title: Tregs_ATACseq_WT2


title: Tregs_WT_Input_DNA

status: Public on Oct 01 2020

type: SRA

city: Chicago

first: Fotini

last: Gounari

state: IL

address: 924 E 27th Street, JFK

department: Medicine

country: USA

institute: University of Chicago

library_source: genomic

data_processing:
Fastq files were grommed and aligned to the mm10 genome using FastqGroomer Bowtie via Galaxy V1.1.1
Aligned bam files were filtered and indices were generated using the Filter SAM or BAM file tool via Galaxy V1.1.1
Peak_Bed files were generated using Homer (ChIPseq, -style factor -o -F 5 -P .00001 -gsize 1.87e9) and MACS2 (ATACseq, peaks calling parameters: -p .00001 --broad --broad-cutoff .00001 -f BAM  ) from filtered bam files, bedGraphs were generatd using Homer, FPKM tacking and differential gene expression analysis was performed with CufLinks/Cuffdiff2,
Genome_build: mm10
Supplementary_files_format_and_content: Peak_Bed files were generated using Homer (ChIPseq) and MACS2 (ATACseq) and contain chr, start end information of each peak, bedGraphs were generatd using Homer, FPKM tacking and differential  expression analysis was performed with CufLinks/Cuffdiff2 (CAT over WT)

molecule: genomic DNA

organism: Mus musculus

source_name: ex vivo peripheral regulatory T cells

growth_protocol: N/A - primary cells were used

extract_protocol:
ChIPseq: 1×107 CD25+YFP+ Tregs were FACS sorted from LN and SPL isolated CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) of 10-12-week-old Foxp3YFP-Cre WT mice. ATACseq/RNAseq: For ATAC–seq, 5-10x104 YFP+CD25+ Tregs were FACS sorted from MACS-pre-purified CD4+ T cells (CD4+ T Cell Isolation Kit, mouse, 130-104-454, Miltenyi) isolated from LNs of Foxp3YFP-Cre Ctnnb1fl(ex3) and Foxp3YFP-Cre WT mice
ChIPseq: Emmanuel, A.O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4(+)CD8(+) thymocytes. Nature immunology 19, 1366-1378 (2018)., ATACseq: Cells were centrifuged at 500g at 4°C for 5 min, washed with 1 x PBS, and centrifuged again. Cells were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and immediately centrifuged at 500 g at 4 °C for 10 min. Pellets were resuspended in transposition reaction buffer (25 μl 2× Tagment Buffer (FC-121-1030, Illumina), 2.5 μl Tagment DNA Enzyme, and 22.5 μl nuclease-free H2O) for 30 min at 37 °C. DNA was purified with a Qiagen MinElute Kit and amplified with Nextera PCR primers (Illumina Nextera Index Kit) and NEBNext PCR Master Mix (M0541, New England BioLabs). Amplified DNA was purified with a Qiagen PCR cleanup kit. Libraries were sequenced on a HiSeq 4000 sequencer at the University of Chicago Genomics Facility, RNAseq: Total RNA was isolated using the PicoPureTM RNA Isolation Kit (KIT0202, Arcturus) following the manufacturer’s instructions. Libraries were generated and sequenced by the University of Chicago Genomics Facility.

tag: strain

tag: Sex

value: male

tag: genotype/variation

value: Foxp3Cre-YFP (WT)

tag: tissue

value: ex vivo peripheral regulatory T cells

tag: chip antibody

value: none (input)


title: Neratinib_Dose3_Rep2

first: Sonia

last: Brockway

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

organism: Homo sapiens

source_name: Pool of 5 breast cancer cell lines

growth_protocol: Cell line pools were cultured in RPMI-1640, 10% Tet System Approved FBS, 1% Penicillin/Streptomycin, 100 ng/mL doxycycline for 7 days prior to compound treatment.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

treatment_protocol: Cell line pools were treated with compound or DMSO over a four-point concentration range (10-fold dilutions) in duplicate using either a standard dose range (10 nM to 10 μM) or a low dose range (1 nM to 1 μM). Dose1=lowest dose. Dose4=highest dose. Cells were treated for 72 hours.

tag: cell lines

tag: sgrnas

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2

tag: compound treatment


title: Tregs_WT_TCF1_ChIPseq

value: anti-Tcf1/TCF7 Cell Signaling, C63D9 (2203)


title: Spautin1_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad007

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: age


title: MLL4SET-MKO, biological rep3

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

country: China

institute: Nanjing University

description:
MLL4SET-MKO rep3
mRNA-Seq
Gastrocnemius muscle total RNA from MLL4SET muscle-specific knock-out mouse.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx

library_source: transcriptomic

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
Quality control using fastQC version 0.11.3.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

molecule: total RNA

source_name: Gastrocnemius muscle from MLL4SET-MKO mouse

extract_protocol:
Gastrocnemius muscle were harvested and flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Muscle-specific MLL4SET knock-out

value: Gastrocnemius muscle

value: 8 weeks


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad006


title: WT, biological rep2

description:
WT rep2
mRNA-Seq
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx

source_name: Gastrocnemius muscle from wild-type mouse

value: Wild-type


title: MLL4SET-MKO, biological rep2

description:
MLL4SET-MKO rep2
mRNA-Seq
Gastrocnemius muscle total RNA from MLL4SET muscle-specific knock-out mouse.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx


title: DMSOPlate14WellF6_Dose3_Rep2


title: SB743921_Dose3_Rep2


title: WT, biological rep1

description:
WT rep1
mRNA-Seq
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx


title: WT, biological rep3

description:
WT rep3
mRNA-Seq
Gastrocnemius muscle total RNA from wild-type mouse - control mouse for muscle specific MLL4SET knock-out.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad012


title: MLL4SET-MKO, biological rep1

description:
MLL4SET-MKO rep1
mRNA-Seq
Gastrocnemius muscle total RNA from MLL4SET muscle-specific knock-out mouse.
processed data file: MLL4SET-MKO_VS_WT_genes.fpkm_tracking
processed data file: MLL4SET-MKO_VS_WT_gene_exp.xlsx


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H4_ad004


title: c-myc-cd19-trb3-ko-1

city: bei jing

first: wang

last: feng

address: nan wei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calcula
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: lymphoma cells

extract_protocol:
The mouse' Lymph nodes tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 months

value: Lymph nodes


title: AZD7545_Dose3_Rep2


title: c-myc-cd19-trb3-ko-3


title: c-myc-3


title: DMSOPlate14WellC6_Dose3_Rep2


title: c-myc-cd19-trb3-ko-2


title: c-myc-1


title: MG132_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad007


title: As_Dc

first: Chen

last: Ling

address: 163 Xianlin Avenue

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Then, those read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below:(1) Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW:  4:10) (2) Remove trailing low quality or N bases (below quality 3) (TRAILING:3) (3) Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa:  2: 30: 7) (4) Drop reads below the 26 bases long (5) Discard those reads that can not form paired
The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the clean reads.
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts, looking for compatibility. A read that is compatible with the exons of an annotated transcript, and aligned to the same strand, is considered mapped to the transcriptome. If the read is compatible with a single gene annotation, it is considered uniquely (confidently) mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting.
Cell Ranger takes as input the expected number of recovered cells, N (see -- expect-cells). Let m be a robust estimate of the maximum total UMI counts, taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group (library) and, if the reference contains multiple genomes, for each genome.
Genome_build: Danio_rerio_Ensemble_91
Supplementary_files_format_and_content: gene-barcode expression matrix

organism: Danio rerio

source_name: liver cells

extract_protocol:
The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument(10x Genomics, USA) to generate single cell Gel bead in Emulsion (GEMs).
ScRNA-seq libraries were prepared using the GemCode Single-Cell 3’ Gel Bead, Chip and Library Kits (10x Genomics, USA) as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.

treatment_protocol: Exposure solutions were prepared by adding 100μg/L arsenic, 300μg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days.  After 23-d exposure, zebrafish were collected and liver were rapidly extracted on ice.

value: liver single cell suspension

tag: exposed pollutants

value: 100ug/L arsenic and 300ug/L DCAcAm


title: WAY362450_Dose3_Rep2


title: CK

description: CK


title: As100

value: 100ug/L arsenic


title: SNS032_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad006


title: KU0063794_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad004


title: Abraxane+Phenelzine_3

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days and Phenelzine (40mg/kg) daily from day 15.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: F267
A+P_3

data_processing:
Reads were cleaned with trimmomatic (v0.36) and tagdust (v2.33) .
Reads were separately mapped to the human (Hg38) and mouse (mm10) genomes (HISAT2 v2.04). Only concordantly mapped reads were kept, and reads that mapped to both genomes were discarded (Picard)
Gene counts were obtained using Stringtie and Ballgown
TMM and library size normalized in EdgeR
Genome_build: Hg38 and mm10
Supplementary_files_format_and_content: normalised counts for Human and Mouse reads.

organism:
Homo sapiens
Mus musculus

source_name: mammary gland

extract_protocol:
The tumor tissues were collected in Allprotect tissue reagent kit and then processed using the Rneasy Microarray Tissue Mini Kit according to manufacturer’s protocol (tissues were lysed mechanically using the Tissue Lyser II).
Libraries were constructed with theTruSeq mRNA Paired-End kit per manufacturers instructions.

treatment_protocol: MDA-MB-231 Cells 2 x 10^6 in 50µl (50:50 PBS:Matrigel) were transplanted subcutaneously into the mammary fat pads of balb/c nude mice and 50 days later the tumour was excised from the sacrificed mouse.

tag: cell line

tag: host mouse strain

value: balb/c nude

value: mammary gland


title: Abraxane+Phenelzine_1

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days and Phenelzine (40mg/kg) daily from day 15.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: F265
A+P_1


title: Phenelzine_4

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of phenelzine 40 mg/kg daily after 15 days.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: C253
PHE_4


title: SN38_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad002

value: male


title: Abraxane+Phenelzine_4

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days and Phenelzine (40mg/kg) daily from day 15.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: F268
A+P_4


title: Dc300

value: 300ug/L DCAcAm


title: Erastin_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad001


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad007


title: Phenelzine_1

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of phenelzine 40 mg/kg daily after 15 days.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: C250
PHE_1


title: Phenelzine_3

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of phenelzine 40 mg/kg daily after 15 days.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: C252
PHE_3


title: Abraxane_4

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days. .
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: B249
ABX_4


title: PifithrinAlpha_Dose3_Rep2


title: BMS345541_Dose3_Rep2


title: Abraxane_3

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days. .
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: B248
ABX_3


title: Purmorphamine_Dose3_Rep2


title: Abraxane_2

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days. .
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: B246
ABX_2


title: Phenelzine_2

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of phenelzine 40 mg/kg daily after 15 days.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: C251
PHE_2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad006


title: Abraxane+Phenelzine_2

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days and Phenelzine (40mg/kg) daily from day 15.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: F266
A+P_2


title: Abraxane_1

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of nab-paclitaxel (30mg/kg) at 15, 22 and 29 days. .
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: B245
ABX_1


title: Canertinib_Dose3_Rep2


title: Vehicle_4

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: A244
VEH_4


title: Methotrexate_Dose3_Rep2


title: Vehicle_3

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: A243
VEH_3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad004


title: Vehicle_2

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: A241
VEH_2


title: Etomoxir_Dose3_Rep2


title: Vehicle_1

description:
MDA-MB-231 cells were transplanted subcutaneously into the mammary fat pads of Balb/c nude mice and treated with intraperitoneal injections of vehicle control only.
gene_count_matrix_human.csv
gene_count_matrix_mouse.csv
Sample name: A240
VEH_1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad012


title: TG101348_Dose3_Rep2


title: LF82 in stationary replicat 1

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description:
NC_011993.1
A272T2

data_processing:
Reads alignment was performed using Bowtie 2 (Langmead &  Salzberg, 2012) and significant fold changes accessed with the DE-seq pipeline (Anders & Huber, 2010).
Genome_build: hg19  and NC_011993.1
Supplementary_files_format_and_content: Custom interface id, gene name, NCBI ID https://www.ncbi.nlm.nih.gov/nuccore/NC_011993.1, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq  P value
Genome_build: hg19
Supplementary_files_format_and_content: gene_id (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25), gene type, gene name, RPKM Condition 1, RPKM condition 2, Fold change (condition 2/condition 1), Deseq  P value

organism: Escherichia coli LF82

growth_protocol: Macrophages were  infected and imaged as previously described (Demarre et al., 2017). Infections were performed at MOI 30 (measured by CFU), resulting in the observation of 3 LF82 bacteria per macrophage on average at 1 h P.I..

extract_protocol:
Total RNA were extracted from THP1 macrophages infected by WT LF82 at 1 h and 6h P.I. Control experiments were performed with macrophages alone and bacteria alone cultivated for 1 h and 6 h in DMEM medium at 37°C and 5% CO2 without agitation. RNA extraction was performed as described before (Demarre et al, 2019).
Experiments were performed from biological duplicate. Human rRNAs were depleted using the Ribo-Zero kit, then strand-specific libraries were constructed using the TruSeq Stranded Total RNA kit (Illumina).
Paired-end sequencing (2 x 100 nt) was performed on a HiSeq 2500 sequencer.

tag: sample name

tag: cell type

value: bacterial culture


title: LF82 6h in growth medium replicat 1

description:
NC_011993.1
A272T3


title: LF82 6h in growth medium replicat 2

description:
NC_011993.1
A272T10


title: Necrostatin1_Dose3_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: SU11274_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad010


title: Donor5_8_TRB_Th1

city: Moscow

first: Sofya

middle: A.

last: Kasatskaya

address: Bolshoy Boulevard 30, bld. 1

department: Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Illumina software was used for barcode identification and sample demultiplexing.
Sequenced reads were processed with MiGEC software v.1.2.9 for Unique Molecular Identifiers (UMI) extraction with MiGEC Checkout and Assemble utilities.
Reads assembled in UMI groups were aligned and errors were corrected with MIXCR software v.2.1.1 using built-in reference library.
VDJtools v.1.2.1 Convert utility was used to convert processed txt files to widey used vdjtools format of cloneset tables.
Supplementary_files_format_and_content: tab-delimited text files for each Sample present cloneset tables in standart VDJtools format

source_name: memory Th subsets sorted from PBMC

extract_protocol:
T cell subsets were FACS sorted from fresh PBMC samples from 5 healthy donors. Effector/memory functional subsets were sorted at >98% purity into RLT  537 buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich).  after exclusion of naive CCR7+CD45RA+ were sorted in lysis buffer
TCRα and TCRβ cDNA libraries were 569 prepared using a Human TCR Kit (MiLaboratory LLC)  with template switch-based incorporation of UMIs.
OTHER: target RNA-seq (RACE)

tag: subset

tag: tcr chain

value: TCR beta

tag: donor

value: Donor 5


title: LF82 1h in growth medium replicat 2

description:
NC_011993.1
A272T8


title: Donor5_7_TRB_Th22


title: LF82 in stationary replicat 2

description:
NC_011993.1
A272T9


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad006

value: ACA,PL,ILA

tag: Sex

tag: strain


title: SJ172550_Dose3_Rep2


title: Donor5_6_TRB_Th2


title: Donor5_5_TRB_Th17


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H2_ad002


title: SixMercaptopurine_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad008


title: Donor5_3_TRB_Th1-17


title: Donor5_2_TRB_TREG

value: Treg


title: Donor5_4_TRB_Th2a


title: BMS536924_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad002


title: LF82 1h in growth medium replicat 1

description:
NC_011993.1
A272T1


title: PAC1_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H12_ad001


title: Donor4_7_TRB_Th22

value: Donor 4


title: Donor4_8_TRB_Th1


title: GSK2636771_Dose3_Rep2


title: Donor4_6_TRB_Th2


title: Donor5_1_TRB_Tfh

value: Tfh


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H11_ad008


title: Donor4_5_TRB_Th17

description: biological replicate for Donor4_5_2_TRB_Th17


title: Donor4_5_2_TRB_Th17

description: biological replicate for Donor4_5_TRB_Th17


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H11_ad007


title: Donor4_4_TRB_Th2a


title: DMSOPlate14WellF3_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H11_ad006


title: Donor4_3_TRB_Th1-17

description: biological replicate for Donor4_3_2_TRB_Th1-17


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H11_ad004


title: Donor4_3_2_TRB_Th1-17

description: biological replicate for Donor4_3_TRB_Th1-17


title: Donor4_2_TRB_TREG

description: biological replicate for Donor4_2_2_TRB_TREG


title: Curcumin_Dose3_Rep2


title: ETP46464_Dose3_Rep2


title: DMSOPlate14WellC3_Dose3_Rep2


title: Donor4_2_2_TRB_TREG

description: biological replicate for Donor4_2_TRB_TREG


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H11_ad001


title: Donor3_6_TRB_Th2

value: Donor 3


title: Donor3_7_TRB_Th22


title: Donor3_8_TRB_Th1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad012


title: TPCA1_Dose3_Rep2


title: Donor3_4_TRB_Th2a


title: Donor3_5_TRB_Th17


title: JQ1_Dose3_Rep2


title: LRRK2IN1_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad010


title: Donor3_3_TRB_Th1-17


title: c-myc-2

value: 4 months

tag: tissue

value: Lymph nodes'cells


title: Donor2_8_TRB_Th1

value: Donor 2


title: Donor3_1_TRB_Tfh


title: PI103_Dose3_Rep2

tag: cell lines


title: Donor3_2_TRB_TREG


title: Donor4_1_TRB_Tfh


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad006


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H3_ad001


title: Donor2_7_TRB_Th22


title: Donor2_5_TRB_Th17


title: Donor2_6_TRB_Th2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad007


title: Ifosfamide_Dose3_Rep2

tag: sgrnas


title: Donor2_4_TRB_Th2a


title: AT7867_Dose3_Rep2

tag: compound treatment


title: Gossypol_Dose3_Rep2


title: ABT737_Dose3_Rep2


title: Donor2_3_TRB_Th1-17


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad002

tag: brain region


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad001

tag: age


title: Donor1_8_TRB_Th1

value: Donor 1


title: DBeQ_Dose3_Rep2


title: Donor1_7_TRB_Th22


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H10_ad004


title: Donor1_6_TRB_Th2


title: Donor1_5_TRB_Th17


title: Donor2_1_TRB_Tfh


title: Donor1_2_TRB_TREG


title: IC87114_Dose3_Rep2


title: Donor1_1_TRB_Tfh


title: APY29_Dose3_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad001


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad006


title: Donor1_4_TRB_Th2a


title: Donor 9671 pre-vaccination

city: Oxford

first: Nicholas

last: Provine

state: Oxfordshire

address: John Radcliffe Hospital

department: NDM - Experimental Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Trimming was performed using Trimmomatic v. 0.39
Pseudoalignment was performed using Kallisto v. 0.46.1
Differential expression analysis was performed using DESeq2 (v. 1.26), with cut-offs of log2 fold-change >1 and p-adjusted <0.05
As appropriate for cross-comparisons, mouse gene symbols were converted to human using biomaRt (v. 2.42.0) and matching on Ensemble gene ID
Genome_build: GRCh38 was used for human data; GRCm38 was used for mouse data
Supplementary_files_format_and_content: Normalized read counts

molecule: polyA RNA

source_name: mucosal-associated invariant T cells

extract_protocol:
RNA extraction was performed as described in: R. A. Barnitz, S. Imam, K. Yates, W. N. Haining, Isolation of RNA and the synthesis and amplification of cDNA from antigen-specific T cells for genome-wide expression analysis. Methods Mol Biol. 979, 161–173 (2013).
cDNA library preparation was performed as described in: S. Picelli et al., Full-length RNA-seq from single cells usingSmart-seq2. Nat Protoc. 9, 171–181 (2014).

treatment_protocol: Treatment protocols listed on a per-sample basis

value: peripheral blood

tag: treatment

value: one day pre-immunization


title: Donor 9671 post-vaccination

value: one day post-immunization with 5x10^10 vp ChAdOx1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad010

value: male


title: Donor1_3_TRB_Th1-17


title: Donor 9499 post-vaccination


title: RO4929097_Dose3_Rep2


title: Donor2_2_TRB_TREG


title: Donor 9499 pre-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad004


title: Donor 6612 post-vaccination


title: Entrectinib_Dose3_Rep2


title: Donor 6612 pre-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad002


title: GDC0879_Dose3_Rep2


title: AZD8186_Dose3_Rep2


title: Donor 6256 post-vaccination


title: Donor 6256 pre-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_H1_ad008


title: ABT199_Dose3_Rep2


title: Donor 4821 pre-vaccination


title: Donor 3517 post-vaccination


title: PF573228_Dose3_Rep2


title: Donor 3517 pre-vaccination


title: Phloretin_Dose3_Rep2


title: Donor 3093 pre-vaccination


title: Donor 3093 post-vaccination


title: Veliparib_Dose3_Rep2


title: Donor 9274 post-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad012


title: Donor 7720 pre-vaccination


title: Donor 7720 post-vaccination


title: Ganetespib_Dose3_Rep1


title: YM155_Dose3_Rep1


title: Donor 7484 pre-vaccination


title: Donor 4074 post-vaccination


title: Donor 4074 pre-vaccination


title: Donor 4821 post-vaccination


title: GSK4112_Dose3_Rep1


title: CAL101_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G9_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad006


title: Donor 3405 post-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G9_ad002


title: StemRegenin1_Dose3_Rep1


title: Donor 9274 pre-vaccination


title: Donor 3405 pre-vaccination


title: Donor 1449 post-vaccination


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad004


title: Donor 1449 pre-vaccination


title: Donor 1272 post-vaccination


title: GSKJ4_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G9_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad001


title: Donor 1272 pre-vaccination


title: ZSTK474_Dose3_Rep1


title: Donor 2794 unstimulated


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad010


title: Istradefylline_Dose3_Rep1


title: Donor 2437 unstimulated


title: Donor 2794 ChAdOx1 stimulation

value: 24h in vitro stim with MOI=10^3 vp ChAdOx1-GFP


title: Donor 7484 post-vaccination


title: OSI027_Dose3_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad001


title: Donor 2437 ChAdOx1 stimulation


title: Donor 2267 unstimulated


title: Triptolide_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad007


title: Donor 2267 ChAdOx1 stimulation


title: BIX01294_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G8_ad008


title: Palbociclib_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad004


title: Donor 2255 ChAdOx1 stimulation


title: Semagacestat_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad006


title: ZM12 [sgNC-8-RFP + CC-122]

city: San Diego

first: Rajkumar

last: Balakrishnan

state: California

address: 10300 Campus Point Drive, Suite 100,

department: Informatics & Predictive Sciences

institute: Bristol Myers Squibb

data_processing:
Raw fastq files were merged so that each sample had one R1 and one R2 files. The quality of the fastq files was evaluated using FastqQC (v 0.11.5). The fastq files were tested using bbmap reformat (v.37.24) for compliance with the fastq format and to convert the quality encoding to q33. Illumina adapters were trimmed using cutadapt (v1.15) and used for Salmon and any other downstream process.    In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option, STAR was also used to trim the reads on the fly using the clip3pAdapterSequence option. Salmon (v 0.7) was used to obtain pseudoalignments on genes on the trimmed fastq files.
Supplementary_files_format_and_content: Salmon Raw Counts

source_name: B lymphocyte

growth_protocol: SU-DHL-4 was maintained in RPMI 1640 medium (RPMI; #11875085, Thermo Fisher) supplemented with 10% fetal bovine serum, 1X sodium pyruvate, 1X non-essential amino acids, 100 U/mL penicillin, and 100 µg/mL streptomycin. When applicable, puromycin (#A1113803, Thermo Fisher), blasticidin (#A1113903, Thermo Fisher) or Hygromycin B (#10687010, Thermo Fisher) was added to the cell culture medium at 2 µg/ml, 10-50 µg/ml and 400 µg/ml respectively .Cells were cultured at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Duplicates of about 1 million freshly frozen, pelleted cells for each condition were shipped to GENEWIZ (South Plainfield, NJ). The RNA extraction was performed using QIAGEN RNeasy Plus Mini Kit and the mRNA was enriched through poly-A+ mRNA.
The RNA extractio library preparation, and mRNAseq were performed by GENEWIZ using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (#7765, New England Biolabs). ERCC RNA spike-in mix (#4456653, invitrogen) was spiked into each sample after RNA extraction and universal human reference RNA (#14919, Thermal fisher) was included for quality control purpose.

treatment_protocol: SU-DHL-4 cells were transduced with a lentiviral vector expressing either sgNT-1 or sgNC-8 and then selected by puromycin (2µg/mL) for three days.  Cells were then spin down and resuspended with fresh medium and seeded in  6 well plates at one million cells per mL and treated with either DMSO or 10 µM CC-122 for 24 hours. Cells were washed once by ice cold PBS and then the cell pellets were snap frozen and kept at -80 °C. One cell pellet from each condition was subjected to western blot to check the CRISPR editing of target genes and Ikaros degradation.


title: ZM11 [sgNC-8-RFP + CC-122]


title: MCF7-PSFFV clone - replica 1

city: Dublin

first: Jochen

last: Prehn

address: 123 St. Stephen's Green

department: Physiology and Medical Physics

country: Ireland

institute: Royal College of Surgeons in Ireland (RCSI)

data_processing:
Transcriptome profiles were created using an existing in-house bioinformatic pipeline. More specifically, after removing the optical duplicates with Clumpify and removing sequencing adapters, the reads were mapped to the human reference genome using TopHat-Bowtie and HTSeq-count was used to create gene-count matrices.
Raw counts were normalized using DESeq2 (R library, version 1.26.0) using ‘rlog’ as normalization method and ‘~ cell_line’ as design formula, including only genes (ENSEMBL identifiers) with non-zero counts in more than 20% of the samples.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts: one tab-separated file for each sample with a ENSEMBL identifier and corresponding count per line
Normalized expression: a single comma-separated file with one sample per line and ENSEMBL identifiers as columns.

growth_protocol: MCF7-pSFFV, MCF7-BCL2, MCF7-BCL(X)L were kindly provided by Dr Donat Koegel. Cells were cultured in RPMI 1640 supplemented with 100 U/mL of penicillin/streptomycin, 10% fetal bovine serum and incubated at 37˚C in humidified atmosphere with 5% of CO2.

extract_protocol:
MCF7 clones were seeded in t25 flasks and let adhere overnight. On the following day, cells were trypsinised, collected in eppendorf tubes and centrifuged. RNA was extracted with TRIzol reagent (ThermoFisher Scientific) and samples mechanically disrupted using a homogeniser. Subsequently, chloroform was added to separate an upper acqueous phase (containing RNA) from the rest. This was mixed with isoprophanol and centrifuged at 12,000g at 4°C; the resulting pellet was put in 75% ethanol and centrifuged again at 7,500 g at 4°C. Pellet was let to air dry and resuspended in RNase free water for further quantification with Nanodrop 2000
Whole transcript RNA-seq was performed on the samples. Specifically, poly-A containing mRNA was purified from the RNA samples and RNA sequencing libraries were created using the KAPA stranded mRNAseq Kit (Illumina), according to the manufacturer’s instructions. Briefly, sequencing libraries were prepared by converting the RNA to cDNA followed by adapter ligation and enrichment of exon coding sequences by PCR using sequence-specific probes. The resulted cDNA libraries were sequenced on a HiSeq 4000 using a flow-cell generating 1 X 50 bp reads.

treatment_protocol: untreated

value: breast cancer

value: MCF7 breast cancer cell line

tag: clone

tag: genotype

value: control (parental)


title: MCF7-BCLXL overexpressing clone - replica 1

tag: cell line

value: BCLXL-overexpressing


title: MCF7-BCL2 overexpressing clone - replica 2


title: MCF7-BCL2 overexpressing clone - replica 1


title: MCF7-BCLXL overexpressing clone - replica 2


title: PF3758309_Dose3_Rep1


title: Afatinib_Dose3_Rep1


title: MCF7-PSFFV clone - replica 2


title: ZM8 [sgNC-8-RFP + DMSO]


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad012

value: ACA,PL,ILA


title: Donor 2255 unstimulated


title: KU60019_Dose3_Rep1


title: ZM6 [sgNT-1-RFP + CC-122]


title: ZM7 [sgNC-8-RFP + DMSO]


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad001


title: ZM5 [sgNT-1-RFP + CC-122]


title: ZM2 [sgNT-1-RFP + DMSO]


title: Linifanib_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G7_ad008


title: Lomeguatrib_Dose3_Rep1


title: DMSOPlate13WellF10_Dose3_Rep1


title: shSMARCB1 Neuron Day 0 1

first: Frank

last: Furnari

address: 9500 Gilman Drive

institute: UC San Diego

description:
sh905 Neuron 1 Day 0
GEO_rawcounts_allfiles.csv

data_processing:
Reads were aligned to hg19 reference genome using STAR alignment software
Output files were sorted and converted to BAM format using Samtools software package
Counts file of reads associated with each gene was generated using featurecounts package
Genome_build: hg19
Supplementary_files_format_and_content: BAM

source_name: iPS12 iPSCs

growth_protocol: Cells were cultured on matrigel-coated plates in mTESR Plus culture medium for iPSCs, or respective NPC or Neuron maintenance medias as described in Reinhardt et al. 2013

extract_protocol:
Cells were harvested and RNA extracted using the Qiagen Rneasy Plus RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were engineered with a doxycycline-inducible non-targeting control or SMARCB1 knockdown construct. ShControl or shSMARCB1 cells were treated with 1 ug/mL doxycycline for 3-5 days

value: iPS-derived Neuron

tag: condition

value: SMARCB1 Knockdown


title: KW2449_Dose3_Rep1


title: shSMARCB1 Neuron Day 0 2

description:
sh905 Neuron 2 Day 0
GEO_rawcounts_allfiles.csv

tag: cell type


title: ZM1 [sgNT-1-RFP + DMSO]


title: shControl Neuron Day 0 2

description:
sh116 Neuron 2 Day 0
GEO_rawcounts_allfiles.csv

value: Control


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad004


title: shControl Neuron Day 0 1

description:
sh116 Neuron 1 Day 0
GEO_rawcounts_allfiles.csv


title: shSMARCB1 NPC Day 0 1

description:
sh905 NPC 1 Day 0
GEO_rawcounts_allfiles.csv

value: iPS-derived NPC


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad006


title: TubastatinA_Dose3_Rep1


title: shSMARCB1 NPC Day 0 2

description:
sh905 NPC 2 Day 0
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad010


title: DMSOPlate13WellC10_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad008


title: shRNA Rescue NPC Day 0 2

description:
sh905m3 NPC 2 Day 0
GEO_rawcounts_allfiles.csv

value: Rescue


title: shRNA Rescue NPC Day 0 1

description:
sh905m3 NPC 1 Day 0
GEO_rawcounts_allfiles.csv


title: shControl NPC Day 0 2

description:
sh116 NPC 2 Day 0
GEO_rawcounts_allfiles.csv


title: shSMARCB1 NPC post-diff.3

description:
sh905 NPC 3
GEO_rawcounts_allfiles.csv


title: EX527_Dose3_Rep1


title: NSC74859_Dose3_Rep1


title: AZD5363_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad012


title: shSMARCB1 NPC post-diff.2

description:
sh905 NPC 2
GEO_rawcounts_allfiles.csv


title: shSMARCB1 NPC post-diff.1

description:
sh905 NPC 1
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad001


title: shControl NPC 2

description:
sh116 NPC 2
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G6_ad007


title: shSMARCB1 NPC Day 0 3

description:
sh905 NPC 3 Day 0
GEO_rawcounts_allfiles.csv


title: CRISPRi SMARCB1 knockdown iPSC 3

description:
UTR1 iPSC 3
GEO_rawcounts_allfiles.csv

value: iPSC


title: shControl NPC Day 0 1

description:
sh116 NPC 1 Day 0
GEO_rawcounts_allfiles.csv


title: CRISPRi SMARCB1 knockdown iPSC 2

description:
UTR1 iPSC 2
GEO_rawcounts_allfiles.csv


title: Olaparib_Dose3_Rep1


title: GSK1059615_Dose3_Rep1


title: CRISPRi SMARCB1 knockdown iPSC 1

description:
UTR1 iPSC 1
GEO_rawcounts_allfiles.csv


title: shControl NPC 1

description:
sh116 NPC 1
GEO_rawcounts_allfiles.csv


title: CRISPRi control iPSC 3

description:
pgRNA iPSC 3
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad004


title: Teniposide_Dose3_Rep1


title: CRISPRi control iPSC 2

description:
pgRNA iPSC 2
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad006


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad002


title: shSMARCB1 iPSC 3

description:
sh905 iPSC 3
GEO_rawcounts_allfiles.csv


title: Belinostat_Dose3_Rep1


title: GDC0941_Dose3_Rep1


title: CRISPRi control iPSC 1

description:
pgRNA iPSC 1
GEO_rawcounts_allfiles.csv


title: BT16 1

description:
BT16 1
GEO_rawcounts_allfiles.csv

value: Cancer cell line


title: BetulinicAcid_Dose3_Rep1


title: shSMARCB1 iPSC 2

description:
sh905 iPSC 2
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G5_ad008


title: BT16 2

description:
BT16 2
GEO_rawcounts_allfiles.csv


title: shSMARCB1 iPSC 1

description:
sh905 iPSC 1
GEO_rawcounts_allfiles.csv


title: shControl iPSC 3

description:
sh116 iPSC 2
GEO_rawcounts_allfiles.csv


title: AZD4547_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G4_ad012


title: shControl iPSC 2

description:
sh116 iPSC 2
GEO_rawcounts_allfiles.csv


title: PX12_Dose3_Rep1


title: shControl iPSC 1

description:
sh116 iPSC 1
GEO_rawcounts_allfiles.csv


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G4_ad010


title: Im-GCT-4072__E3-OE-WT__p15__G34W-repair-OE-H3.3WT__H3K27me3

city: Montreal

first: Nada

last: Jabado

state: Québec

address: 1001 Décarie Boulevard

department: Department of Pediatrics

country: Canada

institute: McGill University

description: Corresponding input is: Im-GCT-4072__E3-OE-WT__p15__G34W-repair-OE-H3.3WT__Input

data_processing:
The ChIP-seq pipeline from C3G’s GenPipes toolset6 (v3.1.0) was used to trim, merge and align ChIP-seq data. Clean reads were aligned to the human genome (hg19) using bwa-mem. Duplicates were marked using picardtools and samtools.  We used the “bamCoverage” functionality of deeptools (v3.1.3) to produce duplicate-depleted RPKM-normalized BigWig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Tumor-derived cell-line

extract_protocol:
ChIP-seq was performed as previously described5. Briefly, cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at −80 °C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off. Samples were checked for sonication efficiency using the criteria of 150–500 bp by gel electrophoresis. After sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples.  ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Twenty-five microliter Protein A beads (Invitrogen) were washed and then incubated with antibodies (anti-H3K27me3 (1:40, CST 9733), (anti-H3K27ac (1:80, Diagenode C15410196)), (anti-H3K36me3 (1:100, Active Motif 61021)), (anti-H3.3 (1:66, Millipore 09–838)), (anti-H3.3G34W (1:100, RevMAb 31-1145-00)), (anti-H3K36me2 (1:50, CST 2901)), (anti-H3K9me3 (1:66, Abcam 8898)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 h, followed by 20 min wash cycle with provided wash buffers.   Reverse cross linking took place on a heat block at 65°C for 4 h. ChIP samples were then treated with 2 µl RNase Cocktail at 65°C for 30 min followed by 2 µl Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents, following manufacturer’s instructions. Briefly, 25 µl of ChIP sample was incubated with 45 µl end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50 µl buffer enzyme mix at 30°C for 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead-bound sample was incubated with 45 µl buffer enzyme mix and 5 µl of TruSeq DNA adapters (Illumina), for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6 × /0.8x ratio of Ampure XP beads (double size selection) set to collect 250–450 bp fragments. 50-bp single end sequencing was performed on the Illumina HiSeq 2500/4000 platforms, whereas paired-end sequencing was peformed on the Illumina NovaSeq 6000 S4 platform.

value: G34W repair to WT + O/E H3.3WT

tag: chip antibody

value: H3K27me3 (Rabbit monoclonal/Cell signaling technology 9733S)


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G4_ad006

value: male


title: MK1775_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G4_ad008


title: Navitoclax_Dose3_Rep1


title: Im-GCT-4072__D6-OE-WT__p15__G34W-repair-OE-H3.3WT__H3K27me3

description: Corresponding input is: Im-GCT-4072__D6-OE-WT__p15__G34W-repair-OE-H3.3WT__Input


title: Im-GCT-4072__D6-OE-G34W__p15__G34W-repair-OE-H3.3G34W__H3K27me3

description: Corresponding input is: Im-GCT-4072__D6-OE-G34W__p15__G34W-repair-OE-H3.3G34W__Input

value: G34W repair to WT + O/E H3.3G34W


title: Im-GCT-4072__E3-OE-G34W__p15__G34W-repair-OE-H3.3G34W__H3K27me3

description: Corresponding input is: Im-GCT-4072__E3-OE-G34W__p15__G34W-repair-OE-H3.3G34W__Input


title: MLN2238_Dose3_Rep1

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: 1807TSS1

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Reads were converted from the native Illumina BCL format to fastq format, which were processed with a standard RNA-Seq pipeline, available through the open-source ‘bcbio-nextgen’ project (https://github.com/chapmanb/bcbio-nextgen).
The bcbio-nextgen pipeline runs qualimap, a computational tool that examines SAM/BAM alignment files and provides an overview of the data to detect common QC problems. Reads were aligned against the hg38 reference genomes using the ultra-rapid STAR aligner and concurrently pseudo-align reads to the transcriptome using the Salmon aligner.
Following alignment, expression values were summarized at the gene and transcript level. FeatureCounts was used for STAR-aligned data while Salmon performed its own internal quantitation, yielding estimated counts and values in length-normalized TPM (transcripts per million).
Raw counts at the gene and transcript level were used for differential gene expression analysis using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: keratinocytes_S. aureus TSST-1

growth_protocol: Primary human keratinocytes at passage 3 were cultured in KSFM

extract_protocol:
RNA was extracted using Trizol followed by Dnase treatment and column purification using Qiagen RNeasy columns
cDNA generation and sequencing: 500 ng of Dnase treated total RNA was used to enrich for polyA containing transcripts using beads coated with oligo(dT) primers. The enriched RNA pool was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample prep kit. The molar concentrations of the indexed libraries were measured using the 2100 Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and combined equally into pools for sequencing.  The concentration of the pools were measured using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced on the Illumina HiSeq 4000 genome sequencer using 150 bp paired-end SBS chemistry.

treatment_protocol: Cells were treated with 100 ug/ml of SEB, TSST-1, or vehicle in 100mm tissue culture plates for 6 hours at 37C

value: female

value: adult skin

value: keratinocytes

value: S. aureus TSST-1


title: Im-GCT-4072__D6-OE-G34W__p15__G34W-repair-OE-H3.3G34W__Input


title: 1807TSS3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad012

value: ACA,PL,ILA


title: Im-GCT-4072__E3-OE-G34W__p15__G34W-repair-OE-H3.3G34W__Input


title: Im-GCT-4072__D6-OE-WT__p15__G34W-repair-OE-H3.3WT__Input


title: BGJ398_Dose3_Rep1


title: 1807TSS4


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad010


title: 1807SEB3

source_name: keratinocytes_S. aureus SEB

value: S. aureus SEB


title: Bortezomib_Dose3_Rep1


title: 1807SEB2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G4_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad006


title: Im-GCT-4072__E3-OE-WT__p15__G34W-repair-OE-H3.3WT__Input


title: 1807SEB4


title: 1807NT4

value: Vehicle


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad001


title: Entinostat_Dose3_Rep1


title: Mdivi1_Dose3_Rep1


title: FourHydroxytamoxifen_Dose3_Rep1


title: 1807NT1


title: Masitinib_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad002


title: PDAC_PBMC_16

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

data_processing:
Samples were run using paired end 50 cycle reads on HiSeq 4000 or the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.
The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 3.0.0 with default settings was used, with an initial expected cell count of 10,000. In all casesthe hg19 reference supplied with the cellranger software was used for alignment.
Genome_build: Genome Reference Consortium Human Build 37 (GRCh37)
Supplementary_files_format_and_content: Zipped .tar containing .mtx.gz, and .tsv.gz files for reading into R using the Seurat Pipeline

source_name: PBMC

extract_protocol:
Tissues  were  mechanically  minced  and  enzymatically  digested  with  collagenase  P (1mg/mL DMEM) and subsequently filtered through a 40µm mesh to obtain single cells. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.).
Single-cell cDNA libraries were  prepared  and sequenced using  the  10x Genomics  Platform

value: Treatment Naïve PDA


title: Isoliquiritigenin_Dose3_Rep1


title: 1807NT2


title: PDAC_PBMC_13


title: PDAC_TISSUE_16

source_name: PANCREAS TUMOR

value: Treatment Naïve


title: GSK461364_Dose3_Rep1


title: PDAC_TISSUE_13


title: IBET151_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G3_ad008


title: MET06: Metastatic lesion 06 (10x 3' v2)

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

data_processing:
Cell Ranger
Genome_build: hg19
Supplementary_files_format_and_content: csv format that contains the umi count for each gene in each barcodes (cells)

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Tumor dissociated using a dissociation kit from Miltenyi Biotec
10x Genomics Chromium v2

tag: tissue type

value: Metastasis

tag: gender

value: M

tag: disease state

value: Pancreatic ductal adenocarcinoma


title: PDAC_PBMC_15


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad001

tag: Sex

tag: strain


title: 1807SEB1

tag: tissue


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad007


title: MET04: Metastatic lesion 04 (10x 3' v2)

value: F


title: Spautin1_Dose3_Rep1

source_name: Pool of 5 breast cancer cell lines

tag: cell lines

tag: sgrnas


title: MET05: Metastatic lesion 05 (10x 3' v2)


title: MET03: Metastatic lesion 03 (10x 3' v2)


title: STF083010_Dose3_Rep1

tag: compound treatment


title: MET01: Metastatic lesion 01 (10x 3' v2)

tag: age


title: MET02: Metastatic lesion 02 (10x 3' v2)


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad010

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: Neratinib_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad006


title: SB743921_Dose3_Rep1


title: BMS754807_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad002


title: DMSOPlate13WellF6_Dose3_Rep1


title: AZD7545_Dose3_Rep1


title: SNS032_Dose3_Rep1


title: DMSOPlate13WellC6_Dose3_Rep1


title: Fatal_2

city: Los Angeles

first: Angela

last: Park

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

description: single-cell RNA-seq

data_processing:
Fastq files were directly used for Cell Ranger v.2.1.1.
Output from Cell Ranger was used for analysis in Seurat v3.1
Dead cells were removed by excluding cells with a mitochondrial gene content greater than 10% of the total UMI count.
Genome_build: A custom reference genome that combines the hg38 human reference genome and the SFTSV KASJH reference genome (accession numbers KP663731-KP663733)
Supplementary_files_format_and_content: Cell ranger outputs:  filtered matrix of gene by cell expression, barcode file, expressed gene file

source_name: PBMCs

extract_protocol:
Blood samples were collected from SFTS-suspected patients between 2014 and 2019. All work with human subjects was approved by the Chungbuk National University Hospital (IRB approval number: 2017-05-002-001) and Asan Hospital (IRB approval number: 2016-0046). PBMCs were extracted using Ficoll-Paque PLUS (GE Healthcare, Uppsala Sweden), and stored at - 80 ºC.
PBMC from each individual were processed separately through the ChromiumTM Single Cell Platform with the 10X Genomics ChromiumTM Single Cell 3’ Library and Gel Bead Kit v2 and the Chromium Single Cell A Chip Kit (PN-120267) using the standard manufacturer’s protocol. The constructed libraries were sequenced on Hiseq 4000 (Illumina, San Diego, CA) system in a 2 x 150 paired-end with average of 50,000 reads per cell.
single-cell RNA-seq

value: fatal


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad012

value: male


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad010


title: Fatal_3

description: single-cell RNA-seq


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad008


title: Fatal_1

description: single-cell RNA-seq


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad007


title: Recovery_1

description: single-cell RNA-seq

value: recovery


title: Infection_2

description: single-cell RNA-seq

value: infection


title: MG132_Dose3_Rep1

first: Sonia

last: Brockway

address: 303 E Superior St, SQBRC 7-500

data_processing:
Library strategy: QMAP-Seq
Individual samples were demultiplexed based on i5 and i7 index sequences by running bcl2fastq Conversion Software (Illumina).
Data was processed using QMAP-Seq bioinformatic analysis pipeline (https://github.com/mendillolab/QMAP-Seq). Briefly, sgRNA and cell line barcode sequences were extracted from Read 1 sequences as follows: [ACACCG][sgRNA:20][Interval:102][CellLineBarcode:8]. The number of reads for each cell line-sgRNA pair was counted, allowing up to one nucleotide mismatch per barcode. Cell number was interpolated from sequencing reads using sample-specific standard curves. The number of cells for a compound-treated sample was normalized to the median number of cells for the DMSO-treated samples.
Data was filtered using the following exclusion criteria. First, samples with low read counts were excluded. Second, cell line-sgRNA pairs with high variation (standard deviation of log2(cell number) > 0.7) were excluded. Third, compounds with an AUC > 550 for any cell line-sgRNA pair were excluded. Fourth, noncytotoxic cell line-compound pairs (relative cell number of sgNT with highest dose ≥ 90%) were excluded. Fifth, cell line-compound pairs without a dose-dependent reduction in cell viability (difference in relative cell number of sgNT between lowest and highest dose < 25%) were excluded.
Genome_build: N/A (sgRNA library sequencing)
Supplementary_files_format_and_content: Plain text document (.txt) files with read counts for each cell line-sgRNA pair. Individual files for each sample.
Supplementary_files_format_and_content: Comma-separated values (.csv) file with relative cell numbers (i.e., cell number (%DMSO)) for each cell line-sgRNA-compound-dose-replicate combination. Matrix table with data for all samples.

extract_protocol:
Cell line pools were lysed with lysis buffer (10% 10x Taq DNA Polymerase Buffer, 0.45% IGEPAL CA-630, 0.45% TWEEN 20, 10% Proteinase K, 79.1% Nuclease-Free Water) containing cell spike-in standards. Cells were incubated at 60°C for 1 hour. Proteinase K from lysis buffer was inactivated at 95°C for 15 minutes.
Barcoded region was PCR amplified with a unique set of indexed primers for each sample. PCR products were pooled and purified twice. Sequencing library was diluted, combined with PhiX, denatured, and sequenced on a NovaSeq 6000 (Illumina).

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Recovery_2

description: single-cell RNA-seq


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad006

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: WAY362450_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G2_ad004


title: Infection_1

description: single-cell RNA-seq


title: KU0063794_Dose3_Rep1


title: Control_3

description: single-cell RNA-seq

value: control


title: Control_2

description: single-cell RNA-seq


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad004


title: SN38_Dose3_Rep1


title: Control_1

description: single-cell RNA-seq


title: Erastin_Dose3_Rep1


title: Im-GCT-3504__4F5__T2-T8__G34W-repair__RNA

description:
Ensembl.ensGene.exon.raw.tsv.gz
Ensembl.ensGene.exon.rpkm.tsv.gz

data_processing:
Trimmomatic14 (v0.32) was used to remove adaptor sequences as well as the first four nucleotides of each read. Reads were truncated when the average quality (phred33) of a 4-nucleotide sliding window fell below 30. Short reads (<30bp) were discarded. Multiple quality control metrics were obtained using FASTQC (v0.11.2), samtools15 (v0.1.19), BEDtools16 (v2.17.0) and custom scripts.  The remaining read sets were aligned to the reference genome build hg19 (GRCh37) using the default parameters of STAR17 (v2.3.0e). Primary alignments of reads mapping to 9 or fewer locations in the genome were retained, and the rest was discarded. We quantified gene expression by counting the number of reads (primary alignments; MAPQ>3) over genes described in Ensembl’s ensGene “exon” reference (GRCh37; n=60234 genes) using featureCounts18 (v1.4.4). Bigwig tracks from BAM files were generated and normalized to library depth using BEDtools16 (v2.17.0) and UCSC tools and visualized using Integrative Genomic Viewer (IGV)13.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts
Supplementary_files_format_and_content: bigWig files

extract_protocol:
Total RNA was extracted from cell pellets using the Aurum Total RNA Mini Kit (Bio-Rad) according to manufacturer’s instructions.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 4000 platform.

value: G34W repair to WT


title: Im-GCT-3504__4F5__T3-T8__G34W-repair__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad002


title: Im-GCT-3504__4F5__T1-T8__G34W-repair__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G12_ad001


title: Im-GCT-3504__4C7__T3-T9__G34W-repair__RNA


title: Purmorphamine_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad010


title: Im-GCT-3504__4C7__T2-T9__G34W-repair__RNA


title: Im-GCT-3504__4C7__T1-T9__G34W-repair__RNA


title: Im-GCT-3504__U1__T1-P12T3__G34W-unedited__RNA

value: G34W unedited


title: BMS345541_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad008

value: ACA,PL,ILA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad007


title: Im-GCT-3504__parental__T3-p11__G34W-parental__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad006


title: Canertinib_Dose3_Rep1


title: Im-GCT-3504__parental__T2-p11__G34W-parental__RNA


title: Im-GCT-3504__parental__T1-p11__G34W-parental__RNA


title: Im-GCT-4072__E3__p7-T2__G34W-repair__RNA


title: Methotrexate_Dose3_Rep1


title: Im-GCT-4072__E3__p10__G34W-repair__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad002


title: Im-GCT-4072__D6__p8__G34W-repair__RNA


title: Im-GCT-4072__D6__p18__G34W-repair__RNA


title: Im-GCT-4072__D6__p16__G34W-repair__RNA


title: Etomoxir_Dose3_Rep1


title: TG101348_Dose3_Rep1


title: Im-GCT-4072__A1__p8__G34W-KO__RNA


title: Im-GCT-3504__U1__T2-P12T3__G34W-unedited__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad012


title: Im-GCT-3504__U1__T3-P12T3__G34W-unedited__RNA


title: Im-GCT-4072__A1__p18__G34W-KO__RNA


title: PifithrinAlpha_Dose3_Rep1


title: Im-GCT-4072__A1__p16__G34W-KO__RNA


title: Necrostatin1_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad010


title: Im-GCT-4072__parental__p3__G34W-parental__RNA


title: SU11274_Dose3_Rep1


title: Im-GCT-4072__parental__p23__G34W-parental__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad007


title: Im-GCT-4072__parental__p16__G34W-parental__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad008


title: Im-GCT-4072__E3__p7-T1__G34W-repair__RNA


title: Im-GCT-4072__parental__p14__G34W-parental__RNA


title: Im-GCT-4072__2B2__T3-11__G34W-unedited__RNA


title: SixMercaptopurine_Dose3_Rep1


title: BMS536924_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad006


title: Im-GCT-4072__2B2__T11__G34W-unedited__RNA


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G11_ad001


title: Im-GCT-4072__2B2__T14__G34W-unedited__RNA


title: PAC1_Dose3_Rep1


title: P-5874

data_processing:
Raw base call files from were demultiplexed into FASTQ files using CellRangers mkfastq function (v3.0.2) with default parameters. The FASTQ files were aligned to the reference human genome hg19 using CellRanger’s count function (v3.0.2), in order to create a matrix of gene read counts per cell.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts of post-QC cells

source_name: Patient tumor

extract_protocol:
Fresh GCT tumours collected after surgery were dissociated in Collagenase-Dispase (Sigma-Aldrich). Red blood cells were lysed by ammonium chloride treatment for 5 min on ice. Cell viability was assessed with Trypan Blue. For samples with low viability (<60%), dissociated cells were enriched for live cells using the Dead Cell Removal kit (Miltenyi Biotech).
10,000 dissociated cells per sample were loaded on the 10X Genomics Chromium controller. The Chromium Single Cell 3′ (10X Genomics, Version 3) protocol was strictly followed to prepare libraries. The 10X libraries were sequenced on the Illumina HiSeq 4000 sequencing platform.


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad004


title: P-6028


title: P-5071


title: P-4671


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad001


title: SJ172550_Dose3_Rep1


title: Im-GCT-4072__parental__p15__G34W-parental__H3K9me3

description: Corresponding input is: Im-GCT-4072__parental__p14__G34W-parental__Input

data_processing:
The ChIP-seq pipeline from C3G’s GenPipes toolset6 (v3.1.0) was used to trim, merge and align ChIP-seq data. Clean reads were aligned to the human genome (hg19) using bwa-mem. Duplicates were marked using picardtools and samtools.  We used the “bamCoverage” functionality of deeptools (v3.1.3) to produce duplicate-depleted RPKM-normalized BigWig tracks
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values containing raw read counts

extract_protocol:
ChIP-seq was performed as previously described5. Briefly, cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at −80 °C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off. Samples were checked for sonication efficiency using the criteria of 150–500 bp by gel electrophoresis. After sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples.  ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Twenty-five microliter Protein A beads (Invitrogen) were washed and then incubated with antibodies (anti-H3K27me3 (1:40, CST 9733), (anti-H3K27ac (1:80, Diagenode C15410196)), (anti-H3K36me3 (1:100, Active Motif 61021)), (anti-H3.3 (1:66, Millipore 09–838)), (anti-H3.3G34W (1:100, RevMAb 31-1145-00)), (anti-H3K36me2 (1:50, CST 2901)), (anti-H3K9me3 (1:66, Abcam 8898)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 h, followed by 20 min wash cycle with provided wash buffers.   Reverse cross linking took place on a heat block at 65°C for 4 h. ChIP samples were then treated with 2 µl RNase Cocktail at 65°C for 30 min followed by 2 µl Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP Illumina library preparation reagents, following manufacturer’s instructions. Briefly, 25 µl of ChIP sample was incubated with 45 µl end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50 µl buffer enzyme mix at 30°C for 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead-bound sample was incubated with 45 µl buffer enzyme mix and 5 µl of TruSeq DNA adapters (Illumina), for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6 × /0.8x ratio of Ampure XP beads (double size selection) set to collect 250–450 bp fragments. Single end sequencing was performed on the Illumina HiSeq 2500/4000 platforms.

value: H3K9me3 (Rabbit polyclonal/Abcam ab8898)


description: Corresponding input is: Im-GCT-4072__D6__p11__G34W-repair__Input


title: Im-GCT-4072__E3__p7__G34W-repair__Input

description: Corresponding input is: Im-GCT-4072__E3__p7__G34W-repair__Input


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad007


title: Im-GCT-4072__E3__p7__G34W-repair__H3K9me3


title: DMSOPlate13WellF3_Dose3_Rep1


title: Im-GCT-4072__D6__p11__G34W-repair__H3K9me3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad001


title: Im-GCT-4072__2B2__T19__G34W-unedited__H3K9me3

description: Corresponding input is: Im-GCT-4072__2B2__T19__G34W-unedited__Input


description: Corresponding input is: Im-GCT-3504__parental__p20__G34W-parental__Input


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad006


title: DMSOPlate13WellC3_Dose3_Rep1


title: ETP46464_Dose3_Rep1


description: Corresponding input is: Im-GCT-3504__U1__p17-T8__G34W-unedited__Input


title: TPCA1_Dose3_Rep1


title: Im-GCT-3504__U1__p17-T8__G34W-unedited__H3.3

value: H3.3 (Rabbit polyclonal/Millipore 09-838)


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G10_ad002


description: Corresponding input is: Im-GCT-3504__4F5__T15__G34W-repair__Input


title: Im-GCT-3504__4F5__T15__G34W-repair__H3.3


description: Corresponding input is: Im-GCT-3504__4C7__T18__G34W-repair__Input


title: GSK2636771_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_G1_ad008


title: Im-GCT-3504__4C7__T18__G34W-repair__H3.3


title: Curcumin_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad012


title: Im-GCT-4072__parental__p7__G34W-parental__H3K36me3

description: Corresponding input is: Im-GCT-4072__parental__p7__G34W-parental__Input

value: H3K36me3 (Mouse monoclonal/GeneTex MABI0333-GTX50908)


title: Gossypol_Dose3_Rep1


title: Im-GCT-4072__parental__p14__G34W-parental__H3K36me2

value: H3K36me2 (Rabbit monoclonal/Cell signaling technology  2901)


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad001


title: Ifosfamide_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad007


title: Im-GCT-4072__E3__p10__G34W-repair__H3K27ac

description: Corresponding input is: Im-GCT-4072__E3__p10__G34W-repair__Input

value: H3K27ac (Rabbit polyclonal/Diagenode C15410196)


title: Im-GCT-4072__D6__p16__G34W-repair__H3K27ac

description: Corresponding input is: Im-GCT-4072__D6__p16__G34W-repair__Input


title: AT7867_Dose3_Rep1


title: Im-GCT-4072__parental__p14__G34W-parental__H3.3G34W

value: H3.3G34W (Rabbit Monoclonal/RevMAb Biosciences RM263)


title: JQ1_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad004


title: ABT737_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad002


title: LRRK2IN1_Dose3_Rep1


title: DBeQ_Dose3_Rep1


title: Im-GCT-4072__E3__p5__G34W-repair__Input

description: Corresponding input is: Im-GCT-4072__E3__p5__G34W-repair__Input


title: Im-GCT-4072__parental__p7__G34W-parental__Input


title: Im-GCT-4072__E3__p5__G34W-repair__H3K36me2


title: Im-GCT-4072__E3__p10__G34W-repair__Input


title: Im-GCT-3504__parental__p20__G34W-parental__H3.3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad012


title: Im-GCT-4072__E3__p10__G34W-repair__H3K36me3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F9_ad008


title: Im-GCT-4072__A1__p16__G34W-KO__H3K27ac

description: Corresponding input is: Im-GCT-4072__A1__p16__G34W-KO__Input

value: G34W KO


title: GDC0879_Dose3_Rep1


title: Im-GCT-4072__parental__p14__G34W-parental__Input


title: Im-GCT-4072__parental__p14__G34W-parental__H3K27ac


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad007


title: IC87114_Dose3_Rep1


title: Im-GCT-4072__D6__p8__G34W-repair__Input

description: Corresponding input is: Im-GCT-4072__D6__p8__G34W-repair__Input


title: Im-GCT-4072__parental__p14__G34W-parental__H3K27me3

value: H3K27me3 (Rabbit monoclonal/Cell signaling technology 9733S)


title: Im-GCT-4072__D6__p8__G34W-repair__H3K36me3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad006


title: Im-GCT-4072__E3__p5__G34W-repair__H3K27me3


title: Im-GCT-4072__D6__p16__G34W-repair__Input


title: Im-GCT-4072__2B2__T19__G34W-unedited__H3K27ac


title: Entrectinib_Dose3_Rep1


title: Im-GCT-4072__D6__p16__G34W-repair__H3K27me3


title: Im-GCT-4072__A1__p8__G34W-KO__Input

description: Corresponding input is: Im-GCT-4072__A1__p8__G34W-KO__Input


title: Phloretin_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad004


title: Im-GCT-4072__A1__p8__G34W-KO__H3K36me3


title: Im-GCT-4072__A1__p8__G34W-KO__H3K36me2


title: AZD8186_Dose3_Rep1


title: Im-GCT-4072__A1__p16__G34W-KO__Input


title: Im-GCT-4072__A1__p16__G34W-KO__H3K27me3


title: APY29_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F8_ad008


title: Im-GCT-4072__E3__p10__G34W-repair__H3.3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad001


title: PI103_Dose3_Rep1


title: Im-GCT-4072__D6__p8__G34W-repair__H3K36me2


title: PF573228_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad007


title: RO4929097_Dose3_Rep1


title: Im-GCT-4072__A1__p16__G34W-KO__H3.3


title: Im-GCT-4072__parental__p14__G34W-parental__H3.3


title: Im-GCT-4072__D6__p8__G34W-repair__H3.3


description: Corresponding input is: Im-GCT-4072__2B2__T11__G34W-unedited__Input


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad006


title: YM155_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad004


description: Corresponding input is: Im-GCT-4072__2B2__none__G34W-unedited__Input


title: Im-GCT-4072__2B2__none__G34W-unedited__H3K36me3


title: Im-GCT-4072__2B2__none__G34W-unedited__H3K36me2


title: Im-GCT-4072__2B2__T11__G34W-unedited__H3K27me3


title: ABT199_Dose3_Rep1


title: GSK4112_Dose2_Rep2


title: Veliparib_Dose3_Rep1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad010


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F6_ad001


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad008


title: CAL101_Dose2_Rep2


description: Corresponding input is: Im-GCT-3504__parental__p15__G34W-parental__Input


title: Im-GCT-3504__parental__p15__G34W-parental__H3K27me3


title: Im-GCT-3504__parental__p15__G34W-parental__H3K27ac


title: StemRegenin1_Dose2_Rep2


title: Im-GCT-4072__2B2__none__G34W-unedited__H3.3G34W


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F6_ad006


title: Im-GCT-3504__parental__p15__G34W-parental__H3K36me2


title: GSKJ4_Dose2_Rep2


title: Im-GCT-3504__U1__T8__G34W-unedited__H3K36me3

description: Corresponding input is: Im-GCT-3504__U1__T8__G34W-unedited__Input


title: Im-GCT-3504__parental__p15__G34W-parental__H3K36me3


title: Im-GCT-3504__U1__T8__G34W-unedited__Input


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F6_ad004


title: Im-GCT-4072__2B2__T19__G34W-unedited__Input


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F6_ad002


title: Istradefylline_Dose2_Rep2


description: Corresponding input is: Im-GCT-3504__4F5__T11__G34W-repair__Input


title: Im-GCT-3504__U1__T8__G34W-unedited__H3K27me3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F6_ad008


title: Im-GCT-3504__U1__T8__G34W-unedited__H3K27ac


title: ZSTK474_Dose2_Rep2


title: OSI027_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F7_ad002


title: Im-GCT-3504__4F5__T11__G34W-repair__H3K36me2


title: Im-GCT-4072__2B2__T11__G34W-unedited__H3.3


title: Im-GCT-3504__4C7__T11__G34W-repair__H3K36me3

description: Corresponding input is: Im-GCT-3504__4C7__T11__G34W-repair__Input


title: Im-GCT-3504__4C7__T11__G34W-repair__H3K27ac


title: Im-GCT-3504__4F5__T11__G34W-repair__H3K36me3


title: Im-GCT-3504__U1__T8__G34W-unedited__H3K36me2


title: Semagacestat_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad007


title: Triptolide_Dose2_Rep2


title: BIX01294_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad006


title: Im-GCT-3504__4F5__T11__G34W-repair__H3K27me3


title: Im-GCT-3504__4F5__T11__G34W-repair__H3K27ac


title: Jurkat-ad-ube3b-1

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: jurkat cells

extract_protocol:
cells were collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T lymphocyte

value: peripheral blood

tag: morphology

value: lymphoblast


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad001

value: male


title: Jurkat-ad-ube3b-2


title: Linifanib_Dose2_Rep2

value: sgNT, sgHSF1, sgHSF2, sgERN1, sgXBP1, sgATF3, sgATF4, sgATF6, sgNFE2L2, sgKEAP1, sgATG7, sgSLC35F2


title: Im-GCT-3504__4C7__T11__G34W-repair__Input

tag: genotype


title: Jurkat-ad-ube3b-3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad010


title: Palbociclib_Dose2_Rep2


title: Im-GCT-3504__4C7__T11__G34W-repair__H3K27me3

tag: cell line


title: PF3758309_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad008


title: KU60019_Dose2_Rep2


title: Lomeguatrib_Dose2_Rep2


title: Jurkat-ad-con-3


title: DMSOPlate12WellF10_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad012


title: Jurkat-control-3


title: Jurkat CM4-2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad001


title: Afatinib_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F5_ad002


title: Jurkat-ad-con-1


title: Im-GCT-3504__4C7__T11__G34W-repair__H3K36me2


title: Jurkat CM4-1


title: Jurkat-c-Myc-si-2

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...


title: Jurkat-control-1


title: Jurkat-control-2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad007


title: Jurkat-c-Myc-si-3


title: Jurkat-ad-con-2


title: KW2449_Dose2_Rep2


title: TubastatinA_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad010


title: Jurkat-control-si-3


title: DMSOPlate12WellC10_Dose2_Rep2


title: Jurkat-control-si-2


title: Jurkat CM4-3


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad006


title: Jurkat-control-si-1


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad004


title: Jurkat-t3-cas9-2

source_name: peripheral blood

value: jurkat cells


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad002


title: Jurkat-t3-cas9-1


title: Jurkat-t3-cas9-3


title: NSC74859_Dose2_Rep2


title: Ganetespib_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F4_ad008


title: Jurkat-control-2


title: Jurkat-control-3


title: AZD5363_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad001


title: Jurkat-control-1


title: Belinostat_Dose2_Rep2


title: RCMB20_primary

type: RNA

first: Edwin

middle: Francisco

last: Juarez

address: 9500 Gilman Dr

institute: University of California San Diego

hyb_protocol: not provided

scan_protocol: not provided

data_processing: RMA and Quantile Normalization of gene expression.

label: biotin

source_name: human tumor

label_protocol: not provided

extract_protocol: total RNA extraction

value: human medulloblastoma tumor

tag: tumor subgroup


title: RCMB28_primary


title: MED211FH_primary


title: RCMB38_primary


title: RCMB18_primary


title: GSK1059615_Dose2_Rep2

institute: Northwestern University


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad012

institute: HHMI-Salk-Institute


title: Jurkat-c-Myc-si-1

first: wang

last: feng

address: nan wei road

tag: cell type


title: Teniposide_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad007


title: MED1911FH_primary


title: EX527_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad010


title: Olaparib_Dose2_Rep2


title: GDC0941_Dose2_Rep2


title: RCMB38

source_name: Patient Derived Xenograph

value: Patient Derived Xenograph


title: RCMB32


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad006

value: ACA,PL,ILA


title: RCMB24


title: RCMB28


title: BetulinicAcid_Dose2_Rep2


title: RCMB40


title: RCMB20


title: AZD4547_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad002


title: MED2312FH


title: MED211FH


title: PX12_Dose2_Rep2


title: RCMB18


title: MED411FH


title: MED1911FH


title: Bortezomib_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad001


title: MB009


title: MED1712FH


title: DMB006


title: MK1775_Dose2_Rep2


title: MB002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad007


title: Mdivi1_Dose2_Rep2


title: ICB-1572MB


title: ICB-1487MB


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad006


title: ICB-984MB


title: ICB-1299MB


title: Navitoclax_Dose2_Rep2


title: BT084


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F3_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F2_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F12_ad012


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F12_ad010


title: MLN2238_Dose2_Rep2


title: FourHydroxytamoxifen_Dose2_Rep2


title: Entinostat_Dose2_Rep2


title: BGJ398_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F12_ad006


title: GSK461364_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F12_ad004


title: Masitinib_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F12_ad001


title: Isoliquiritigenin_Dose2_Rep2


title: IBET151_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad012


title: Spautin1_Dose2_Rep2


title: TACE_Non-Response_307

city: Singapore

first: Kam

last: Hui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Centre Singapore

description: Gene expression data from HCC Tissue sample of  TACE_Non-Response patient

hyb_protocol: The final cRNA obtained was hybridized to the GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix, USA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
The data was analysed using Partek Genomics Suite version 6.6.  CEL files were imported into Partek with GCRMA background correction, quantile normalisation, log2-transformation, and batch effects were removed based on scan date factor.
GCRMA processed log2 signal intensity after batch effect removal using Partek Genomics Suite version 6.6.

source_name: Tissue RNA sample from HCC TACE_Non-Response patient

label_protocol: Five micrograms of total RNA were reversely-transcribed and labeled with biotin.

growth_protocol: Comprehensive gene expression profiling was conducted using biopsied tumor tissues obtained from patients with unresectable HCC prior to TACE treatment.  The present study was performed as a continuing study, according to the clinical trial registered at http://ClinicalTrials.gov (No. NCT00493402).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.

treatment_protocol: All patients recruited in this study were treated with the same TACE regimen.

tag: subject status

value: hepatocellular carcinoma (HCC) patient

tag: subject subgroup

value: TACE non-responders

tag: sample source

value: Liver Tissue; tumor biopsy


title: TACE_Non-Response_313


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad008


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad010


title: TACE_Non-Response_301


title: TACE_Non-Response_325


title: TACE_Non-Response_337


title: TACE_Non-Response_321


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad007


title: TACE_Non-Response_304


title: BMS754807_Dose2_Rep2


title: STF083010_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad006


title: SB743921_Dose2_Rep2


title: Neratinib_Dose2_Rep2


title: TACE_Non-Response_215


title: TACE_Non-Response_205


title: TACE_Non-Response_198


title: MED1712FH_primary


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad002


title: TACE_Non-Response_193


title: TACE_Non-Response_176


title: AZD7545_Dose2_Rep2


title: TACE_Non-Response_173


title: DMSOPlate12WellF6_Dose2_Rep2


title: TACE_Non-Response_204


title: TACE_Non-Response_202


title: SNS032_Dose2_Rep2


title: TACE_Non-Response_182


title: TACE_Non-Response_172


title: TACE_Non-Response_195


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F11_ad001


title: TACE_Non-Response_181


title: DMSOPlate12WellC6_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad010


title: MG132_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad006


title: SN38_Dose2_Rep2


title: KU0063794_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad004


title: TACE_Non-Response_153


title: TACE_Non-Response_156


title: TACE_Non-Response_167


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad008


title: WAY362450_Dose2_Rep2


title: Erastin_Dose2_Rep2


title: TACE_Non-Response_131


title: TACE_Non-Response_166


title: TACE_Non-Response_157


title: TACE_Non-Response_168


title: TACE_Non-Response_113


title: TACE_Non-Response_154


title: Purmorphamine_Dose2_Rep2


title: TACE_Non-Response_165


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad012


title: TACE_Non-Response_155


title: TACE_Non-Response_126


title: TACE_Non-Response_105


title: TACE_Non-Response_106


title: TACE_Non-Response_111


title: TACE_Non-Response_101


title: TACE_Non-Response_114


title: TACE_Non-Response_108


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad002


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F10_ad001


title: PifithrinAlpha_Dose2_Rep2


title: BMS345541_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad004


title: Canertinib_Dose2_Rep2


title: Methotrexate_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad006


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad002


title: TG101348_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad010


title: Etomoxir_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad001


title: TACE_Non-Response_59


title: SU11274_Dose2_Rep2


title: Necrostatin1_Dose2_Rep2


title: TACE_Non-Response_92


title: TACE_Non-Response_90


title: TACE_Non-Response_85


title: TACE_Non-Response_67


title: TACE_Non-Response_81


title: TACE_Non-Response_56


title: TACE_Non-Response_55


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad012


title: TACE_Non-Response_77


title: TACE_Non-Response_35


title: TACE_Non-Response_41


title: TACE_Non-Response_86


title: TACE_Non-Response_95


title: TACE_Non-Response_51


title: TACE_Non-Response_53


title: SJ172550_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_F1_ad008


title: TACE_Non-Response_58


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad001


title: TACE_Non-Response_36


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad007


title: SixMercaptopurine_Dose2_Rep2


title: TACE_Non-Response_33


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad010


title: PAC1_Dose2_Rep2


title: BMS536924_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad006


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad004


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad002


title: JQ1_Dose2_Rep2


title: TACE_Non-Response_34


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad012


title: DMSOPlate12WellF3_Dose2_Rep2


title: Curcumin_Dose2_Rep2


title: ETP46464_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E9_ad008


title: DMSOPlate12WellC3_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad007


title: TACE_Non-Response_133


title: TACE_Non-Response_19


title: TPCA1_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad001


title: TACE_Non-Response_30


title: TACE_Non-Response_23


title: TACE_Non-Response_32


title: TACE_Response_324

description: Gene expression data from HCC Tissue sample of TACE_Response patient

source_name: Tissue RNA sample from HCC TACE_Response patient

value: TACE responders


title: TACE_Non-Response_16


title: TACE_Response_332


title: TACE_Response_331


title: TACE_Non-Response_18


title: TACE_Response_326


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad010


title: TACE_Non-Response_17


title: TACE_Response_327


title: TACE_Response_319


title: TACE_Non-Response_29


title: TACE_Response_320


title: TACE_Response_317


title: TACE_Response_334


title: TACE_Response_315


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad006


title: PI103_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad004


title: Gossypol_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad002


title: Ifosfamide_Dose2_Rep2


title: LRRK2IN1_Dose2_Rep2


title: TACE_Response_311


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E8_ad008


title: TACE_Response_336


title: AT7867_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad012


title: TACE_Response_323


title: TACE_Response_309


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad001


title: DBeQ_Dose2_Rep2


title: ABT737_Dose2_Rep2


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad007


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad010


title: GDC0879_Dose2_Rep2


title: TACE_Response_214


title: APY29_Dose2_Rep2


title: TACE_Response_217


title: TACE_Response_308


title: TACE_Response_210


title: IC87114_Dose2_Rep2


title: TACE_Response_303


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad004


title: TACE_Response_213


title: TACE_Response_306


title: TACE_Response_216


title: TACE_Response_211


title: TACE_Response_208


title: CEMBA190205_5A_3_CEMBA190205_5A_4_E7_ad006