheroplasts were washed by PBS, subjected to long-crosslinker fixation for 40min, and quenched with 250 mM glycine for 5 min. Cells were pelleted again, washed with PBS, and treated with a level of MNase yielding >95% mononucleosomes. After stopping MNase, chromatin pellet and supernatant was dephosphorylated using rSAP separately. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Chromatin was diluted into 2.5 mL and treated with T4 DNA ligase. Ligated products were treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated at 65 C overnight.

tag: strain

tag: media

value: YPD


title: tDNA690_rep1


title: ME_JH_112315_1109-ATACSlice03-04-10whole

description:
Insert Size - 50-400
011718_MERGED_2reps_081817_RemDUP_041217_Bowtie2_ME_JH_112315_10whole_shifted_lessthan130_10MNorm.wig

value: 10 whole embryos


title: ME_JH_112315_1109-ATACSlice03-02-20Post

description:
Insert Size - 50-400
011718_MERGED_2reps_081817_RemDUP_041217_Bowtie2_ME_JH_112315_20Post_shifted_lessthan130_10MNorm_linregwhole.wig


title: tDNA690_rep2


title: ME_JH_112315_1105-ATACSlice2-01-20a


title: ME_JH_112315_1105-ATACSlice2-7-10whole


title: N3

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the canine canFam3 reference genome+transcriptome (Ensembl).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the canFam3 reference transcriptome (Ensembl).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the canFam3 reference transcriptome (Ensembl).
Genome_build: Canine canFam3 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

organism: Canis lupus familiaris

source_name: normal meninges

extract_protocol:
RNA was purified from 2x15uM scrolls from each FFPE block using the Agencourt FormaPure kit (Beckman Coulter) using a BioMek 4000 Automated Liquid Handling System (Beckman Coulter).  For fresh-frozen control meninges samples, RNA was purified using Trizol (Invitrogen). Samples with high molecular weight material based on QC on an Fragment Analyzer (Advanced Analytical) were treated with RapidOUT DNAse (ThermoFisher Scientific). Ribosomal RNA was subtracted by hybridization from 1-2.5ug total RNA per sample using the RiboZero Magnetic Gold HMR Kit (Illumina).
Directional RNA-seq libraries were prepared from 50-100 ug rRNA-depleted RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: All meningioma specimens were collected in 10% neutral buffered formalin and were embedded in paraffin wax within 24 hours of arrival at the New York State Animal Health Diagnostic Center (Cornell University College of Veterinary Medicine, Section of Anatomic Pathology).  Diagnoses were made based on hematoxylin and eosin stained sections.  Control samples of meninges were collected fresh from three healthy research beagle dogs shortly after euthanasia for an unrelated project.

tag: tumor grade

tag: tumor subtype


title: N1


title: ChIPSeq IN2 CD4T +IL2 H3K27Ac

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were aligned to the mm9 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to bam format using samtools. MACS was used to call peaks for ChIP-Seq data. HOMER is used to perform super-enhancer analysis. RPKM model (reads per kilobase per million reads) was used to normalize gene expression values for RNA-Seq data.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements for RNA-seq; peak bedGraph for ChIP-seq

source_name: CD4T H3K27Ac +IL2, IN2 deletion

growth_protocol: T cells were isolated from spleen by standard methods using kits from Miltenyi. Cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum.

extract_protocol:
For ChIP-Seq, and cross-linked with 1% formaldehyde (methanol-free, Pierce, Rockford, IL) at room temperature for 10 min. After sonication, fragmented chromatin equivalent to 10 million cells was immunoprecipitated with control rabbit IgG (Santa Cruz Biotechnology, Dallas TX) or indicated antibodies and Magna ChIPTM Protein A+G Magnetic Beads (Millipore, Billerica MA). ChIP-Seq DNA libraries were prepared using KAPA LTP Library Preparation Kit (Kapa Biosystems, Wilmington, MA) and indexed primers (BIOO Scientific, Austin, TX), and the libraries were then sequenced. For RNA-Seq, KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems, Wilmington, MA), and each library was indexed using barcoded primers (BIOO Scientific, Austin, TX). Barcoded PCR products were purified on 2% E-Gel, 250-400 bp fragments were purified, quantified on Qbit (Invitrogen), mixed, and sequenced on an Illumina Genome Analyzer II or HiSeq2000 platform.
PCR products were barcoded (indexed) and sequenced on Illumina Genome Analyzer II or HiSeq 2000 platform.

treatment_protocol: For pre-activation, cells were stimulated with plate-bound anti-CD3 (2 μg/ml) + anti-CD28 (1 μg/ml) for 3 days, rested overnight, and then stimulated with IL-2 (100 U/ml, 2 nM) or IL-21 (100 ng/ml) for 1h (ChIP-Seq). RNA-Seq experiments were performed with total RNA isolated from mouse CD4+ T cells, pre-activated, treated without or with IL-2 or IL-21 for 0.5, 2, 4, or 24 h.

tag: strain background

value: IN2 deletion

value: Spleen

tag: cell type

value: pre-activated T cells

tag: treated with

value: IL-2 (100 U/ml, 2 nM) for 1hr

tag: chip antibody

value: anti-H3K27Ac (Abcam)


title: Person 5 hypothyroid

tag: condition

tag: tissue

value: Whole blood


title: ME_JH_112315_1105-ATACSlice2-02-20p


title: P13

source_name: meningioma

value: II

value: atypical


title: ChIPSeq UP CD4T +IL2 H3K27Ac

source_name: CD4T H3K27Ac +IL2, UP deletion

tag: genotype/variation

value: UP deletion


title: P12


title: ChIPSeq IN1 CD4T +IL2 H3K27Ac

source_name: CD4T H3K27Ac +IL2, IN1 deletion

value: IN1 deletion


title: ChIPSeq WT CD4T +IL2 H3K27Ac 2

source_name: CD4T H3K27Ac +IL2, Wild Type

value: Wild Type


title: P11


title: ChIPSeq IN2 CD4T +IL2 STAT5B

source_name: CD4T STAT5B, +IL2, IN2 deletion

value: anti-STAT5B (R&D systems)


title: P10


title: ChIPSeq IN1 CD4T +IL2 STAT5B

source_name: CD4T STAT5B, +IL2, IN1 deletion


title: P9


title: ChIPSeq WT CD4T +IL2 STAT5B 2

source_name: CD4T STAT5B, +IL2, Wild Type

value: wild type


title: P7


title: P8


title: N2


title: P5

value: I

value: transitional


title: P4


title: P6


title: ChIPSeq WT CD4T -IL2 H3K27Ac

source_name: CD4T H3K27Ac -IL2


title: P3


title: RNASeq CD4T IL21 24h

source_name: CD4T treated with IL21 for 24h

value: pre-activated CD4+ T cells

value: IL21 for 24h


title: ChIPSeq WT CD8T -IL2 STAT5B

source_name: CD8T STAT5B, -IL2


title: P2

value: meningothelial


title: P1


title: RNASeq CD4T IL21 4h

source_name: CD4T treated with IL21 for 4h

value: Spleen

value: IL21 for 4h


title: RNASeq CD4T IL2 24h

source_name: CD4T treated with IL2 for 24h

value: IL2 for 24h


title: pDAB447-030 T3 (pool)

city: Indianapolis

first: Lyudmila

middle: V

last: Sidorenko

state: Indiana

address: 9330 Zionsville Rd

institute: DOW AgroSciences

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

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, ZmHiGC


title: tDNA2334_rep2

value: YPD


title: pDAB447-023 T3 (pool)


title: pDAB447-012  T3 (pool)


title: RNASeq CD4T IL2 2h

source_name: CD4T treated with IL2 for 2h

value: IL2 for 2h


title: ChIPSeq UP CD4T +IL2 STAT5B

source_name: CD4T STAT5B, +IL2, UP deletion

value: UP deletion

value: pre-activated T cells

value: IL-2 (100 U/ml, 2 nM) for 1hr


title: pDAB447-002 T3 (pool)


title: pDAB447-010 T3 (pool)


title: RNASeq CD4T IL2 0.5h

source_name: CD4T treated with IL2 for 0.5h

value: wild type

value: IL2 for 0.5h


title: chid+deci

city: Shanghai

first: Meng-Meng

last: Ji

address: Ruijin No.2 Road

country: China

institute: Shanghai Ruijin Hospital

data_processing:
Paired-end reads were harvested from Illumina HiSeq Sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9),  the high quality trimmed reads were aligned to the reference genome (UCSC hg19) guided by the Ensembl GFF gene annotation file with hisat2 software (v2.0.4).
Then, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA，and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: mRNA Expression Profiling.xlsx：mRNA Expression (FPKM values) of genes for all samples

source_name: Jurkat cell

growth_protocol: Cells were grown in RPMI-1640 medium, supplemented with 10% heat-inactivated fetal bovine serum in a humidified atmosphere containing 95% air-5% CO2 at 37°C.

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

treatment_protocol: Jurkat (KMT2D V5486M) cells were treated with Chidamide (5nm)，Decitabine (5μm)，Chidamide (5nm)+Decitabine (5μm)，respectively.

value: Jurkat cell (KMT2D V5486M)

tag: treatment

value: Chidamide (5nm)+Decitabine (5μm)


title: ChIPSeq WT CD4T +IL2 H3K27Ac 1

source_name: CD4T H3K27Ac +IL2

value: anti-H3K27Ac (Abcam)


title: ChIPSeq WT CD8T +IL2 STAT5B

source_name: CD8T STAT5B, +IL2

value: Spleen

value: anti-STAT5B (R&D systems)


title: ChIPSeq WT CD4T +IL21 STAT3

source_name: CD4T STAT3 +IL21

value: IL-21 (100 ng/ml) for 1h

value: anti-STAT3 (Invitrogen)


title: ChIPSeq WT CD4T -IL21 STAT3

source_name: CD4T STAT3 -IL21


title: RNASeq CD4T Cont

source_name: CD4T no cytokine

value: pre-activated CD4+ T cells


title: deci

value: Decitabine (5μm)


title: chid

value: Chidamide (5nm)


title: E7_8wks_289

data_processing:
bcl2fastq-1.8.4 software used for basecalling.
Reads were trimmed using the Trimmomatic tool
Read pairs were mapped to the mouse reference genome (mm10) using Rsubread.
Reads were also mapped to HPV16 E7 gene sequence (https://www.ncbi.nlm.nih.gov/nuccore/333031?from=562&to=858&sat=4&sat_key=66313949) to obtain expression level of E7 oncogene
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the raw counts of sequencing reads for mouse genes and HPV16 E7 gene

source_name: E7, 8wks, Ear Skin

value: Whole Ear Skin

tag: genotype


title: ChIPSeq WT CD4T +IL2 H3K4me3

source_name: CD4T H3K4me3 +IL2

value: anti-H3K4me3 (Millipore)


title: untreated

value: untreated


title: RNASeq CD4T IL2 4h

source_name: CD4T treated with IL2 for 4h

value: IL2 for 4h


title: E7_8wks_288


title: ChIPSeq WT CD4T +IL2 STAT5B 1

source_name: CD4T STAT5B, +IL2

value: pre-activated T cells

value: IL-2 (100 U/ml, 2 nM) for 1hr


title: ChIPSeq WT CD4T -IL2 STAT5B

source_name: CD4T STAT5B, -IL2

value: wild type


title: C57_8wks_286

source_name: C57, 8wks, Ear Skin

value: control


title: RNASeq CD4T IL21 2h

source_name: CD4T treated with IL21 for 2h

value: IL21 for 2h


title: C57_8wks_287


title: ChIPSeq WT CD4T IgG

source_name: CD4T IgG

value: rabbit IgG (Santa Cruz)


title: C57_8wks_285


title: RNASeq CD4T IL21 0.5h

source_name: CD4T treated with IL21 for 0.5h

value: Spleen

value: IL21 for 0.5h


title: UT-5

city: Clemson

first: William

middle: S

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

data_processing:
FastQC-quality check
Trimmomatic-trim low quality bases and adapter sequences
GSNAP alignment to reference genome (GCA_001632505.1)
Subread Feature Counts- generate raw counts from alignment
EdgeR-determine differential gene expression
Genome_build: GCA_001632505.1
Supplementary_files_format_and_content: Comma separated table (.csv) of the raw counts and normalized counts

organism: Daphnia magna

source_name: Whole Daphnia magna

growth_protocol: Daphnia magna were cultured in moderately hard water at 21C ambient temperature and 16:8 light:dark cycle.

extract_protocol:
Each sample consisted of three animals. Samples were placed in RNAlater Stabalization Solution and stored at -80C. RNA was extracted using Rneasy Plus Mini Kit according to manufacturer's instructions.
TruSeq RNA library prep kit v2

treatment_protocol: Treated Daphnia magna were exposed to 40 µM atrazine for 96 hours using DMSO as a solvent carrier.

value: whole organism

tag: age

value: 7 day old

value: No exposure

tag: development stage

value: adult


title: UT-1


title: Antler tip 2

city: Changchun

first: Yu

last: Zhao

address: No.1035 Boshuo Road, Jingyuetan tourism economic development district

institute: Changchun University of Chinese Medicine

description: growth

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence
smallRNA tag was mapped to miRBase database to detect miRNA
use a perl package named Comparison to find out the differentially expressed miRNA
predicted miRNA target mRNA by miRanda and targetscan
Genome_build: non
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample

organism: Cervus nippon

source_name: deer antler

growth_protocol: Antler tips of 4-year-old Chinese Sika deer at various time points during antler growth (15 d and 60 d)

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using the 2100 Bioanalyzer (Agilent Technologies) with RNA integrated number (RIN) values greater than or equal to 8
MiRNA-sequencing was performed by Nanjing Geneseeq Inc., Nanjing, China. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: Antler tips were cut into 1 mm3 pieces. All samples were immediately stored in liquid nitrogen after washing with PBS buffer.

value: antler tip

tag: Stage

value: 15 day


title: AT40-2

value: 96 hours of 40 µM atrazine exposure


title: AT40-4

value: 96 hours of 40 µM utrazine exposure


title: Antler tip 1

description: growth

value: 60 day


title: WT Vehicle Tibialis mRNA rep10

status: Public on Oct 29 2017

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 B.38, gene models version Ensembl R.75
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: Tibialis Muscle

tag: strain

value: Tibialis Muscle

value: Wild Type

value: 12 weeks

tag: Sex

value: female

value: Vehicle


title: WT Vehicle Tibialis mRNA rep8


title: WT Vehicle Tibialis mRNA rep5


title: WT Vehicle Tibialis mRNA rep6


title: WT Vehicle Tibialis mRNA rep9


title: WT Vehicle Tibialis mRNA rep4


title: WT Vehicle Tibialis mRNA rep1


title: E7_8wks_290

value: Whole Ear Skin


title: ChIPSeq WT CD4T -IL2 H3K4me3

source_name: CD4T H3K4me3 -IL2

tag: strain background

value: wild type

value: Spleen

value: pre-activated T cells

value: anti-H3K4me3 (Millipore)


title: WT Vehicle Tibialis mRNA rep7


title: WT Vehicle Quadriceps mRNA rep9

source_name: Quadriceps Muscle

value: Quadriceps Muscle


title: WT Vehicle Quadriceps mRNA rep10


title: WT Vehicle Quadriceps mRNA rep8


title: WT Vehicle Quadriceps mRNA rep7


title: WT Vehicle Tibialis mRNA rep3


title: WT Vehicle Quadriceps mRNA rep4


title: WT Vehicle Quadriceps mRNA rep5


title: WT Vehicle Quadriceps mRNA rep3


title: WT Vehicle Quadriceps mRNA rep2


title: WT Vehicle Quadriceps mRNA rep1


title: WT ActRIIB Tibialis mRNA rep10

value: ActRIIB decoy


title: WT ActRIIB Tibialis mRNA rep9


title: WT ActRIIB Tibialis mRNA rep6


title: WT ActRIIB Tibialis mRNA rep7


title: WT ActRIIB Tibialis mRNA rep8


title: WT ActRIIB Tibialis mRNA rep5


title: WT ActRIIB Tibialis mRNA rep4


title: WT ActRIIB Quadriceps mRNA rep9


title: WT ActRIIB Quadriceps mRNA rep6


title: WT ActRIIB Quadriceps mRNA rep7


title: WT ActRIIB Quadriceps mRNA rep5


title: WT ActRIIB Quadriceps mRNA rep10


title: WT ActRIIB Quadriceps mRNA rep4


title: WT ActRIIB Tibialis mRNA rep1


title: WT ActRIIB Quadriceps mRNA rep1


title: WT ActRIIB Quadriceps mRNA rep2


title: R6/2 Vehicle Tibialis mRNA rep9


title: R6/2 Vehicle Tibialis mRNA rep10


title: R6/2 Vehicle Tibialis mRNA rep8


title: R6/2 Vehicle Tibialis mRNA rep5


title: R6/2 Vehicle Tibialis mRNA rep3


title: R6/2 Vehicle Tibialis mRNA rep6


title: WT ActRIIB Quadriceps mRNA rep3


title: R6/2 Vehicle Tibialis mRNA rep2


title: R6/2 Vehicle Tibialis mRNA rep7


title: R6/2 Vehicle Tibialis mRNA rep4


title: WT ActRIIB Tibialis mRNA rep3


title: R6/2 Vehicle Tibialis mRNA rep1


title: WT ActRIIB Tibialis mRNA rep2


title: R6/2 Vehicle Quadriceps mRNA rep10


title: R6/2 Vehicle Quadriceps mRNA rep7


title: R6/2 Vehicle Quadriceps mRNA rep6


title: R6/2 Vehicle Quadriceps mRNA rep9


title: R6/2 Vehicle Quadriceps mRNA rep8


title: WT ActRIIB Quadriceps mRNA rep8


title: R6/2 Vehicle Quadriceps mRNA rep4


title: R6/2 Vehicle Quadriceps mRNA rep1


title: R6/2 ActRIIB Tibialis mRNA rep10


title: R6/2 ActRIIB Tibialis mRNA rep8


title: R6/2 ActRIIB Tibialis mRNA rep9


title: R6/2 Vehicle Quadriceps mRNA rep2


title: R6/2 Vehicle Quadriceps mRNA rep3


title: WT Vehicle Quadriceps mRNA rep6


title: R6/2 ActRIIB Tibialis mRNA rep6


title: R6/2 ActRIIB Tibialis mRNA rep5


title: R6/2 ActRIIB Tibialis mRNA rep3


title: R6/2 ActRIIB Tibialis mRNA rep1


title: R6/2 ActRIIB Tibialis mRNA rep4


title: R6/2 ActRIIB Quadriceps mRNA rep10


title: R6/2 ActRIIB Quadriceps mRNA rep8


title: R6/2 ActRIIB Quadriceps mRNA rep9


title: R6/2 ActRIIB Tibialis mRNA rep2


title: R6/2 ActRIIB Quadriceps mRNA rep6


title: R6/2 ActRIIB Quadriceps mRNA rep3


title: R6/2 ActRIIB Quadriceps mRNA rep2


title: R6/2 ActRIIB Quadriceps mRNA rep1


title: R6/2 ActRIIB Quadriceps mRNA rep5


title: R6/2 ActRIIB Quadriceps mRNA rep4


title: 10 mg/ml curcumin treatment _12h  : replicate 2

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
After demultiplexing, the data was mapped to the D. discoideum genome with bowtie version 1.0.0. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_rc.tab" contain raw expression values while files ending with "_nor.tab" contain normalized expression values.

organism: Dictyostelium discoideum

source_name: 10 ug/ml curcumin treatment  12h

growth_protocol: Wild-type strain (AX4) were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared  two sets of Illumina multiplexed libraries. We prepared 48 individual libraries separately and deveided two sets. In each set, we added a unique barcode to each library at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced one pool per lane of a flow cell on Illumina Genome Analyzer II (read length = 50 bases).

treatment_protocol: Cells were treated with curcumin at multiple concentrations (0, 2.5, 5.0, 7.5 and 10.0 µg/ml)  and samples at different time points (0, 4, 8 and 12 hour).

value: WT

tag: replicate

tag: treatment concentreation

value: 10 mg/ml

tag: different durations

value: 12 hr


title: R6/2 ActRIIB Tibialis mRNA rep7


title: R6/2 Vehicle Quadriceps mRNA rep5


title: 10 mg/ml curcumin treatment _8h  : replicate 2

source_name: 10 ug/ml curcumin treatment  8h

value: 8 hr


title: 10 mg/ml curcumin treatment _12h  : replicate 3


title: 10 mg/ml curcumin treatment _8h : replicate 1


title: 10 mg/ml curcumin treatment _12h : replicate 1


title: WT Vehicle Tibialis mRNA rep2


title: 10 mg/ml curcumin treatment _8h  : replicate 3


title: 10 mg/ml curcumin treatment _4h  : replicate 2

source_name: 10 ug/ml curcumin treatment  4h

value: 4 hr


title: R6/2 ActRIIB Quadriceps mRNA rep7


title: 7.5 mg/ml curcumin treatment _8h  : replicate 2

source_name: 7.5 ug/ml curcumin treatment  8h

value: 7.5 mg/ml


title: 7.5 mg/ml curcumin treatment _8h  : replicate 3


title: 7.5 mg/ml curcumin treatment _8h : replicate 1


title: 7.5 mg/ml curcumin treatment _4h : replicate 1

source_name: 7.5 ug/ml curcumin treatment  4h


title: 5 mg/ml curcumin treatment _12h  : replicate 3

source_name: 5 ug/ml curcumin treatment  12h

value: 5 mg/ml


title: 5 mg/ml curcumin treatment _12h  : replicate 2


title: 7.5 mg/ml curcumin treatment _12h : replicate 1

source_name: 7.5 ug/ml curcumin treatment  12h


title: 5 mg/ml curcumin treatment _12h : replicate 1


title: 7.5 mg/ml curcumin treatment _12h  : replicate 2


title: 7.5 mg/ml curcumin treatment _4h  : replicate 3


title: 5 mg/ml curcumin treatment _8h  : replicate 3

source_name: 5 ug/ml curcumin treatment  8h


title: 5 mg/ml curcumin treatment _8h  : replicate 2


title: 10 mg/ml curcumin treatment _4h : replicate 1


title: 5 mg/ml curcumin treatment _4h  : replicate 3

source_name: 5 ug/ml curcumin treatment  4h


title: 5 mg/ml curcumin treatment _4h  : replicate 2


title: 7.5 mg/ml curcumin treatment _4h  : replicate 2


title: 7.5 mg/ml curcumin treatment _12h  : replicate 3


title: 10 mg/ml curcumin treatment _4h  : replicate 3


title: 5 mg/ml curcumin treatment _8h : replicate 1


title: 5 mg/ml curcumin treatment _4h : replicate 1


title: 2.5 mg/ml curcumin treatment _12h  : replicate 3

source_name: 2.5 ug/ml curcumin treatment  12h

value: 2.5 mg/ml


title: 2.5 mg/ml curcumin treatment _12h  : replicate 2


title: 2.5 mg/ml curcumin treatment _12h : replicate 1


title: 2.5 mg/ml curcumin treatment _8h  : replicate 2

source_name: 2.5 ug/ml curcumin treatment  8h


title: 2.5 mg/ml curcumin treatment _8h : replicate 1


title: 2.5 mg/ml curcumin treatment _8h  : replicate 3


title: 2.5 mg/ml curcumin treatment _4h  : replicate 2

source_name: 2.5 ug/ml curcumin treatment  4h


title: cyt.10.4_S12

first: Raghavendra

last: Mirmira

state: IN

address: 635 Barnhill Drive

department: Biochemistry

institute: Indiana University School of Medicine

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control.
Then all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner  with the following parameter: “--outSAMmapqUnique 60”.
The reads distribution across the genome was assessed using bamutils (from ngsutils).
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread)  with the following parameters: “–p –Q 10”.
Genes with read count per million (CPM) < 0.5 in more than 3 of the samples were removed. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using DESeq2. P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: Pancreatic islets

growth_protocol: Mouse islets were isolated from collagenase-perfused pancreata

extract_protocol:
and/or with ML351 for 24hrs.
Dual-indexed nonstranded cDNA libraries were prepared using SMARTSeq v4 Ultra Low input RNA Kit (Clontech)

treatment_protocol: Islets were treated with a cytokine cocktail containing 5 ng/ml IL-1β, 10 ng/ml TNF-α, and 100 ng/ml IFN-γ and/or mL351 for 24 hours

tag: agent

value: cytokines+mL351 10uM


title: 2.5 mg/ml curcumin treatment _4h  : replicate 3


title: 2.5 mg/ml curcumin treatment _4h : replicate 1


title: 0 mg/ml curcumin treatment _12h  : replicate 2

source_name: 0 ug/ml curcumin treatment  12h

value: 0 mg/ml


title: cyt.10.1_S10


title: cyt.10.2_S11


title: cyt.4_S9

value: cytokines


title: 0 mg/ml curcumin treatment _8h  : replicate 3

source_name: 0 ug/ml curcumin treatment  8h


title: cyt.3_S8


title: 0 mg/ml curcumin treatment _12h : replicate 1


title: 0 mg/ml curcumin treatment _12h  : replicate 3


title: 10uM.3_S6


title: 0 mg/ml curcumin treatment _4h  : replicate 3

source_name: 0 ug/ml curcumin treatment  4h


title: 0 mg/ml curcumin treatment _8h : replicate 1


title: cyt.1_S7


title: 0 mg/ml curcumin treatment _8h  : replicate 2


title: 10uM.2_S5


title: 0 mg/ml curcumin treatment _4h  : replicate 2


title: 10uM.1_S4


title: 0 mg/ml curcumin treatment _0h  : replicate 3

source_name: 0 ug/ml curcumin treatment  0h

value: 0 hr


title: NT.2_S2

value: Vehicle


title: NT.4_S3


title: NT.1_S1


title: 0 mg/ml curcumin treatment _0h  : replicate 2


title: A549.1735.2

status: Public on Oct 28 2017

description: microRNAs

data_processing:
miRNA sequencing short reads were aligned to human reference genome (GRCh38) using Bowtie2 (v2.2.3) ;
Aligned sequences were mapped to mature miRNAs with annotation from miRBase (v.21);
The relative expression abundances of miRNAs were calculated as Count-Per-Million (CPM).
Supplementary_files_format_and_content: CPM

source_name: Lung epithelial cells

growth_protocol: A549 cells were plated in T-25 flask at 2x106 density and cultivated in Dulbecco's minimal essential medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL penicillin and 100 mg/mL streptomycin at 37°C in 5% CO2 overnight. Then, cells were washed 3 times with PBS and cultured in DMEM media supplemented with 10% exosome-depleted FBS (System Biosciences, Inc. (SBI), Palo Alto, CA) for 48 hours

tag: cell type

value: Carcinoma cells

tag: cellular portion

value: Exosomes

tag: passages


title: 0 mg/ml curcumin treatment _0h : replicate 1


title: 0 mg/ml curcumin treatment _4h : replicate 1


title: A549.1735.1

description: microRNAs


title: A549.Scrb.4

description: microRNAs


title: A549.Scrb.2

description: microRNAs


title: A549.Scrb.3

description: microRNAs


title: A549.1735.3

description: microRNAs


title: A549.1735.4

description: microRNAs


title: A549.Scrb.1

description: microRNAs


title: HK-2 AGO2-PAR-CLIP CsA2

city: Boston

first: Christopher

middle: J

last: Benway

state: MA

address: 300 Longwood Ave, Enders 510

department: Nephrology

institute: Children's Hospital

data_processing:
Library strategy: PAR-CLIP
Base-calling and de-multiplexing were completed using CASAVA-1.8.2 software.
Reads were pre-processed by adapter clipping with the package 'cutadapt.' miRNA-seq reads were filtered by size (greater than 16 nt).
Alignment of miRNA reads to the hg19 reference genome was performed using Bowtie. Counts of reads mapping to mature miRNAs was obtained using HTSeq and GFF data obtained from miRBase (v 21). mRNA reads were aligned using TopHat and counted using HTSeq with a hg19 GTF reference based on UCSC gene exons obtained from Illumina iGenomes. DESeq2 was used to compute differential expression.
PAR-CLIP reads greater than 13 nt were aligned with Bowtie to the hg19 reference genome, allowing for 2 mismatches. AGO bound clusters of sequences were identified using the PIPE-CLIP bioinformatics pipeline. Crosslinking clutsters are defined as enriched clusters (p value < 0.05). containing reliable T>C crossliinking mutations (p value < 0.05)/
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq count matrices indicate the read counts aligned to mRNAs of miRNAs. DESeq2 output files indicate the calculated log2 fold change in expression and adjusted p-values. PAR-CLIP files contain, in BED format, the crosslinking sites determined by PIPE-CLIP analysis, including PeakScore and Annotation of the genes which are identified.

source_name: human kidney proximal tubular cell line

growth_protocol: Human kidney proximal tubular epithelial cells (HK-2, ATCC) were grown in Keratinocyte-SFM supplemented with 5 ng/ml Epidermal Growth Factor 1-53 (EGF 1-53) and 0.05 mg/ml Bovine Pituitary Extract (BPE). Cells were maintained in 15 cm dishes until ~80% confluency.

extract_protocol:
Total RNAs were isolated from cells grown in 15 cm culture dishes using miRNeasy Kit (Qiagen) according to manufacturer's instructions. Small RNAs, including miRNAs, were isolated using the manufacturer's enrichment protocol. The larger RNA fraction (>200 nt) was enriched for mRNAs using NEBNext Poly(A)mRNA Magnetic Isolation Module (New England Biolabs). For PAR-CLIP, crosslinked cells were resuspended in NP40 lysis buffer and incubated on ice for 10 minutes. The lysates were cleared by centrifugation and syringe filter. RNAs in the cleared lysate were partially degraded by treatment with RNAse T1 for 15 minutes at 22°C followed by 5 minutes on ice. Immunoprecipitation of target Argonaute (AGO) protein was accomplished using antibody-bound Dynabeads Protein G magnetic particles (Thermo Fisher) for 2 hours in lysis buffer (lower salt concentration than IP buffer) at 4°C. The complete RNA isolation protocol was completed as described by Hafner et. al, 2010 (PMCID: PMC4180672).
mRNAs and miRNA libraries were constructed using NEBnext Multiplex Small RNA and mRNA Library Prep Sets for Illumina (New England Biolabs). PAR-CLIP cDNA libraries were constructed from recovered RNA by sequentially ligating a preadenylated 3'-adapter using T4 Rnl2(1-249)K227Q ligase (New England Biolabs) and an RNA 5'-adapter using T4 RNA ligase. Adapters are designed to be compatible with Illumina Small RNA library and sequencing protocols. After PCR amplification the libraries were size fractionated by agarose gel electrophoresis.

treatment_protocol: 24 hours prior to crosslinking, cells were treated with 5 ug/mL cyclosporine A (CsA, Sigma-Aldrich) or vehicle control (0.1% ethanol). ~16-18 hours prior to crosslinking, cells were treated with 100 uM 4-thiouridine (4-SU, Sigma-Aldrich). For UV crosslinking, attached cells were rinsed once with ice-cold PBS. PBS was removed completely and cells were irradiated on ice with 365 nm UV light (0.15 J/cm2) in a Stratalinker 2400 (Stratagene). Cells were scraped off in 1 ml PBS per plate and collected by centrifugation at 500 × g for 5 min. For mRNA-seq and miRNA-seq cells were treated with 5 ug/mL CsA or vehicle control (0.1% ethanol) for 48 hours.

tag: cell line

tag: crosslinker and crosslinked wavelength

tag: par-clip antibody

value: anti-AGO2 (Cell Signaling C34C6, #2897)


title: PostWL Subject 1

city: New York

first: Yupu

last: Liang

address: 1230 York Avenue

institute: The Rockefeller University

description:
Human abdominal adipose tissue
Sample name: 01B

data_processing:
Aligning the input reads to reference genome using STAR
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genome_build: hg19
Supplementary_files_format_and_content: text file summarizing count information of gene presented after aligning samples to the reference genome, normalized by DESeq2

extract_protocol:
RNEasy Lipid Mini Kit
NY Genome Center

treatment_protocol: Diet-Induced Weight Loss

tag: subject id

tag: timepoint

value: PostWL

tag: tissue

value: Subcutaneous adipose

tag: tissue source

value: Modified liposuction aspirate

tag: tissue preparation

value: Rinsed with saline, snap frozen

value: female


title: PreWL Subject 3

description:
Human abdominal adipose tissue
Sample name: 03A

value: PreWL

tag: Sex


title: PreWL Subject 11

description:
Human abdominal adipose tissue
Sample name: 11A


title: HK-2 AGO2-PAR-CLIP Veh1


title: HK-2 AGO2-PAR-CLIP Veh2


title: PostWL Subject 3

description:
Human abdominal adipose tissue
Sample name: 03B


title: HK-2 miRNA CsA4

data_processing:
Base-calling and de-multiplexing were completed using CASAVA-1.8.2 software.
Reads were pre-processed by adapter clipping with the package 'cutadapt.' miRNA-seq reads were filtered by size (greater than 16 nt).
Alignment of miRNA reads to the hg19 reference genome was performed using Bowtie. Counts of reads mapping to mature miRNAs was obtained using HTSeq and GFF data obtained from miRBase (v 21). mRNA reads were aligned using TopHat and counted using HTSeq with a hg19 GTF reference based on UCSC gene exons obtained from Illumina iGenomes. DESeq2 was used to compute differential expression.
PAR-CLIP reads greater than 13 nt were aligned with Bowtie to the hg19 reference genome, allowing for 2 mismatches. AGO bound clusters of sequences were identified using the PIPE-CLIP bioinformatics pipeline. Crosslinking clutsters are defined as enriched clusters (p value < 0.05). containing reliable T>C crossliinking mutations (p value < 0.05)/
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq count matrices indicate the read counts aligned to mRNAs of miRNAs. DESeq2 output files indicate the calculated log2 fold change in expression and adjusted p-values. PAR-CLIP files contain, in BED format, the crosslinking sites determined by PIPE-CLIP analysis, including PeakScore and Annotation of the genes which are identified.


title: PreWL Subject 9

description:
Human abdominal adipose tissue
Sample name: 09A


title: HK-2 miRNA CsA3


title: HK-2 miRNA CsA2


title: PreWL Subject 4

description:
Human abdominal adipose tissue
Sample name: 04A


title: PostWL Subject 2

description:
Human abdominal adipose tissue
Sample name: 02B


title: HK-2 miRNA CsA1


title: Toddler mutant 7 hpf

city: Salt Lake City

first: James

middle: A

last: Gagnon

state: UT

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

institute: University of Utah

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

organism: Danio rerio

source_name: Whole embryos (n=50)

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

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

tag: developmental stage

value: 7 hpf

tag: genotype

value: Toddler mutant

value: Whole embryo


title: Wild type 7 hpf

value: wild type


title: PreWL Subject 12

description:
Human abdominal adipose tissue
Sample name: 12A


title: HK-2 PAN-AGO-PAR-CLIP

value: Anti-pan Ago (Millipore 2A8, MABE56)


title: Toddler mutant 6 hpf

value: 6 hpf