title: SN12C_sunitinib_0nM_2h

description: gene expression data from SN12C treated with 0nM sunitinib for 2h


title: SN12C_sunitinib_0nM_24h

status: Public on Oct 09 2018

type: RNA

city: Rockville

first: Anne

last: Monks

state: MD

address: 9609 Medical Center Dr

department: Developmental Therapeutics Program

country: USA

institute: National Cancer Institute

description: gene expression data from SN12C treated with 0nM sunitinib for 24h

hyb_protocol: Biotin labeled antisense cRNA (4 µg per sample) was hybridized to Affymetrix GeneChip HT Human Genome U133A 96-Array plates overnight

scan_protocol: Plates were washed, stained, then scanned on an Affymetrix GeneTitan HT array plate scanner

data_processing: Data were collected using Affymetrix AGCC software.  Initial data quality control was performed using percent present calls generated by Affymetrix Quality Reporter software. Samples failing QC were repeated (R2)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human tumor cell line SN12C

label_protocol: Samples (96-well format, 1 µg each) were labeled using Affymetrix (Cleveland OH) HT One-Cycle Eukaryotic Labeling Kit on Biomek FX Target Prep Express system following manufacturer’s suggested protocols

growth_protocol: All cell lines were cultured in RPMI-1640 media with 10% FBS and L-Glutamine and incubated at 37oC, 5%CO2.

extract_protocol: Total RNA was isolated using the Qiagen Rneasy mini kit, quantitated by measuring absorbance at A260, quality of RNA was determined on a Caliper LabChip GX all samples used had an RQS>7.5

treatment_protocol: All drugs were dissolved in DMSO, diluted to their appropriate concentrations in culture media and added to the cells pre-plated for 24h (DMSO final concentration of 0.25%) , and incubated for the indicated times

tag: group

value: member of the NCI-60 cell line panel

tag: tissue

value: Renal


title: SK-MEL-5_sunitinib_200nM_2h

description: gene expression data from SK-MEL-5 treated with 200nM sunitinib for 2h

source_name: human tumor cell line SK-MEL-5

value: Melanoma


title: SK-MEL-5_sunitinib_2000nM_24h

description: gene expression data from SK-MEL-5 treated with 2000nM sunitinib for 24h


title: SN12C_sunitinib_0nM_6h

description: gene expression data from SN12C treated with 0nM sunitinib for 6h


title: SK-MEL-5_sunitinib_2000nM_2h

description: gene expression data from SK-MEL-5 treated with 2000nM sunitinib for 2h


title: SK-MEL-5_sunitinib_200nM_24h

description: gene expression data from SK-MEL-5 treated with 200nM sunitinib for 24h


title: SK-MEL-5_sunitinib_2000nM_6h

description: gene expression data from SK-MEL-5 treated with 2000nM sunitinib for 6h


title: SN12C_sunitinib_200nM_24h

description: gene expression data from SN12C treated with 200nM sunitinib for 24h


title: SK-MEL-2_sunitinib_200nM_6h

description: gene expression data from SK-MEL-2 treated with 200nM sunitinib for 6h

source_name: human tumor cell line SK-MEL-2


title: SK-MEL-2_sunitinib_200nM_24h

description: gene expression data from SK-MEL-2 treated with 200nM sunitinib for 24h


title: SK-MEL-5_sunitinib_0nM_6h

description: gene expression data from SK-MEL-5 treated with 0nM sunitinib for 6h


title: SK-MEL-5_sunitinib_0nM_24h

description: gene expression data from SK-MEL-5 treated with 0nM sunitinib for 24h


title: SK-MEL-5_sunitinib_0nM_2h

description: gene expression data from SK-MEL-5 treated with 0nM sunitinib for 2h


title: SK-MEL-2_sunitinib_200nM_2h

description: gene expression data from SK-MEL-2 treated with 200nM sunitinib for 2h


title: SK-MEL-2_sunitinib_2000nM_2h

description: gene expression data from SK-MEL-2 treated with 2000nM sunitinib for 2h


title: SK-MEL-2_sunitinib_2000nM_6h

description: gene expression data from SK-MEL-2 treated with 2000nM sunitinib for 6h


title: SK-MEL-2_sunitinib_2000nM_24h

description: gene expression data from SK-MEL-2 treated with 2000nM sunitinib for 24h


title: SK-MEL-28_sunitinib_200nM_2h

description: gene expression data from SK-MEL-28 treated with 200nM sunitinib for 2h

source_name: human tumor cell line SK-MEL-28


title: SK-MEL-2_sunitinib_0nM_6h

description: gene expression data from SK-MEL-2 treated with 0nM sunitinib for 6h


title: SK-MEL-28_sunitinib_200nM_6h

description: gene expression data from SK-MEL-28 treated with 200nM sunitinib for 6h


title: SK-MEL-28_sunitinib_2000nM_6h

description: gene expression data from SK-MEL-28 treated with 2000nM sunitinib for 6h


title: SK-MEL-28_sunitinib_2000nM_2h

description: gene expression data from SK-MEL-28 treated with 2000nM sunitinib for 2h


title: SK-MEL-28_sunitinib_200nM_24h

description: gene expression data from SK-MEL-28 treated with 200nM sunitinib for 24h


title: SK-MEL-28_sunitinib_2000nM_24h

description: gene expression data from SK-MEL-28 treated with 2000nM sunitinib for 24h


title: SK-MEL-28_sunitinib_0nM_2h

description: gene expression data from SK-MEL-28 treated with 0nM sunitinib for 2h


title: SK-MEL-28_sunitinib_0nM_6h

description: gene expression data from SK-MEL-28 treated with 0nM sunitinib for 6h


title: SF-539_sunitinib_200nM_2h

description: gene expression data from SF-539 treated with 200nM sunitinib for 2h

source_name: human tumor cell line SF-539

value: CNS


title: SF-539_sunitinib_200nM_6h

description: gene expression data from SF-539 treated with 200nM sunitinib for 6h


title: SK-MEL-28_sunitinib_0nM_24h

description: gene expression data from SK-MEL-28 treated with 0nM sunitinib for 24h


title: SF-539_sunitinib_200nM_24h

description: gene expression data from SF-539 treated with 200nM sunitinib for 24h


title: SF-539_sunitinib_2000nM_6h

description: gene expression data from SF-539 treated with 2000nM sunitinib for 6h


title: C2C12 H3K4me3 ChIP at 1k cells replicate 1

type: SRA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

library_source: genomic

data_processing:
The raw sequence reads were aligned to the mouse and human reference genomes (GRCm38 and GRCh38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained.
The bigWig files were generated using bamCoverage command of deepTools (ver. 2.4.2) with the option: --smoothLength x --binSize y, where x and y are specified in the file names.
The csv countmatrix files were generated with multiBamSummary with the option bins -bs 4000 (or 10000).
ChILT peaks were generated with Homer findPeaks with the options -style histone -style histone -gsize 3e9 -size 4000 -regionRes 1 -minDist 1 -fdr 0.2.
ChIP peaks were generated with MACS2 (ver. 2.1.1) with the options -g hs -q 0.01 --nomodel --shift 0 --extsize 200 --keep-dup all.
Genome_build: GRCm38/mm10 and GRCh38/hg38
Supplementary_files_format_and_content: bigWig files contain signal data for visualization via tools such as the Integrative Genomics Viewer, csv files include comma-delimited matrices, the bed file contains the peak data for C2C12, MCF-7 and MDA-MB-231 data.

molecule: genomic DNA

organism: Mus musculus

source_name: Immortal cell line

extract_protocol:
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.

tag: cell line

tag: antibody target

tag: primary antibody

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: C2C12 H3K4me3 ChIP at 10k cells replicate 2


title: C2C12 H3K4me3 ChIP at 1k cells replicate 2


title: SF-539_sunitinib_2000nM_2h

description: gene expression data from SF-539 treated with 2000nM sunitinib for 2h


title: SF-539_sunitinib_0nM_2h

description: gene expression data from SF-539 treated with 0nM sunitinib for 2h


title: C2C12 H3K4me3 at 100 cells (0.5ul of Tn5 added) replicate 1

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz

extract_protocol:
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Immunostaining half of the protocol includes cell dispensing, fixation, permeabilization, blocking, reaction to primary anti-body and the ChILT probe. The reactive probe are integrated into a proximal genomic region to where the primary antibody is bound upon Tn5 activation. The integrated ChILT DNA is used for the linear amplification of genomic sequences and the transcribed RNAs are utilized for library preparation for deep-sequencing.
Fixed cells were lysed and histone-DNA complexes were isolated with antibodies.
Libraries were prepared on the Illumina HiSeq1500 and 2500 platforms.


title: C2C12 H3K4me3 ChIP at 10k cells replicate 1


title: SF-295_sunitinib_200nM_6h

description: gene expression data from SF-295 treated with 200nM sunitinib for 6h

source_name: human tumor cell line SF-295


title: SK-MEL-2_sunitinib_0nM_2h

description: gene expression data from SK-MEL-2 treated with 0nM sunitinib for 2h


title: C2C12 H3K4me3 at 100 cells (0.5ul of Tn5 added) replicate 2


title: SF-295_sunitinib_200nM_2h

description: gene expression data from SF-295 treated with 200nM sunitinib for 2h


title: C2C12 H3K4me3 at 100 cells (0.5M KCl salt concentration) replicate 1


title: C2C12 H3K4me3 at 100 cells (0.5M KCl salt concentration) replicate 2


title: C2C12 H3K4me3 at 100 cells (0.5ul of EzTn5 added) replicate 2


title: SF-295_sunitinib_2000nM_2h

description: gene expression data from SF-295 treated with 2000nM sunitinib for 2h


title: SF-295_sunitinib_200nM_24h

description: gene expression data from SF-295 treated with 200nM sunitinib for 24h


title: SF-295_sunitinib_2000nM_6h

description: gene expression data from SF-295 treated with 2000nM sunitinib for 6h


title: SF-539_sunitinib_2000nM_24h

description: gene expression data from SF-539 treated with 2000nM sunitinib for 24h


title: SK-MEL-2_sunitinib_0nM_24h

description: gene expression data from SK-MEL-2 treated with 0nM sunitinib for 24h


title: SF-539_sunitinib_0nM_6h

description: gene expression data from SF-539 treated with 0nM sunitinib for 6h


title: SF-295_sunitinib_2000nM_24h

description: gene expression data from SF-295 treated with 2000nM sunitinib for 24h


title: C2C12 H3K4me3 at 100 cells (0.5ul of EzTn5 added) replicate 1


title: SF-539_sunitinib_0nM_24h

description: gene expression data from SF-539 treated with 0nM sunitinib for 24h


title: C2C12 H3K4me3 at 100 cells (1M KCl salt concentration) replicate 2


title: C2C12 H3K4me3 at 100 cells (1M NaCl salt concentration) replicate 2


title: C2C12 H3K4me3 at 100 cells (1M NaCl salt concentration) replicate 1


title: C2C12 H3K4me3 at 100 cells (1M KCl salt concentration) replicate 1


title: SF-295_sunitinib_0nM_2h

description: gene expression data from SF-295 treated with 0nM sunitinib for 2h


title: C2C12 H3K27me3 at 100 cells (0.5M KCl salt concentration) replicate 2

value: mouse monoclonal anti-H3K27me3 (Hayashi-Takanaka et al., Nucleic Acids Res. 2011 Aug;39(15):6475-88., CMA323)


title: C2C12 H3K27me3 at 100 cells (0.5M KCl salt concentration) replicate 1


title: C2C12 H3K27me3 at 100 cells (1M NaCl salt concentration) replicate 1


title: C2C12 H3K27me3 at 100 cells (1M KCl salt concentration) replicate 2


title: C2C12 ChILT-DNA at 100 cells (1M NaCl salt concentration) replicate 2

value: ChILT-DNA


title: C2C12 ChILT-DNA at 100 cells (1M NaCl salt concentration) replicate 1


title: C2C12 ChILT-DNA at 100 cells (0.5M KCl salt concentration) replicate 1


title: C2C12 ChILT-DNA at 100 cells (0.5M KCl salt concentration) replicate 2


title: UO-31_vorinostat_5000nM_6h

description: gene expression data from UO-31 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line UO-31


title: UO-31_vorinostat_5000nM_2h

description: gene expression data from UO-31 treated with 5000nM vorinostat for 2h


title: C2C12 H3K27me3 at 100 cells (1M NaCl salt concentration) replicate 2


title: UO-31_vorinostat_1000nM_2h

description: gene expression data from UO-31 treated with 1000nM vorinostat for 2h


title: UO-31_vorinostat_1000nM_24h

description: gene expression data from UO-31 treated with 1000nM vorinostat for 24h


title: UO-31_vorinostat_5000nM_24h

description: gene expression data from UO-31 treated with 5000nM vorinostat for 24h


title: SF-295_sunitinib_0nM_6h

description: gene expression data from SF-295 treated with 0nM sunitinib for 6h


title: UO-31_vorinostat_0nM_24h

description: gene expression data from UO-31 treated with 0nM vorinostat for 24h


title: C2C12 ChILT-DNA at 100 cells (1M KCl salt concentration) replicate 2

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz


title: C2C12 ChILT-DNA at 100 cells (1M KCl salt concentration) replicate 1


title: UO-31_vorinostat_0nM_6h

description: gene expression data from UO-31 treated with 0nM vorinostat for 6h


title: C2C12 H3K27me3 at 100 cells (1M KCl salt concentration) replicate 1


title: C2C12 H3K27ac at 1 cell replicate 2

value: mouse monoclonal anti-H3K27ac (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA309)


title: C2C12 H3K27ac at 1 cell replicate 1


title: UACC-62_vorinostat_1000nM_6h

description: gene expression data from UACC-62 treated with 1000nM vorinostat for 6h

source_name: human tumor cell line UACC-62


title: UACC-62_vorinostat_5000nM_24h

description: gene expression data from UACC-62 treated with 5000nM vorinostat for 24h


title: C2C12 H3K4me3 at 1 cell replicate 2


title: UACC-62_vorinostat_5000nM_6h

description: gene expression data from UACC-62 treated with 5000nM vorinostat for 6h


title: UACC-62_vorinostat_5000nM_2h

description: gene expression data from UACC-62 treated with 5000nM vorinostat for 2h


title: UO-31_vorinostat_1000nM_6h

description: gene expression data from UO-31 treated with 1000nM vorinostat for 6h


title: UO-31_vorinostat_0nM_2h

description: gene expression data from UO-31 treated with 0nM vorinostat for 2h


title: UACC-62_vorinostat_1000nM_2h

description: gene expression data from UACC-62 treated with 1000nM vorinostat for 2h


title: C2C12 H3K4me3 at 1 cell replicate 1


title: UACC-62_vorinostat_0nM_6h

description: gene expression data from UACC-62 treated with 0nM vorinostat for 6h


title: UACC-62_vorinostat_1000nM_24h

description: gene expression data from UACC-62 treated with 1000nM vorinostat for 24h


title: UACC-62_vorinostat_0nM_24h

description: gene expression data from UACC-62 treated with 0nM vorinostat for 24h


title: UACC-62_vorinostat_0nM_2h

description: gene expression data from UACC-62 treated with 0nM vorinostat for 2h


title: UACC-257_vorinostat_5000nM_6h

description: gene expression data from UACC-257 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line UACC-257


title: NIH3T3_1k_MyoD_plus-2

value: NIH 3T3

value: MyoD plus

value: rabbit polyclonal anti-MyoD (Santa Cruz, M-318)


title: UACC-257_vorinostat_5000nM_24h

description: gene expression data from UACC-257 treated with 5000nM vorinostat for 24h


title: NIH3T3_1k_MyoD_plus-1


title: C2C12 IgG at 100 cells replicate 2

description:
countMatrix10k_C2C12_cellnumbers.csv.gz
countMatrix4k_C2C12_cellnumbers.csv.gz

value: Control IgG


title: C2C12 IgG at 100 cells replicate 1


title: C2C12 CTCF at 1k cells replicate 2

value: CTCF

value: rabbit polyclonal anti-CTCF (Abcam, ab70303)


title: C2C12 CTCF at 1k cells replicate 1


title: UACC-257_vorinostat_1000nM_24h

description: gene expression data from UACC-257 treated with 1000nM vorinostat for 24h


title: C2C12 IgG at 1k cells replicate 1


title: UACC-257_vorinostat_5000nM_2h

description: gene expression data from UACC-257 treated with 5000nM vorinostat for 2h


title: C2C12 IgG at 1k cells replicate 2


title: NIH3T3_1k_MyoD_minus-2

value: MyoD minus


title: C2C12 IgG at 10k cells replicate 2


title: UACC-257_vorinostat_1000nM_6h

description: gene expression data from UACC-257 treated with 1000nM vorinostat for 6h


title: U251_vorinostat_5000nM_6h

description: gene expression data from U251 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line U251


title: UACC-257_vorinostat_1000nM_2h

description: gene expression data from UACC-257 treated with 1000nM vorinostat for 2h


title: UACC-257_vorinostat_0nM_24h

description: gene expression data from UACC-257 treated with 0nM vorinostat for 24h


title: C2C12 IgG at 100k cells replicate 2


title: UACC-257_vorinostat_0nM_2h

description: gene expression data from UACC-257 treated with 0nM vorinostat for 2h


title: C2C12 IgG at 10k cells replicate 1


title: U251_vorinostat_5000nM_24h

description: gene expression data from U251 treated with 5000nM vorinostat for 24h


title: UACC-257_vorinostat_0nM_6h

description: gene expression data from UACC-257 treated with 0nM vorinostat for 6h


title: C2C12 ChILT-DNA at 100 cells replicate 2


title: C2C12 IgG at 100k cells replicate 1


title: U251_vorinostat_1000nM_6h

description: gene expression data from U251 treated with 1000nM vorinostat for 6h


title: C2C12 ChILT-DNA at 1k cells replicate 2


title: C2C12 ChILT-DNA at 10k cells replicate 2


title: C2C12 ChILT-DNA at 1k cells replicate 1


title: U251_vorinostat_1000nM_24h

description: gene expression data from U251 treated with 1000nM vorinostat for 24h


title: C2C12 ChILT-DNA at 10k cells replicate 1


title: C2C12 ChILT-DNA at 100k cells replicate 2


title: C2C12 no Ab at 100 cells replicate 2

description:
countMatrix4k_C2C12_cellnumbers.csv.gz
countMatrix10k_C2C12_cellnumbers.csv.gz


title: C2C12 ChILT-DNA at 100k cells replicate 1


title: U251_vorinostat_0nM_2h

description: gene expression data from U251 treated with 0nM vorinostat for 2h


title: C2C12 no Ab at 1k cells replicate 2


title: U251_vorinostat_0nM_24h

description: gene expression data from U251 treated with 0nM vorinostat for 24h


title: C2C12 no Ab at 100 cells replicate 1


title: U251_vorinostat_5000nM_2h

description: gene expression data from U251 treated with 5000nM vorinostat for 2h


title: NIH3T3_1k_MyoD_minus-1


title: C2C12 no Ab at 1k cells replicate 1


title: TK-10_vorinostat_5000nM_24h

description: gene expression data from TK-10 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line TK-10


title: TK-10_vorinostat_5000nM_2h

description: gene expression data from TK-10 treated with 5000nM vorinostat for 2h


title: U251_vorinostat_0nM_6h

description: gene expression data from U251 treated with 0nM vorinostat for 6h


title: TK-10_vorinostat_1000nM_6h

description: gene expression data from TK-10 treated with 1000nM vorinostat for 6h


title: TK-10_vorinostat_1000nM_2h

description: gene expression data from TK-10 treated with 1000nM vorinostat for 2h


title: TK-10_vorinostat_1000nM_24h

description: gene expression data from TK-10 treated with 1000nM vorinostat for 24h


title: TK-10_vorinostat_0nM_6h

description: gene expression data from TK-10 treated with 0nM vorinostat for 6h


title: C2C12 no Ab at 10k cells replicate 1


title: C2C12 no Ab at 10k cells replicate 2


title: U251_vorinostat_1000nM_2h

description: gene expression data from U251 treated with 1000nM vorinostat for 2h


title: TK-10_vorinostat_0nM_2h

description: gene expression data from TK-10 treated with 0nM vorinostat for 2h


title: C2C12 no Ab at 100k cells replicate 1


title: T-47D_vorinostat_5000nM_6h

description: gene expression data from T-47D treated with 5000nM vorinostat for 6h

source_name: human tumor cell line T-47D

value: Breast


title: TK-10_vorinostat_5000nM_6h

description: gene expression data from TK-10 treated with 5000nM vorinostat for 6h


title: C2C12 H3K27me3 at 100 cells replicate 1


title: C2C12 H3K27ac at 100 cells replicate 1


title: C2C12 H3K27ac at 100 cells replicate 2


title: T-47D_vorinostat_1000nM_6h

description: gene expression data from T-47D treated with 1000nM vorinostat for 6h


title: T-47D_vorinostat_5000nM_2h

description: gene expression data from T-47D treated with 5000nM vorinostat for 2h


title: C2C12 no Ab at 100k cells replicate 2

description:
countMatrix4k_C2C12_cellnumbers.csv.gz
countMatrix10k_C2C12_cellnumbers.csv.gz


title: C2C12 H3K27me3 at 100 cells replicate 2


title: T-47D_vorinostat_5000nM_24h

description: gene expression data from T-47D treated with 5000nM vorinostat for 24h


title: bmj21L

city: Fujisawa

first: Hideaki

last: Takano

state: KANAGAWA

address: 1866, Kameino

department: College of Bioresource Sciences

institute: Nihon University

description: This sample is of wild-type Burkholderia multivorans cultured under the light condition for 21 h.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Burkholderia multivorans

source_name: cDNA prepared from light culture of B. multivorans in middle stationary phase

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: B. multivorans ATCC 17616 strain was grown in LB at 28°C at 135 strokes/min for 14 or 21 hrs under dark and light conditions.

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA). Total RNA was extracted using RNeasy Midi kit (Qiagen).

tag: strain

tag: growth phase

value: middle stationary

tag: light status

value: light culture


title: bmj21D

description: This sample is of wild-type Burkholderia multivorans cultured under the dark condition for 21 h.

source_name: cDNA prepared from dark culture of B. multivorans in middle stationary phase

value: dark culture


title: bmj14L

description: This sample is of wild-type Burkholderia multivorans cultured under the light condition for 14 h.

source_name: cDNA prepared from light culture of B. multivorans in early stationary phase

value: early stationary


title: T-47D_vorinostat_1000nM_2h

description: gene expression data from T-47D treated with 1000nM vorinostat for 2h

value: member of the NCI-60 cell line panel


title: T-47D_vorinostat_0nM_24h

description: gene expression data from T-47D treated with 0nM vorinostat for 24h


title: T-47D_vorinostat_0nM_6h

description: gene expression data from T-47D treated with 0nM vorinostat for 6h


title: C2C12 ChILT-DNA at 100 cells replicate 1

description:
countMatrix10k_C2C12_cellnumbers.csv.gz
countMatrix4k_C2C12_cellnumbers.csv.gz


title: C2C12 H3K4me3 at 100 cells replicate 2

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: C2C12 H3K4me3 at 100 cells replicate 1


title: Pp2FbFP_ROS_5min_III

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For calculation and normalization of ratios reflecting the relative mRNA levels (Ratio of Medians, GenePix Pro), GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Neusser T., Polen T., Geissen R., Wagner R. (2010)  Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery.  BMC Genomics 11: 165; doi: 10.1186/1471-2164-11-165

growth_protocol: To analyze differences in global oxidative stress response in E. coli that were induced by Pp2FbFP and DsFbFP M49I, a DNA microarray-based analysis was conducted. E. coli cells expressing the respective photosensitizers were cultivated in LB media, supplemented with 50 μg ml-1 kanamycin (25 ml culture volume in 500 ml Erlenmeyer flasks, start OD580 = 0.05). The cultures were incubated at 37 °C and under continuous shaking (130 rpm) in the dark. LOV-FP expression was induced by addition of 0.4 mM IPTG during the  logarithmic growth phase (~OD580 = 0.7). Three hours after induction, cultures were divided into two test cultures with a volume of 25 ml in 500 ml Erlenmeyer flaks and an OD580 of 0.5. For light treatment one of these cultures was placed between two blue-light emitting LED-panels (λ = 462 nm, 100 mW cm-2, Insta Elektro, Lüdenscheid, Germany, panel distance: 30 cm), whereas the second culture was kept in the dark. To ensure optimal oxygen supply of cells during irradiation process, cultures were supplemented with stirring bars and placed on magnetic stirrers. Since the selectivity and efficiency of light-driven ROS formation strongly vary between those proteins, we first evaluated different exposure times (5, 10, 15 and 30 minutes) for full induction of LOV-FP-mediated stress-response in E.coli. To this end, samples containing an OD580 of 3 were harvested after light treatment by centrifugation and the cell pellets were shock frozen in liquid nitrogen and subsequently stored at -80°C. RNA isolation, cDNA synthesis, microarray hybridization and data analyses were performed as described before92 except the utilization of DNA-microarrays carrying probes for the genes of E. coli MG1655 strain. Detailed transcriptome analyses of light-induced stress-response based on independent biological triplicates were finally carried out under best illumination conditions (i.e. Pp2FbFP: 5 min, DsFbFP M49I: 15 min) as described above.

extract_protocol: The preparation of total RNA was performed with the RNeasy Kit from Qiagen as described (Hanke T., Nöh K., Noack S., Polen T., Bringer S., Sahm H., Wiechert W., Bott M. (2013)  Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H. Appl Environ Microbiol 79: 2336-48; doi: 10.1128/AEM.03414-12)

treatment_protocol: see growth protocol

tag: induced by

tag: treatment

value: plus 5min blue light

value: no blue light


title: TK-10_vorinostat_0nM_24h

description: gene expression data from TK-10 treated with 0nM vorinostat for 24h

value: Renal


title: SW-620_vorinostat_1000nM_24h

description: gene expression data from SW-620 treated with 1000nM vorinostat for 24h

source_name: human tumor cell line SW-620

value: Colon


title: Pp2FbFP_ROS_5min_II


title: T-47D_vorinostat_0nM_2h

description: gene expression data from T-47D treated with 0nM vorinostat for 2h


title: SW-620_vorinostat_5000nM_24h

description: gene expression data from SW-620 treated with 5000nM vorinostat for 24h


title: SW-620_vorinostat_1000nM_2h

description: gene expression data from SW-620 treated with 1000nM vorinostat for 2h


title: SW-620_vorinostat_5000nM_2h

description: gene expression data from SW-620 treated with 5000nM vorinostat for 2h


title: SW-620_vorinostat_0nM_2h

description: gene expression data from SW-620 treated with 0nM vorinostat for 2h


title: SW-620_vorinostat_0nM_6h

description: gene expression data from SW-620 treated with 0nM vorinostat for 6h


title: SW-620_vorinostat_0nM_24h

description: gene expression data from SW-620 treated with 0nM vorinostat for 24h


title: T-47D_vorinostat_1000nM_24h

description: gene expression data from T-47D treated with 1000nM vorinostat for 24h


title: Pp2FbFP_ROS_5min_I


title: SR_vorinostat_5000nM_6h

description: gene expression data from SR treated with 5000nM vorinostat for 6h

source_name: human tumor cell line SR

value: Leukemia


title: M49I_ROS_15min_III

value: pET28a-DsFbFP M49I

value: plus 15min blue light


title: M49I_ROS_15min_II


title: M49I_ROS_15min_I


title: SR_vorinostat_5000nM_2h

description: gene expression data from SR treated with 5000nM vorinostat for 2h


title: SR_vorinostat_5000nM_24h

description: gene expression data from SR treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3C7

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv

library_source: transcriptomic

data_processing:
NextSeq 500
bcl2fastq v.20.0.422
cutadapt v.1.15
BWA-mem v0.7.16
python  3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: Feature counts of all RNA seq data from 1, 10 and 50 cells can be found in Feature_counts_scRNAseq_set_two.tsv. Single-cell samples with appropriate coverage (more than 500 genes captured with at least 10 read counts per gene) were considered for VSG expression analysis and are listed in VSG_raw_counts_scRNAseq_set_two.tsv.
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq II

organism: Trypanosoma brucei brucei

source_name: single cell

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1, 10 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.

value: Lister 427 MITat 1.2

tag: genotyope

tag: life cycle stage

value: bloodstream form


title: ΔH3.V/ΔH4.V_T3C10


title: ΔH3.V/ΔH4.V_T3C9


title: ΔH3.V/ΔH4.V_T3C12

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv

source_name: 50 cells


title: ΔH3.V/ΔH4.V_T3C6


title: ΔH3.V/ΔH4.V_T3C11


title: ΔH3.V/ΔH4.V_T3C8


title: ΔH3.V/ΔH4.V_T3C4


title: SR_vorinostat_1000nM_2h

description: gene expression data from SR treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3C5


title: ΔH3.V/ΔH4.V_T3C3


title: SR_vorinostat_0nM_6h

description: gene expression data from SR treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T3C2


title: SR_vorinostat_1000nM_24h

description: gene expression data from SR treated with 1000nM vorinostat for 24h


title: SNB-75_vorinostat_5000nM_6h

description: gene expression data from SNB-75 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line SNB-75

value: CNS


title: SR_vorinostat_0nM_2h

description: gene expression data from SR treated with 0nM vorinostat for 2h


title: SNB-75_vorinostat_5000nM_24h

description: gene expression data from SNB-75 treated with 5000nM vorinostat for 24h


title: SR_vorinostat_0nM_24h

description: gene expression data from SR treated with 0nM vorinostat for 24h


title: SNB-75_vorinostat_5000nM_2h

description: gene expression data from SNB-75 treated with 5000nM vorinostat for 2h


title: SNB-75_vorinostat_1000nM_6h

description: gene expression data from SNB-75 treated with 1000nM vorinostat for 6h


title: SNB-75_vorinostat_1000nM_2h

description: gene expression data from SNB-75 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3B12


title: SNB-75_vorinostat_0nM_6h

description: gene expression data from SNB-75 treated with 0nM vorinostat for 6h


title: SNB-75_vorinostat_1000nM_24h

description: gene expression data from SNB-75 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3B11


title: ΔH3.V/ΔH4.V_T3B9


title: ΔH3.V/ΔH4.V_T3B8


title: ΔH3.V/ΔH4.V_T3B10


title: ΔH3.V/ΔH4.V_T3B7


title: ΔH3.V/ΔH4.V_T3B6


title: SNB-75_vorinostat_0nM_2h

description: gene expression data from SNB-75 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3C1


title: SNB-19_vorinostat_5000nM_6h

description: gene expression data from SNB-19 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line SNB-19


title: ΔH3.V/ΔH4.V_T3B5


title: SNB-19_vorinostat_5000nM_24h

description: gene expression data from SNB-19 treated with 5000nM vorinostat for 24h


title: SNB-19_vorinostat_5000nM_2h

description: gene expression data from SNB-19 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3B3

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T3B2


title: SR_vorinostat_1000nM_6h

description: gene expression data from SR treated with 1000nM vorinostat for 6h


title: SNB-19_vorinostat_1000nM_2h

description: gene expression data from SNB-19 treated with 1000nM vorinostat for 2h


title: SNB-19_vorinostat_1000nM_24h

description: gene expression data from SNB-19 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3A12


title: ΔH3.V/ΔH4.V_T3A11

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T3A8


title: ΔH3.V/ΔH4.V_T3A9


title: SNB-19_vorinostat_0nM_6h

description: gene expression data from SNB-19 treated with 0nM vorinostat for 6h


title: SNB-19_vorinostat_0nM_24h

description: gene expression data from SNB-19 treated with 0nM vorinostat for 24h


title: SNB-75_vorinostat_0nM_24h

description: gene expression data from SNB-75 treated with 0nM vorinostat for 24h


title: SN12C_vorinostat_5000nM_2h

description: gene expression data from SN12C treated with 5000nM vorinostat for 2h

source_name: human tumor cell line SN12C


title: SNB-19_vorinostat_1000nM_6h

description: gene expression data from SNB-19 treated with 1000nM vorinostat for 6h


title: SNB-19_vorinostat_0nM_2h

description: gene expression data from SNB-19 treated with 0nM vorinostat for 2h


title: SN12C_vorinostat_5000nM_6h

description: gene expression data from SN12C treated with 5000nM vorinostat for 6h


title: SN12C_vorinostat_5000nM_24h

description: gene expression data from SN12C treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T3A10


title: ΔH3.V/ΔH4.V_T3A6


title: ΔH3.V/ΔH4.V_T3A7


title: ΔH3.V/ΔH4.V_T3A5


title: ΔH3.V/ΔH4.V_T3B1


title: SN12C_vorinostat_1000nM_24h

description: gene expression data from SN12C treated with 1000nM vorinostat for 24h


title: SN12C_vorinostat_1000nM_2h

description: gene expression data from SN12C treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3A4


title: ΔH3.V/ΔH4.V_T3B4


title: SN12C_vorinostat_0nM_2h

description: gene expression data from SN12C treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T3A3


title: ΔH3.V/ΔH4.V_T3A2


title: SN12C_vorinostat_1000nM_6h

description: gene expression data from SN12C treated with 1000nM vorinostat for 6h


title: bmj14D

description: This sample is of wild-type Burkholderia multivorans cultured under the dark condition for 14 h.

source_name: cDNA prepared from dark culture of B. multivorans in early stationary phase


title: SN12C_vorinostat_0nM_6h

description: gene expression data from SN12C treated with 0nM vorinostat for 6h


title: SN12C_vorinostat_0nM_24h

description: gene expression data from SN12C treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2H12

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T3A1


title: ΔH3.V/ΔH4.V_T2H9


title: ΔH3.V/ΔH4.V_T2H8


title: ΔH3.V/ΔH4.V_T2H10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T2H11


title: SK-OV-3_vorinostat_5000nM_2h

description: gene expression data from SK-OV-3 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line SK-OV-3

value: Ovarian


title: SK-OV-3_vorinostat_5000nM_6h

description: gene expression data from SK-OV-3 treated with 5000nM vorinostat for 6h


title: SK-OV-3_vorinostat_1000nM_6h

description: gene expression data from SK-OV-3 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2H7


title: ΔH3.V/ΔH4.V_T2H5


title: ΔH3.V/ΔH4.V_T2H4


title: ΔH3.V/ΔH4.V_T2H6


title: ΔH3.V/ΔH4.V_T2H2


title: SK-OV-3_vorinostat_0nM_2h

description: gene expression data from SK-OV-3 treated with 0nM vorinostat for 2h


title: SK-OV-3_vorinostat_1000nM_2h

description: gene expression data from SK-OV-3 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2H3


title: SK-MEL-5_vorinostat_5000nM_24h

description: gene expression data from SK-MEL-5 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line SK-MEL-5

value: Melanoma


title: SK-OV-3_vorinostat_0nM_24h

description: gene expression data from SK-OV-3 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2H1


title: SK-MEL-5_vorinostat_5000nM_6h

description: gene expression data from SK-MEL-5 treated with 5000nM vorinostat for 6h


title: SK-OV-3_vorinostat_1000nM_24h

description: gene expression data from SK-OV-3 treated with 1000nM vorinostat for 24h


title: SK-MEL-5_vorinostat_5000nM_2h

description: gene expression data from SK-MEL-5 treated with 5000nM vorinostat for 2h


title: SK-OV-3_vorinostat_5000nM_24h

description: gene expression data from SK-OV-3 treated with 5000nM vorinostat for 24h


title: SK-MEL-5_vorinostat_1000nM_6h

description: gene expression data from SK-MEL-5 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2G12


title: SK-MEL-5_vorinostat_1000nM_24h

description: gene expression data from SK-MEL-5 treated with 1000nM vorinostat for 24h


title: SK-OV-3_vorinostat_0nM_6h

description: gene expression data from SK-OV-3 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2G9


title: ΔH3.V/ΔH4.V_T2G10


title: ΔH3.V/ΔH4.V_T2G11


title: ΔH3.V/ΔH4.V_T2G8


title: ΔH3.V/ΔH4.V_T2G7


title: ΔH3.V/ΔH4.V_T2G6


title: SK-MEL-2_vorinostat_5000nM_24h

description: gene expression data from SK-MEL-2 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line SK-MEL-2


title: SK-MEL-2_vorinostat_5000nM_2h

description: gene expression data from SK-MEL-2 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2G5

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: SK-MEL-5_vorinostat_1000nM_2h

description: gene expression data from SK-MEL-5 treated with 1000nM vorinostat for 2h


title: SK-MEL-2_vorinostat_5000nM_6h

description: gene expression data from SK-MEL-2 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2G4

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: SK-MEL-2_vorinostat_1000nM_6h

description: gene expression data from SK-MEL-2 treated with 1000nM vorinostat for 6h


title: SK-MEL-5_vorinostat_0nM_24h

description: gene expression data from SK-MEL-5 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2G3


title: SK-MEL-5_vorinostat_0nM_6h

description: gene expression data from SK-MEL-5 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2G2


title: ΔH3.V/ΔH4.V_T2G1


title: SK-MEL-2_vorinostat_1000nM_2h

description: gene expression data from SK-MEL-2 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2F12


title: SK-MEL-5_vorinostat_0nM_2h

description: gene expression data from SK-MEL-5 treated with 0nM vorinostat for 2h


title: SK-MEL-2_vorinostat_0nM_2h

description: gene expression data from SK-MEL-2 treated with 0nM vorinostat for 2h


title: SK-MEL-2_vorinostat_0nM_6h

description: gene expression data from SK-MEL-2 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2F10


title: ΔH3.V/ΔH4.V_T2F9


title: SK-MEL-2_vorinostat_1000nM_24h

description: gene expression data from SK-MEL-2 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2F11


title: ΔH3.V/ΔH4.V_T2F8


title: SK-MEL-2_vorinostat_0nM_24h

description: gene expression data from SK-MEL-2 treated with 0nM vorinostat for 24h


title: SK-MEL-28_vorinostat_5000nM_24h

description: gene expression data from SK-MEL-28 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line SK-MEL-28


title: ΔH3.V/ΔH4.V_T2F6


title: ΔH3.V/ΔH4.V_T2F5


title: ΔH3.V/ΔH4.V_T2F4


title: SK-MEL-28_vorinostat_1000nM_2h

description: gene expression data from SK-MEL-28 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2F2


title: SK-MEL-28_vorinostat_1000nM_6h

description: gene expression data from SK-MEL-28 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2F1


title: SK-MEL-28_vorinostat_1000nM_24h

description: gene expression data from SK-MEL-28 treated with 1000nM vorinostat for 24h


title: SK-MEL-28_vorinostat_5000nM_2h

description: gene expression data from SK-MEL-28 treated with 5000nM vorinostat for 2h


title: SK-MEL-28_vorinostat_0nM_24h

description: gene expression data from SK-MEL-28 treated with 0nM vorinostat for 24h


title: SK-MEL-28_vorinostat_0nM_6h

description: gene expression data from SK-MEL-28 treated with 0nM vorinostat for 6h


title: SF-539_vorinostat_5000nM_6h

description: gene expression data from SF-539 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line SF-539


title: SF-539_vorinostat_5000nM_2h

description: gene expression data from SF-539 treated with 5000nM vorinostat for 2h


title: SK-MEL-28_vorinostat_0nM_2h

description: gene expression data from SK-MEL-28 treated with 0nM vorinostat for 2h


title: SF-539_vorinostat_5000nM_24h

description: gene expression data from SF-539 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2F7

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T2E10


title: ΔH3.V/ΔH4.V_T2E9


title: SF-539_vorinostat_1000nM_6h

description: gene expression data from SF-539 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2E7


title: ΔH3.V/ΔH4.V_T2E12


title: ΔH3.V/ΔH4.V_T2E11


title: ΔH3.V/ΔH4.V_T2F3


title: ΔH3.V/ΔH4.V_T2E8


title: SF-539_vorinostat_1000nM_2h

description: gene expression data from SF-539 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2E5


title: SF-539_vorinostat_1000nM_24h

description: gene expression data from SF-539 treated with 1000nM vorinostat for 24h


title: SF-539_vorinostat_0nM_2h

description: gene expression data from SF-539 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2E6


title: ΔH3.V/ΔH4.V_T2E4


title: SF-539_vorinostat_0nM_6h

description: gene expression data from SF-539 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2E3


title: ΔH3.V/ΔH4.V_T2E2


title: SF-295_vorinostat_1000nM_6h

description: gene expression data from SF-295 treated with 1000nM vorinostat for 6h

source_name: human tumor cell line SF-295


title: ΔH3.V/ΔH4.V_T2E1


title: SF-295_vorinostat_5000nM_24h

description: gene expression data from SF-295 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2D12

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: SF-295_vorinostat_5000nM_6h

description: gene expression data from SF-295 treated with 5000nM vorinostat for 6h


title: SF-539_vorinostat_0nM_24h

description: gene expression data from SF-539 treated with 0nM vorinostat for 24h


title: SF-295_vorinostat_1000nM_2h

description: gene expression data from SF-295 treated with 1000nM vorinostat for 2h


title: SF-295_vorinostat_1000nM_24h

description: gene expression data from SF-295 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2D9


title: ΔH3.V/ΔH4.V_T2D10


title: SF-295_vorinostat_0nM_2h

description: gene expression data from SF-295 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2D8


title: ΔH3.V/ΔH4.V_T2D5


title: ΔH3.V/ΔH4.V_T2D11


title: ΔH3.V/ΔH4.V_T2D7


title: SF-295_vorinostat_0nM_24h

description: gene expression data from SF-295 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2D4


title: SF-268_vorinostat_5000nM_2h

description: gene expression data from SF-268 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line SF-268


title: ΔH3.V/ΔH4.V_T2D3


title: ΔH3.V/ΔH4.V_T2D1


title: ΔH3.V/ΔH4.V_T2C12


title: SF-295_vorinostat_5000nM_2h

description: gene expression data from SF-295 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2D6


title: SF-268_vorinostat_1000nM_6h

description: gene expression data from SF-268 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2C10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T2C11


title: ΔH3.V/ΔH4.V_T2C9


title: ΔH3.V/ΔH4.V_T2C8


title: ΔH3.V/ΔH4.V_T2C7


title: SF-268_vorinostat_1000nM_24h

description: gene expression data from SF-268 treated with 1000nM vorinostat for 24h


title: SF-268_vorinostat_1000nM_2h

description: gene expression data from SF-268 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2D2


title: SF-268_vorinostat_0nM_6h

description: gene expression data from SF-268 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2C6


title: SF-295_vorinostat_0nM_6h

description: gene expression data from SF-295 treated with 0nM vorinostat for 6h


title: SF-268_vorinostat_5000nM_6h

description: gene expression data from SF-268 treated with 5000nM vorinostat for 6h


title: SF-268_vorinostat_0nM_24h

description: gene expression data from SF-268 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2C5


title: RXF-393_vorinostat_5000nM_2h

description: gene expression data from RXF-393 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line RXF-393


title: RXF-393_vorinostat_0nM_6h

description: gene expression data from RXF-393 treated with 0nM vorinostat for 6h


title: SF-268_vorinostat_5000nM_24h

description: gene expression data from SF-268 treated with 5000nM vorinostat for 24h


title: RXF-393_vorinostat_0nM_2h

description: gene expression data from RXF-393 treated with 0nM vorinostat for 2h


title: RXF-393_vorinostat_5000nM_6h

description: gene expression data from RXF-393 treated with 5000nM vorinostat for 6h


title: SF-268_vorinostat_0nM_2h

description: gene expression data from SF-268 treated with 0nM vorinostat for 2h


title: RXF-393_vorinostat_1000nM_2h

description: gene expression data from RXF-393 treated with 1000nM vorinostat for 2h


title: RXF-393_vorinostat_1000nM_6h

description: gene expression data from RXF-393 treated with 1000nM vorinostat for 6h


title: RXF-393_vorinostat_5000nM_24h

description: gene expression data from RXF-393 treated with 5000nM vorinostat for 24h


title: RXF-393_vorinostat_1000nM_24h

description: gene expression data from RXF-393 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2C4

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: RXF-393_vorinostat_0nM_24h

description: gene expression data from RXF-393 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T2C3


title: ΔH3.V/ΔH4.V_T2C2


title: ΔH3.V/ΔH4.V_T2C1


title: ΔH3.V/ΔH4.V_T2B12


title: PC-3_vorinostat_5000nM_24h

description: gene expression data from PC-3 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line PC-3

value: Prostate


title: ΔH3.V/ΔH4.V_T2B11


title: ΔH3.V/ΔH4.V_T2B10


title: ΔH3.V/ΔH4.V_T2B9


title: ΔH3.V/ΔH4.V_T2B7


title: PC-3_vorinostat_5000nM_2h

description: gene expression data from PC-3 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2B8


title: ΔH3.V/ΔH4.V_T2B4


title: ΔH3.V/ΔH4.V_T2B6


title: PC-3_vorinostat_0nM_6h

description: gene expression data from PC-3 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2B5


title: PC-3_vorinostat_1000nM_6h

description: gene expression data from PC-3 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2B3


title: ΔH3.V/ΔH4.V_T2B2


title: PC-3_vorinostat_1000nM_24h

description: gene expression data from PC-3 treated with 1000nM vorinostat for 24h


title: PC-3_vorinostat_0nM_24h

description: gene expression data from PC-3 treated with 0nM vorinostat for 24h


title: PC-3_vorinostat_5000nM_6h

description: gene expression data from PC-3 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2B1


title: PC-3_vorinostat_1000nM_2h

description: gene expression data from PC-3 treated with 1000nM vorinostat for 2h


title: PC-3_vorinostat_0nM_2h

description: gene expression data from PC-3 treated with 0nM vorinostat for 2h


title: OVCAR-8_vorinostat_5000nM_6h

description: gene expression data from OVCAR-8 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line OVCAR-8


title: OVCAR-8_vorinostat_5000nM_2h

description: gene expression data from OVCAR-8 treated with 5000nM vorinostat for 2h


title: OVCAR-8_vorinostat_5000nM_24h

description: gene expression data from OVCAR-8 treated with 5000nM vorinostat for 24h


title: OVCAR-8_vorinostat_1000nM_6h

description: gene expression data from OVCAR-8 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2A11


title: OVCAR-8_vorinostat_0nM_6h

description: gene expression data from OVCAR-8 treated with 0nM vorinostat for 6h


title: OVCAR-8_vorinostat_1000nM_24h

description: gene expression data from OVCAR-8 treated with 1000nM vorinostat for 24h


title: SK-MEL-28_vorinostat_5000nM_6h

description: gene expression data from SK-MEL-28 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2A10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T2A9


title: ΔH3.V/ΔH4.V_T2A8


title: ΔH3.V/ΔH4.V_T2A6


title: ΔH3.V/ΔH4.V_T2A7


title: ΔH3.V/ΔH4.V_T2A4


title: ΔH3.V/ΔH4.V_T2A5


title: ΔH3.V/ΔH4.V_T2A12


title: OVCAR-5_vorinostat_5000nM_6h

description: gene expression data from OVCAR-5 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line OVCAR-5


title: ΔH3.V/ΔH4.V_T2A3

source_name: single cell


title: OVCAR-8_vorinostat_1000nM_2h

description: gene expression data from OVCAR-8 treated with 1000nM vorinostat for 2h


title: OVCAR-5_vorinostat_5000nM_24h

description: gene expression data from OVCAR-5 treated with 5000nM vorinostat for 24h


title: OVCAR-8_vorinostat_0nM_24h

description: gene expression data from OVCAR-8 treated with 0nM vorinostat for 24h


title: OVCAR-5_vorinostat_5000nM_2h

description: gene expression data from OVCAR-5 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1H12


title: OVCAR-5_vorinostat_1000nM_6h

description: gene expression data from OVCAR-5 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T2A2


title: OVCAR-5_vorinostat_1000nM_24h

description: gene expression data from OVCAR-5 treated with 1000nM vorinostat for 24h


title: OVCAR-5_vorinostat_1000nM_2h

description: gene expression data from OVCAR-5 treated with 1000nM vorinostat for 2h


title: OVCAR-8_vorinostat_0nM_2h

description: gene expression data from OVCAR-8 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T2A1


title: OVCAR-5_vorinostat_0nM_2h

description: gene expression data from OVCAR-5 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1H11


title: OVCAR-5_vorinostat_0nM_24h

description: gene expression data from OVCAR-5 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1H10


title: ΔH3.V/ΔH4.V_T1H9


title: ΔH3.V/ΔH4.V_T1H8


title: OVCAR-4_vorinostat_5000nM_24h

description: gene expression data from OVCAR-4 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line OVCAR-4


title: ΔH3.V/ΔH4.V_T1H7


title: ΔH3.V/ΔH4.V_T1H6


title: OVCAR-4_vorinostat_1000nM_6h

description: gene expression data from OVCAR-4 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1H5


title: OVCAR-5_vorinostat_0nM_6h

description: gene expression data from OVCAR-5 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1H4


title: OVCAR-4_vorinostat_1000nM_2h

description: gene expression data from OVCAR-4 treated with 1000nM vorinostat for 2h


title: OVCAR-4_vorinostat_5000nM_2h

description: gene expression data from OVCAR-4 treated with 5000nM vorinostat for 2h


title: OVCAR-4_vorinostat_0nM_2h

description: gene expression data from OVCAR-4 treated with 0nM vorinostat for 2h


title: OVCAR-4_vorinostat_1000nM_24h

description: gene expression data from OVCAR-4 treated with 1000nM vorinostat for 24h


title: OVCAR-4_vorinostat_0nM_6h

description: gene expression data from OVCAR-4 treated with 0nM vorinostat for 6h


title: OVCAR-4_vorinostat_5000nM_6h

description: gene expression data from OVCAR-4 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1H1

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T1H2


title: ΔH3.V/ΔH4.V_T1G12


title: ΔH3.V/ΔH4.V_T1G10


title: ΔH3.V/ΔH4.V_T1G11


title: OVCAR-3_vorinostat_5000nM_6h

description: gene expression data from OVCAR-3 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line OVCAR-3


title: ΔH3.V/ΔH4.V_T1G9


title: ΔH3.V/ΔH4.V_T1G8


title: ΔH3.V/ΔH4.V_T1G7


title: ΔH3.V/ΔH4.V_T1G6


title: OVCAR-3_vorinostat_1000nM_2h

description: gene expression data from OVCAR-3 treated with 1000nM vorinostat for 2h


title: OVCAR-3_vorinostat_1000nM_24h

description: gene expression data from OVCAR-3 treated with 1000nM vorinostat for 24h


title: OVCAR-3_vorinostat_5000nM_24h

description: gene expression data from OVCAR-3 treated with 5000nM vorinostat for 24h


title: OVCAR-4_vorinostat_0nM_24h

description: gene expression data from OVCAR-4 treated with 0nM vorinostat for 24h


title: OVCAR-3_vorinostat_0nM_2h

description: gene expression data from OVCAR-3 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1G5


title: ΔH3.V/ΔH4.V_T1G4


title: ΔH3.V/ΔH4.V_T1H3


title: ΔH3.V/ΔH4.V_T1G3


title: ΔH3.V/ΔH4.V_T1G2


title: OVCAR-3_vorinostat_1000nM_6h

description: gene expression data from OVCAR-3 treated with 1000nM vorinostat for 6h


title: NCI-H522_vorinostat_5000nM_6h

description: gene expression data from NCI-H522 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line NCI-H522

value: Lung


title: OVCAR-3_vorinostat_0nM_24h

description: gene expression data from OVCAR-3 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1F12

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: NCI-H522_vorinostat_5000nM_2h

description: gene expression data from NCI-H522 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1F11


title: OVCAR-3_vorinostat_5000nM_2h

description: gene expression data from OVCAR-3 treated with 5000nM vorinostat for 2h


title: NCI-H522_vorinostat_1000nM_6h

description: gene expression data from NCI-H522 treated with 1000nM vorinostat for 6h


title: NCI-H522_vorinostat_5000nM_24h

description: gene expression data from NCI-H522 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1F10


title: NCI-H522_vorinostat_1000nM_2h

description: gene expression data from NCI-H522 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1F9


title: OVCAR-3_vorinostat_0nM_6h

description: gene expression data from OVCAR-3 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1F8

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T1F7


title: NCI-H522_vorinostat_1000nM_24h

description: gene expression data from NCI-H522 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1F6


title: ΔH3.V/ΔH4.V_T1F5


title: NCI-H522_vorinostat_0nM_2h

description: gene expression data from NCI-H522 treated with 0nM vorinostat for 2h


title: NCI-H522_vorinostat_0nM_24h

description: gene expression data from NCI-H522 treated with 0nM vorinostat for 24h


title: NCI-H460_vorinostat_5000nM_6h

description: gene expression data from NCI-H460 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line NCI-H460


title: NCI-H460_vorinostat_5000nM_2h

description: gene expression data from NCI-H460 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1G1


title: NCI-H460_vorinostat_1000nM_6h

description: gene expression data from NCI-H460 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1F3


title: NCI-H460_vorinostat_5000nM_24h

description: gene expression data from NCI-H460 treated with 5000nM vorinostat for 24h


title: NCI-H460_vorinostat_1000nM_2h

description: gene expression data from NCI-H460 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1F4


title: ΔH3.V/ΔH4.V_T1F2


title: NCI-H460_vorinostat_1000nM_24h

description: gene expression data from NCI-H460 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1F1


title: ΔH3.V/ΔH4.V_T1E12


title: NCI-H460_vorinostat_0nM_6h

description: gene expression data from NCI-H460 treated with 0nM vorinostat for 6h


title: NCI-H522_vorinostat_0nM_6h

description: gene expression data from NCI-H522 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1E11

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: NCI-H460_vorinostat_0nM_24h

description: gene expression data from NCI-H460 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1E10


title: NCI-H460_vorinostat_0nM_2h

description: gene expression data from NCI-H460 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1E9


title: ΔH3.V/ΔH4.V_T1E8


title: NCI-H322M_vorinostat_5000nM_24h

description: gene expression data from NCI-H322M treated with 5000nM vorinostat for 24h

source_name: human tumor cell line NCI-H322M


title: NCI-H322M_vorinostat_5000nM_2h

description: gene expression data from NCI-H322M treated with 5000nM vorinostat for 2h


title: NCI-H322M_vorinostat_5000nM_6h

description: gene expression data from NCI-H322M treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1E7

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: NCI-H322M_vorinostat_1000nM_2h

description: gene expression data from NCI-H322M treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1E6


title: ΔH3.V/ΔH4.V_T1E5


title: ΔH3.V/ΔH4.V_T1E4


title: NCI-H322M_vorinostat_1000nM_24h

description: gene expression data from NCI-H322M treated with 1000nM vorinostat for 24h


title: NCI-H322M_vorinostat_0nM_6h

description: gene expression data from NCI-H322M treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1E3


title: ΔH3.V/ΔH4.V_T1E2


title: NCI-H322M_vorinostat_0nM_24h

description: gene expression data from NCI-H322M treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1E1


title: ΔH3.V/ΔH4.V_T1D12

source_name: 50 cells


title: ΔH3.V/ΔH4.V_T1D11


title: ΔH3.V/ΔH4.V_T1D10


title: NCI-H23_vorinostat_5000nM_24h

description: gene expression data from NCI-H23 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line NCI-H23


title: ΔH3.V/ΔH4.V_T1D9


title: NCI-H322M_vorinostat_0nM_2h

description: gene expression data from NCI-H322M treated with 0nM vorinostat for 2h


title: NCI-H23_vorinostat_5000nM_6h

description: gene expression data from NCI-H23 treated with 5000nM vorinostat for 6h


title: NCI-H322M_vorinostat_1000nM_6h

description: gene expression data from NCI-H322M treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1D7


title: NCI-H23_vorinostat_5000nM_2h

description: gene expression data from NCI-H23 treated with 5000nM vorinostat for 2h


title: NCI-H23_vorinostat_1000nM_6h

description: gene expression data from NCI-H23 treated with 1000nM vorinostat for 6h


title: NCI-H23_vorinostat_1000nM_2h

description: gene expression data from NCI-H23 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1D6

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T1D5


title: NCI-H23_vorinostat_0nM_6h

description: gene expression data from NCI-H23 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1D2


title: NCI-H23_vorinostat_1000nM_24h

description: gene expression data from NCI-H23 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1C12


title: ΔH3.V/ΔH4.V_T1C11


title: ΔH3.V/ΔH4.V_T1D8


title: ΔH3.V/ΔH4.V_T1C10


title: NCI-H23_vorinostat_0nM_24h

description: gene expression data from NCI-H23 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1C9


title: ΔH3.V/ΔH4.V_T1C8


title: NCI-H226_vorinostat_5000nM_24h

description: gene expression data from NCI-H226 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line NCI-H226


title: NCI-H226_vorinostat_5000nM_6h

description: gene expression data from NCI-H226 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1C7

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: NCI-H226_vorinostat_5000nM_2h

description: gene expression data from NCI-H226 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1D4


title: ΔH3.V/ΔH4.V_T1C6


title: ΔH3.V/ΔH4.V_T1D3


title: NCI-H226_vorinostat_1000nM_6h

description: gene expression data from NCI-H226 treated with 1000nM vorinostat for 6h


title: NCI-H226_vorinostat_1000nM_2h

description: gene expression data from NCI-H226 treated with 1000nM vorinostat for 2h


title: NCI-H226_vorinostat_1000nM_24h

description: gene expression data from NCI-H226 treated with 1000nM vorinostat for 24h


title: NCI-H23_vorinostat_0nM_2h

description: gene expression data from NCI-H23 treated with 0nM vorinostat for 2h


title: NCI-ADR-RES_vorinostat_5000nM_6h

description: gene expression data from NCI-ADR-RES treated with 5000nM vorinostat for 6h

source_name: human tumor cell line NCI-ADR-RES


title: NCI-H226_vorinostat_0nM_6h

description: gene expression data from NCI-H226 treated with 0nM vorinostat for 6h


title: NCI-ADR-RES_vorinostat_5000nM_2h

description: gene expression data from NCI-ADR-RES treated with 5000nM vorinostat for 2h


title: NCI-H226_vorinostat_0nM_24h

description: gene expression data from NCI-H226 treated with 0nM vorinostat for 24h


title: NCI-ADR-RES_vorinostat_1000nM_6h

description: gene expression data from NCI-ADR-RES treated with 1000nM vorinostat for 6h


title: NCI-H226_vorinostat_0nM_2h

description: gene expression data from NCI-H226 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1C5


title: ΔH3.V/ΔH4.V_T1D1


title: NCI-ADR-RES_vorinostat_5000nM_24h

description: gene expression data from NCI-ADR-RES treated with 5000nM vorinostat for 24h


title: NCI-ADR-RES_vorinostat_1000nM_2h

description: gene expression data from NCI-ADR-RES treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1C4


title: NCI-ADR-RES_vorinostat_1000nM_24h

description: gene expression data from NCI-ADR-RES treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1C3


title: ΔH3.V/ΔH4.V_T1C2


title: NCI-ADR-RES_vorinostat_0nM_6h

description: gene expression data from NCI-ADR-RES treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1B12


title: ΔH3.V/ΔH4.V_T1B11


title: NCI-ADR-RES_vorinostat_0nM_24h

description: gene expression data from NCI-ADR-RES treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1B10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T1B9


title: ΔH3.V/ΔH4.V_T1B8


title: ΔH3.V/ΔH4.V_T1B7


title: ΔH3.V/ΔH4.V_T1B6


title: ΔH3.V/ΔH4.V_T1B5


title: MOLT-4_vorinostat_5000nM_24h

description: gene expression data from MOLT-4 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line MOLT-4


title: MOLT-4_vorinostat_1000nM_6h

description: gene expression data from MOLT-4 treated with 1000nM vorinostat for 6h


title: MOLT-4_vorinostat_5000nM_6h

description: gene expression data from MOLT-4 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1B4


title: ΔH3.V/ΔH4.V_T1B3


title: ΔH3.V/ΔH4.V_T1B2


title: MOLT-4_vorinostat_1000nM_24h

description: gene expression data from MOLT-4 treated with 1000nM vorinostat for 24h


title: MOLT-4_vorinostat_5000nM_2h

description: gene expression data from MOLT-4 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1B1


title: MOLT-4_vorinostat_1000nM_2h

description: gene expression data from MOLT-4 treated with 1000nM vorinostat for 2h


title: MOLT-4_vorinostat_0nM_24h

description: gene expression data from MOLT-4 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1C1


title: MDA-MB-468_vorinostat_5000nM_6h

description: gene expression data from MDA-MB-468 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line MDA-MB-468

value: Breast


title: MOLT-4_vorinostat_0nM_2h

description: gene expression data from MOLT-4 treated with 0nM vorinostat for 2h

value: member of the NCI-60 cell line panel


title: MOLT-4_vorinostat_0nM_6h

description: gene expression data from MOLT-4 treated with 0nM vorinostat for 6h


title: MDA-MB-468_vorinostat_5000nM_24h

description: gene expression data from MDA-MB-468 treated with 5000nM vorinostat for 24h


title: NCI-ADR-RES_vorinostat_0nM_2h

description: gene expression data from NCI-ADR-RES treated with 0nM vorinostat for 2h


title: MDA-MB-468_vorinostat_5000nM_2h

description: gene expression data from MDA-MB-468 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_T1A11


title: ΔH3.V/ΔH4.V_T1A10


title: MDA-MB-468_vorinostat_1000nM_2h

description: gene expression data from MDA-MB-468 treated with 1000nM vorinostat for 2h


title: MDA-MB-468_vorinostat_1000nM_6h

description: gene expression data from MDA-MB-468 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1A8


title: ΔH3.V/ΔH4.V_T1A7


title: MDA-MB-468_vorinostat_1000nM_24h

description: gene expression data from MDA-MB-468 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1A6

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_T1A5


title: MDA-MB-468_vorinostat_0nM_6h

description: gene expression data from MDA-MB-468 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_T1A12


title: MDA-MB-468_vorinostat_0nM_2h

description: gene expression data from MDA-MB-468 treated with 0nM vorinostat for 2h


title: MDA-MB-468_vorinostat_0nM_24h

description: gene expression data from MDA-MB-468 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_T1A4


title: ΔH3.V/ΔH4.V_T1A3


title: ΔH3.V/ΔH4.V_T1A1


title: ΔH3.V/ΔH4.V_H12


title: MDA-MB-435_vorinostat_5000nM_2h

description: gene expression data from MDA-MB-435 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line MDA-MB-435


title: MDA-MB-435_vorinostat_1000nM_6h

description: gene expression data from MDA-MB-435 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_H11

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_H10


title: MDA-MB-435_vorinostat_5000nM_24h

description: gene expression data from MDA-MB-435 treated with 5000nM vorinostat for 24h


title: MDA-MB-435_vorinostat_1000nM_2h

description: gene expression data from MDA-MB-435 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_H9


title: ΔH3.V/ΔH4.V_T1A9


title: ΔH3.V/ΔH4.V_H8


title: ΔH3.V/ΔH4.V_H7


title: MDA-MB-231_vorinostat_5000nM_6h

description: gene expression data from MDA-MB-231 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line MDA-MB-231


title: ΔH3.V/ΔH4.V_T1A2


title: ΔH3.V/ΔH4.V_H6


title: MDA-MB-435_vorinostat_0nM_6h

description: gene expression data from MDA-MB-435 treated with 0nM vorinostat for 6h


title: MDA-MB-435_vorinostat_1000nM_24h

description: gene expression data from MDA-MB-435 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_H5


title: ΔH3.V/ΔH4.V_H4


title: ΔH3.V/ΔH4.V_H3


title: MDA-MB-435_vorinostat_5000nM_6h

description: gene expression data from MDA-MB-435 treated with 5000nM vorinostat for 6h


title: MDA-MB-435_vorinostat_0nM_24h

description: gene expression data from MDA-MB-435 treated with 0nM vorinostat for 24h


title: MDA-MB-435_vorinostat_0nM_2h

description: gene expression data from MDA-MB-435 treated with 0nM vorinostat for 2h


title: MDA-MB-231_vorinostat_5000nM_2h

description: gene expression data from MDA-MB-231 treated with 5000nM vorinostat for 2h


title: MDA-MB-231_vorinostat_5000nM_24h

description: gene expression data from MDA-MB-231 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_H1

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: MDA-MB-231_vorinostat_1000nM_6h

description: gene expression data from MDA-MB-231 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_H2


title: ΔH3.V/ΔH4.V_G12


title: MDA-MB-231_vorinostat_1000nM_2h

description: gene expression data from MDA-MB-231 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_G10


title: ΔH3.V/ΔH4.V_G11


title: MDA-MB-231_vorinostat_0nM_2h

description: gene expression data from MDA-MB-231 treated with 0nM vorinostat for 2h


title: MDA-MB-231_vorinostat_0nM_24h

description: gene expression data from MDA-MB-231 treated with 0nM vorinostat for 24h


title: MDA-MB-231_vorinostat_1000nM_24h

description: gene expression data from MDA-MB-231 treated with 1000nM vorinostat for 24h


title: MDA-MB-231_vorinostat_0nM_6h

description: gene expression data from MDA-MB-231 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_G9


title: ΔH3.V/ΔH4.V_G8


title: MCF7_vorinostat_5000nM_6h

description: gene expression data from MCF7 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line MCF7


title: MCF7_vorinostat_5000nM_2h

description: gene expression data from MCF7 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_G6


title: ΔH3.V/ΔH4.V_G7


title: MCF7_vorinostat_1000nM_2h

description: gene expression data from MCF7 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_G5

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_G4


title: ΔH3.V/ΔH4.V_G3


title: ΔH3.V/ΔH4.V_G1


title: ΔH3.V/ΔH4.V_G2


title: ΔH3.V/ΔH4.V_F12


title: MCF7_vorinostat_5000nM_24h

description: gene expression data from MCF7 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_F11


title: ΔH3.V/ΔH4.V_F9


title: MCF7_vorinostat_1000nM_6h

description: gene expression data from MCF7 treated with 1000nM vorinostat for 6h


title: MALME-3M_vorinostat_5000nM_6h

description: gene expression data from MALME-3M treated with 5000nM vorinostat for 6h

source_name: human tumor cell line MALME-3M


title: MCF7_vorinostat_1000nM_24h

description: gene expression data from MCF7 treated with 1000nM vorinostat for 24h


title: MCF7_vorinostat_0nM_24h

description: gene expression data from MCF7 treated with 0nM vorinostat for 24h


title: MCF7_vorinostat_0nM_6h

description: gene expression data from MCF7 treated with 0nM vorinostat for 6h


title: MCF7_vorinostat_0nM_2h

description: gene expression data from MCF7 treated with 0nM vorinostat for 2h


title: MALME-3M_vorinostat_5000nM_2h

description: gene expression data from MALME-3M treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_F8

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: MALME-3M_vorinostat_1000nM_6h

description: gene expression data from MALME-3M treated with 1000nM vorinostat for 6h


title: MALME-3M_vorinostat_1000nM_24h

description: gene expression data from MALME-3M treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_F6


title: ΔH3.V/ΔH4.V_F7


title: MALME-3M_vorinostat_0nM_2h

description: gene expression data from MALME-3M treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_F5


title: MALME-3M_vorinostat_0nM_6h

description: gene expression data from MALME-3M treated with 0nM vorinostat for 6h


title: MALME-3M_vorinostat_0nM_24h

description: gene expression data from MALME-3M treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_F10


title: MALME-3M_vorinostat_5000nM_24h

description: gene expression data from MALME-3M treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_F3


title: M14_vorinostat_5000nM_24h

description: gene expression data from M14 treated with 5000nM vorinostat for 24h

source_name: human tumor cell line M14


title: M14_vorinostat_5000nM_2h

description: gene expression data from M14 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_F2

source_name: single cell


title: M14_vorinostat_5000nM_6h

description: gene expression data from M14 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_F1

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: MALME-3M_vorinostat_1000nM_2h

description: gene expression data from MALME-3M treated with 1000nM vorinostat for 2h


title: M14_vorinostat_1000nM_2h

description: gene expression data from M14 treated with 1000nM vorinostat for 2h


title: M14_vorinostat_1000nM_24h

description: gene expression data from M14 treated with 1000nM vorinostat for 24h


title: M14_vorinostat_1000nM_6h

description: gene expression data from M14 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_E12


title: ΔH3.V/ΔH4.V_E7


title: ΔH3.V/ΔH4.V_E9


title: ΔH3.V/ΔH4.V_E10


title: ΔH3.V/ΔH4.V_F4


title: M14_vorinostat_0nM_6h

description: gene expression data from M14 treated with 0nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_E8


title: ΔH3.V/ΔH4.V_E3


title: LOX_vorinostat_5000nM_6h

description: gene expression data from LOX treated with 5000nM vorinostat for 6h

source_name: human tumor cell line LOX


title: ΔH3.V/ΔH4.V_E2


title: M14_vorinostat_0nM_24h

description: gene expression data from M14 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_E6

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_E4


title: LOX_vorinostat_5000nM_24h

description: gene expression data from LOX treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_E5


title: ΔH3.V/ΔH4.V_D12

source_name: 10 cells


title: LOX_vorinostat_1000nM_2h

description: gene expression data from LOX treated with 1000nM vorinostat for 2h


title: LOX_vorinostat_1000nM_24h

description: gene expression data from LOX treated with 1000nM vorinostat for 24h


title: LOX_vorinostat_1000nM_6h

description: gene expression data from LOX treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_E11


title: LOX_vorinostat_0nM_6h

description: gene expression data from LOX treated with 0nM vorinostat for 6h


title: KM12_vorinostat_5000nM_2h

description: gene expression data from KM12 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line KM12


title: M14_vorinostat_0nM_2h

description: gene expression data from M14 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_D7


title: ΔH3.V/ΔH4.V_D11


title: LOX_vorinostat_0nM_2h

description: gene expression data from LOX treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_D5


title: ΔH3.V/ΔH4.V_D9


title: LOX_vorinostat_0nM_24h

description: gene expression data from LOX treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_D10


title: KM12_vorinostat_5000nM_6h

description: gene expression data from KM12 treated with 5000nM vorinostat for 6h


title: LOX_vorinostat_5000nM_2h

description: gene expression data from LOX treated with 5000nM vorinostat for 2h


title: KM12_vorinostat_1000nM_24h

description: gene expression data from KM12 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_D8


title: ΔH3.V/ΔH4.V_D3


title: KM12_vorinostat_5000nM_24h

description: gene expression data from KM12 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_D2


title: ΔH3.V/ΔH4.V_E1

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: KM12_vorinostat_1000nM_2h

description: gene expression data from KM12 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_D1


title: ΔH3.V/ΔH4.V_D6


title: KM12_vorinostat_1000nM_6h

description: gene expression data from KM12 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_C12


title: K-562_vorinostat_5000nM_6h

description: gene expression data from K-562 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line K-562


title: ΔH3.V/ΔH4.V_C9

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: KM12_vorinostat_0nM_6h

description: gene expression data from KM12 treated with 0nM vorinostat for 6h


title: K-562_vorinostat_5000nM_24h

description: gene expression data from K-562 treated with 5000nM vorinostat for 24h


title: KM12_vorinostat_0nM_2h

description: gene expression data from KM12 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_C10


title: ΔH3.V/ΔH4.V_D4


title: ΔH3.V/ΔH4.V_C11


title: ΔH3.V/ΔH4.V_C7


title: K-562_vorinostat_1000nM_2h

description: gene expression data from K-562 treated with 1000nM vorinostat for 2h


title: K-562_vorinostat_1000nM_6h

description: gene expression data from K-562 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_C6


title: ΔH3.V/ΔH4.V_C8


title: KM12_vorinostat_0nM_24h

description: gene expression data from KM12 treated with 0nM vorinostat for 24h


title: K-562_vorinostat_5000nM_2h

description: gene expression data from K-562 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_C4


title: ΔH3.V/ΔH4.V_C5


title: ΔH3.V/ΔH4.V_C3


title: IGR-OV1_vorinostat_5000nM_6h

description: gene expression data from IGR-OV1 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line IGR-OV1


title: K-562_vorinostat_1000nM_24h

description: gene expression data from K-562 treated with 1000nM vorinostat for 24h


title: IGR-OV1_vorinostat_5000nM_2h

description: gene expression data from IGR-OV1 treated with 5000nM vorinostat for 2h


title: K-562_vorinostat_0nM_24h

description: gene expression data from K-562 treated with 0nM vorinostat for 24h


title: K-562_vorinostat_0nM_2h

description: gene expression data from K-562 treated with 0nM vorinostat for 2h


title: K-562_vorinostat_0nM_6h

description: gene expression data from K-562 treated with 0nM vorinostat for 6h


title: IGR-OV1_vorinostat_5000nM_24h

description: gene expression data from IGR-OV1 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_C2


title: IGR-OV1_vorinostat_1000nM_2h

description: gene expression data from IGR-OV1 treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_C1


title: ΔH3.V/ΔH4.V_B11

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv


title: IGR-OV1_vorinostat_1000nM_6h

description: gene expression data from IGR-OV1 treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_B10

description:
ERCC spike-in control added
Feature_counts_scRNAseq_set_two.tsv
VSG_raw_counts_scRNAseq_set_two.tsv


title: ΔH3.V/ΔH4.V_B6


title: ΔH3.V/ΔH4.V_B9


title: IGR-OV1_vorinostat_0nM_6h

description: gene expression data from IGR-OV1 treated with 0nM vorinostat for 6h


title: IGR-OV1_vorinostat_1000nM_24h

description: gene expression data from IGR-OV1 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_B7


title: ΔH3.V/ΔH4.V_B4


title: ΔH3.V/ΔH4.V_B8


title: ΔH3.V/ΔH4.V_B3


title: HT29_vorinostat_1000nM_6h

description: gene expression data from HT29 treated with 1000nM vorinostat for 6h

source_name: human tumor cell line HT29


title: HT29_vorinostat_1000nM_2h

description: gene expression data from HT29 treated with 1000nM vorinostat for 2h


title: IGR-OV1_vorinostat_0nM_2h

description: gene expression data from IGR-OV1 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_B2


title: HT29_vorinostat_5000nM_24h

description: gene expression data from HT29 treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_A11


title: ΔH3.V/ΔH4.V_B1


title: ΔH3.V/ΔH4.V_A10


title: HT29_vorinostat_1000nM_24h

description: gene expression data from HT29 treated with 1000nM vorinostat for 24h


title: HT29_vorinostat_0nM_2h

description: gene expression data from HT29 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_B5


title: ΔH3.V/ΔH4.V_A7


title: ΔH3.V/ΔH4.V_A9


title: IGR-OV1_vorinostat_0nM_24h

description: gene expression data from IGR-OV1 treated with 0nM vorinostat for 24h


title: HT29_vorinostat_5000nM_6h

description: gene expression data from HT29 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V_A6

source_name: 50 cells


title: HS-578T_vorinostat_5000nM_2h

description: gene expression data from HS-578T treated with 5000nM vorinostat for 2h

source_name: human tumor cell line HS-578T


title: ΔH3.V/ΔH4.V_A5


title: HS-578T_vorinostat_5000nM_24h

description: gene expression data from HS-578T treated with 5000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V_A2


title: HS-578T_vorinostat_1000nM_2h

description: gene expression data from HS-578T treated with 1000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_A4


title: ΔH3.V/ΔH4.V_A3


title: HT29_vorinostat_5000nM_2h

description: gene expression data from HT29 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V_A8


title: ΔH3.V/ΔH4.V_A1


title: Tbx5_Mut_2

city: Chicago

first: Xinan

middle: Holly

last: Yang

state: IL

address: 900 East 57th Street, KCBD Room 5121

department: Pediatrics

institute: universty of Chicago

description: Mice were raised and maintained in the KCBD Animal Facilities at the University of Chicago as per IACUC (Institutional Animal Care and Use Committee)  guidelines. Female mice  were superovulated at 5-6 weeks of age and mated for timed dissection at embryonic day 9.5.

data_processing:
After quality assessment using FastQC  v1.10.1, we masked the over-represented (>1%, 100% over 38bp) TruSeq adapter from one sample (IM-2_TGACCA) which is CACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC. The clean fastq file is submitted.
Align 38-bp short reads to the mouse genome mm10 using Tophat v 2.0.6 (--segment-length 19  --segment-mismatches 1 --no-coverage-search  --keep-fasta-order -p 2).
Calculate the accepted hits for each sample using the 'Rsubread' package (v1.14.1).
Analyze expression with the 'DEseq2' package with the by default parameters that designs the batch effect as a potential variable. The normalized counts are calculated by dividing the raw counts by the DESeq estimated size factors.
Genome_build: mm10
Supplementary_files_format_and_content: Scores represent cross-sample normalized values which are the raw counts divided by the estimated size factors using the 'DESeq2' package, and raw counts are calculatd from Tophat accepted hits using the 'Rsubread' package (v1.14.1).

source_name: embryonic CPP

extract_protocol:
CPP tissue was microdissected from E9.5 timed matings. Pools of tissue were mechanically homogenized in TRIzol Reagent (Invitrogen) and then RNA was isolated in accordance to the manufacturer’s instructions. Libraries were prepared from this RNA starting with 1μg per sample and using the mRNA-seq Sample Prep Kit (Illumina) as per recommended instructions.
Barcoded Libraries were prepared according to Illumina's instructions (2013) accompanying the TruSeq RNA Sample prep kit v2  (Part# RS-122-2001). Libraries were quantitated using the Agilent Bio-analyzer (model 2100) and pooled in equimolar amounts. The pooled libraries were sequenced on the HiSeq2500 in Rapid Run Mode following the manufacturer's protocols (2013).

value: C56B/6 and CD-1 mixed

tag: embryonic day

tag: micro-dissected tissue

value: CPP

tag: library strategy

value: RNA-seq

tag: genotype


title: WT_CPP_5


title: WT_CPP_6


title: HS-578T_vorinostat_5000nM_6h

description: gene expression data from HS-578T treated with 5000nM vorinostat for 6h


title: HS-578T_vorinostat_0nM_6h

description: gene expression data from HS-578T treated with 0nM vorinostat for 6h


title: HS-578T_vorinostat_1000nM_24h

description: gene expression data from HS-578T treated with 1000nM vorinostat for 24h


title: HOP-92_vorinostat_5000nM_6h

description: gene expression data from HOP-92 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line HOP-92


title: HS-578T_vorinostat_0nM_2h

description: gene expression data from HS-578T treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V 1 cell N711/S508

description:
processed data column: H11
ERCC spike-in control added

data_processing:
Demultiplexing: bcl2fastq v.20.0.422
Read trimming: cutadapt v.1.15
Read alignment: BWA-mem v0.7.16
scRNAseq analysis: python  3.6
samtools v1.8
bedtools v2.26.0
picard v2.9.0
Genome_build: Tb427v9
Supplementary_files_format_and_content: txt; scRNA-seq normalization and quantification from scRNA-seq I

extract_protocol:
Cells were sorted and lysed in lysis buffer ((0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water) and RNA was extracted from 1 and 50 cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara) with a fourth of the recommended volumes of reagents. PCR amplification was performed for 26 cycles.
Libraries were constructed using a Nextera XT kit (Illumina) according to the manufacturer's instructions, but using only one fourth of the recommended voulmens and 1 ng of cDNA.


title: ΔH3.V/ΔH4.V 1 cell N7012/S508

description:
processed data column: H12
ERCC spike-in control added


title: WT_CPP_1


title: WT_CPP_2


title: WT_CPP_3


title: HOP-92_vorinostat_5000nM_24h

description: gene expression data from HOP-92 treated with 5000nM vorinostat for 24h


title: HOP-92_vorinostat_5000nM_2h

description: gene expression data from HOP-92 treated with 5000nM vorinostat for 2h


title: Tbx5_Mut_1


title: ΔH3.V/ΔH4.V 1 cell N710/S508

description:
processed data column: H10
ERCC spike-in control added


title: HS-578T_vorinostat_1000nM_6h

description: gene expression data from HS-578T treated with 1000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V 1 cell N709/S508

description:
processed data column: H9
ERCC spike-in control added


title: HOP-92_vorinostat_1000nM_6h

description: gene expression data from HOP-92 treated with 1000nM vorinostat for 6h


title: HS-578T_vorinostat_0nM_24h

description: gene expression data from HS-578T treated with 0nM vorinostat for 24h


title: C2C12 input at 1k cells replicate 2

source_name: Immortal cell line


title: TAC Veh

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

data_processing:
Base calling was done with illumina bcl2fastq2 version 2.17.1.14 using the recommended settings
Adapter trimming, QC metrics, and RNA seq analysis were done using CLC Bio Genomics Workbench version 11 (64-bit) using the recommended settings
Genome_build: Reference genome/ transcriptome was mm10
Supplementary_files_format_and_content: Original reads in fastq format; processed data in Excel format.

molecule: polyA RNA

source_name: mouse left ventricle

growth_protocol: Adult male mice were housed in standard 12h light/12h dark cycle.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) by following manufacturer's protocol, followed by clean-up and DNase I treatment with Ambion kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Library construction was performed using Illumina Truseq mRNA-LT (cat. RS-122-2101) kit by following manufactuer's protocol.

treatment_protocol: 6-8 week old mice were subjected to Sham or TAC surgery and then randomly divided into Vehicle (Veh) or JIB-04 treated groups. Veh or JIB-04 was administered to mice by oral gavage one/two dasy after surgery followed by gavage every-other day for 6 weeks. AT week 6, mice were sacrificed and hearts were removed quickly, left ventricles sliced out and snap frozen in liquid nitrogen. The heart samples were store at -80C for RNA extraction.

tag: strain background

tag: age

value: adult

tag: Sex

value: male

value: TAC surgery + vehicle

value: heart left ventricle


title: TAC JIB-04

value: TAC surgery + JIB-04

tag: tissue


title: Sham Veh

value: sham surgery + vehicle


title: C2C12 input at 1k cells replicate 1

tag: cell line

tag: antibody target


title: C2C12 input at 10k cells replicate 2

tag: primary antibody


title: ΔH3.V/ΔH4.V 1 cell N708/S508

description:
processed data column: H8
ERCC spike-in control added

tag: strain

value: Lister 427 MITat 1.2

value: bloodstream form


title: Sham JIB-04

value: sham surgery + JIB-04


title: C2C12 input at 10k cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N7012/S507

description:
processed data column: G12
ERCC spike-in control added


title: C2C12 input at 100k cells replicate 2


title: C2C12 input at 100k cells replicate 1


title: ΔH3.V/ΔH4.V 1 cell N707/S508

description:
processed data column: H7
ERCC spike-in control added


title: C2C12 H3K4me3 ChIP at 100k cells replicate 2

value: mouse monoclonal anti-H3K4me3 (Kimura et al., Cell Struct Funct. 2008;33(1):61-73., CMA304)


title: ΔH3.V/ΔH4.V 1 cell N711/S507

description:
processed data column: G11
ERCC spike-in control added


title: HOP-92_vorinostat_0nM_6h

description: gene expression data from HOP-92 treated with 0nM vorinostat for 6h

tag: group


title: HT29_vorinostat_0nM_6h

description: gene expression data from HT29 treated with 0nM vorinostat for 6h

value: Colon


title: C2C12 H3K4me3 at 100 cells (0.1ul of Tn5 added) replicate 2

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz


title: ΔH3.V/ΔH4.V 1 cell N710/S507

description:
processed data column: G10
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells (0.1ul of Tn5 added) replicate 1


title: HT29_vorinostat_0nM_24h

description: gene expression data from HT29 treated with 0nM vorinostat for 24h


title: HOP-92_vorinostat_0nM_2h

description: gene expression data from HOP-92 treated with 0nM vorinostat for 2h

value: Lung


title: HOP-92_vorinostat_1000nM_2h

description: gene expression data from HOP-92 treated with 1000nM vorinostat for 2h


title: HOP-62_vorinostat_5000nM_6h

description: gene expression data from HOP-62 treated with 5000nM vorinostat for 6h

source_name: human tumor cell line HOP-62


title: C2C12 H3K4me3 at 100 cells (0.02ul of Tn5 added) replicate 2


title: C2C12 H3K4me3 at 100 cells (Tn5 integration at RT) replicate 2


title: C2C12 H3K4me3 at 100 cells (0.02ul of Tn5 added) replicate 1


title: HOP-92_vorinostat_1000nM_24h

description: gene expression data from HOP-92 treated with 1000nM vorinostat for 24h


title: HOP-62_vorinostat_5000nM_2h

description: gene expression data from HOP-62 treated with 5000nM vorinostat for 2h


title: ΔH3.V/ΔH4.V 1 cell N708/S507

description:
processed data column: G8
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells (0.1ul of EzTn5 added) replicate 2


title: HOP-62_vorinostat_5000nM_24h

description: gene expression data from HOP-62 treated with 5000nM vorinostat for 24h


title: C2C12 H3K4me3 at 100 cells (0.1ul of EzTn5 added) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N707/S507

description:
processed data column: G7
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells (with PAGE purified probes) replicate 2


title: HOP-92_vorinostat_0nM_24h

description: gene expression data from HOP-92 treated with 0nM vorinostat for 24h


title: C2C12 H3K4me3 at 100 cells (with PAGE purified probes) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N7012/S506

description:
processed data column: F12
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells  (with probes with excessive DNA oligos) replicate 2


title: C2C12 H3K4me3 at 100 cells  (with probes with excessive DNA oligos) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N711/S506

description:
processed data column: F11
ERCC spike-in control added


title: HOP-62_vorinostat_1000nM_2h

description: gene expression data from HOP-62 treated with 1000nM vorinostat for 2h


title: C2C12 H3K4me3 at 100 cells (with probes with PEG13 linkers) replicate 2


title: HOP-62_vorinostat_1000nM_24h

description: gene expression data from HOP-62 treated with 1000nM vorinostat for 24h


title: C2C12 H3K4me3 at 100 cells (with probes with PEG13 linkers) replicate 1


title: C2C12 H3K4me3 at 100 cells (with probes without PEG linkers) replicate 2


title: ΔH3.V/ΔH4.V 1 cell N710/S506

description:
processed data column: F10
ERCC spike-in control added


title: C2C12 H3K4me3 at 100 cells (with probes without PEG linkers) replicate 1

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz


title: ΔH3.V/ΔH4.V 1 cell N709/S506

description:
processed data column: F9
ERCC spike-in control added


title: HOP-62_vorinostat_0nM_6h

description: gene expression data from HOP-62 treated with 0nM vorinostat for 6h


title: HOP-62_vorinostat_0nM_2h

description: gene expression data from HOP-62 treated with 0nM vorinostat for 2h


title: C2C12 H3K4me3 at 100 cells (Tn5 integration at 4 degrees) replicate 2


title: C2C12 H3K4me3 at 100 cells (Tn5 integration at 4 degrees) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N708/S506

description:
processed data column: F8
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.5ul of Tn5 added) replicate 2

value: mouse monoclonal anti-H3K27me3 (Hayashi-Takanaka et al., Nucleic Acids Res. 2011 Aug;39(15):6475-88., CMA323)


title: HOP-62_vorinostat_0nM_24h

description: gene expression data from HOP-62 treated with 0nM vorinostat for 24h

value: member of the NCI-60 cell line panel


title: ΔH3.V/ΔH4.V 1 cell N707/S506

description:
processed data column: F7
ERCC spike-in control added


title: ΔH3.V/ΔH4.V 1 cell N709/S507

description:
processed data column: G9
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.1ul of Tn5 added) replicate 2


title: ΔH3.V/ΔH4.V 1 cell N7012/S505

description:
processed data column: E12
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.1ul of Tn5 added) replicate 1


title: HL-60_vorinostat_5000nM_2h

description: gene expression data from HL-60 treated with 5000nM vorinostat for 2h

source_name: human tumor cell line HL-60

value: Leukemia


title: C2C12 H3K27me3 at 100 cells (0.02ul of Tn5 added) replicate 2


title: C2C12 H3K27me3 at 100 cells (0.02ul of Tn5 added) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N711/S505

description:
processed data column: E11
ERCC spike-in control added


title: ΔH3.V/ΔH4.V 1 cell N710/S505

description:
processed data column: E10
ERCC spike-in control added


title: HL-60_vorinostat_5000nM_24h

description: gene expression data from HL-60 treated with 5000nM vorinostat for 24h


title: C2C12 H3K27me3 at 100 cells (Tn5 integration at RT) replicate 1


title: C2C12 H3K27me3 at 100 cells (Tn5 integration at RT) replicate 2


title: HL-60_vorinostat_1000nM_6h

description: gene expression data from HL-60 treated with 1000nM vorinostat for 6h


title: C2C12 H3K27me3 at 100 cells (0.5ul of EzTn5 added) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N709/S505

description:
processed data column: E9
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.5ul of Tn5 added) replicate 1


title: C2C12 H3K27me3 at 100 cells (0.5ul of EzTn5 added) replicate 2


title: HL-60_vorinostat_5000nM_6h

description: gene expression data from HL-60 treated with 5000nM vorinostat for 6h


title: ΔH3.V/ΔH4.V 1 cell N708/S505

description:
processed data column: E8
ERCC spike-in control added


title: HL-60_vorinostat_1000nM_2h

description: gene expression data from HL-60 treated with 1000nM vorinostat for 2h


title: HL-60_vorinostat_1000nM_24h

description: gene expression data from HL-60 treated with 1000nM vorinostat for 24h


title: ΔH3.V/ΔH4.V 1 cell N707/S505

description:
processed data column: E7
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.1ul of EzTn5 added) replicate 1

description:
countMatrix10k_C2C12_conditions.csv.gz
countMatrix4k_C2C12_conditions.csv.gz


title: C2C12 H3K27me3 at 100 cells (with PAGE purified probes) replicate 2


title: ΔH3.V/ΔH4.V 50 cells N7012/S504

description:
processed data column: D12
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (with PAGE purified probes) replicate 1


title: HL-60_vorinostat_0nM_6h

description: gene expression data from HL-60 treated with 0nM vorinostat for 6h


title: C2C12 H3K27me3 at 100 cells (with probes with PEG13 linkers) replicate 1


title: HL-60_vorinostat_0nM_2h

description: gene expression data from HL-60 treated with 0nM vorinostat for 2h


title: ΔH3.V/ΔH4.V 1 cell N711/S504

description:
processed data column: D11
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (with probes without PEG linkers) replicate 2


title: C2C12 H3K27me3 at 100 cells (with probes with PEG13 linkers) replicate 2


title: HL-60_vorinostat_0nM_24h

description: gene expression data from HL-60 treated with 0nM vorinostat for 24h


title: ΔH3.V/ΔH4.V 1 cell N710/S504

description:
processed data column: D10
ERCC spike-in control added


title: C2C12 H3K27me3 at 100 cells (0.1ul of EzTn5 added) replicate 2


title: C2C12 H3K27me3 at 100 cells (Tn5 integration at 4 degrees) replicate 1


title: ΔH3.V/ΔH4.V 1 cell N709/S504

description:
processed data column: D9
ERCC spike-in control added


title: C2C12 ChILT-DNA at 100 cells (0.5ul of Tn5 added) replicate 2

value: ChILT-DNA


title: ΔH3.V/ΔH4.V 1 cell N708/S504

description:
processed data column: D8
ERCC spike-in control added


title: C2C12 H3K4me3 ChIP at 100k cells replicate 1


title: C2C12 H3K27me3 at 100 cells (Tn5 integration at 4 degrees) replicate 2