title: BRG1-mES-ChIPseq

status: Public on Oct 19 2018

description: ChIP-seq of BRG1 from v6.5 mESCs

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for BRD9, BRG1 and ARID1A were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background. For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

source_name: v6.5 mESCs

growth_protocol: v6.5 mouse or Arid1af/f:CreERT2 ESCs were cultured in Knockout™ DMEM (Thermo Fisher Sci #10829018) supplemented with 15% ESC-Sure FBS serum (Applied Stem Cell #ASM-5007) and Knockout™ Serum Replacement (Thermo Fisher Sci #10828028), 2 mM L-glutamine (Gibco #35050061), 10 mM HEPES (Gibco #15630080), 1 mM sodium pyruvate (Gibco #11360070), 100 U/mL penicillin/streptomycin (Gibco #15140122), 0.1 mM non-essential amino acids (Gibco #11140050), 0.1 mM beta-mercaptoethanol (Gibco 21985023) and leukemia inhibitory factor (LIF). ESCs were maintained on gamma-irradiated mouse embryonic fibroblast (MEF) feeders at 37°C, 5% CO2 with daily media changes and passaged every other day.

extract_protocol:
RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research). For ChIP-Seq, ~20E6 v6.5 mouse ESCs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against BRG1, BRD9 and ARID1A bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions. RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.

treatment_protocol: For RNA-seq, v6.5 mouse ESCs were transduced in suspension with shcontrol or shBrd9 virus for 1-2 hours with 5 µg/mL of Polybrene then plated onto MEF feeders for incubation with the virus overnight. RNA was collected four days post-puromycin (1 µg/mL) selection.  For RNA-seq, Arid1af/f:CreERT2 ESCs were treated with either ethanol or 1 µM 4-hydroxytamoxifen for 24 hours then passaged. RNA was collected 72 hours after treatment. For RNA-seq, v6.5 mESCs were treated with either DMSO or 10 µM I-BRD9 and RNA was collected either 24 or 48 hours after treatment. For ChIP-seq, v6.5 mESCs were treated with either DMSO or 3 µM I-BRD9 for 6 or 24 hours or 500 nM JQ1 for 24 hours.


title: Input-for-BRG1-mES-ChIPseq

type: SRA

city: San Diego

first: Diana

middle: C.

last: Hargreaves

state: CA

address: 10010 North Torrey Pines Road

country: USA

institute: The Salk Institute for Biological Studies

description: Input for BRG1 ChIP-seq from v6.5 mESCs

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: treatment

tag: shRNA

tag: antibody source


title: Arid1aff-Tam-replicate2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of tamoxifen treated Arid1af/f:CreERT2 ESCs replicate 2
Arid1afpkm.txt.gz
processed data file sample name: 1_TAM_2

library_source: transcriptomic

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5) for RNA-seq and ChIP-seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for BRD9, BRG1, ARID1A and BRD4 were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background. For RNA-Seq, Reads Per Kilobase of exon per million mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph file Columns: (1) chrom (2) chromStart (3) chromEnd (4) dataValue. FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

molecule: polyA RNA

source_name: Arid1af/f:CreERT2 mESCs

extract_protocol:
RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
RNA-Seq libraries were prepared using either Illumina TruSeq RNA Library Prep Kit v2 or Illumina TruSeq Stranded mRNA Kit following the manufacturer's instructions.

treatment_protocol: For RNA-seq, v6.5 mouse ESCs were transduced in suspension with shcontrol or shBrd9 virus for 1-2 hours with 5 µg/mL of Polybrene then plated onto MEF feeders for incubation with the virus overnight. RNA was collected four days post-puromycin (1 µg/mL) selection.  For RNA-seq, Arid1af/f:CreERT2 ESCs were treated with either ethanol or 1 µM 4-hydroxytamoxifen for 24 hours then passaged. RNA was collected 72 hours after treatment. For RNA-seq, v6.5 mESCs were treated with either DMSO or 10 µM I-BRD9 and RNA was collected either 24 or 48 hours after treatment.

tag: cell type

value: mESC

tag: genotype


title: BRD9-24hr-JQ1-Experiment1-ChIPseq

description: ChIP-seq of BRD9 from v6.5 mESCs treated with 500 nM JQ1 for 24 hours

value: Active Motif 61537


title: BRD4-mES-ChIPseq

description: ChIP-seq of BRD4 from v6.5 mESCs

extract_protocol:
For ChIP-Seq, ~20E6 v6.5 mouse ESCs were collected and cross-linked first in 3mM disuccinimidyl glutarate (DSG) then in 1% formaldehyde. After quenching the excess formaldehyde with 125 mM glycine, the fixed cells were washed, pelleted and flash-frozen. Upon thawing, the cells were resuspended in lysis solution (50 mM HEPES-KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100 and incubated on ice for ten minutes. The isolated nuclei were washed with wash solution (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8) then sheared in a Covaris E229 sonicator for 10-20 minutes to generate DNA fragments between ~ 200-1000 bp. After clarification of insoluble material by centrifugation, the chromatin was immunoprecipitated overnight at 4C with antibodies against BRG1, BRD9 and ARID1A bound to Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM HEPES-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS). Antibody bound DNA were washed and treated with Proteinase K and RNase A and the purified ChIP DNA was used for library generation for subsequent sequencing.
ChIP-Seq libraries were generated using the NuGen Ovation Ultralow Library System V2 following the manufacturer's instructions.

treatment_protocol: For ChIP-seq, v6.5 mESCs were treated with either DMSO or 3 µM I-BRD9 for 6 or 24 hours or 500 nM JQ1 for 24 hours.

tag: cell line

value: Bethyl A301-985A


title: Input-mES-replicate1-ChIPseq

description: Input ChIP-seq replicate 1


title: Input-IBRD9-Experiment2-ChIPseq

description: Input ChIP-seq I-BRD9 24 hr, experiment 2

value: 3 uM I-BRD9-2, 24 hours


title: ARID1A-mES-replicate2-ChIPseq

description: ChIP-seq of ARID1A from v6.5 mESCs replicate 2

value: Santa Cruz sc-32761


title: DC.8an103n.PP.4

status: Public on Nov 03 2018

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: CD8- Dendritic Cell

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

molecule: total RNA

source_name: Peyer's Patch

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: strain

tag: age

value: 7 weeks old

tag: sorting markers

value: Dendritic Cell


title: ARID1A-mES-replicate1-ChIPseq

description: ChIP-seq of ARID1A from v6.5 mESCs replicate 1


title: Input-IBRD9-Experiment3-ChIPseq

description: Input ChIP-seq I-BRD9 24 hr, experiment 3

value: 3 uM I-BRD9-3, 24 hours


title: Input-DMSO-Experiment2-ChIPseq

description: Input ChIP-seq DMSO, experiment 2

value: DMSO-2, 24 hours


title: BRG1-IBRD9-Experiment3-ChIPseq

description: ChIP-seq of BRG1 from 24 hr I-BRD9-treated v6.5 mESCs, experiment 3


title: BRD4-DMSO-Experimet2-ChIPseq

description: ChIP-seq of BRD4 from DMSO-treated v6.5 mESCs, experiment 2


title: BRG1-DMSO-Experiment3-ChIPseq

description: ChIP-seq of BRG1 from DMSO-treated v6.5 mESCs, experiment 3

value: DMSO-3, 24 hours


title: Input-DMSO-Experiment3-ChIPseq

description: Input ChIP-seq DMSO, experiment 3


title: BRD4-IBRD9-Experiment2-ChIPseq

description: ChIP-seq of BRD4 from 24 hr I-BRD9-treated v6.5 mESCs, experiment 2


title: Input-mES-replicate2-ChIPseq

description: Input ChIP-seq replicate 2


title: Input-for-BRD4-mES-ChIPseq

description: Input ChIP-seq from v6.5 mESCs


title: Input-24hr-JQ1-Experiment1-ChIPseq

description: Input from v6.5 mESCs treated with 500 nM JQ1 for 24 hours


title: 48hrIBRD9-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 48 hr I-BRD9 treated v6.5 mESCs replicate 2
48hr-IBRD9-fpkm.txt.gz
processed data file sample name: 48iB10_Rep2

value: I-BRD9 for 48 hours


title: Arid1aff-EtOH-replicate2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of ethanol treated Arid1af/f:CreERT2 ESCs replicate 2
Arid1afpkm.txt.gz
processed data file sample name: 1_EtOH_2

value: ethanol


title: 48hrDMSO-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 48 hr DMSO treated v6.5 mESCs replicate 2
48hr-IBRD9-fpkm.txt.gz
processed data file sample name: 48DMSO_Rep2

value: DMSO for 48 hours


title: 24hrIBRD9-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 24 hr I-BRD9 treated v6.5 mESCs replicate 1
24hr-IBRD9-fpkm.txt.gz
processed data file sample name: 24iB10_Rep2

value: I-BRD9 for 24 hours


title: 24hrIBRD9-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 24 hr I-BRD9 treated v6.5 mESCs replicate 2
24hr-IBRD9-fpkm.txt.gz
processed data file sample name: 24iB10_Rep1


title: Arid1aff-Tam-replicate1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of tamoxifen treated Arid1af/f:CreERT2 ESCs replicate 1
Arid1afpkm.txt.gz
processed data file sample name: 1_TAM_1


title: 48hrDMSO-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 48 hr DMSO treated v6.5 mESCs replicate 1
48hr-IBRD9-fpkm.txt.gz
processed data file sample name: 48DMSO_Rep1


title: Arid1aff-EtOH-replicate1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of ethanol treated Arid1af/f:CreERT2 ESCs replicate 1
Arid1afpkm.txt.gz
processed data file sample name: 1_EtOH_1


title: 24hrDMSO-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 24 hr DMSO treated v6.5 mESCs replicate 1
24hr-IBRD9-fpkm.txt.gz
processed data file sample name: 24DMSO_Rep1

value: DMSO for 24 hours


title: shBrd9-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of shBrd9 treated v6.5 mESCs replicate 2
shRNAfpkm.txt.gz
processed data file sample name: shbrd9_mef_rep2

value: shRNA Brd9 pooled


title: shcontrol-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of shcontrol treated v6.5 mESCs replicate 2
shRNAfpkm.txt.gz
processed data file sample name: shcontrol_mef_rep2

value: shRNA scrambled control


title: shcontrol-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of shcontrol treated v6.5 mESCs replicate 1
shRNAfpkm.txt.gz
processed data file sample name: shcontrol_mef_rep1

value: mESC


title: BRD9-6hr-IBRD9-Experiment1-ChIPseq

description: ChIP-seq of BRD9 from 6hr I-BRD9-treated v6.5 mESCs

value: I-BRD9 for six hours

value: Active Motif 61537


title: Input-DMSO-Experiment1-ChIPseq

description: Input ChIP-seq DMSO

value: DMSO


title: Input-6hr-IBRD9-Experiment1-ChIPseq

description: Input ChIP-seq 6hr I-BRD9


title: BRD9-24hr-IBRD9-Experiment1-ChIPseq

description: ChIP-seq of BRD9 from 24hr I-BRD9-treated v6.5 mESCs


title: Lane 2 RPI26

status: Public on Oct 10 2018

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

description: AR scRNAseq transcript counts.csv

data_processing:
Basecalls performed using CASAVA version 1.4
Unique molecular identifiers (UMIs) and sample barcodes were extracted from the first read of each read pair using a custom R script. The second read of each read pair were aligned to the AGPv4 genome assembly using HiSat2
The number of UMIs for each gene and each sample were counted, allowing for a 1 bp mismatch in UMIs to avoid over-counting artifacts resulting from sequencing errors
Genome_build: AgpV4
Supplementary_files_format_and_content: csv file containing transcript counts for each each gene and split-cell sample

organism: Zea mays

source_name: Isolated maize male germinal cell

growth_protocol: Maize (Zea mays) inbred line W23 bz2 was grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle

extract_protocol:
Maize anthers were dissected and placed in protoplasting enzymes. Released archesporial (AR) cell and pollen mother cell (PMC) protoplasts were then recognized by their large size, picked up manually using blunted syringe needles, and placed on the cap of an 8-tube PCR strip.
Library protocol based on CelSeq2, modified to allow for split-cell technical replicates. Read 1 contains a 10 bp unique molecular identifier (UMI) followed by a 6-7 bp sample barcode. Read 2 contains transcript sequence.

tag: tissue

value: anther


title: 24hrDMSO-rep2-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 24 hr DMSO treated v6.5 mESCs replicate 2
24hr-IBRD9-fpkm.txt.gz
processed data file sample name: 24DMSO_Rep2


title: Lane 2 RPI24

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI18

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI28

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI20

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI23

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI19

description: AR scRNAseq transcript counts.csv


title: 48hrIBRD9-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of 48 hr I-BRD9 treated v6.5 mESCs replicate 1
48hr-IBRD9-fpkm.txt.gz
processed data file sample name: 48iB10_Rep1


title: Lane 2 RPI29

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI21

description: AR scRNAseq transcript counts.csv


title: BRD9-DMSO-Experiment1-ChIPseq

description: ChIP-seq of BRD9 from DMSO-treated v6.5 mESCs


title: Lane 2 RPI17

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI14

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI13

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI15

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI22

description: AR scRNAseq transcript counts.csv


title: shBrd9-rep1-RNAseq

description:
strand specific polyA+ RNA
RNA-seq of shBrd9 treated v6.5 mESCs replicate 1
shRNAfpkm.txt.gz
processed data file sample name: shbrd9_mef_rep1


title: Lane 2 RPI12

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI11

description: AR scRNAseq transcript counts.csv


title: Input-24hr-IBRD9-Experiment1-ChIPseq

description: Input ChIP-seq 24hr I-BRD9


title: Lane 2 RPI10

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI27

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI9

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI8

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI5

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI6

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI7

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI4

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI2

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI29

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI28

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI1

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI3

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI26

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI24

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI19

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI20

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI18

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI21

description: AR scRNAseq transcript counts.csv


title: Lane 2 RPI16

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI22

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI16

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI13

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI27

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI12

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI11

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI23

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI10

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI8

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI15

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI5

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI7

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI6

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI3

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI4

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI17

description: AR scRNAseq transcript counts.csv


title: Lane 1 RPI2

description: AR scRNAseq transcript counts.csv


title: Sample4-RNAseq-ARID1AffTam2

status: Public on Jul 27 2018

description: RNA-seq of tamoxifen treated Arid1af/f:CreERT2 ESCs replicate 2

data_processing:
Basecalls performed using RTA (Illumina)
Fastq files were evaluated for quality using FastQC and trimmed using Trimmomatic.
Trimmed sequences were mapped to the mm10 reference genome using HISAT2 in single-end mode with default parameters.
Average counts per million (cpm) was calculated for each sample condition using custom R scripts, and differentially expressed genes were identified using the edgeR package in Bioconductor. A false discovery threshold of 0.05 was imposed using the toptags function of edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains the output from edgeR including mean counts per million for both treatments, fold changes for the knockout vs. control, and FDR-adjusted p-values.

growth_protocol: Arid1af/f:CreERT2 ESCs were cultured in Knockout™ DMEM (Thermo Fisher Sci #10829018) supplemented with 15% ESC-Sure FBS serum (Applied Stem Cell #ASM-5007) and Knockout™ Serum Replacement (Thermo Fisher Sci #10828028), 2 mM L-glutamine (Gibco #35050061), 10 mM HEPES (Gibco #15630080), 1 mM sodium pyruvate (Gibco #11360070), 100 U/mL penicillin/streptomycin (Gibco #15140122), 0.1 mM non-essential amino acids (Gibco #11140050), 0.1 mM beta-mercaptoethanol (Gibco 21985023) and leukemia inhibitory factor (LIF). ESCs were maintained on gamma-irradiated mouse embryonic fibroblast (MEF) feeders at 37°C, 5% CO2 with daily media changes and passaged every other day.

treatment_protocol: For RNA-seq, Arid1af/f:CreERT2 ESCs were treated with either ethanol or 1 µM 4-hydroxytamoxifen for 24 hours then passaged. RNA was collected 72 hours after treatment.

value: embryonic stem cells (ESCs)


title: Lane 1 RPI1

description: AR scRNAseq transcript counts.csv


title: Sample3-RNAseq-ARID1AffTam1

description: RNA-seq of tamoxifen treated Arid1af/f:CreERT2 ESCs replicate 1


title: Sample2-RNAseq-ARID1AffEtoh2

description: RNA-seq of ethanol treated Arid1af/f:CreERT2 ESCs replicate 2


title: Lane 1 RPI14

description: AR scRNAseq transcript counts.csv


title: Sample1-RNAseq-ARID1AffEtoh1

description: RNA-seq of ethanol treated Arid1af/f:CreERT2 ESCs replicate 1


title: Utricle_WT_4

status: Public on Jun 28 2018

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

data_processing:
STAR v2.5.2a aligner was used to map reads to the GRCm38.v11 release of mouse genome (GENCODE).
Transcripts were quantified using the STAR v2.5.2a aligner and the --quantMode GeneCounts parameter.
Gene level counts were filtered to remove genes that had lower than 5 counts in all compared samples.
Differential gene expression was evaluated using the DESeq2 tool.
Genome_build: GRCm38.p4 Release M11
Supplementary_files_format_and_content: Tab-delimited text file includes DESeq2-normalized counts for all samples, and tab-delimited text file of raw counts for each sample.

source_name: utricle

extract_protocol:
Utricles were dissected from the rest of the inner ear, and RNA was harvested using the RNeasy Micro Kit (Qiagen). RNA was pooled from 7–9 mice to obtain a single sample.
200-300 ng of total RNA were reverse transcribed using SuperScript IV reverse transcriptase (Thermo Fisher Scientific), oligo dT primer, and template switching oligo. Second strand cDNA was amplified using LongAmp DNA polymerase (New England BioLabs) for 12 PCR cycles, and purified on SPRI Select Beads (Beckman Coulter). The size distribution and concentration of second strand cDNA was evaluated on a Fragment Analyzer instrument using High Sensitivity Large Fragment Analysis Kit (Advanced Analytical). 125 pg of second strand cDNA was tagmented, PCR amplified, and indexed using the Nextera XT Library Prep Kit (Illumina). Following AMPure XP Bead purification (Beckman Coulter), the size distribution and concentration of cDNA Libraries were evaluated on a Fragment Analyzer instrument using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical). All libraries were normalized, pooled and sequenced in a HiSeq1500 instrument (126x126 paired end mode).

tag: organ

value: utricle

value: embryonic day E15.6

value: wild-type


title: WTcon3

source_name: organ of Corti culture

growth_protocol: Organs of Corti were dissected from P0 mice and placed on Matrigel-coated transwell plates (Corning). Organ cultures were maintained in neurobasal-A medium supplemented with B-27, N-2, 0.5 mM L-glutamine (all from Thermo Fisher Scientific), and 100 U/mL penicillin (Sigma).

extract_protocol:
The RNeasy Micro Kit (Qiagen) was used for the isolation of RNA from organ of Corti cultures. RNA was pooled from 6–8 organ of Corti cultures to obtain a single sample.
200-300 ng of total RNA were reverse transcribed using SuperScript IV reverse transcriptase (Thermo Fisher Scientific), oligo dT primer, and template switching oligo. Second strand cDNA was amplified using LongAmp DNA polymerase (New England BioLabs) for 12 PCR cycles, and purified on SPRI Select Beads (Beckman Coulter). The size distribution and concentration of second strand cDNA was evaluated on a Fragment Analyzer instrument using High Sensitivity Large Fragment Analysis Kit (Advanced Analytical). 125 pg of second strand cDNA was tagmented, PCR amplified, and indexed using the Nextera XT Library Prep Kit (Illumina). Following AMPure XP Bead purification (Beckman Coulter), the size distribution and concentration of cDNA Libraries were evaluated on a Fragment Analyzer instrument using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical). All libraries were normalized, pooled and sequenced in a HiSeq1500 instrument (126x126 paired end mode).

treatment_protocol: Organs of Corti were incubated with 2 nM FK228 (APExBIO) or solvent only (0.1% DMSO) from day in vitro (DIV)1 to DIV1.5 and from DIV3 to DIV3.5. RNA was isolated from these cultures at DIV3.5.

value: organ of Corti

tag: age of mice

value: postnatal day 0

tag: compound exposure

value: solvent only (0.1% DMSO)

tag: duration of exposure

value: day in vitro (DIV)1-1.5 and DIV3-3.5

tag: duration of culture

value: 3.5 days


title: Utricle_WT_1

value: embryonic day E15.5


title: Utricle_KO_3


title: WTFK2


title: WTFK1


title: Utricle_KO_2


title: WTcon4


title: Utricle_KO_1


title: Utricle_KO_4


title: R4FK4


title: WTcon2


title: WTcon1


title: R4FK3


title: R4FK5


title: R4FK2


title: WTFK4


title: Utricle_WT_2


title: Utricle_WT_3


title: R4con5


title: R4con4


title: R4con2


title: Lane 1 RPI9

description: AR scRNAseq transcript counts.csv


title: R4con1


title: WTFK7


title: Cortex_WT_3

source_name: neocortex

extract_protocol:
The neocortex of 3 WT and 3 Rest(+/deltaExon4) mice (E15.5) was dissected from the rest of the brain, and RNA was isolated from the dissected tissue using Trizol Reagent (Thermo Fisher Scientific). RNA was further purified on the separation column of the RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions.
200-300 ng of total RNA were reverse transcribed using SuperScript IV reverse transcriptase (Thermo Fisher Scientific), oligo dT primer, and template switching oligo. Second strand cDNA was amplified using LongAmp DNA polymerase (New England BioLabs) for 12 PCR cycles, and purified on SPRI Select Beads (Beckman Coulter). The size distribution and concentration of second strand cDNA was evaluated on a Fragment Analyzer instrument using High Sensitivity Large Fragment Analysis Kit (Advanced Analytical). 125 pg of second strand cDNA was tagmented, PCR amplified, and indexed using the Nextera XT Library Prep Kit (Illumina). Following AMPure XP Bead purification (Beckman Coulter), the size distribution and concentration of cDNA Libraries were evaluated on a Fragment Analyzer instrument using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical). All libraries were normalized, pooled and sequenced in a HiSeq1500 instrument (126x126 paired end mode).

value: neocortex


title: Cortex_KO_2


title: Cortex_WT_2


title: Cortex_KO_1


title: Cortex_KO_3


title: SKF2

status: Public on Feb 22 2018

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

description:
processed data file: GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: SKF2-30489506 and SKF2-30694684

data_processing:
Raw Illumina files were processed by Genotypic Technology Ltd. (Bangalore, India) for read mapping and the identification of differentially expressed transcripts. Raw data were downloaded and processed by GT proprietary tool for adapters and low quality bases trimming towards 3'-end.
Biological replicates were pooled together to generate a reference transcriptome using Trinity (Grabherr et al., 2011) using all default parameters with a k-mer of 25. Once assembled, the sequences were clustered based on similarity between sequences with CD-Hit v4.5.4 (Niu et al., 2010) using the following parameters: 95 % coverage and 90 % identity, -r 1, and others the default setting. The longest sequences for each cluster was used as the representative sequence. The clustered transcripts with ≥ 300 bp in length were considered for the analysis.
DESeq was used for differential gene exppression (DGE) analysis After the variance calculation for each gene, DGE is calculated by negative binomial distribution. Once the DGE is calculated, results are separated as up regulated, down regulated and neutral based on log2 fold change. Once the DGE was calculated, results were separated as up-regulated and down-regulated based on a |log2| > 0.5 cut off. A false discovery rate (FDR) at 5 % was used for multiple hypothesis testing.
Genome_build: The transcripts were annotated using the Basic Local Alignment Search Tool (BLAST+2.2.29) (E-value < 1.0e-4) using Chordata protein sequences from the Uniprot database (Altschul et al., 1990). The remaining unannotated transcripts were further annotated using Pfam database. The file Unigenes.fasta contains transcript sequence.
Supplementary_files_format_and_content: DGE analysis output; a FASTA file with the unigene transcript sequences is available on the series record.

organism: Carassius auratus

source_name: Primary hypothalamic and telencephalic radial glial cell culture_SKF

growth_protocol: The hypothalamus and telencephalon were dissection from adult female goldfish and rinsed twice with Hanks Balanced Salt with Antibiotic-Antimycotic solution and minced into small explants. Radial glial cells were dissociated with 0.25 % trypsin and cultured in Leibovitz’s L-15 medium with 15 % Fetal Bovine Serum and Antibiotic-Antimycotic. Cell culture medium was changed 4–7 days after isolation and then once a week thereafter. Radial glial cells were subcultured by trypsinization (0.125 %) for 3 passages, and then were used for experimentation.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen) including an on-column DNase treatment to remove genomic DNA. The concentration of total RNA was determined using the Qubit RNA Assay Kit (Life Technologies). In order to evaluate the quality of the total RNA, RNA integrity number (RIN) was assessed using Agilent RNA 600 Nano Reagents and RNA Nano Chips in Agilent 2100 Bioanalyzer (Agilent Technologies).
Sequencing of 10 RGC cultures was performed by MR DNA (www.mrdnalab.com) following the manufacturer’s guidelines (Illumina HiSeq) for paired end sequencing (151 bp).

treatment_protocol: Cells were exposed to either 1000 nM SNa (n=3) or 10uM (n=3) SKF for 24hrs.

value: hypothalamus and telencephalon

value: radial glial cell

tag: Sex

value: female


title: SKF5

description:
processed data file: GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: SKF5-30501509 and SKF5-30684718


title: Cortex_WT_1


title: SKF1

description:
processed data file: GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: SKF1-30493508 and SKF1-30693686


title: SN4

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report
One library run on two separate lanes: SN4-30507520 and SN4-30696691

source_name: Primary hypothalamic and telencephalic radial glial cell culture_SNa


title: SN1

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report
One library run on two separate lanes: SN1-30499520 and SN1-30695685


title: Control5

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report, GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: Control5-30507519 and Control5-30680716

source_name: Primary hypothalamic and telencephalic radial glial cell culture_untreated


title: Control4

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report, GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: Control4-30493507 and Control4-30694685


title: SN5

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report
One library run on two separate lanes: SN5-30514526 and SN5-30684717


title: Control1

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report, GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on two separate lanes: Control1-30507518 and Control1-30692690


title: Control-RGC_S25_L002_R1_001

description:
processed data file: GT_SO_5230_Control_vs_SN_DGE_Report, GT_SO_5230_Control_vs_SKF_DGE_Report
One library run on one lane (RGC_S25_L002_R1_001)


title: High_17

status: Public on Jan 31 2018

type: RNA

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.

data_processing:
Agilent Feature Extraction Software (v10.7) was used (GRID: 026437_D_F_20140627). Normalized signal intensity provided here is quantile Normalization.
Cut off of 2.1 intensity as limit of detection of intensity

organism: Danio rerio

source_name: larval zebrafish 9 days old

label_protocol: Agilent one color protocol for Cy3 following manufacturer's protocol

extract_protocol: Trizol protocol for total RNA following manufacturer's protocol

treatment_protocol: Three doses of fipronil: Ethanol control (n=6), low (0.2 ug/L) (n=5), medium (200 ug/L) (n=6) and high (2000 ug/L) (n=6)

tag: agent

value: fipronil

tag: dose

tag: developmental stage

value: larval

value: 9 days old


title: High_19


title: Medium_15


title: Control_26

value: control

value: 0 ug/L


title: Control_27


title: Medium_13


title: High_22


title: Control_32


title: Medium_9


title: Control_31


title: High_20


title: High_21


title: Low_6


title: TOV21G RNA-seq-WT-Rep1

status: Public on Sep 29 2017

description: RNA-seq of TOV21G cells with scrambled shRNA replicate 1

data_processing:
Basecalls performed using RTA (Illumina)
Reads were aligned to the human genome (hg38) using STAR (v2.2.0c) for ATAC-seq, ChIP-seq, and RNA-Seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate tag directories and peak files. ATAC-seq peaks were found using the findPeaks program in HOMER with the following options "-style dnase -o auto". ChIP-Seq regions were found using the findPeaks program in HOMER using the paramter "-style histone" to find broad peaks for H3K4me, H3K4me3, H3K27ac, and H3K27me3 using input as background.  For RNA-Seq, Fragments Per Kilobase of transcript per milion mapped reads (FPKM) were calculated for annotated genes using HOMER.
Genome_build: hg38
Supplementary_files_format_and_content: peaks.txt file Columns: (1) PeakID (2) chr (3) start (4) end (5) strand (6) Normalized Tag Count (7) Not used (8) findPeaks Score (9) Fold Change vs Local (10) p-value vs Local (11) Clonal Fold Change. regions.txt file columns: (1) PeakID (2) chr (3) start (4) end (5) strand (6) Normalized Tag Count (7) region size (8) findPeaks Score (9) Total Tags (normalized to Control Experiment) (10) Control Tags (11) Fold Change vs Control (12) p-value vs Control (13) Clonal Fold Change. FPKM Tab delimited text file, Columns: (1) Transcript/RepeatID (2) chr (3) start (4) end (5) strand (6) Length (7) Copies (8) Annotation/Divergence (9-16) FPKM for each experiment.

organism: Homo sapiens

growth_protocol: TOV21G cells were grown in 1:1 mixture of Medium 199 (Life Technologies) containing 2.2g/L sodium bicarbonate and MCDB 105 (Life Technologies) containing 1.5g/L sodium bicarbonate, supplemented with 15% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
ATAC-Seq: Cells were washed with cold PBS, collected by centrifugation then resuspended in resuspension buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). After collection, cells were lysed in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and collected before incubating in transposition mix containing Tn5 transposase. ChIP-seq: Cells were harvested and crosslinked in 1% formaldehyde for 10 min before quenching with glycine for 5 min on ice. Cells were pelleted by centrifugation and snap frozen in dry ice before storage at -80˚C. Pellets were thawed on ice and resuspended in rinse buffer 1 (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X100), collected by centrifugation then resuspended in rinse buffer 2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Cells were washed and resuspended in shearing buffer before sonication using Covaris E220 (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8). For ChIPs using antibodies for histone modifications, 106 cells in 1ml shearing buffer were added to 1ml Covaris tubes and sheared for 12 mins at 140W with 10% duty factor. For FRA1 ChIPs, cells were sheared for 8 mins at 140W with 5% duty factor. DNA was then made up to 1x IP buffer (50 mM HEPES/KOH pH 7.5, 150 mM NaCl , 1 mM EDTA, 1 % Triton X100, 0.1 % DOC, 0.1% SDS, supplemented with protease inhibitors) and 3ug antibody added for overnight incubation with rolling at 4˚C. Antibody bound DNA was recovered using a 1:1 mixture of Protein A and Protein G beads, washed and treated with Proteinase K and RNAse A. Purified ChIP DNA was then used for library generation for ChIP-seq. RNA-Seq: RNA was isolated using Quick-RNA Miniprep Kit (Zymo Research).
ATAC-seq: Purified DNA was ligated with adapters (NuGEN), amplified and size selected for sequencing. Library DNA was sequenced with paired end 42 bp reads. RNA-seq: mRNA was isolated using NEBnext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) with 5 μg input RNA according to the manufacturer’s guidelines. Libraries were prepared for RNA-seq using NEBnext® UltraTM RNA Library Prep Kit for Illumina® following the manufacturer’s instructions. mRNA was fragmented and purified before first strand and second strand synthesis. Double-stranded cDNA was then purified and ends repaired before dA tailing and adapter ligation. After cleanup and size selection, cDNA libraries were amplified and purified before sequencing with single end 51 bp reads. ChIP-seq: 5 ng ChIP DNA was used to prepare libraries using the NuGen Ovation® Ultralow Library System V2 following the manufacturer’s instructions. Briefly, DNA ends were repaired before ligation of adapters for sequencing. Following bead purification, libraries were amplified by PCR then purified and size-selected for sequencing with single end 51 bp reads.

treatment_protocol: shRNA-mediated gene silencing was performed by lentiviral infection of GIPZ shRNAs (Dharmacon, GE) targeting ARID1B (V3LHS_306691) or scrambled control (RHS4346). 48 hours after infection, puromycin (TOV21G: 4μg/ml) was added to select infected cells.

tag: RNAi

value: scrambled control

tag: antibody source


title: TOV21G RNA-seq-ARID1BKD-Rep2

description: RNA-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2

value: ARID1B RNAi


title: TOV21G H3K27ac-ChIP-seq-ARID1BKD-Rep2

description: H3K27ac ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2

value: H3K27ac (Abcam, ab4729)


title: Low_5


title: Control_28


title: Medium_12


title: Medium_10


title: Medium_16


title: TOV21G RNA-seq-ARID1BKD-Rep1

description: RNA-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: High_18


title: Control_30


title: TOV21G Input-ChIP-seq-WT-Rep1

description: Input control for ChIP-seq of TOV21G cells with scrambled shRNA replicate 1


title: Low_1


title: TOV21G H3K27ac-ChIP-seq-ARID1BKD-Rep1

description: H3K27ac ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: Low_3


title: TOV21G H3K27ac-ChIP-seq-WT-Rep2

description: H3K27ac ChIP-seq of TOV21G cells with scrambled shRNA replicate 2


title: TOV21G H3K4me3-ChIP-seq-ARID1BKD-Rep2

description: H3K4me3 ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2

value: H3K4me3 (Millipore, #05-745)


title: TOV21G H3K27ac-ChIP-seq-WT-Rep1

description: H3K27ac ChIP-seq of TOV21G cells with scrambled shRNA replicate 1


title: TOV21G H3K4me3-ChIP-seq-WT-Rep1

description: H3K4me3 ChIP-seq of TOV21G cells with scrambled shRNA replicate 1


title: TOV21G H3K4me3-ChIP-seq-WT-Rep2

description: H3K4me3 ChIP-seq of TOV21G cells with scrambled shRNA replicate 2


title: TOV21G H3K4me-ChIP-seq-ARID1BKD-Rep2

description: H3K4me ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2

value: H3K4me (Abcam, ab8895)


title: TOV21G H3K4me3-ChIP-seq-ARID1BKD-Rep1

description: H3K4me3 ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: TOV21G H3K4me-ChIP-seq-WT-Rep1

description: H3K4me ChIP-seq of TOV21G cells with scrambled shRNA replicate 1


title: HCT116 RNA-seq-ARID1BKD-Rep1

description: RNA-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1

growth_protocol: HCT116 cells were cultured in RPMI (Corning CellGro), 10% FBS (Omega Scientific, Inc), supplemented with 1% Penicllin/Streptavidin (Life Technologies).

treatment_protocol: shRNA-mediated gene silencing was performed by lentiviral infection of GIPZ shRNAs (Dharmacon, GE) targeting ARID1B (V3LHS_306691) or scrambled control (RHS4346). 48 hours after infection, puromycin (HCT116: 2μg/ml) was added to select infected cells.


title: HCT116 RNA-seq-ARID1BKD-Rep2

description: RNA-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- RNA-seq-ARID1AKO-ARID1BKD-Rep1

description: RNA-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1

source_name: HCT116 ARID1A-/-


title: HCT116 RNA-seq-WT-Rep2

description: RNA-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- Input-ChIP-seq-ARID1AKO-ARID1BKD-Rep1

description: Input control for ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 ARID1A-/- RNA-seq-ARID1AKO-ARID1BKD-Rep2

description: RNA-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 RNA-seq-WT-Rep1

description: RNA-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- Input-ChIP-seq-ARID1AKO-Rep1

description: Input control for ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- RNA-seq-ARID1AKO-Rep1

description: RNA-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: HCT116 Input-ChIP-seq-ARID1BKD-Rep1

description: Input control for ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 Input-ChIP-seq-WT-Rep1

description: Input control for ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- H3K27me3-ChIP-seq-ARID1AKO-ARID1BKD-Rep1

description: H3K27me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1

value: H3K27me3 (Active Motif, #39155)


title: HCT116 ARID1A-/- H3K27me3-ChIP-seq-ARID1AKO-Rep2

description: H3K27me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 H3K27me3-ChIP-seq-ARID1BKD-Rep2

description: H3K27me3 ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- H3K27me3-ChIP-seq-ARID1AKO-Rep1

description: H3K27me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: TOV21G H3K4me-ChIP-seq-WT-Rep2

description: H3K4me ChIP-seq of TOV21G cells with scrambled shRNA replicate 2


title: TOV21G H3K4me-ChIP-seq-ARID1BKD-Rep1

description: H3K4me ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 ARID1A-/- RNA-seq-ARID1AKO-Rep2

description: RNA-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 H3K27me3-ChIP-seq-ARID1BKD-Rep1

description: H3K27me3 ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K27me3-ChIP-seq-WT-Rep2

description: H3K27me3 ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- H3K27ac-ChIP-seq-ARID1AKO-ARID1BKD-Rep1

description: H3K27ac ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 ARID1A-/- H3K27ac-ChIP-seq-ARID1AKO-Rep2

description: H3K27ac ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 H3K27me3-ChIP-seq-WT-Rep1

description: H3K27me3 ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- H3K27me3-ChIP-seq-ARID1AKO-ARID1BKD-Rep2

description: H3K27me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- H3K27ac-ChIP-seq-ARID1AKO-Rep1

description: H3K27ac ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- H3K4me3-ChIP-seq-ARID1AKO-ARID1BKD-Rep2

description: H3K4me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 H3K27ac-ChIP-seq-ARID1BKD-Rep1

description: H3K27ac ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K27ac-ChIP-seq-WT-Rep1

description: H3K27ac ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 H3K27ac-ChIP-seq-WT-Rep2

description: H3K27ac ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- H3K4me3-ChIP-seq-ARID1AKO-Rep2

description: H3K4me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- H3K4me3-ChIP-seq-ARID1AKO-ARID1BKD-Rep1

description: H3K4me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 ARID1A-/- H3K4me-ChIP-seq-ARID1AKO-ARID1BKD-Rep2

description: H3K4me ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 H3K4me3-ChIP-seq-WT-Rep1

description: H3K4me3 ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 H3K4me3-ChIP-seq-ARID1BKD-Rep1

description: H3K4me3 ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K4me3-ChIP-seq-WT-Rep2

description: H3K4me3 ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- H3K4me-ChIP-seq-ARID1AKO-Rep1

description: H3K4me ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- H3K4me-ChIP-seq-ARID1AKO-Rep2

description: H3K4me ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- H3K4me-ChIP-seq-ARID1AKO-ARID1BKD-Rep1

description: H3K4me ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K4me-ChIP-seq-ARID1BKD-Rep2

description: H3K4me ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- H3K27ac-ChIP-seq-ARID1AKO-ARID1BKD-Rep2

description: H3K27ac ChIP-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 H3K4me-ChIP-seq-ARID1BKD-Rep1

description: H3K4me ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K4me-ChIP-seq-WT-Rep2

description: H3K4me ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 H3K27ac-ChIP-seq-ARID1BKD-Rep2

description: H3K27ac ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: TOV21G ATAC-seq-ARID1BKD-Rep2

description: ATAC-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- ATAC-seq-ARID1AKO-ARID1BKD2-Rep2

description: ATAC-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 H3K4me3-ChIP-seq-ARID1BKD-Rep2

description: H3K4me3 ChIP-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ARID1A-/- H3K4me3-ChIP-seq-ARID1AKO-Rep1

description: H3K4me3 ChIP-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: TOV21G ATAC-seq-ARID1BKD-Rep1

description: ATAC-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: TOV21G ATAC-seq-WT-Rep1

description: ATAC-seq of TOV21G cells with scrambled shRNA replicate 1


title: TOV21G ATAC-seq-WT-Rep2

description: ATAC-seq of TOV21G cells with scrambled shRNA replicate 2


title: HCT116 ARID1A-/- ATAC-seq-ARID1AKO-ARID1BKD2-Rep1

description: ATAC-seq of homozygous ARID1A knockout HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 ARID1A-/- ATAC-seq-ARID1AKO-Rep1

description: ATAC-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ARID1A-/- ATAC-seq-ARID1AKO-Rep2

description: ATAC-seq of homozygous ARID1A knockout HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ATAC-seq-ARID1BKD-Rep2

description: ATAC-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 2


title: HCT116 ATAC-seq-WT-Rep2

description: ATAC-seq of WT HCT116 cells with scrambled shRNA replicate 2


title: HCT116 ATAC-seq-ARID1BKD-Rep1

description: ATAC-seq of WT HCT116 cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1


title: HCT116 H3K4me-ChIP-seq-WT-Rep1

description: H3K4me ChIP-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: HCT116 ATAC-seq-WT-Rep1

description: ATAC-seq of WT HCT116 cells with scrambled shRNA replicate 1


title: P5_RRC_40

status: Public on Sep 11 2017

description:
Single cell
S061L3D01

data_processing:
Basecalls by bcl2fastq v2.15
Reads aligned to mm10 genome (NCBI GRCm38) with RefSeq coordinates.
Reads aligned with STAR v.2.4, using following parameters:  --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMmode Full outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 10000000000  --outSAMstrandField intronMotif --outSAMattributes All --outSAMattrRGline ID:${i}${j} SM:${i}${j} PL:Illumina LB:${i}${j} --quantMode TranscriptomeSAM
Transcripts per Million (TPM) calculated with RSEM v1.2, using following parameters:  rsem-calculate-expression -p 8 --bam --paired-end --no-bam-output --estimate-rspd Aligned.toTranscriptome.out.bam
Outlier analysis performed with SINGuLAR analysis toolset 3.0 (Fluidigm) and cross-sample normalization conducted using DESeq resulting in normalized TPM (nTPM)
Genome_build: NCBI GRCm38 (mm10)
Supplementary_files_format_and_content: Expression matrix of single cells and RefSeq genes, with values in TPM

source_name: Endolymphatic sac epithelium

growth_protocol: All cells used were from acute isolations from E12.5, E16.5, P5, P30 endolymphatic sac epithelia of C57BL/6J mice using a mechanical/enzymatic dissociation technique.

extract_protocol:
Following dissociation of tissue into a single-cell suspension, target cells were enriched by purification as described, cells were lysed, total RNA reverse-transcribed with oligo-dT primers, and cDNA amplified using SMARTer ultra-low input cDNA synthesis (Clontech) on the C1 microfluidics platform (Fluidigm).
cDNA libraries were prepared for sequencing using Nextera XT tagmentation and 96-barcode indexing (Illumina). Barcoded samples were pooled, cleaned with Agencourt AMPure XP magnetic bead isolation (Beckman Coulter).

treatment_protocol: All cells are stained with LIVE/DEAD cell viability assay before lysis.

value: endolymphatic sac

value: Postnatal day 5

tag: classification

value: P5 RRC

tag: c1 ifc #

value: IFC 5


title: P5_RRC_41

description:
Single cell
S061L3D04

tag: strain


title: P5_MRC_33

description:
Single cell
S061L3F05

tag: age

value: P5 MRC


title: P5_MRC_34

description:
Single cell
S061L3G02


title: P5_RRC_44

description:
Single cell
S061L3G03


title: P5_RRC_47

description:
Single cell
S061L3H05


title: P5_RRC_39

description:
Single cell
S061L3C03


title: P5_RRC_43

description:
Single cell
S061L3G01


title: P5_RRC_45

description:
Single cell
S061L3H03


title: P5_RRC_38

description:
Single cell
S061L3C01


title: P5_MRC_35

description:
Single cell
S061L3H02


title: E16.5_ProC_16

description:
Single cell
S061L3E06

value: Embryonic day 16.5

value: E16.5 ProC

value: IFC 2


title: P5_MRC_31

description:
Single cell
S061L3C02


title: P5_MRC_30

description:
Single cell
S061L3A06


title: P5_RRC_36

description:
Single cell
S061L3B01


title: P5_RRC_37

description:
Single cell
S061L3B03


title: P5_RRC_46

description:
Single cell
S061L3H04


title: P5_MRC_32

description:
Single cell
S061L3F04


title: P5_RRC_34

description:
Single cell
S061L3A02


title: P5_MRC_29

description:
Single cell
S061L3A01


title: E16.5_ProC_14

description:
Single cell
S061L2H11


title: E12.5_cell_44

description:
Single cell
S061L2H07

value: Embryonic day 12.5

value: E12.5 cell

value: IFC 8


title: E16.5_ProC_13

description:
Single cell
S061L2H05


title: E16.5_MRC_07

description:
Single cell
S061L2H12

value: E16.5 MRC


title: P5_RRC_42

description:
Single cell
S061L3F03


title: E16.5_ProC_15

description:
Single cell
S061L3B06


title: P5_RRC_35

description:
Single cell
S061L3A05


title: E12.5_cell_43

description:
Single cell
S061L2G11


title: E16.5_nonMRC_18

description:
Single cell
S061L2H04

value: E16.5 nonMRC


title: E12.5_cell_23

description:
Single cell
S061L2D10


title: E12.5_cell_22

description:
Single cell
S061L2D05


title: E12.5_cell_26

description:
Single cell
S061L2E04


title: E12.5_cell_33

description:
Single cell
S061L2F04


title: E12.5_cell_32

description:
Single cell
S061L2F03


title: E12.5_cell_39

description:
Single cell
S061L2F12


title: E12.5_cell_31

description:
Single cell
S061L2F01


title: E12.5_cell_29

description:
Single cell
S061L2E11


title: E12.5_cell_24

description:
Single cell
S061L2D11


title: E12.5_cell_38

description:
Single cell
S061L2F11


title: E12.5_cell_34

description:
Single cell
S061L2F05


title: E12.5_cell_36

description:
Single cell
S061L2F08


title: E12.5_cell_27

description:
Single cell
S061L2E06


title: E12.5_cell_25

description:
Single cell
S061L2D12


title: E12.5_cell_40

description:
Single cell
S061L2G06


title: E12.5_cell_28

description:
Single cell
S061L2E08


title: E12.5_cell_37

description:
Single cell
S061L2F09


title: E12.5_cell_30

description:
Single cell
S061L2E12


title: E12.5_cell_35

description:
Single cell
S061L2F06


title: E16.5_MRC_06

description:
Single cell
S061L2G10


title: E12.5_cell_42

description:
Single cell
S061L2G09


title: E12.5_cell_20

description:
Single cell
S061L2D03


title: E12.5_cell_21

description:
Single cell
S061L2D04


title: TOV21G RNA-seq-WT-Rep2

description: RNA-seq of TOV21G cells with scrambled shRNA replicate 2

value: scrambled control


title: E12.5_cell_41

description:
Single cell
S061L2G07


title: E12.5_cell_18

description:
Single cell
S061L2C11


title: E12.5_cell_19

description:
Single cell
S061L2C12


title: E12.5_cell_17

description:
Single cell
S061L2C10


title: TOV21G Input-ChIP-seq-ARID1BKD-Rep1

description: Input control for ChIP-seq of TOV21G cells with ARID1B KD (shRNA V3LHS_306691, Dharmacon, GE) replicate 1

value: ARID1B RNAi


title: E12.5_cell_13

description:
Single cell
S061L2B12


title: E12.5_cell_16

description:
Single cell
S061L2C09


title: E12.5_cell_15

description:
Single cell
S061L2C06


title: E12.5_cell_14

description:
Single cell
S061L2C05


title: E12.5_cell_07

description:
Single cell
S061L2B06


title: E12.5_cell_06

description:
Single cell
S061L2B05


title: E12.5_cell_01

description:
Single cell
S061L2A04


title: E12.5_cell_08

description:
Single cell
S061L2B07


title: E12.5_cell_10

description:
Single cell
S061L2B09


title: E12.5_cell_04

description:
Single cell
S061L2B02


title: E12.5_cell_02

description:
Single cell
S061L2A05


title: P30_RRC_30

description:
Single cell
S061L1H11

value: Postnatal day 30

value: P30 RRC

value: IFC 7


title: E12.5_cell_09

description:
Single cell
S061L2B08

value: endolymphatic sac


title: E12.5_cell_03

description:
Single cell
S061L2A12


title: E12.5_cell_11

description:
Single cell
S061L2B10


title: P30_MRC_13

description:
Single cell
S061L1G09

value: P30 MRC


title: P30_MRC_14

description:
Single cell
S061L1G12


title: P30_RRC_31

description:
Single cell
S061L1H12


title: P30_RRC_28

description:
Single cell
S061L1H03

value: IFC 6


title: E12.5_cell_05

description:
Single cell
S061L2B04


title: P30_RRC_29

description:
Single cell
S061L1H09


title: P30_RRC_26

description:
Single cell
S061L1G03


title: P30_RRC_25

description:
Single cell
S061L1G01


title: P30_MRC_15

description:
Single cell
S061L1H02


title: P30_RRC_24

description:
Single cell
S061L1F09


title: P30_RRC_22

description:
Single cell
S061L1F07


title: E12.5_cell_12

description:
Single cell
S061L2B11


title: P30_RRC_27

description:
Single cell
S061L1G06


title: P30_MRC_11

description:
Single cell
S061L1F01


title: P30_RRC_21

description:
Single cell
S061L1E10


title: P30_RRC_20

description:
Single cell
S061L1E09


title: Low_4

value: fipronil

value: larval

value: 9 days old


title: P30_MRC_08

description:
Single cell
S061L1E03


title: P30_MRC_12

description:
Single cell
S061L1F02


title: P30_RRC_19

description:
Single cell
S061L1E07


title: P30_RRC_18

description:
Single cell
S061L1D12


title: P30_RRC_17

description:
Single cell
S061L1D11


title: P30_MRC_10

description:
Single cell
S061L1E08


title: P30_MRC_09

description:
Single cell
S061L1E06


title: P30_RRC_13

description:
Single cell
S061L1C09


title: P30_RRC_14

description:
Single cell
S061L1C12


title: P30_MRC_07

description:
Single cell
S061L1D10


title: P30_MRC_06

description:
Single cell
S061L1D09


title: P30_MRC_05

description:
Single cell
S061L1D07


title: P30_RRC_15

description:
Single cell
S061L1D03


title: P30_RRC_23

description:
Single cell
S061L1F08


title: P30_RRC_12

description:
Single cell
S061L1C08


title: P30_MRC_03

description:
Single cell
S061L1C10


title: P30_MRC_01

description:
Single cell
S061L1B09


title: P30_RRC_10

description:
Single cell
S061L1B07


title: P30_RRC_11

description:
Single cell
S061L1B11


title: P30_RRC_08

description:
Single cell
S061L1B03


title: P30_RRC_07

description:
Single cell
S061L1B02


title: P30_MRC_04

description:
Single cell
S061L1D05


title: P30_RRC_16

description:
Single cell
S061L1D04


title: P30_RRC_05

description:
Single cell
S061L1A10


title: P30_RRC_06

description:
Single cell
S061L1A12


title: P30_RRC_03

description:
Single cell
S061L1A07


title: P30_RRC_04

description:
Single cell
S061L1A08


title: P30_MRC_02

description:
Single cell
S061L1C04


title: P30_RRC_02

description:
Single cell
S061L1A06


title: P5_RRC_31

description:
Single cell
S034H04

value: Postnatal day 5

value: P5 RRC

value: IFC 4


title: P5_RRC_30

description:
Single cell
S034H01

value: IFC 3


title: P5_RRC_33

description:
Single cell
S034H09


title: E16.5_nonMRC_17

description:
Single cell
S034H05

value: Embryonic day 16.5

value: IFC 1


title: P5_RRC_32

description:
Single cell
S034H08


title: P30_RRC_01

description:
Single cell
S061L1A01


title: P5_MRC_27

description:
Single cell
S034H03

value: P5 MRC


title: P5_MRC_28

description:
Single cell
S034H10


title: P30_RRC_09

description:
Single cell
S061L1B04


title: P5_MRC_26

description:
Single cell
S034G04


title: P5_MRC_25

description:
Single cell
S034G03


title: P5_RRC_26

description:
Single cell
S034F08


title: P5_MRC_20

description:
Single cell
S034E11


title: P5_MRC_17

description:
Single cell
S034E07


title: P5_RRC_29

description:
Single cell
S034G10


title: P5_RRC_27

description:
Single cell
S034F10


title: P5_RRC_22

description:
Single cell
S034E04


title: P5_RRC_28

description:
Single cell
S034G02


title: P5_RRC_25

description:
Single cell
S034F03


title: P5_MRC_24

description:
Single cell
S034F09


title: P5_MRC_19

description:
Single cell
S034E09


title: P5_MRC_15

description:
Single cell
S034E01


title: P5_MRC_18

description:
Single cell
S034E08


title: P5_RRC_24

description:
Single cell
S034E10


title: P5_MRC_22

description:
Single cell
S034F02


title: P5_MRC_21

description:
Single cell
S034F01


title: P5_RRC_23

description:
Single cell
S034E06


title: P5_MRC_16

description:
Single cell
S034E02


title: P5_MRC_23

description:
Single cell
S034F04


title: P5_RRC_19

description:
Single cell
S034D08


title: P5_RRC_18

description:
Single cell
S034D05


title: P5_RRC_16

description:
Single cell
S034D01


title: P5_RRC_15

description:
Single cell
S034C12


title: P5_MRC_13

description:
Single cell
S034D06


title: P5_RRC_17

description:
Single cell
S034D02


title: P5_RRC_21

description:
Single cell
S034D12


title: P5_MRC_14

description:
Single cell
S034D09


title: P5_RRC_14

description:
Single cell
S034C09


title: P5_MRC_11

description:
Single cell
S034C11


title: P5_MRC_08

description:
Single cell
S034B04


title: P5_MRC_09

description:
Single cell
S034C04


title: P5_MRC_06

description:
Single cell
S034A12


title: P5_RRC_13

description:
Single cell
S034C08


title: P5_RRC_03

description:
Single cell
S034A10


title: P5_RRC_09

description:
Single cell
S034B11


title: P5_RRC_04

description:
Single cell
S034A11


title: P5_RRC_11

description:
Single cell
S034C03


title: P5_RRC_07

description:
Single cell
S034B06


title: P5_MRC_07

description:
Single cell
S034B01


title: P5_MRC_10

description:
Single cell
S034C07


title: P5_RRC_08

description:
Single cell
S034B09


title: P5_RRC_20

description:
Single cell
S034D10


title: P5_RRC_12

description:
Single cell
S034C06


title: P5_RRC_06

description:
Single cell
S034B05


title: P5_MRC_12

description:
Single cell
S034D03


title: P5_RRC_05

description:
Single cell
S034B03


title: P5_MRC_01

description:
Single cell
S034A01


title: P5_RRC_01

description:
Single cell
S034A06


title: P5_RRC_02

description:
Single cell
S034A08


title: E16.5_ProC_12

description:
Single cell
S032H12

value: E16.5 ProC

value: IFC 2


title: E16.5_nonMRC_16

description:
Single cell
S032H11

value: E16.5 nonMRC


title: P5_MRC_03

description:
Single cell
S034A05


title: P5_MRC_02

description:
Single cell
S034A03


title: E16.5_nonMRC_15

description:
Single cell
S032H10


title: P5_MRC_04

description:
Single cell
S034A07


title: P5_RRC_10

description:
Single cell
S034B12


title: P5_MRC_05

description:
Single cell
S034A09


title: E16.5_MRC_05

description:
Single cell
S032H02

value: E16.5 MRC


title: E16.5_nonMRC_13

description:
Single cell
S032G07

value: endolymphatic sac


title: E16.5_MRC_04

description:
Single cell
S032G12


title: E16.5_ProC_10

description:
Single cell
S032G10


title: E16.5_nonMRC_14

description:
Single cell
S032G09


title: E16.5_ProC_09

description:
Single cell
S032F08


title: E16.5_nonMRC_11

description:
Single cell
S032F07


title: E16.5_nonMRC_12

description:
Single cell
S032F12


title: E16.5_nonMRC_09

description:
Single cell
S032E03


title: E16.5_MRC_03

description:
Single cell
S032G02


title: E16.5_nonMRC_10

description:
Single cell
S032F06


title: E16.5_ProC_08

description:
Single cell
S032F04


title: E16.5_MRC_02

description:
Single cell
S032E10


title: E16.5_ProC_03

description:
Single cell
S032B11


title: E16.5_ProC_06

description:
Single cell
S032C09


title: E16.5_nonMRC_07

description:
Single cell
S032D06


title: E16.5_nonMRC_06

description:
Single cell
S032D04


title: E16.5_nonMRC_08

description:
Single cell
S032D12


title: E16.5_nonMRC_02

description:
Single cell
S032B02


title: E16.5_nonMRC_04

description:
Single cell
S032B06


title: E16.5_nonMRC_05

description:
Single cell
S032B10


title: E16.5_MRC_01

description:
Single cell
S032A06


title: E16.5_ProC_11

description:
Single cell
S032H06


title: E16.5_ProC_02

description:
Single cell
S032A05


title: E16.5_nonMRC_01

description:
Single cell
S032B01


title: E16.5_nonMRC_03

description:
Single cell
S032B05


title: E16.5_ProC_01

description:
Single cell
S032A03


title: E16.5_ProC_05

description:
Single cell
S032C08


title: E16.5_ProC_04

description:
Single cell
S032C03


title: BaCl1

status: Public on Aug 31 2017

data_processing:
Raw Illumina files were processed by Genotypic Technology Ltd. (Bangalore, India) for read mapping and the identification of differentially expressed transcripts. Raw data were downloaded and processed (Adapter, B-block and low quality base filtering) using Genotypic's proprietary Perl script for removing adapter and low quality base trimming.
RNA-Seq reads were then mapped using the ultra-high-throughput short read aligner Bowtie (Langmead 2010) and reference alignment was conducted with TopHat-2.0.13 (Trapnell et al. 2009), a fast splice junction mapper for RNA-Seq reads. Processed data were inputted into TopHat and default parameters for directional libraries were used. Cufflinks-2.2.1 was used to assemble transcripts and to identify transcripts that were differentially expressed using default settings and -G option to facilitate read mapping.
Biological replicates were combined using Cuffmerge and then analyzed using CuffDiff for replicate samples by modeling the variance in fragment counts across replicates as a function of the mean fragment count. Each replicated condition was first used to build a model. Models were generated from each biological replicate and were averaged to provide a single global model for all conditions in the experiment. Cuffdiff was then used to determine significant changes in transcript levels.
Expression level estimation was reported as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) value together with confidence intervals. The false discovery rate or FDR-adjusted p-value of the test statistic (q-value) was also generated. An in-house pipeline was developed to automate the abovementioned mapping and assembly process.
Genome_build: The 138,026 transcript sequences of Dugesia japonica were subjected to blast against the 385,255 sequences of Platyhelminthes database extracted from Uniprot as a reference
Supplementary_files_format_and_content: fragments per kilobase of transcript sequence per million mapped fragments (FPKM)

organism: Dugesia japonica

source_name: Worn heads

growth_protocol: Whole worms were treated in 1mM BaCl2 solution, refreshed weekly. No more than 25 worms were kept in 50 mL of 1mM BaCl2 solution in untreated tissue culture plates at 10oC, and degenerated tissues were pipetted out of plates on a regular basis.

extract_protocol:
Total RNA was extracted using Trizol reagent (Ambion/ThermoFisher) purification (0.5 mL/25 worms). RNA was pelleted and then suspended in 80% ethanol. Samples (n=2/experimental group) were then shipped to the MIT sequencing core. Quality control for RNA was conducted using a 2100 Agilent Bioanalyzer and RNA was deemed to be of high quality for sequencing.
The library prep workflow used was the TruSeq PolyA, a commercially available kit from Illumina.

treatment_protocol: Total RNA was extracted from wild type D. japonica and from D. japonica with BaCl2-insensitive heads. Biological replicates were collected for each treatment, with 25 worms per replicate. For the RNAseq experiment, worms were kept in 1mM BaCl2 for 35 days, when BaCl2-insensitive heads had fully regenerated. Heads were then amputated, and RNA was extracted.

value: head

tag: treatment


title: WT1

tag: tissue

value: control


title: E16.5_ProC_07

description:
Single cell
S032D10


title: BaCl2


title: WT2


title: D0

status: Public on Jul 31 2017

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. There was 825 ng of Cy3-labeled cRNA used.

data_processing: Agilent Feature Extraction Software (v10.7) was used. Quantile normalized.

organism: Rattus norvegicus

source_name: Striatum

treatment_protocol: Rats were randomly assigned to 1 of 3 treatment groups (saline, acute, repeated/chronic). Saline rats received one daily saline injection (i.p.) on 5 days, acute rats received one daily saline injection on 4 days and a final MDPV injection on a 5th day, repeated MDPV rats received one daily MDPV injection on 5 days. MDPV dose was 1 mg/kg. Twenty four hours after the final injection, rats were euthanized, brains removed, flash frozen and stored at -80C until  day of assay. For assay, left dorsal striatum was manually dissected to process in the following steps.

tag: treatment group

value: Saline

value: brain

tag: tissue compartment

value: Striatum

value: male

value: 80-90 days old

value: Long Evans


title: F1

value: Acute


title: H5


title: A0

value: Chronic


title: COLO320_AA_DCLK3

status: Public on Feb 15 2017

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description: DCLK3 amplicon; FW primer: GTCCACATGCACGACAAGAG; Rev primer: TCCAAAATCAGCCAATTTCA

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy (H3K27ac ChIP-seq): mapping: bwa-aln (0.7.10-r789), peak calling: macs2 (version 2.0.10.20130306) q=0.01 --broad option
Library strategy (ChIP-seq/Dnase I-seq/Target RNA or DNA-seq): mapping: bwa-aln (0.7.10-r789), peak calling: macs2 (version 2.0.10.20130306) q=0.01; Allele-specific read counts: IGV (version 2.3)
Library strategy (ATAC-seq): mapping: bwa-mem (0.7.10-r789), peak calling: macs2 (version 2.0.10.20130306) q=0.01; Allele-specific read counts: IGV (version 2.3)
Library strategy (4C-seq): mapping: bwa-aln (0.7.10-r789), data analysis: R package 'r3Cseq' (version 3.3)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using "bam2bw" script (https://bitbucket.org/simonvh/bam2bw/src),  bedGraph files were generated using R package "r3Cseq".

source_name: Colorectal cancer cell line

growth_protocol: RPMI medium supplemented with 10% fetal bovine, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
Libraries were purified using QIA quick column (DNase I-seq, ATAC-seq, Targeted RNA-/DNA-seq, and 4C-seq), QIA minElute column (ChIP-seq) or SPRI beads (ATAC-seq).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: COLO320 isogenic lines (G/G, A/A) were generated by CRISPR-CAS9 site specific mutation. COLO320 (G/A) was mocked with the empty vector.

tag: cell line

tag: cell type

value: Colorectal cancer cell line

tag: genetic modification

value: CRISPR-CAS9 site specific mutation at rs1800734

tag: library strategy

value: targeted RNA-seq


title: COLO320_rs35149869_genomic

description: Amplicon containing rs35149869; FW primer: TACCAGGGAAAACCGCAAT; REV primer: TGACCTTCACAGTCATTCTGC

value: targeted DNA-seq


title: COLO320_GG_DCLK3


title: COLO320_GA_DCLK3

value: Mocked with CRISPR-CAS9 vector


title: H11

tag: Sex


title: H8


title: H3


title: H9


title: C1


title: D1


title: A1


title: H2


title: F0


title: H4


title: E1


title: H12


title: E0


title: C0


title: H7


title: B1


title: H10


title: B0


title: H6


title: H1


title: COLO320_rs1800734_genomic

description: Amplicon containing rs1800734; FW primer: TGGATGGCGTAAGCTACA, REV primer: CAGTTCTCAATCATCTCTTTG


title: SNU175_rs35149869_genomic


title: SNU175_rs1800734_genomic


title: COLO320_GA_rs1800734_4C_2

description: 1st restriction enzyme: NLAIII, 2nd restriction enzyme: CSP6I; FW primer: GCGGCGGGGGAAGTTATC, REV primer: GGGACTTTGTATACCAGTGCATG.


title: COLO320_rs35149869_rtPCR


title: COLO320_AA_rs1800734_4C_1


title: COLO320_GA_rs1800734_4C_1


title: SNU175_rs1800734_rtPCR


title: COLO320_rs1800734_rtPCR


title: COLO320_AA_rs1800734_4C_2


title: COLO320_GG_rs1800734_4C_2


title: COLO320_GG_rs1800734_4C_1


title: SNU175_ATAC

description: 2 µl Tn5 (illumina) treatment at 37 °C for 1 h; SPRI bead purification smear library; paired-end sequencing.

value: ATAC-seq


title: T-84_DNaseI

description: 0.12 Unit of DNase I (Roche) at 37 °C for 15 min; library size: 200 bp; single-end sequencing.

growth_protocol: DMEM medium supplemented with 10% fetal bovine, 100 U/ml penicillin and 100 µg/ml streptomycin.

value: DNase I-seq


title: SW480_DNaseI


title: COLO320_GG_ATAC


title: COLO320_AA_ATAC

description: 4 µl Tn5 (illumina) treatment at 37 °C for 1 h; SPRI bead purification smear library; paired-end sequencing.


title: COLO320_ATAC


title: HUTU80_DNaseI


title: RKO_DNaseI

value: RKO


title: SW1116_DNaseI


title: HT-29_DNaseI


title: COLO205_DNaseI


title: CaCO2_DNaseI


title: LoVo_DNaseI

description: 80 U/ml DNase I (Sigma-Aldrich) at 37 °C for 3 min; library size: 300 bp; single-end sequencing.

value: LoVo


title: SNU175_rs35149869_rtPCR


title: GP5d_DNaseI


title: COLO320_ELF1

description: crosslinking ChIP; chromatin size: 300 bp; library size: 300 bp; single-end sequencing.

value: transcription factor ChIP-seq

tag: chip antibody

value: anti-ELF1 (Santa Cruz Biotechnology, sc-631X)


title: SNU175_ELF1


title: COLO320_TFAP4

value: anti-TFAP4 (Santa Cruz Biotechnology, sc-18593X)


title: COLO320_GA_ATAC

description: 3 µl Tn5 (illumina) treatment at 37 °C for 1 h; SPRI bead purification smear library; paired-end sequencing.


title: SNU175_TFAP4


title: HCT116_H3K27ac

value: histone ChIP-seq

value: anti-H3K27ac (Diagenode, C15410196)


title: SK-CO-1_DNaseI


title: LoVo_H3K27ac


title: A4_aged oil sands 20ppm

status: Public on Oct 31 2016

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used May, 2010.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) at 100% PMT (Agilent Microarray Scanner with SureScan Technology).  Agilent Feature Extraction Software (v10.7)  calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization with an minimum intensity cutoff of 3.5

organism: Pimephales promelas

source_name: newly hatched FHM_aged oil sands 20ppm

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Trizol protocol for total RNA

tag: developmental stage

value: newly hatched FHM

tag: embryo exposed to

value: aged oil sands 20ppm


title: F1_fresh oil sands10ppm

source_name: newly hatched FHM_fresh oil sands10ppm

value: fresh oil sands10ppm


title: M3_pure naphthenic acids 1.25ppm

source_name: newly hatched FHM_pure naphthenic acids 1.25ppm

value: pure naphthenic acids 1.25ppm


title: M4_pure naphthenic acids 2.5ppm

source_name: newly hatched FHM_pure naphthenic acids 2.5ppm

value: pure naphthenic acids 2.5ppm


title: A6_aged oil sands 20ppm


title: A1_aged oil sands 10ppm

source_name: newly hatched FHM_aged oil sands 10ppm

value: aged oil sands 10ppm


title: A7_aged oil sands salt

source_name: newly hatched FHM_aged oil sands salt

value: aged oil sands salt


title: M9_pure naphthenic acids salt

source_name: newly hatched FHM_pure naphthenic acids salt

value: pure naphthenic acids salt


title: F7_fresh oil sands salt

source_name: newly hatched FHM_fresh oil sands salt

value: fresh oil sands salt


title: F4_fresh oil sands 5ppm

source_name: newly hatched FHM_fresh oil sands 5ppm

value: fresh oil sands 5ppm


title: A3_aged oil sands 10ppm


title: F9_fresh oil sands salt


title: M5_pure naphthenic acids 2.5ppm


title: M7_pure naphthenic acids salt


title: A8_aged oil sands salt


title: F5_fresh oil sands 5ppm


title: F8_fresh oil sands salt


title: A9_aged oil sands salt


title: A2_aged oil sands 10ppm


title: M2_pure naphthenic acids 1.25ppm


title: F6_fresh oil sands 5ppm


title: M6_pure naphthenic acids 2.5ppm


title: F2_fresh oil sands10ppm


title: M8_pure naphthenic acids salt


title: F3_fresh oil sands10ppm


title: M1_pure naphthenic acids 1.25ppm


title: 1.8 ug/g_8

status: Public on Sep 24 2016

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID:028639_D_F_20100525). Normalized signal intensity provided here is quantile Normalization.

source_name: Heart_1.8 ug/g

treatment_protocol: Fish fed dieldrin laced feed: Three treatments, control, 0.15 and 1.8 ug measured DLD in feed.

value: AB strain

value: 6 months

tag: gender

value: female

tag: diet

value: 1.8 μg/g dose diet for 21d

value: heart


title: 0.15 ug/g_16

source_name: Heart_0.15 ug/g

value: 0.15 μg/g dose diet for 21d


title: 1.8 ug/g_13


title: A5_aged oil sands 20ppm


title: 1.8 ug/g_2


title: 38C-control

status: Public on Aug 25 2016

data_processing: Normalized signal intensity provided here is Loess Normalization with a minimum intensity cut off of 4 (female hypothalami), 3 (male hypothalami), 2.8 (female liver). Each of the three datasets were normalized and analyzed within experiment.

value: female FHM sexually mature

tag: exposed to

value: solvent control for 7 weeks

value: Liver


title: 0.15 ug/g_9

tag: strain


title: 47C-control


title: 0.15 ug/g_10

tag: age


title: 5P-phenanthrene

value: waterbourne phenanthrene (201.8 µg/L) for 7 wks


title: 1.8 ug/g_5


title: 2P-phenanthrene


title: 12C-control


title: 41P-phenanthrene


title: 0 ug/g_1

source_name: Heart_0 ug/g

value: control for 21d


title: 56C-control


title: 0 ug/g_11


title: 0 ug/g_3


title: 18P-phenanthrene


title: 0.15 ug/g_15


title: 0 ug/g_14


title: 0.15 ug/g_7


title: 10P-phenanthrene


title: 23C-control


title: 44P-phenanthrene


title: 0 ug/g_4


title: 32P-phenanthrene


title: 28P-phenanthrene


title: 54-Control

value: male FHM sexually mature

value: hypothalamus


title: 34C-control


title: 50C-control


title: 16-Phenanthrene Exposed


title: 9-Phenanthrene Exposed


title: 26-Phen


title: 39-Control


title: 51-Control


title: 30-Phenanthrene Exposed


title: 22-Control


title: 29-Phen


title: 31-Phenanthrene Exposed


title: 46-Phen


title: 49-Control


title: 20-Control


title: 7-Phenanthrene Exposed


title: 47-Control


title: 42-Phenanthrene Exposed


title: 32-Phen


title: 13-Control


title: 33-Control


title: 56-Control


title: 37-Control


title: 10-Phen


title: 5-Phen


title: 2-Phen


title: 35-Control


title: 3-Phenanthrene Exposed


title: 50-Control


title: 40-Phenanthrene Exposed


title: 41-Phen


title: 14-Control


title: 19-Control


title: 25-Control


title: KO3 [hypothalamus]

status: Public on Jul 01 2016

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. 1.6 ug of Cy3-labeled cRNA was used.

data_processing: Agilent Feature Extraction Software (v10.7) was used.

source_name: animals that received new bone marrow from double adrenergic receptor knockout (treated KO chimera)

treatment_protocol: Whole bone marrow cells from Adrb1tm1BkkAdrb2tm1Bkk/J mice were reconstituted into lethally- irradiated (950 Rad) C57BL/6J mice using a single retro-orbital injection at a ratio of 1:4 (Adrb1tm1BkkAdrb2tm1Bkk/J to C57BL/6J). All reconstituted mice were recovered for 2-3 months prior to tissue collection for microarrays.

tag: bone marrow cell source strain

tag: bone marrow cell receiver (or control) strain

value: lethally- irradiated (950 Rad) C57BL/6J

tag: tissue harvested


title: C3 [hypothalamus]

description: Whole bone marrow cells from Adrb1tm1BkkAdrb2tm1Bkk/J mice were reconstituted into lethally- irradiated (950 Rad) C57BL/6J mice

source_name: control mouse


title: C2 [distal colon]

value: Distal Colon


title: C1 [hypothalamus]


title: C8 [distal colon]


title: KO5 [hypothalamus]


title: C4 [hypothalamus]


title: KO3 [distal colon]


title: KO4 [hypothalamus]


title: KO8 [distal colon]


title: C7 [hypothalamus]


title: KO6 [hypothalamus]


title: C2 [hypothalamus]


title: C4 [distal colon]


title: C5 [hypothalamus]


title: KO6 [distal colon]


title: C9 [distal colon]


title: KO7 [hypothalamus]


title: C8 [hypothalamus]


title: K02 [hypothalamus]


title: KO4 [distal colon]


title: C6 [hypothalamus]


title: KO5 [distal colon]


title: C3 [distal colon]


title: KO7 [distal colon]


title: KO1 [hypothalamus]


title: KO8 [hypothalamus]


title: KO2 [distal colon]


title: C5 [distal colon]


title: 0.15 ug/g_6

tag: tissue


title: C4 [bone marrow]

description: Q. Norm. of C4

value: Bone marrow


title: C1 [distal colon]


title: C3 [bone marrow]

description: Q. Norm. of C3


title: C8 [bone marrow]

description: Q. Norm. of C8


title: KO4 [bone marrow]

description: Q. Norm. of KO4


title: C5 [bone marrow]

description: Q. Norm. of C5


title: C7 [bone marrow]

description: Q. Norm. of C7


title: KO6 [bone marrow]

description: Q. Norm. of KO6


title: KO3 [bone marrow]

description: Q. Norm. of KO3


title: KO5 [bone marrow]

description: Q. Norm. of KO5


title: C6 [bone marrow]

description: Q. Norm. of C6


title: KO2 [bone marrow]

description: Q. Norm. of KO2


title: KO8 [bone marrow]

description: Q. Norm. of KO8


title: C1 [bone marrow]

description: Q. Norm. of C1


title: Control 14

status: Public on May 31 2016

scan_protocol: Array were scanned using an Agilent microarray scanner and raw array data were obtained using Agilent Feature Extraction Software v10.1

data_processing: Raw data were analyzed using Agilent Genespring® GX Software version 12.6.1. Quantile normalization was performed on the data to reduce variance between arrays.

source_name: Liver

label_protocol: Following the manufacturer’s instructions, the Low Input Quick Amp Labeling Kit (Agilent Technologies, Mississauga, ON, Canada) was used to label 100 ng of total RNA from each sample using Cyanine-3 dye. Subsequently, 600 ng of labelled cRNA from each sample was hybridized to the microarrays (Agilent HD 8x60k format, AMADID: 36574) following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Mississauga, ON, Canada).

extract_protocol: RNA was extracted from liver tissues using QIAzol®-chloroform and RNeasy Mini Kit (QIAGEN). RNA samples with concentrations < 50 ng/ul were reconcentrated via sodium acetate and ethanol precipitation.

treatment_protocol: Males exposed to 25 ng/L EE2 for 96 hours

tag: treatment

value: control


title: EE2 12

hyb_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, Mississauga, ON, Canada) was used to label 100 ng of total RNA from each sample using Cyanine-3 dye


title: KO1 [bone marrow]

description: Q. Norm. of KO1


title: C2 [bone marrow]

description: Q. Norm. of C2


title: EE2 16


title: EE2 17


title: Control 9 rep


title: Control 13


title: EE2 6


title: EE2 10


title: EE2 18


title: Control 9


title: EE2 11


title: KO7 [bone marrow]

description: Q. Norm. of KO7


title: Control 3 rep


title: EE2 5


title: Control 3


title: Control 8


title: Control 1


title: Lab C T17

data_processing:
BG correction (in a smooth monotonic transformation of the background subtracted intensities such that all the corrected intensities are positive), between-array quantile normalization, and averaging duplicated spots  (both items were done using limma package)
filtering out control probes and low expressed probes. To get an idea of how bright expression   probes should be, we compute the 95% percentile of the negative control probes on each array. We  keep probes that are at least 10% brighter than the negative controls on at least 7 arrays (  there are 8 biological replicates per condition)

source_name: liver

value: liver


title: Lab E EE2-11

hyb_protocol: Low Input Quick Amp Labeling Kit was used to label 100 ng of total RNA from each sample using Cyanine-3 dye

data_processing: The scanned images were analyzed withFeature extraction (Agilent) using default parameters and Agilient-provided GEML grid file 036574_D_F_20110917.xml to obtain signal intensities. GeneSpring GX (Agilent Technologies) was used to normalize data by quantile normalizaton and baseline transformation to the median of all samples. Statistical analysis was also performed in GeneSpring utilizing data from all microarray probes and consisted of t-test analysis to test for significant differential expression of microarray targets.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Qiagen Rneasy


title: Lab E EE2-17


title: Lab E C8


title: Lab E C1


title: Lab E C5


title: Lab E EE2-18


title: Lab E EE2-12


title: Lab C T10


title: Lab E C3


title: Lab C T16


title: Lab E EE2-16


title: Lab C T18


title: Lab C T12


title: Lab C T5


title: Lab E C9


title: Lab E C6


title: Lab C C3


title: Lab C T11


title: Lab C T6


title: Lab E EE2-13


title: Lab E C2


title: Lab E EE2-10


title: Lab C C14


title: Lab C C7


title: Lab C C8


title: Lab C C13


title: Lab C C2


title: EE2_18

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID:028639_D_F_20100525).


title: EE2_16


title: Lab C C9


title: EE2_12


title: Control_13


title: Control_3


title: Lab C C1


title: Control_7


title: EE2_5


title: EE2_11


title: Control_9


title: Control_8


title: Control_2


title: Lab E C7


title: Control_1


title: Control_14


title: EE2_17


title: EE2_6


title: Lab E EE2-14


title: T16

hyb_protocol: Agilent one color protocol; Microarrays were washed after 17 hours.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

data_processing: First, raw data was log2 transformed.  Then, data from non-uniform features (probes), probes flagged by the extraction algorithm as below background, and quality control probes, and probes that did not have at least 5 of 8 data points remaining in at least one of the treatments were removed from the data set.  Missing value imputation was performed in Jmp Genomics, setting missing values to the minimum of that probe in that treatment.  The probes that had no values for a single treatment were assigned the minimum above background value for that sample on the array.  Next, non-annotated probes were removed from the data set.  After all pre-processing steps there were 45911 of 62976 original probes remaining.  Then, the data were normalized to the 75th percentile.

value: 25 ng/L EE2


title: T10


title: C14


title: T11


title: T12


title: C8


title: C7


title: C9


title: T17


title: C2


title: C3


title: C13


title: T5


title: T6


title: T18


title: C1


title: EE2_10


title: 15 Cntl

status: Public on May 11 2016

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID:028639_D_F_20100525). Normalized signal intensity provided here is Quantile Normalization.

source_name: testis

value: adult

value: Testis


title: 19 EE2

value: 17alpha-ethinylestradiol (EE2)


title: 5 EE2


title: 8 Cntl


title: 14 Cntl


title: 12 EE2


title: 10 EE2


title: 6 EE2


title: 11 EE2


title: 13 Cntl


title: 16 EE2


title: 3 Cntl


title: 9 Cntl


title: 7 Cntl


title: 21 EE2


title: 2 Cntl


title: Rat Hair 394, 20psi

status: Public on May 07 2016

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. 1.54 ug of Cy3-labeled cRNA was used.

data_processing: Agilent Feature Extraction Software (v10.7) was used (GRID: 028279_D_F_20140721). Normalized signal intensity provided here is Quantile Normaization.

source_name: hair and blood

treatment_protocol: Male adult Sprague-Dawley (SD) rats (Rattus norvegicus) (QC, Canada) were used as the animal model. All rats were 9 to 10 week of age with a weight between 350 and 400 g.  The animals were acclimated under the lab environment for at least one week before the experiment. An advanced blast simulator (ABS) system was used for multiple single pulse shockwave generation (Zhang et al., 2014; Pham et al., 2015). Both control (0 psi) and experimental conditions contained five individual animals (n = 5 per treatment). All rats were stabilized in plastic sleeves and treated with 3% isoflurane anaesthetic (mixed with oxygen) for 8 min prior to exposure. The sleeves from the experimental groups were then placed inside the ABS system with the head positioned in the test area for exposure. Individual head impacts were conducted at the intensities of 15 psi, 20 psi, 25 psi, and 30 psi for an approximate 4 ms positive duration.  Rat whisker hair follicles (up to 20 follicles per animal) and whole blood (5 ml) were collected one day after exposure and stored in RNA later solution or RNA protect Animal Blood Tubes (both from Qiagen, ON, Canada), respectively. All animal experiments were conducted under the guidelines of ‘‘Guide to the Care and Use of Experimental Animals’’ and ‘‘The Ethics of Animal Experimentation’’ by Canadian Council on Animal Care. All experimental procedures were approved by the Animal Care Committee at Defense Research and Development Canada (DRDC).

value: Sprague-Dawley

value: 9 to 10 weeks

value: male

tag: weight

tag: stress

value: multiple single pulse shockwaves

tag: intensity

value: hair follicle


title: Rat Hair 382, Sham Control

value: Sham Control

value: Control


title: Rat Blood 523, 25psi

value: blood


title: Rat Hair 519, 20psi


title: Rat Blood 513, 15psi


title: Rat Blood 520, 20psi


title: Rat Hair 384, Sham Control


title: Rat Hair 403, 30psi


title: Rat Blood 529, 30psi


title: Rat Hair 527, 30psi


title: Rat Hair 397, 25psi


title: Rat Blood 518, 20psi


title: Rat Blood 522, 25psi


title: Rat Hair 389, 15psi


title: Rat Hair 506, Sham Control


title: Rat Hair 522, 25psi


title: Rat Hair 511, 15psi


title: Rat Hair 390, 20psi


title: Rat Blood 517, 20psi


title: Rat Blood 509, Sham Control


title: Rat Blood 507, Sham Control


title: Rat Blood 516, 20psi


title: Rat Hair 386, 15psi


title: Rat Blood 527, 30psi


title: Rat Hair 526, 30psi


title: Rat Blood 514, 15psi


title: Rat Blood 506, Sham Control


title: Rat Blood 521, 25psi


title: Rat Hair 523, 25psi


title: Rat Hair 528, 30spi


title: Rat Blood 510, Sham Control


title: Rat Hair 521, 25psi


title: Rat Blood 511, 15psi


title: Rat Blood 530, 30psi


title: Rat Hair 387, 15psi


title: Rat Blood 528, 30psi


title: Rat Blood 526, 30psi


title: Rat Hair 402, 30psi


title: Rat Hair 383, Sham Control


title: Rat Blood 525, 25psi


title: Rat Hair 381, Sham Control


title: Rat Blood 508, Sham Control


title: Rat Blood 515, 15psi


title: Rat Blood 524, 25psi


title: Rat Hair 385, 15psi


title: HEY Ovarian Cancer 3D Spheroids_10

status: Public on Apr 18 2016

hyb_protocol: cDNA and then amplified and labeled with biotin using Affymetrix 3’IVT Expression System according to the manufacturer’s instructions. Hybridization with the biotin-labeled RNA, staining, and scanning of the chips followed the prescribed procedure outlined in the Affymetrix technical manual.

scan_protocol: The Arrays were scanned using the Affymetrix GCS3000 System (Scanner). Cel files containing normalized intensity data (RMA normalization) were generated using the Gene Expression Console (Affymetrix).

data_processing: Signal intensity was scaled to an average intensity of 500 during comparison analysis.

label: biotin

source_name: HEY Ovarian Cancer 3D Spheroids

label_protocol: RNA was converted to cDNA and then amplified and labeled with biotin using Affymetrix 3’IVT Expression System according to the manufacturer’s instructions.

growth_protocol: The HEY human ovarian cancer cell line was authenticated by short tandem repeat (STR) DNA profiling (Genetica, Inc.) and was compared to ATCC and previously published profiles (Gynecol Oncol. Oct 2012; 127(1): 241–248. ) Cells were cultured in a humidified incubator containing 5% CO2 at 37oC in RPMI with 10% fetal bovine serum and 1% Pen-Strep-Glutamine.  Spheroid formation was accomplished through the hanging drop method.  Briefly, trypsinized HEY cells were resuspended at 1 x 106 cells/mL in supplemented RPMI.  Multiple 25 µl droplets of the cell solution were then placed onto plate lids, inverted, and incubated for 72 hours to allow cells to aggregate into spheroids.

extract_protocol: HEY Human ovarian carcinoma cells treated with TGF-β were cultured on a 2-dimensional substrate or 3-dimensional substrate as described above.  Replicates of 4 separate experiments were performed on 4 different culturing days, cells isolated and stored in RNAlater Soln (Ambion) for no more than 7 days.  Up to 100µg of total RNA was isolated from all 8 samples using Qiagen’s RNeasy Mini Kit according to the manufacturer’s instructions. RNA integrity was verified with 1µl of total RNA on RNA 6000 chips (Agilent) using The Agilent 2100 Bioanalyzer.

treatment_protocol: To induce EMT, a final concentration of 10 ng/µl TGFβ was added to cells and incubated for 72 hours as monolayer cell culture or hanging drops during the creation of spheroids.  Following incubation, monolayer cells and spheroids were photographed using an Evos® FL Cell Imaging microscope (ThermoFisher Scientific) and then collected in 1X PBS.

tag: cell line

value: HEY Ovarian Cancer cells

tag: agent

value: TGFβ

tag: culture conditions

value: 3D Spheroids


title: HEY Ovarian Cancer 3D Spheroids_11


title: HEY Ovarian Cancer 3D Spheroids_12


title: HEY Ovarian Cancer 3D Spheroids_09


title: HEY Ovarian Cancer 2D monolayer_03

source_name: HEY Ovarian Cancer 2D monolayer

value: 2D monolayer


title: HEY Ovarian Cancer 2D monolayer_02


title: HEY Ovarian Cancer 2D monolayer_04


title: Rat Blood 519, 20psi

tag: developmental stage


title: Rat Hair 516, 20psi

tag: gender


title: Rat Hair 395, 25psi


title: IFNβ stimulation for 2.5hr biological rep 2

status: Public on Feb 02 2016

city: Rochester

first: Juilee

last: Thakar

state: New York

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

hyb_protocol: According to standard Affymetrix protocol.

data_processing: Data was normalized using GCRMA from simpleaffy package from Bioconductor

source_name: monocyte derived dendritic cells

label_protocol: Good-quality RNA was reverse transcribed using T7-oligo(dT)24 to yield double-stranded cDNA. cRNA was transcribed and biotinylated from cDNA templates.

growth_protocol: human peripheral blood mononuclear cells were isolated from buffy coats by Ficoll density gradient centrifugation and positive immunomagnetic purification for CD14 followed by a 5 day incubation with 500 U/ml  hGM-CSF  (Preprotech, Rocky Hill NJ) and 1000 U/ml hIL-4 (Preprotech, Rocky Hill NJ)

extract_protocol: Total RNA was purified from 2.5 × 106 DCs per time sample using RNeasyMicro (Qiagen, Valencia, CA) with DNase treatment. RNA was eluted from columns using water and quantified by spectrophotometry.

treatment_protocol: Cells treated with IFNB or control were harvested at 2.5 h. Naive DCs served as negative control.

tag: cell type

value: monocyte derived dendritic cellc (DCs)

tag: stimulation

value: IFNβ


title: IFNβ stimulation for 2.5hr biological rep 1

scan_protocol: According to standard Affymetrix protocol.


title: Naïve DCs biological rep 1


title: IFNβ stimulation for 2.5hr biological rep 3


title: Naïve DCs biological rep 3


title: Naïve DCs biological rep 2