description:
RTF2-Rescued_24h IFN treatment_24h harvest_rep 3
B9


title: Tempus xO assay DNA sequencing [24_T]

status: Public on Aug 27 2020

type: SRA

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

country: USA

institute: Northwestern University

description:
24-AST
Skin
24_AST.vcf
24-AST.soma.pindel.vcf

library_source: genomic

data_processing:
Library strategy: DNA-seq
FASTQ files containing raw sequencing data were generated using BCL2FASTQ version 2.17 from Illumina Inc.
NovoAlign version 3.05.00 was used for reference sequence alignment.
Variant calls were performed using Freebayes version 1.0.2.58-g054b257.
Indel calls were performed using Pindel version 0.2.5.b9.
RNA fusion calls were performed using P.ARC version 2.5.2.
RNA expression analysis was conducted with CRISP version 1.4.2.4.
Variants were filtered using proprietary Tempus VCF filtering code.
Genome_build: GRCh37, GRCh38, 1000 genomes human reference, HG19, ExAC Database V 0.3.1, Tempus Knowledge database (KDB) V.0.1 COSMIC database version 79 GRCh37
Supplementary_files_format_and_content: .txt files containing RNA counts were generated from FASTQ files using CRISP version 1.4.2.4.
Supplementary_files_format_and_content: VCF files containing DNA variants were generated using Freebayes version 1.0.2.58-g054b257.

molecule: genomic DNA

organism: Homo sapiens

source_name: Sptitz Tumor

extract_protocol:
Tumor total nucleic acid was extracted from at least ten 5-micron FFPE tissue sections with tumor cellularity > 20% by a Chemagic360 instrument (PerkinElmer, MA) using a source-specific magnetic bead protocol and digested with proteinase K. Nucleic acid is quantified by a Quant-iT picogreen dsDNA reagent Kit or Quant-iT Ribogreen RNA Kit (Life Technologies, CA). A Covaris ultrasonicator mechanically sheared 100 nanograms of DNA from each tumor and normal sample to an average size of 200 base pairs (bp).
Libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems, MA). DNA underwent enzymatic end-repair and A-tailing, adapter ligation, bead-based size selection, PCR and probe hybridization. KAPA HiFi HotStart ReadyMix (Kapa Biosystems, MA) was used to amplify captured DNA targets which were then sequenced to an average depth of 500X on the Illumina HiSeq 4000 System (Illumina, Inc., CA) utilizing patterned flow cell technology. One hundred nanograms of RNA per tumor sample was fragmented in the presence of magnesium to an average size of 200 bp. The RNA then underwent first strand cDNA synthesis using random primers, followed by combined second strand synthesis and A-tailing, adapter ligation, bead-based cleanup and library amplification. Samples were then hybridized with the IDT xGEN Exome Research Panel (IDT Inc., CA) and sequenced to obtain > 50 million reads on the Illumina HiSeq 4000 System (Illumina, Inc., San Diego, CA) utilizing patterned flow cell technology.
Next-generation sequencing (DNA with 1711 gene panel and whole transcriptome RNA sequencing).

tag: tissue

value: Sptitz Tumor (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD001_indexed

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

organism: Mus musculus

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: MOs

tag: Sex

value: male

tag: age

tag: strain


city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description:
RTF2-KO_24h IFN treatment_24h harvest_rep 1
B4

library_source: transcriptomic

data_processing:
Short sequencing reads were aligned to the hg38 genome (GENCODE v21) using STAR v2.6
Genomic coordinates were then converted to transcriptomic coordinates, and transcript abundances were quantified using RSEM v1.3.1
Transcript abundances were then aggregated to gene abundances
Genome_build: hg38
Supplementary_files_format_and_content: counts, TPMs

molecule: total RNA

source_name: RTF2-KO A549

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
The Smart-Seq2 protocol (Picelli, Nat Protoc, 2014) was employed to perform transcriptomic analyses of the different cells. The cDNA was synthesized from 1ng of total RNA using SuperScript II reverse transcription, followed by PCR amplification and quality check using high-sensitivity DNA Bioanalyzer chip (Agilent). 0.15 ng of cDNA was then used for the tagmentation reaction carried out with the Nextera XT DNA sample preparation kit (Illumina) and further PCR amplification.

tag: cell line

tag: genotype

tag: treatment

value: IFN 24h 200U/ml

tag: infection

tag: harvest time


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD001_indexed


description:
WT A549_24h IFN treatment_24h harvest_rep 3
B3

source_name: WT A549

value: WT


title: Tempus xO assay DNA sequencing [23_N]

description:
23-AST
Skin
23_AST.vcf
23-AST.soma.pindel.vcf

value: Sptitz Tumor (normal)


title: Tempus xO assay DNA sequencing [23_T]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD012_indexed


description:
WT A549_24h IFN treatment_24h harvest_rep 2
B2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD010_indexed


title: Tempus xO assay DNA sequencing [236_T]

description:
236-SM
Skin
236_SM.vcf
236-SM.soma.pindel.vcf

source_name: Spitzoid Melanoma

value: Spitzoid Melanoma (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D2_AD010_indexed


description:
WT A549_24h IFN treatment_24h harvest_rep 1
B1


description:
RTF2-Rescued_no treatment_24h harvest_rep 3
A9

source_name: RTF2-Rescued A549


title: Tempus xO assay DNA sequencing [234_T]

description:
234-SM
Skin
234_SM.vcf
234-SM.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [235_T]

description:
235-SM
Skin
235_SM.vcf
235-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D12_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D12_AD012_indexed


description:
RTF2-Rescued_no treatment_24h harvest_rep 2
A8


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D11_AD006_indexed


description:
RTF2-Rescued_no treatment_24h harvest_rep 1
A7


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D11_AD001_indexed


title: Tempus xO assay DNA sequencing [24_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D12_AD001_indexed


title: Tempus xO assay DNA sequencing [233_T]

description:
233-SM
Skin
233_SM.vcf
233-SM.soma.pindel.vcf


title: RTF2-KO_no treatment_24h harvest_rep 3

description:
RTF2-KO_no treatment_24h harvest_rep 3
A6


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D1_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D11_AD004_indexed


title: RTF2-KO_no treatment_24h harvest_rep 1

description:
RTF2-KO_no treatment_24h harvest_rep 1
A4


title: Tempus xO assay DNA sequencing [231_T]

description:
231-MWS
Skin
231_SM.vcf
231-SM.soma.pindel.vcf

source_name: Melanoma with Spitzoid Features

value: Melanoma with Spitzoid Features (tumor)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D11_AD002_indexed


title: RTF2-KO_no treatment_24h harvest_rep 2

description:
RTF2-KO_no treatment_24h harvest_rep 2
A5


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD012_indexed


title: WT A549_no treatment_24h harvest_rep 2

description:
WT A549_no treatment_24h harvest_rep 2
A2


title: Tempus xO assay DNA sequencing [229_T]

description:
229-SM
Skin
229_SM.vcf
229-SM.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [225_T]

description:
225-SM
Skin
225_SM.vcf
225-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D10_AD006_indexed


title: Tempus xO assay DNA sequencing [228_T]

description:
228-SM
Skin
228_SM.vcf
228-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD010_indexed


title: Tempus xO assay DNA sequencing [226_T]

description:
226-SM
Skin
226_SM.vcf
226-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD006_indexed


title: HiChIP YY1-TMPYP4 rep2

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

description: processed data file: HiChIP_TMP_Interaction_Matrix_5kb_bin.cool

data_processing:
Library strategy: HiChIP
The sequencing reads of ChIP-seq were aligned to human hg19 reference genome using the Bowtie2. Peak calling were generated using the Model-based Analysis of ChIP-Seq (MACS). The UCSC Genome Browser was used to visualize the mapping results.
For HiChIP-seq analysis, the reads were aligned to human hg19 reference genome using the Map with BWA-MEM tool with gap extension penalty setting at 50. Then the interaction matrix was built with hicBuildMatrix tool with restriction site setting to HindIII site. And visualization of the HiChIP data was performed with hicPlotMatrix tool.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, wig files were generated using MACS2, and converted to Bigwig files.For HiChIP, cool files were generatd by hicBuildMatrix tool.

source_name: 293T YY1-TAPTAG

growth_protocol: Cells were cultured at 37 oC in a humidified incubator with 5% CO2.

extract_protocol:
Lysates were clarified from crosslinked and sonicated chromatin. Antibody was used to purify the protein interacted DNA. For HiChIP, crosslinked chromatin were digested with HindIII and ligated before sonication and antibody enrichment.
DNA sequencing library preparation was conducted using NEBNext Ultra™ DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

treatment_protocol: Cells were treated with PDS or TMPYP4 for 12 hours before harvest.

tag: antibody

value: Anti-Flag  (Cell Signaling Technology, 2368S)

tag: cell type

value: Human embryonic kidney cells


title: WT A549_no treatment_24h harvest_rep 3

description:
WT A549_no treatment_24h harvest_rep 3
A3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C4_AD002_indexed


title: Tempus xO assay DNA sequencing [22_T]

description:
22-AST
Skin
22_AST.vcf
22-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [224_T]

description:
224-MWS
Skin
224_MWS.vcf
224-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C4_AD001_indexed


title: Tempus xO assay DNA sequencing [223_N]

description:
223-MWS
Skin
223_MWS.vcf
223-MWS.soma.pindel.vcf

value: Melanoma with Spitzoid Features (normal)


title: HiChIP YY1-TMPYP4 rep1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D10_AD010_indexed


title: Tempus xO assay DNA sequencing [222_T]

description:
222-MWS
Skin
222_MWS.vcf
222-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C4_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C4_AD008_indexed


title: Tempus xO assay DNA sequencing [223_T]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C5_AD007_indexed


title: WT A549_no treatment_24h harvest_rep 1

description:
WT A549_no treatment_24h harvest_rep 1
A1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C3_AD002_indexed


title: HiChIP YY1-PDS rep1

description: processed data file: HiChIP_PDS_Interaction_Matrix_5kb_bin.cool


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD008_indexed


title: HiChIP YY1 rep2

description: processed data file: HiChIP_Kin_Interaction_Matrix_5kb_bin.cool


title: Tempus xO assay DNA sequencing [222_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D10_AD001_indexed


title: HiChIP YY1 rep4


title: Tempus xO assay DNA sequencing [220_T]

description:
220-SM
Skin
220_SM.vcf
220-SM.soma.pindel.vcf


title: HiChIP YY1-PDS rep2


title: HiChIP YY1 rep1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD006_indexed


title: HiChIP YY1 rep3


title: Tempus xO assay DNA sequencing [220_N]

value: Spitzoid Melanoma (normal)


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD001_indexed


title: ChIP-seq YY1-TMPYP4 rep2

data_processing:
The sequencing reads of ChIP-seq were aligned to human hg19 reference genome using the Bowtie2. Peak calling were generated using the Model-based Analysis of ChIP-Seq (MACS). The UCSC Genome Browser was used to visualize the mapping results.
For HiChIP-seq analysis, the reads were aligned to human hg19 reference genome using the Map with BWA-MEM tool with gap extension penalty setting at 50. Then the interaction matrix was built with hicBuildMatrix tool with restriction site setting to HindIII site. And visualization of the HiChIP data was performed with hicPlotMatrix tool.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, wig files were generated using MACS2, and converted to Bigwig files.For HiChIP, cool files were generatd by hicBuildMatrix tool.


title: ChIP-seq YY1-TMPYP4 rep1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD008_indexed


title: Tempus xO assay DNA sequencing [215_T]

description:
215-SM
Skin
215_SM.vcf
215-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD007_indexed


title: Tempus xO assay DNA sequencing [221_T]

description:
221-MWS
Skin
221_MWS.vcf
221-MWS.soma.pindel.vcf


title: ChIP-seq YY1-PDS rep2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C2_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD001_indexed


title: Tempus xO assay DNA sequencing [212_T]

description:
212-MWS
Skin
212_MWS.vcf
212-MWS.soma.pindel.vcf


title: ChIP-seq YY1-PDS rep1


title: ChIP-seq YY1 rep2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD001_indexed


title: Tempus xO assay DNA sequencing [20_T]

description:
20-AST
Skin
20_AST.vcf
20-AST.soma.pindel.vcf


title: Tempus xO assay DNA sequencing [20_N]


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD006_indexed


title: ChIP-seq control rep2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD007_indexed


title: ChIP-seq YY1 rep1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD004_indexed


title: Tempus xO assay DNA sequencing [217_T]

description:
217-MWS
Skin
217_MWS.vcf
217-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD008_indexed


title: Tempus xO assay DNA sequencing [204_T]

description:
204-SM
Skin
204_SM.vcf
204-SM.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C12_AD012_indexed


title: CD4 Treg_KO1

city: Boston

first: George

middle: C.

last: Tsokos

address: CLS-928, 3 Blackfan Circle

department: Medicine

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

data_processing:
Adapter sequences were trimmed from the raw reads with CutAdapt (v2.7). Trimmed reads of each sample were mapped to the reference house mouse genome build GRCm38 (mm10) by using Bowtie2 (v2.3.5) BAM files were generated and sorted by query name with SAMtools (v1.9).
Genrich (v0.6) was used for peak calling using multiple replicates for one condition with default threshold. PCR duplicated reads and reads mapping to mitochondrial DNA and the Y chromosome were filtered.
Genomic location of peaks was determined using R package ChIPseeker (v1.22.1). The integrative genomics viewer (IGV) was used to analyze the genomic context of specific differentially accessible regions.
Peaks called from ATAC-Seq profiles were annotated using ChIPseeker. In detail, the “TxDb.Mmusculus.UCSC.mm10.knowGene” was used as the annotation database, and the promoter region was defined as ±3 kb around the transcriptional start site (TSS).
Affinity-based analysis was performed using R package Diffbind (v2.14.0) with the DESeq2 method (V1.26.0). TF binding motif analysis of ATAC-seq data was performed using HOMER v4.7.217. Only known motifs from HOMER’s motif database were considered.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: CD4 Regulatory T cells

growth_protocol: CD4 Tconv cells which were sorted out by flow cytometry, were stimulated with plate bound CD3 (1 μg/ml) and CD28 (1 μg/ml) antibodies for 4 hours. Treg cells  which were sorted out by flow cytometry, were stimulated with IL-2 (20 ng/ml) and plate bound CD3 (1 μg/ml) and CD28(1 μg/ml)  antibodies for 4 hours

extract_protocol:
50,000 viable cells were lysed using 50 ul cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and the nuclei was Pellet.
We followed the Omni-ATAC protocol (Corces et al., 2017) to construct the library. Deep sequencing was performed using PE35-bp reads on Illumina NextSeq500 at Boston Nutrition Obesity Research Center Functional Genomics Core.

value: Splenic CD4 Regulatory T cells

value: 9-10 weeks

value: PPP2R2D KO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD007_indexed


title: CD4 Treg_KO2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD012_indexed


title: CD4 Treg_WT2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD008_indexed


title: Tempus xO assay DNA sequencing [211_T]

description:
211-MWS
Skin
211_MWS.vcf
211-MWS.soma.pindel.vcf


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD006_indexed


title: CD4 Treg_WT1


title: CD4 Tconv_KO2

source_name: CD4 Conventional T cells

value: Splenic CD4 Conventional T cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B4_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C11_AD001_indexed


title: CD4 Tconv_KO1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD004_indexed


title: ChIP-seq control rep1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B4_AD010_indexed


title: CD4 Tconv_WT2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B4_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD008_indexed


title: ELF3 expressing_03

type: RNA

city: Suita

first: Masami

last: Suzuki

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

description: Gene expression in ELF3 expressing cells

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Bile duct cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: HBDEC2 cells was maintained in F-medium supplemented with 10 µM Y-27632 (Liu et al., 2012) without feeder cells.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit  (QIAGEN, Valencia, CA).

value: Bile duct cells

value: ELF3 expressing


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD002_indexed

value: MOs


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD010_indexed

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD010_indexed


title: FLCN KO MCD 6

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling
Adaptor sequences and low-quality score bases (Phred score < 30) were first trimmed using Trimmomatic
The resulting reads were aligned to the GRCm38 mouse reference genome assembly, using STAR
Read counts for each sample are obtained using HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: All procedures for generating the Flcn knockout mouse model were performed at McGill University. Maintenance and experimental manipulation of mice were performed according to the guidelines and regulations of the McGill University Research and Ethic Animal Committee and the Canadian Council on Animal Care. All studies were carried out using C57BL/6 mice housed on a 12-h light:12-h dark cycle at 22°C.  To generate liver-specific Flcn knockout mice, Flcn f/f mice were crossed with Albumin-Cre transgenic mice (kind gift from Dr. André Marette, Laval University, Quebec, Canada). Flcn knockout mice were generated by crossing Flcnf/f mice homozygous for the floxed allele with Flcnf/f; Albumin-Cre+/− mice.

extract_protocol:
Total RNA Mini Kit (Geneaid, cat# RT100)
KAPA mRNAseq Hyperprep Kit

treatment_protocol: Mice were fed on a chow diet containing 10 kcal percent fat (Research Diet, cat# D12450B) or a Methionine/Choline Deficient (MCD) diet (Envigo, cat# TD.90262) beginning at 6 weeks of age and fed ad libidum. Controls used were FlcnWT/WT; Albumin-cre+/- mice raised in identical conditions.

value: liver

value: FLCN KO

tag: diet

value: MCD


title: ELF3 expressing_01


title: Control_for_induced_expression_01

description: Gene expression in  control cells

value: control


title: ELF3 expressing_02


title: Control_for_induced_expression_02

description: Gene expression in control cells


title: ELF3 KD_02

description: Gene expression in ELF3 KD cells

value: bile duct cells

tag: genotype/variation

value: ELF3 KD


title: ELF3 KD_03

description: Gene expression in ELF3 KD cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD010_indexed


title: FLCN KO MCD 4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD001_indexed


title: FLCN KO MCD 3


title: Control_for_induced_expression_03

description: Gene expression in control cells


title: ELF3 KD_01

description: Gene expression in ELF3 KD cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD012_indexed


title: CD4 Tconv_WT1

value: WT


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD008_indexed


title: FLCN KO MCD 2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B4_AD002_indexed


title: Control_02

description: Gene expression in control cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD004_indexed


title: FLCN KO MCD 1


title: FLCN KO MCD 5


title: Control_03

description: Gene expression in control cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B1_AD010_indexed


title: FLCN KO Chow 5

value: Chow


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B12_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B12_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B1_AD001_indexed


title: FLCN KO Chow 4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B1_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD001_indexed


title: ELF3 KO_02

description: Gene expression in ELF3 KO cells

value: ELF KO


title: FLCN KO Chow 3


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B1_AD007_indexed


title: FLCN KO Chow 2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B3_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B2_AD002_indexed


title: WT_03

description: Gene expression in WT cells


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B1_AD004_indexed


title: Untreat.Hep.no3

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Alignment-independent quantification using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: TPM as txt file

growth_protocol: Cells were directly sorted from liver of mice without in vitro growth. Mice were injected with AAV-TBG-Cre to label cells at 4 weeks. At 5 weeks, DDC-treated mice were moved to DDC chow for four weeks before livers were harvested and cells isolated.

extract_protocol:
RNA was extracted using QiagenRNeasy micro Kit.
RNA-seq libraries were build by the Next-Generation Sequencing Core at Upenn following standard protocols.

treatment_protocol: Cells were not treated following sorting from liver of mice

value: hepatocytes

value: Untreated


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B12_AD006_indexed


title: Cre MCD 5

value: Cre


title: Untreat.Hep.no1


title: WT_01

description: Gene expression in  WT cells


title: FLCN KO Chow 1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD012_indexed


title: Untreat.Hep.no2


title: Cre MCD 4


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B12_AD001_indexed


title: ELF3 KO_03

description: Gene expression in ELF3 KO cells


title: WT_02

description: Gene expression in WT cells


title: Cre MCD 2


title: Untreat.Bil.no1

value: biliary epithelial cells (BECs)


title: Cre MCD 1


title: Untreat.Bil.no3


title: ColKO3

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

country: Germany

institute: Goethe-University

data_processing:
Sequencing data of isolated CD8+ T cells were analyzed using SeqBox software (Beccuti et al., 2018).
Adapter trimming was done with skewer (Jiang et al., 2014).
For isolated CD8+ T cells STAR (Dobin & Gingeras, 2015) was used to map the reads to the mouse reference genome (mm10). For total colons Tophat2 was used for genome alignment.
For isolated CD8+ T cells RSEM (Li & Dewey, 2011) was used for gene and isoform-level quantification and for total colons HTSeq-count was used.
DESeq2 was used for differential expression analysis.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read counts for each sample.

source_name: AOM/DSS-treated colon

extract_protocol:
Total RNA was isolated from FACS-sorted CD8+ T cells and snap frozen colons using the RNeasy Micro Kit (Qiagen). RNA samples were analyzed on a 2100 Bioanalyzer using Agilent RNA 6000 Pico chip (both from Agilent Technologies, Santa Clara, USA).
Library preparation for isolated CD8+ T cells was performed using the SMARTer® Stranded Total RNA Sample Prep Kit –HI (Takara Bio Europe, Saint-Germain-en-Laye, France). Quantity and quality of the cDNA libraries were determined by Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Dreieich, Germany) and Agilent High Sensitivity DNA chip (Agilent Technologies). Library preparation of total colons was performed by the DKFZ Genomics & Proteomics Core Facility.

treatment_protocol: For the AOM/DSS model, mice were subjected to two AOM/DSS cycles with 10mg/kg i.p. at day 0 and the 0.5% DSS in the drinking water at day 1-6 and repeated at day 21-27 with one additional DSS cycle at day 47-52. PyMT mice were not treated and PyMT tumors were isolated when one tumor reached a diameter of 1.5 cm.

tag: strain/background

value: S1PR4 KO

value: Colon

tag: time point

value: 84 days of treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B12_AD002_indexed

value: MOs

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD006_indexed


title: ColKO2


title: Cre MCD 3

value: liver


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_D10_AD012_indexed


title: ColKO1


title: Control_01

description: Gene expression in  control cells


title: Cre Chow 5


title: Untreat.Bil.no2


title: ELF3 KO_01

description: Gene expression in ELF3 KO cells


title: Cre Chow 4


title: ColWT3


title: Cre Chow 6


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD010_indexed


title: ColWT2


title: Embryo_8cell_rep3

city: Nanjing

first: Mingtian

last: Deng

state: Jiangsu

address: Weigang No.1

department: College of Animal Science and Technology

country: China

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ARS1 whole genome using Hisat2 with defult parameters
Count were generated using htseq-count, Reads Per Kilobase of exon model per Million mapped reads were genenrated using R
Genome_build: ARS1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Capra hircus

source_name: Embryo

growth_protocol: Embryos were washed three times with BO-IVC medium supplemented with 10% FBS and cultured in groups of 20-25 in 75 μL droplet of BO-IVC medium supplemented with 10% FBS at 38.5°C in an atmosphere containing 5% CO2, 5% O2, 90% N2, and 100% humidity. They were collected at 72 h and 168 h post-IVF to obtain embryos for gene expression analysis and RNA-seq.

extract_protocol:
Embryos were directly lysed and used for cDNA synthesis
Smart-seq2

treatment_protocol: In general, 5-10 pL of 20 µM siRNAs that targeted YTHDF2 were microinjected into the cytoplasm of fertilized embryos at 8 h after IVF. The MISSION siRNA universal negative WT was served as a negative WT (NC) for siRNA experiments. These microinjected embryos were cultured in BO-IVC medium supplemented with 10% FBS at 38.5°C in an atmosphere containing 5% CO2, 5% O2, 90% N2, and 100% humidity. Development status was determined at 72 h and 168 h after microinjection.

value: Embryo

value: untreated

tag: Stage


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD008_indexed


title: DDC.Hep.no1

value: DDC


title: DDC.Bil.no3


title: Embryo_8cell_rep2


title: Cre Chow 3

tag: tissue


title: ColWT1


title: Embryo_8cell_rep1


title: DDC.Hep.no3


title: Cre Chow 2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD008_indexed

tag: brain region


title: DDC.Bil.no2


title: DDC.Hep.no2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD012_indexed

tag: Sex


title: DDC.Bil.no1


title: Cre Chow 1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD007_indexed

tag: age


title: DDC.Rep.no3

value: reprogrammed cells


title: Embryo_4cell_rep3


title: DDC.Rep.no2


title: Embryo_4cell_rep2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD006_indexed

tag: strain


title: O453

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
processed data file:
tpm_all.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were alligned using Kallisto, and transcript level tpm values were summed up to gene level tpm values
Genome_build: GRCm38 version 95
Supplementary_files_format_and_content: tpm.tsv contains the transcript per million levels of each gene within each cell that passed quality control, in a tab deliminated matrix. tpm_non_QC.tsv follows the same format, but also contains cells that did not pass quality control. The previous 2 did not contain Cortical or UC cells as those were not part of the analysis. tpm_all.tsv contains their data as well.

source_name: Stratum Oriens

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

tag: gender

value: Female

tag: tissue/layer

value: Stratum Oriens

tag: morphological type

value: UC

tag: axon morphology

tag: dendrite morphology

tag: location

value: Right

tag: quality control

value: Failed


title: O454

description:
processed data file:
tpm.tsv
tpm_non_QC.tsv
tpm_all.tsv

value: vBC

value: BC

value: Vertical

value: Passed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD004_indexed


title: Embryo_4cell_rep1

tag: cell type

tag: treatment


title: O452

description:
processed data file:
tpm_all.tsv


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD002_indexed


title: DDC.Rep.no1


title: 6694c2.KO.KDM3A.no2

data_processing:
alignment using Bowtie2 to generate sam files
sam and bam files were processed with SAMtools
eak calling using MACS2
peaks were merged with BEDTools
read counts were calculated and normalized in the merged peaks for every sample
Genome_build: mm10
Supplementary_files_format_and_content: normalized count for each peaks across samples

source_name: pancreatic cancer tumor cell line

growth_protocol: Tumor cells are cultured in vitro with DMEM + 10% FBS + Glutamax

extract_protocol:
ChIP-seq samples were prepared following previously published report, Li, Jinyang, et al. "Tumor cell-intrinsic factors underlie heterogeneity of immune cell infiltration and response to immunotherapy." Immunity 49.1 (2018): 178-193.
ChIP-seq libraries were prepared following the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) protocol, using NEBNext Multiplex Oligos Index Primers Sets

treatment_protocol: No treatment was used

tag: cell line

value: pancreatic cancer tumor cell line

tag: genotype

tag: chip antibody


title: Oocyte_MII_rep3

source_name: Oocyte

value: Oocyte

tag: Stage

value: mature oocyte


title: Oocyte_MII_rep2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B10_AD001_indexed

tag: brain region

value: MOs

value: male


title: 6694c2.KO.KDM3A.no1


title: 6694c2.WT.KDM3A.no2

value: WT


title: O450

description:
processed data file:
tpm_non_QC.tsv
tpm_all.tsv

value: hBIC

value: BIC

value: Horizontal


title: Oocyte_MII_rep1

value: untreated


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD010_indexed

tag: Sex


title: O449

description:
processed data file:
tpm_all.tsv

tag: age

value: Female

value: Stratum Oriens

value: UC


title: O448

description:
processed data file:
tpm_all.tsv

value: Cortical

value: Failed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD006_indexed

tag: strain


title: H3_UV3

city: Cologne

first: Björn

last: Schumacher

address: Joseph-Stelzmann-Str. 26

institute: CECAD Research Center

data_processing:
ChIP-Seq reads were aligned to the Caenorhabditis elegans ce11 reference genome using bowtie2 version 2.3.4.2
Non-uniquely aligned reads and reads with more than 2 mismatches were filtered and the remaining reads were converted to BAM files by samtools v1.9
Potential PCR duplicates were removed by Picard’s MarkDuplicates v2.20.4-SNAPSHOT
The H3K4me2 peaks were called using THOR v0.11.4 with a bin size of 300, a p-value cutoff of 0.01, the –merge flag and blacklisted regions filtering
The peak annotation was done with Uropa v3.3.2 against WS271 and a distance of 5 kb up- and downstream of the peak
Genome_build: Caenorhabditis elegans (ce11)
Supplementary_files_format_and_content: Bigwig files, generated by deeptools (v3.3) bamCoverage with normalizeUsing BPM

organism: Caenorhabditis elegans

source_name: L1 stage worms

growth_protocol: L1 worms were grown on NGM plates and fed with E. coli bacteria

extract_protocol:
UV-treated or mock-treated L1 worms were washed off from plates at 24h-post treatment. Crosslink with 1% formaldehyde and suspend in 1ml ChIP buffer (50mM HEPES, 300mM NaCl, 1mM EDTA pH 8.0, 1% Trition X, 0.1% Sodium deoxycholate, 10% glycerol, Protease Inhibitors), then freeze with liquid nitrogen at -80°C. On the next day, worms were homogenized and sonicated to generate worm lysate. Protein concentration was measured and 100 μg of sample was separated as input, and the rest samples was incubated with H3K4me2 or H3 antibody and Dynabeads™  Protein G (Invitrogen) at 4°C over-night. After incubation, samples were washed twice with ChIP buffer, 5min for each, and washed 1 time with ChIP buffer with 1M NaCl for 5 mins, and Washed 1 time with 1ml ChIP buffer with 500mM NaCl for 5 mins, then Washed 1 time with LiCl buffer for 5 mins. Subsequently, elution buffer ( 50mM Tris-HCL Ph 8.0, 10mM EDTA, 1%SDS) was applied and incubated at 4 °C for 1h. Boil the sample at 90°C for 30min with shaking, and check the sonication efficiency by running DNA gels. Afterward, 2 µl Rnase A was added to sample and input, and incubated for 30min at 37°C.  Then 10 µl proteinase K was added and incubated for 2h at 55°C. NaCl was added to samples and input to reach 200mM, and incubated over-night at 65°C with shaking. Experiment was carried out in triplicate.
Libraries were prepared according to Illumina's instructions with Cologne Center for Genomics (CCG) modofication.

treatment_protocol: UVB 480mJ/cm2 treatment or mock-treatment was applied on L1 worms.

value: UV treatment

tag: time point

tag: antibody


title: 6694c2.WT.KDM3A.no1


title: 6694c2.KO.H3K9me2.no2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD004_indexed


title: 6694c2.KO.H3K9me2.no1


title: H3_Ctrl3

value: mock treatment


title: 6694c2.KO.H3K9ac.no2

value: pancreatic cancer tumor cell line


title: H3_UV1


title: O447

description:
processed data file:
tpm_all.tsv

tag: gender

tag: tissue/layer

tag: morphological type


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD006_indexed


title: O445

description:
processed data file:
tpm_all.tsv

tag: axon morphology

tag: dendrite morphology

tag: location


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD007_indexed


title: O451

description:
processed data file:
tpm_all.tsv

value: Right

tag: quality control


title: 6694c2.KO.H3K9ac.no1

tag: cell line

tag: cell type


title: O443

description:
processed data file:
tpm_all.tsv


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD010_indexed


title: H3_Ctrl1

tag: treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD002_indexed


title: H3_Ctrl2


title: O441

description:
processed data file:
tpm_all.tsv


title: H3K4me2_UV2


title: 6694c2.KO.input

tag: genotype

tag: chip antibody


title: O442

description:
processed data file:
tpm_all.tsv


title: H3K4me2_UV3


title: H3K4me2_UV1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A4_AD001_indexed

tag: brain region

tag: Sex


title: 6694c2.WT.H3K9me2.no1

tag: strain


title: 6694c2.WT.H3K9ac.no2


title: H3_UV2

tag: time point


title: O439

tag: age

value: Male

value: hBC

value: BC

value: Passed


title: O444

description:
processed data file:
tpm_all.tsv

tag: gender


title: O440

tag: tissue/layer

value: Left


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD012_indexed

value: MOs

value: male


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD004_indexed


title: 6694c2.WT.H3K9ac.no1

value: WT


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD012_indexed


title: H3K4me2_Ctrl2

tag: antibody


title: 6694c2.WT.H3K9me2.no2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD010_indexed


title: H3K4me2_Ctrl1


title: O435

tag: morphological type

value: vBC

tag: axon morphology

value: Vertical


title: O436

description:
processed data file:
tpm_all.tsv

value: Stratum Oriens

value: UC

tag: dendrite morphology

tag: location


title: 6419c5.KO.KDM3A.no3

tag: cell line


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD008_indexed


title: N2UV3

data_processing:
Reads were mapped to the Caenorhabditis elegans reference genome
Differential gene expression was analyzed using DESeq2
Results were uploaded into the QuickNGS database
Genome_build: Caenorhabditis elegans (Ensembl Version 87)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

extract_protocol:
UV-irradiated or mock-treated L1 worms were washed off plates using M9 buffer, and suspended in TRIzol™ reagent (ThermoFisher) with 0.7mm zirconia/silica beads (Biospec Products), and homogenized with Precellys24 (Bertin).  After lysis, total RNA were purified using the RNeasy™ Mini kit (Qiagen) according to the manufacturers’ specification, except for the use of  1-bromo-3-chloropropane (Sigma) instead of chloroform for phase separation. Each sample was run in triplicates. Around 100-150 ng/µl per sample was sent for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: UVB 480mJ/cm2 treatment for 24h, UVB 800mJ/cm2 for 6h or mock-treatment was applied on L1 worms.

value: 800mJ/cm² of UV


title: O434

value: Horizontal

tag: quality control


title: 6419c5.KO.KDM3A.no2

tag: cell type


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD004_indexed


title: 6419c5.KO.KDM3A.no1

tag: genotype


title: O431

description:
processed data file:
tpm_all.tsv

value: Failed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD001_indexed


title: H3K4me2_Ctrl3

tag: treatment

value: mock treatment


title: N2UV1


title: N2C3

value: mock-treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD002_indexed

tag: brain region


title: 6419c5.WT.KDM3A.no3

value: pancreatic cancer tumor cell line

tag: chip antibody


title: O430

value: Male


title: 6419c5.WT.KDM3A.no2

tag: strain


title: O429

value: hBIC

value: BIC


title: 6419c5.WT.KDM3A.no1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A3_AD008_indexed

tag: Sex


title: N2C2

tag: time point


title: O428

description:
processed data file:
tpm_all.tsv

tag: age

tag: gender

value: Right


title: O427

tag: tissue/layer

value: Passed


title: 80290_ctrl3


title: N2C1


title: 6419c5.KO.H3K9me2.no2


title: 6419c5.KO.H3K9me2.no1


title: 6694c2.WT.input


title: N2UV2


title: O433

tag: morphological type

value: Left


title: 6419c5.KO.H3K9ac.no2


title: O426

value: hBC

tag: axon morphology

value: BC


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_C10_AD001_indexed

value: MOs

value: male


title: 80282_ctrl1


title: 6419c5.KO.H3K9ac.no1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A2_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD007_indexed


title: O425

value: Stratum Oriens

tag: dendrite morphology


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A1_AD001_indexed


title: O424

tag: location


title: 80288_tre3

value: 480mJ/cm² of UV


title: 6419c5.KO.input

tag: cell line


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD012_indexed


title: O423

description:
processed data file:
tpm_all.tsv

value: UC

tag: quality control


title: O422

description:
processed data file:
tpm_all.tsv

value: Failed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD008_indexed


title: 80280_tre1


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A1_AD002_indexed


title: 6419c5.WT.H3K9me2.no1

tag: cell type

value: WT


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD006_indexed


title: 80286_ctrl2

value: mock-treatment


title: 6419c5.WT.H3K9ac.no1

value: pancreatic cancer tumor cell line

tag: genotype


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD010_indexed


title: O151

value: Male

value: Horizontal


title: O134

value: vBIC

value: BIC

value: Vertical


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD002_indexed


title: O106

value: Left

value: Passed


title: 6419c5.WT.input


title: Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 5

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_PD1-5_IGO_08381_F_15

data_processing:
Fastq files for Brca1 and Brca2-deficient cells as well as parental cells were aligned and pre-processed to produce a count matrix using 10X Cell Ranger version 3.0.2.  The resulting count matrix was then filtered to exclude all cells with UMI count in mitochondrial genes > than 20% of all counts as described in Azizi et al Cell 2018, and all ribosomal genes were also removed from the analysis.  We further filtered any genes that had a mean log count <= 2.5 to reduce sparsity in the final count matrix.  Following these initial filtering steps, we used Seurat version 2.4 to scale the UMI counts and perform log normalization of the data.  To mitigate batch effects, we adopted a stringent approach whereby each replicate in each condition was treated as a separate batch.  Log-normalized counts for each sample were used as input to the mnnCorrect method Haghverdi et al 2018 from the scran package. The batch-corrected PCA from mnnCorrect was used as input to Phenograph clustering at resolution 1.0. Differential expression analyses were conducted using the FindMarkers function in Seurat.
For mouse tumors, fresh frozen tissue from day 14 tumors were used for isolation of DNA and RNA and submitted to the Integrated Genomic Core for library preparation and sequencing. 3-5 replicates per condition were submitted for sequencing depending on RNA quality.
Reads were aligned against the mm10 assembly by STAR
Gene level count values were then computed by the summarizeOverlaps function from the R package "GenomicAlignments" with UCSC mm10 KnownGene as the base gene model. The Union counting mode was used and only mapped paired reads were considered.
Differentially Expressed Genes (DEG) analyses were done using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized bulk RNA-seq counts

source_name: 4T1 breast tumor mouse model

growth_protocol: 4T1 cells were grown in culture until 60% confluence in RPMI 1640 supplemented with 10% FBS

extract_protocol:
For cells lines , Qiagen RNAeasy kit was used for isolation
RNA libraries were prepared for sequencing using standard Illumina protocols
For mouse single cell analysis, orthotopic implanted tumors in the mammary fat pad were isolated at day 12 after implantation. Single cell suspensions were generated from 2 pooled tumors using the Mouse Tumor Dissociation Kit according to manufacturer instructions (Miltenyi Biotech). Singe cell suspensions were then stained with DAPI and antibodies to CD45 and live lymphoctyes (DAPI-CD45+) cells were sorted on a BD Aria cell sorter (gating strategy below). Single cell library preparation was performed according to manufacturer instructions using the mouse single cell RNAseq kit (10X genomics) with 10,000 cells input per sample. Three replicates of each condition (4T1 Parental, 4T1 Brca2null , and  4T1 Brca1null tumors) were processed although 1 Brca1null  sample failed initially quality control and was excluded.

treatment_protocol: anti PD-1 antibody was injected intraperitoneally twice a week from palpable tumos

tag: treatment

value: immunotherapy-treated

value: Balbc/J

tag: tissue

value: Breast

value: Brca1 KO


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD001_indexed

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: MOs

value: male


title: O104

value: Stratum Oriens

value: hBIC

value: Right


title: O90

source_name: Stratum Pyramidale

value: Stratum Pyramidale

value: vBC

value: BC


title: O87

value: Male

value: vBIC


title: stembase_DXC_42hai_rep3

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

description: Gene expression data from stem base of DXC line 42 h after dexamethasone treatment

hyb_protocol: Following fragmentation and biotin end labeling, 3,8 ug of cDNA were hybridized for 20h at 48C° on Affymetrix® Rice Gene 1.1ST Jp array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 of Affymetrix GeneAtlas system using Hybridization, Wash & Stain kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: Data were generated with Affymetrix Epression Console v 1.4.1 and GCRMA algorithm.

label: biotin

organism: Oryza sativa Japonica Group

source_name: stem base, DXC line, 42hour after dexamethasone treatment

label_protocol: Biotinylated single strand cDNA were prepared according to the Affymetrix WT PLUS protocol from 200 ng total RNA (WT PLUSTechnical Manual, 2010 - 2012, P/N 702935 Rev4 Affymetrix).

growth_protocol: Oryza sativa L. cv. Taichung 65 crl1 mutant (Inukai et al. 2005) was transformed with a binary vector pINDEX2 (Ouwerkerk et al., 2001, Planta 213, 370-378) empty or containing the CRL1 gene (Os03g0149100) to generate DX and DXC lines respectively as described in Coudert et al., 2015 New Phytol 206(1):243-54. The line DXC corresponds to line DXC3 in Coudert et al., 2015, 206(1):243-54). Seeds were dehulled and disinfected (3 min in ethanol 70%, 90 min in 2:3 v/v sodium hypochlorite 9,6%/Milli-Q water plus 500 µL Tween 80, quadruple rinsed in Milli-Q water) and inoculated under sterile conditions in round Petri dishes (ref. 82.1473.001, Starstedt, Germany) containing a filter pad (ref. 1001-090, Whatman paper, GE Healthcare, UK) and 15 mL half strength Murashige and Skoog (MS/2) medium (ref. M0231, Duchefa Biochemie, The Netherlands). Culture chambers were set at 27°C, 70% relative humidity, and 14 hour daylight. After 5 days, the plantlets were transferred into 250 mL wide-collar Erlenmeyer flasks containing 30 mL MS/2 medium, and let to rest for 24 hour.

extract_protocol: Stem bases were collected every 3 hour from 0 to 45 hour after adition of dexamethasone in the medium (hours after induction, hai), according to Coudert et al., 2011, BMC Genomics, 12, e387. The experiment was repeated independently three times with DX and DXC lines. For each biological replicate, ten to fifteen stem bases were collected and immediately frozen in liquid nitrogen. After grounding 8~12 stem bases in liquid nitrogen using a TissueLyser II tissue disruption system (Qiagen, The Netherlands) with 3 mm steel beads for 15 sec at 30 Hz, RNA were extracted using the Plant RNeasy Kit (Qiagen, The Netherlands) with DNAse I treatment (Qiagen) on purification column according to the supplier’s recommendations.

treatment_protocol: Plantlets were treated by adding dexamethasone (DEX) (ref. D4902, Sigma-Aldrich, MO, USA) diluted in absolute ethanol, to obtain a final concentration of 1 µM. After 5 hour, DEX was removed by replacing the culture  medium with a fresh one.

value: stem base

value: cv Taichung 65, crl1 mutant

tag: line

value: DXC

tag: hour after induction


title: 6419c5.WT.H3K9me2.no2

tag: strain

value: pancreatic cancer tumor cell line

value: WT

tag: chip antibody


title: Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 3

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_PD1-3_IGO_08381_F_13

value: immunotherapy-treated

value: Balbc/J

value: Breast


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD004_indexed

value: MOs

tag: Sex

value: male

tag: age


title: 80284_tre2

value: 480mJ/cm² of UV

tag: time point


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD008_indexed


title: Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 4

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_PD1-4_IGO_08381_F_14

value: Brca1 KO


title: Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 2

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_PD1-2_IGO_08381_F_12


title: Mouse 4T1 Brca1 KO Immunotherapy-treated bulk RNA-seq Rep 1

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_PD1-1_IGO_08381_F_11


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD010_indexed


title: O71

tag: gender

value: Female

tag: tissue/layer

value: Stratum Oriens

tag: morphological type

value: hBIC

tag: axon morphology

value: BIC

value: Horizontal

value: Right

value: Passed


title: stembase_DXC_45hai_rep3

description: Gene expression data from stem base of DXC line 45 h after dexamethasone treatment

source_name: stem base, DXC line, 45hour after dexamethasone treatment

value: stem base

value: cv Taichung 65, crl1 mutant

value: DXC


title: O52

value: Stratum Pyramidale

value: vBC

value: BC

tag: dendrite morphology

value: Vertical

tag: location

tag: quality control


title: O43

description:
processed data file:
tpm_all.tsv

value: UC

value: Failed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A1_AD008_indexed

value: MOs

value: male


title: Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 3

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-PD1-5_IGO_08381_D_36

tag: treatment

value: immunotherapy-treated

value: Balbc/J

value: Breast

tag: genotype

value: Brca2 KO

tag: cell line


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_B11_AD010_indexed

tag: brain region


title: O80

source_name: Stratum Radiatum

value: Female

value: Stratum Radiatum

value: Right


title: Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 2

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-PD1-4_IGO_08381_D_35

tag: tissue


title: CD8KO3

source_name: PyMT mammary tumor

tag: strain/background

tag: genotype/variation

value: S1PR4 KO

tag: cell type

value: CD8+ T cells from PyMT tumor

value: When one tumor reached a size of 1.5 cm


title: CD8KO2


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A10_AD008_indexed

tag: Sex

tag: age

tag: strain


title: stembase_DXC_30hai_rep3

description: Gene expression data from stem base of DXC line 30 h after dexamethasone treatment

source_name: stem base, DXC line, 30hour after dexamethasone treatment

value: stem base

value: cv Taichung 65, crl1 mutant

tag: line

value: DXC

tag: hour after induction


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A10_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A11_AD012_indexed


title: Mouse 4T1 Brca2 KO Immunotherapy-treated bulk RNA-seq Rep 1

description:
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-PD1-2_IGO_08381_D_34


title: CD8KO1

tag: time point


title: 4T1 Cell Line Brca1 KO bulk RNA-seq Rep 6

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17QQ_3

source_name: 4T1 Cell Line

value: Brca1 KO


title: 4T1 Cell Line Brca1 KO bulk RNA-seq Rep 5

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17QQ_2


title: stembase_DXC_33hai_rep3

description: Gene expression data from stem base of DXC line 33 h after dexamethasone treatment

source_name: stem base, DXC line, 33hour after dexamethasone treatment


title: stembase_DXC_39hai_rep3

description: Gene expression data from stem base of DXC line 39 h after dexamethasone treatment

source_name: stem base, DXC line, 39hour after dexamethasone treatment


title: stembase_DXC_36hai_rep3

description: Gene expression data from stem base of DXC line 36 h after dexamethasone treatment

source_name: stem base, DXC line, 36hour after dexamethasone treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A12_AD006_indexed


title: stembase_DXC_21hai_rep3

description: Gene expression data from stem base of DXC line 21 h after dexamethasone treatment

source_name: stem base, DXC line, 21hour after dexamethasone treatment


title: stembase_DXC_18hai_rep3

description: Gene expression data from stem base of DXC line 18 h after dexamethasone treatment

source_name: stem base, DXC line, 18hour after dexamethasone treatment


title: CD8WT2

value: WT


title: 4T1 Cell Line Brca1 KO bulk RNA-seq Rep 4

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17QQ_1


title: stembase_DXC_27hai_rep3

description: Gene expression data from stem base of DXC line 27 h after dexamethasone treatment

source_name: stem base, DXC line, 27hour after dexamethasone treatment


title: stembase_DXC_15hai_rep3

description: Gene expression data from stem base of DXC line 15 h after dexamethasone treatment

source_name: stem base, DXC line, 15hour after dexamethasone treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A10_AD007_indexed

value: MOs


title: 4T1 Cell Line Brca1 KO bulk RNA-seq Rep 3

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17Q_3


title: stembase_DXC_9hai_rep3

description: Gene expression data from stem base of DXC line 9 h after dexamethasone treatment

source_name: stem base, DXC line, 9hour after dexamethasone treatment


title: stembase_DXC_24hai_rep3

description: Gene expression data from stem base of DXC line 24 h after dexamethasone treatment

source_name: stem base, DXC line, 24hour after dexamethasone treatment


title: 180626_CEMBA_mm_P56_P63_3B_CEMBA180501_3B_1_CEMBA180501_3B_2_A10_AD006_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: CD8WT3


title: CD8WT1


title: stembase_DXC_12hai_rep3

description: Gene expression data from stem base of DXC line 12 h after dexamethasone treatment

source_name: stem base, DXC line, 12hour after dexamethasone treatment


title: tetON_input

first: Shinichi

last: Yachida

address: Yamadaoka 2-2

description: control

data_processing:
The sequenced reads of single-end 36 bp in length were aligned to the human reference genome assembly (NCBI37/hg19) using bowtie2-align-s (v2.2.4) with default parameters.
Peak detection was performed using the MACS algorithm (v1.4.2) with the option (-g hs -p 0.01).
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain macs-called peaks for each sample.

source_name: HBDEC2 cell line (established from primary culture of biliary epithelium cells)

growth_protocol: Immortalized normal biliary epithelial cell line, established and named HBDEC2, were maintained in F-medium supplemented with 10 µM Y-27632 (Liu et al., 2012) without feeder cells.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit . The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: ELF3 gene knockout clone was edited using CRISPR/Cas9-system which transfect a pRGEN-Cas9_CMV plasmid carrying gRNA silencing ELF3 oligonucleotides to HBDEC2 cells by electroporation. An inducible ELF3-expressing was generated by infection with the retroviral vector pRetroX-TetOne-Puro-ELF3-flag, expressing ELF3 fused to a flag-tag.

tag: cell line background

value: knockout ELF3 gene

tag: variation

value: ELF3-inducible cells with Tet-On system

tag: chip antibody

value: none (input)


title: stembase_DXC_0hai_rep3

description: Gene expression data from stem base of DXC line 0 h after dexamethasone treatment

source_name: stem base, DXC line, 0hour after dexamethasone treatment


title: 4T1 Cell Line Brca1 KO bulk RNA-seq Rep 2

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17Q_2

value: Balbc/J

value: Breast


title: 4T1 Cell Line Brca2 KO bulk RNA-seq Rep 3

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2_3

value: Brca2 KO


title: 4T1 aCell Line Brca1 KO bulk RNA-seq Rep 1

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1_17Q_1


title: tetON_anti-ELF3

description: over expression of ELF3


title: stembase_DXC_6hai_rep3

description: Gene expression data from stem base of DXC line 6 h after dexamethasone treatment

source_name: stem base, DXC line, 6hour after dexamethasone treatment


title: stembase_DXC_3hai_rep3

description: Gene expression data from stem base of DXC line 3 h after dexamethasone treatment

source_name: stem base, DXC line, 3hour after dexamethasone treatment


title: MT_3

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: adult kctd15 mutant testis  replicate 3

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.43.0 employing a transcript cDNA FASTA file called GCF_000002035.5_GRCz10_rna.fna downloaded from the NCBI site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option “countFromAbundance=lengthScaledTPM” using a transcript to gene data.frame generated from GCF_000002035.5_GRCz10_genomic.gff file . The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR.
Genome_build: GCF_000002035.5_GRCz10 using NCBI annotation

organism: Danio rerio

source_name: adult kctd15 mutant testis

growth_protocol: Embryos were collected and staged to 10 somite at 28.5C. Larva were fed and maintained according to SOP regulations in animal facility

extract_protocol:
RNA from embryos/tissues was extracted using TRIzol.
Directional RNA-seq library construction was performed from 100 ng of high quality RNA (RIN > 8.0) using the Illumina Stranded mRNA Library Prep Kit (Illumina). Library construction from three biological replicates for all time points was performed.

value: kctd15 mutant

value: adult

value: testis


title: DWP1

data_processing:
Sequencing data were analyzed using SeqBox software (Beccuti et al., 2018).
Adapter trimming with done with skewer (Jiang et al., 2014)
STAR (Dobin & Gingeras, 2015) was used to map the reads to the mouse reference genome (mm10)
RSEM (Li & Dewey, 2011) was used for gene and isoform-level quantification
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2TPM values for each sample …

source_name: PyMT mammary tumor

extract_protocol:
Total RNA was isolated from snap frozen PyMT tumors using the peqGOLD Total RNA Kit (VWR International, Darmstadt, Germany). RNA samples were analyzed on a 2100 Bioanalyzer using Agilent RNA 6000 Nano chip (both from Agilent Technologies, Santa Clara, USA).
Library preparation was performed using the SMARTer® Stranded Total RNA Sample Prep Kit –HI (Takara Bio Europe, Saint-Germain-en-Laye, France). Quantity and quality of the cDNA libraries were determined by Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific, Dreieich, Germany) and Agilent High Sensitivity DNA chip (Agilent Technologies).

treatment_protocol: PyMT Mice were divided into four groups according to treatment (anti-PD-1 (TWP), IgG1 (TWI), doxorubicin (DOX) + anti-PD-1 (DWP) and DOX + IgG1 (DWI)). For animals receiving immune checkpoint blockade only, treatment was initiated (day 0) once the first tumor reached a size of 0.6 cm in diameter. Antibodies were administrated i.p. at a concentration of 20 mg/kg (on day 0) and 10 mg/kg (on day 6, 12, 18). All mice received either anti-mouse PD-1 antibody (4H2, Ono Pharmaceutical, Osaka, Japan) or anti-mouse IgG1 (BioXcell/Hölzel Diagnostik, Cologne, Germany) diluted in sterile 0.9% NaCl. In the model with the combination of chemotherapy and immune checkpoint blockade treatment started once the first mammary tumor reached a size of 1 cm in diameter. Doxorubicin (Cell Pharm, Bad-Vilbel, Germany) diluted in sterile 0.9% NaCl was administrated i.p. (5 mg/kg) once a week for five weeks. One day after doxorubicin administration, mice were treated with 10 mg/kg of either anti-mouse PD-1 antibody (4H2, Ono Pharmaceutical) or anti-mouse IgG1 (BioXCell). Mice were monitored three times a week for up to five weeks after initial treatment.

value: tumor

tag: treatment

value: DOX + anti-PD-1

tag: treatment duration

value: treatment once-weekly for 5 weeks


title: DWP3


title: MO_2

description: adult kctd15 mutant ovary  replicate 2

source_name: adult kctd15 mutant ovary

tag: genotype

value: ovary


title: DWP2


title: 4T1 Cell Line Brca2 KO bulk RNA-seq Rep 2

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2_2

source_name: 4T1 Cell Line

tag: cell line


title: MT_2

description: adult kctd15 mutant testis  replicate 2

tag: tissue


title: DWI3

value: DOX + IgG1


title: MT_1

description: adult kctd15 mutant testis  replicate 1


title: stembase_DX_45hai_rep3

description: Gene expression data from stem base of DX line 45 h after dexamethasone treatment

source_name: stem base, DX line, 45hour after dexamethasone treatment

value: stem base

value: cv Taichung 65, crl1 mutant

value: DX


title: 4T1 Cell Line Brca2 KO bulk RNA-seq Rep 1

description:
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2_1


title: MO_3

description: adult kctd15 mutant ovary  replicate 3


title: stembase_DX_42hai_rep3

description: Gene expression data from stem base of DX line 42 h after dexamethasone treatment

source_name: stem base, DX line, 42hour after dexamethasone treatment


title: stembase_DX_36hai_rep3

description: Gene expression data from stem base of DX line 36 h after dexamethasone treatment

source_name: stem base, DX line, 36hour after dexamethasone treatment


title: stembase_DX_39hai_rep3

description: Gene expression data from stem base of DX line 39 h after dexamethasone treatment

source_name: stem base, DX line, 39hour after dexamethasone treatment


title: DWI1


title: TWP2


title: TWP3


title: WTT_3

description: adult wildtype testis  replicate 3

source_name: adult wildtype testis

value: wildtype


title: stembase_DX_33hai_rep3

description: Gene expression data from stem base of DX line 33 h after dexamethasone treatment

source_name: stem base, DX line, 33hour after dexamethasone treatment


title: MO_1

description: adult kctd15 mutant ovary  replicate 1


title: TWP1


title: DWI2


title: stembase_DX_30hai_rep3

description: Gene expression data from stem base of DX line 30 h after dexamethasone treatment

source_name: stem base, DX line, 30hour after dexamethasone treatment


title: Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 3

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Par-d14-IgG-3_IGO_08381_D_18

source_name: 4T1 breast tumor mouse model

value: untreated

value: Brca WT


title: Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 2

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Par-d14-IgG-2_IGO_08381_D_17

value: Balbc/J


title: WTT_1

description: adult wildtype testis  replicate 1


title: Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 5

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_IgG-5_IGO_08381_F_10

value: Breast

value: Brca1 KO


title: Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 5

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Par-d14-IgG-5_IGO_08381_D_20


title: WTT_2

description: adult wildtype testis  replicate 2


title: stembase_DX_27hai_rep3

description: Gene expression data from stem base of DX line 27 h after dexamethasone treatment

source_name: stem base, DX line, 27hour after dexamethasone treatment


title: Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 1

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Par-d14-IgG-1_IGO_08381_D_16


title: Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 4

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_IgG-4_IGO_08381_F_9


title: WTO_2

description: adult wildtype ovary  replicate 2

source_name: adult wildtype ovary


title: TWI1


title: stembase_DX_24hai_rep3

description: Gene expression data from stem base of DX line 24 h after dexamethasone treatment

source_name: stem base, DX line, 24hour after dexamethasone treatment


title: TWI3


title: Mouse 4T1 Parental (BRCA WT) Untreated bulk RNA-seq Rep 4

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Par-d14-IgG-4_IGO_08381_D_19


title: stembase_DX_21hai_rep3

description: Gene expression data from stem base of DX line 21 h after dexamethasone treatment

source_name: stem base, DX line, 21hour after dexamethasone treatment


title: WTO_1

description: adult wildtype ovary  replicate 1


title: Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 2

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_IgG-2_IGO_08381_F_7


title: PulseChase_exp_uhrf1_fl_04_GFPpositive_TomatoPositive (RRBS

first: Benjamin

middle: D.

last: Singer

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with BCL2FASTQ v2.17.1.14.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

extract_protocol:
Genomic DNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. Genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.5% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

value: Treg cells


title: WTO_3

description: adult wildtype ovary  replicate 3

value: adult


title: PulseChase_exp_uhrf1_fl_03_GFPpositive_TomatoPositive (RRBS


title: PK_2

description: 10 somites wildtype embryo 5pg AP2-P59 + 100pg kctd15 injected replicate 2

value: 10 somites

value: embryo

value: 5pg AP2-P59 + 100pg kctd15 injected


title: PK_3

description: 10 somites wildtype embryo 5pg AP2-P59 + 100pg kctd15 injected replicate 3


title: PulseChase_exp_uhrf1_fl_04_GFPnegative_TomatoPositive (RRBS

source_name: ex-Foxp3 cells (Foxp3-GFP–tdTomato+)

value: ex-Foxp3 cells


title: PK_1

description: 10 somites wildtype embryo 5pg AP2-P59 + 100pg kctd15 injected replicate 1


title: stembase_DX_15hai_rep3

description: Gene expression data from stem base of DX line 15 h after dexamethasone treatment

source_name: stem base, DX line, 15hour after dexamethasone treatment


title: TWI2

source_name: PyMT mammary tumor

value: tumor

value: treatment once-weekly for 5 weeks


title: Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 1

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_IgG-1_IGO_08381_F_6


title: PulseChase_exp_uhrf1_fl_03_GFPnegative_TomatoPositive (RRBS


title: stembase_DX_12hai_rep3

description: Gene expression data from stem base of DX line 12 h after dexamethasone treatment

source_name: stem base, DX line, 12hour after dexamethasone treatment

value: stem base


title: Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 5

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-IgG-5_IGO_08381_D_33

value: Brca2 KO


title: stembase_DX_18hai_rep3

description: Gene expression data from stem base of DX line 18 h after dexamethasone treatment

source_name: stem base, DX line, 18hour after dexamethasone treatment

value: cv Taichung 65, crl1 mutant

value: DX


title: stembase_DX_9hai_rep3

description: Gene expression data from stem base of DX line 9 h after dexamethasone treatment

source_name: stem base, DX line, 9hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_02_GFPpositive_TomatoPositive (RRBS


title: Mouse 4T1 Brca1 KO Untreated bulk RNA-seq Rep 3

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA1-d14_IgG-3_IGO_08381_F_8

value: untreated


title: P_2

description: 10 somites wildtype embryo 5pg AP2-P59 injected replicate 2

value: wildtype

value: 5pg AP2-P59 injected


title: Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 3

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-IgG-3_IGO_08381_D_31

value: Balbc/J

value: Breast


title: stembase_DX_3hai_rep3

description: Gene expression data from stem base of DX line 3 h after dexamethasone treatment

source_name: stem base, DX line, 3hour after dexamethasone treatment


title: Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 4

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-IgG-4_IGO_08381_D_32


title: P_3

description: 10 somites wildtype embryo 5pg AP2-P59 injected replicate 3


title: Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 2

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-IgG-2_IGO_08381_D_30


title: stembase_DX_6hai_rep3

description: Gene expression data from stem base of DX line 6 h after dexamethasone treatment

source_name: stem base, DX line, 6hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_02_GFPnegative_TomatoPositive (RRBS


title: PulseChase_exp_uhrf1_fl_01_GFPpositive_TomatoPositive (RRBS

value: Treg cells


title: M_3

description: 10 somites kctd15 mutant embryo  replicate 3

source_name: 10 somites kctd15 mutant embryo

value: kctd15 mutant


title: PulseChase_exp_uhrf1_fl_01_GFPnegative_TomatoPositive (RRBS


title: Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 1

description:
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv
Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv
BRCA2-d14-IgG-1_IGO_08381_D_29


title: 6419c5.WT.H3K9ac.no2

source_name: pancreatic cancer tumor cell line

value: pancreatic cancer tumor cell line

value: WT


title: M_2

description: 10 somites kctd15 mutant embryo  replicate 2

value: 10 somites

value: embryo


title: G5.GAL76.SD12hr.56537

city: Philadelphia

first: Allan

middle: I

last: Pack

address: 125 South 31st St

institute: University of Pennsylvania

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 by STAR-v2.5.3a.
Data were quantified using PORT quantification script. The code is available at https://github.com/itmat/Normalization (PORT-v0.8.4-beta)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level contains counts from unique reads that only map to one gene.

source_name: eGFP expressing galanin neurons isolated from VLPO using LCM

growth_protocol: Experiments were performed on male Tg(Gal-EGFP)HX109Gsat mice at 2-4 months housed individually in a 12/12 light/dark room.

extract_protocol:
After cervical dislocation the brains were quickly removed and 3mm coronal section containing VLPO region was cut and post-fixed in ice-cold 4% paraformaldehyde (pH 7.4) for 5 minutes. 10 μm frozen sections were generated with cryostat and GFP+ cells were isolated using LCM. Total RNA was extracted using RNAqueous-Micro kit (Invitrogen).
Total RNA from each sample was prepared for sequencing using theTakara Bio, SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. 1 ng of RNA was used to prepare the RNA libraries. The libraries were sequenced on Illumina HiSeq 4000. Depths of 23-36 million paired-end 150bp reads were generated for each sample.

treatment_protocol: Half of the mice were sleep deprived for various of durations using gentle handling

tag: behavior

value: SD

tag: timepoint

value: VLPO

value: eGFP expressing galanin neurons


title: PulseChase_exp_control_04_GFPnegative_TomatoPositive (RRBS

tag: cell type

value: ex-Foxp3 cells


title: PulseChase_exp_control_04_GFPpositive_TomatoPositive (RRBS


title: G4.GAL71.SD9hr.56531


title: G3.GAL69.SD6hr.56525


title: stembase_DXC_45hai_rep2

description: Gene expression data from stem base of DXC line 45 h after dexamethasone treatment

source_name: stem base, DXC line, 45hour after dexamethasone treatment

value: stem base

value: cv Taichung 65, crl1 mutant

value: DXC


title: M_1

description: 10 somites kctd15 mutant embryo  replicate 1


title: stembase_DX_0hai_rep3

description: Gene expression data from stem base of DX line 0 h after dexamethasone treatment

source_name: stem base, DX line, 0hour after dexamethasone treatment

value: DX


title: stembase_DXC_42hai_rep2

description: Gene expression data from stem base of DXC line 42 h after dexamethasone treatment

source_name: stem base, DXC line, 42hour after dexamethasone treatment


title: PulseChase_exp_control_03_GFPpositive_TomatoPositive (RRBS


title: P_1

description: 10 somites wildtype embryo 5pg AP2-P59 injected replicate 1

value: wildtype

value: 5pg AP2-P59 injected


title: K_1

description: 10 somites wildtype embryo 100pg kctd15 injected replicate 1

value: 100pg kctd15 injected


title: G2.GAL67.SD3hr.56519


title: stembase_DXC_39hai_rep2

description: Gene expression data from stem base of DXC line 39 h after dexamethasone treatment

source_name: stem base, DXC line, 39hour after dexamethasone treatment


title: stembase_DXC_33hai_rep2

description: Gene expression data from stem base of DXC line 33 h after dexamethasone treatment

source_name: stem base, DXC line, 33hour after dexamethasone treatment


title: K_2

description: 10 somites wildtype embryo 100pg kctd15 injected replicate 2


title: PulseChase_exp_control_02_GFPpositive_TomatoPositive (RRBS

value: Treg cells


title: C_3

description: 10 somites wildtype embryo  replicate 3

source_name: 10 somites wildtype embryo


title: F11.GAL62.SS12hr.56567

value: SS


title: PulseChase_exp_control_02_GFPnegative_TomatoPositive (RRBS

source_name: ex-Foxp3 cells (Foxp3-GFP–tdTomato+)


title: stembase_DXC_27hai_rep2

description: Gene expression data from stem base of DXC line 27 h after dexamethasone treatment

source_name: stem base, DXC line, 27hour after dexamethasone treatment


title: stembase_DXC_36hai_rep2

description: Gene expression data from stem base of DXC line 36 h after dexamethasone treatment

source_name: stem base, DXC line, 36hour after dexamethasone treatment


title: K_3

description: 10 somites wildtype embryo 100pg kctd15 injected replicate 3


title: stembase_DXC_30hai_rep2

description: Gene expression data from stem base of DXC line 30 h after dexamethasone treatment

source_name: stem base, DXC line, 30hour after dexamethasone treatment


title: F9.GAL18.SS6hr.56557


title: C_1

description: 10 somites wildtype embryo  replicate 1


title: C_2

description: 10 somites wildtype embryo  replicate 2


title: F8.GAL57.SS3hr.56552


title: PulseChase_exp_control_01_GFPpositive_TomatoPositive (RRBS


title: PulseChase_exp_control_01_GFPnegative_TomatoPositive (RRBS


title: F7.GAL51.0h.56547

value: baseline


title: stembase_DXC_21hai_rep2

description: Gene expression data from stem base of DXC line 21 h after dexamethasone treatment

source_name: stem base, DXC line, 21hour after dexamethasone treatment


title: F6.GAL75.SD12hr.56542


title: AK_3

description: 10 somites wildtype embryo 5pg AP2 + 100pg kctd15 injected replicate 3

value: 5pg AP2 + 100pg kctd15 injected


title: Chimera_exp_uhrf1_chimera_04 (RRBS

source_name: Treg cells (CD25hiFoxp3-YFP+)


title: F10.GAL65.SS9hr.56562


title: AK_1

description: 10 somites wildtype embryo 5pg AP2 + 100pg kctd15 injected replicate 1

value: 10 somites


title: F5.GAL70.SD9hr.56536


title: Chimera_exp_uhrf1_chimera_03 (RRBS


title: Chimera_exp_uhrf1_chimera_02 (RRBS


title: A_3

description: 10 somites wildtype embryo 5pg AP2 injected replicate 3

value: embryo

value: 5pg AP2 injected


title: Chimera_exp_uhrf1_chimera_01 (RRBS


title: A_2

description: 10 somites wildtype embryo 5pg AP2 injected replicate 2


title: F4.GAL38.SD6hr.56530

value: SD

value: VLPO


title: F3.GAL66.SD3hr.56524

value: eGFP expressing galanin neurons


title: stembase_DXC_18hai_rep2

description: Gene expression data from stem base of DXC line 18 h after dexamethasone treatment

source_name: stem base, DXC line, 18hour after dexamethasone treatment

value: stem base


title: F2.GAL61.SS12hr.56518


title: Chimera_exp_control_04 (RRBS

value: Uhrf1+/+Foxp3YFP-Cre/YFP-Cre (control)


title: AK_2

description: 10 somites wildtype embryo 5pg AP2 + 100pg kctd15 injected replicate 2


title: stembase_DXC_12hai_rep2

description: Gene expression data from stem base of DXC line 12 h after dexamethasone treatment

source_name: stem base, DXC line, 12hour after dexamethasone treatment

value: cv Taichung 65, crl1 mutant

value: DXC


title: A_1

description: 10 somites wildtype embryo 5pg AP2 injected replicate 1

value: wildtype


title: stembase_DXC_6hai_rep2

description: Gene expression data from stem base of DXC line 6 h after dexamethasone treatment

source_name: stem base, DXC line, 6hour after dexamethasone treatment


title: stembase_DXC_9hai_rep2

description: Gene expression data from stem base of DXC line 9 h after dexamethasone treatment

source_name: stem base, DXC line, 9hour after dexamethasone treatment


title: Chimera_exp_control_03 (RRBS


title: stembase_DXC_0hai_rep2

description: Gene expression data from stem base of DXC line 0 h after dexamethasone treatment

source_name: stem base, DXC line, 0hour after dexamethasone treatment


title: Chimera_exp_control_02 (RRBS


title: 25hrM_3

description: 25 hpf kctd15 mutant embryos replicate 3

source_name: 25 hpf kctd15 mutant embryos

growth_protocol: Embryos were collected and staged to appropriate timepoint at 28.5C. Larva were fed and maintained according to SOP regulations in animal facility

tag: genotype/variation

value: kctd15 mutant

value: 25 hpf

value: embryos


title: stembase_DXC_3hai_rep2

description: Gene expression data from stem base of DXC line 3 h after dexamethasone treatment

source_name: stem base, DXC line, 3hour after dexamethasone treatment


title: E9.GAL55.SS3hr.56556

source_name: eGFP expressing galanin neurons isolated from VLPO using LCM

value: SS


title: 25hrM_2

description: 25 hpf kctd15 mutant embryos replicate 2

tag: age


title: stembase_DX_45hai_rep2

description: Gene expression data from stem base of DX line 45 h after dexamethasone treatment

source_name: stem base, DX line, 45hour after dexamethasone treatment

value: DX


title: Chimera_exp_control_01 (RRBS

value: Treg cells


title: PulseChase_exp_uhrf1_fl_06_GFPpositive_TomatoPositive (RNA-seq)

data_processing:
Basecalls performed using Illumina RTA2 software.
BCL2FASTQ v2.17.1.14 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the mm10 reference genome using Tophat v.2.1.0, and SeqMonk v1.45.4 was used to generate gene and transcript expression levels for protein-coding genes.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.45.4.

extract_protocol:
RNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
SMARTer Stranded Total RNA-Seq Kit v2 (Takara)


title: 25hrM_1

description: 25 hpf kctd15 mutant embryos replicate 1


title: E8.GAL50.0h.56551

value: baseline


title: stembase_DX_42hai_rep2

description: Gene expression data from stem base of DX line 42 h after dexamethasone treatment

source_name: stem base, DX line, 42hour after dexamethasone treatment


title: E7.GAL74.SD12hr.56546


title: 25hrWT_3

description: 25 hpf wildtype embryos replicate 3

source_name: 25 hpf wildtype embryos


title: stembase_DX_39hai_rep2

description: Gene expression data from stem base of DX line 39 h after dexamethasone treatment

source_name: stem base, DX line, 39hour after dexamethasone treatment


title: 25hrWT_2

description: 25 hpf wildtype embryos replicate 2


title: PulseChase_exp_uhrf1_fl_05_GFPpositive_TomatoPositive (RNA-seq)


title: stembase_DXC_24hai_rep2

description: Gene expression data from stem base of DXC line 24 h after dexamethasone treatment

source_name: stem base, DXC line, 24hour after dexamethasone treatment


title: E6.GAL43.SD9hr.56541


title: PulseChase_exp_uhrf1_fl_06_GFPnegative_TomatoPositive (RNA-seq)

source_name: ex-Foxp3 cells (Foxp3-GFP–tdTomato+)

value: ex-Foxp3 cells


title: 25hrWT_1

description: 25 hpf wildtype embryos replicate 1


title: E5.GAL37.SD6hr.56535


title: E10.GAL16.SS6hr.56561


title: stembase_DX_33hai_rep2

description: Gene expression data from stem base of DX line 33 h after dexamethasone treatment

source_name: stem base, DX line, 33hour after dexamethasone treatment


title: stembase_DX_36hai_rep2

description: Gene expression data from stem base of DX line 36 h after dexamethasone treatment

source_name: stem base, DX line, 36hour after dexamethasone treatment


title: E4.GAL33.SD3hr.56529


title: 1sM_2

description: 1 somite kctd15 mutant embryos replicate 2

source_name: 1 somite kctd15 mutant embryos

value: 1 somite


title: E3.GAL60.SS12hr.56523


title: stembase_DX_27hai_rep2

description: Gene expression data from stem base of DX line 27 h after dexamethasone treatment

source_name: stem base, DX line, 27hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_05_GFPpositive_TomatoNegative (RNA-seq)


title: 1sM_3

description: 1 somite kctd15 mutant embryos replicate 3


title: stembase_DX_30hai_rep2

description: Gene expression data from stem base of DX line 30 h after dexamethasone treatment

source_name: stem base, DX line, 30hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_04_GFPpositive_TomatoPositive (RNA-seq)


title: PulseChase_exp_uhrf1_fl_06_GFPpositive_TomatoNegative (RNA-seq)


title: 1sM_1

description: 1 somite kctd15 mutant embryos replicate 1


title: stembase_DX_24hai_rep2

description: Gene expression data from stem base of DX line 24 h after dexamethasone treatment

source_name: stem base, DX line, 24hour after dexamethasone treatment


title: D11.GAL15.SS6hr.56565


title: 1sWT_3

description: 1 somite wildtype embryos replicate 3

source_name: 1 somite wildtype embryos


title: stembase_DX_21hai_rep2

description: Gene expression data from stem base of DX line 21 h after dexamethasone treatment

source_name: stem base, DX line, 21hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_04_GFPpositive_TomatoNegative (RNA-seq)


title: D10.GAL5.SS3hr.56560


title: 1sWT_2

description: 1 somite wildtype embryos replicate 2


title: PulseChase_exp_uhrf1_fl_04_GFPnegative_TomatoPositive (RNA-seq)


title: 1sWT_1

description: 1 somite wildtype embryos replicate 1


title: stembase_DX_15hai_rep2

description: Gene expression data from stem base of DX line 15 h after dexamethasone treatment

source_name: stem base, DX line, 15hour after dexamethasone treatment


title: stembase_DX_18hai_rep2

description: Gene expression data from stem base of DX line 18 h after dexamethasone treatment

source_name: stem base, DX line, 18hour after dexamethasone treatment


title: stembase_DX_12hai_rep2

description: Gene expression data from stem base of DX line 12 h after dexamethasone treatment

source_name: stem base, DX line, 12hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_05_GFPnegative_TomatoPositive (RNA-seq)


title: D7.GAL41.SD9hr.56545

source_name: eGFP expressing galanin neurons isolated from VLPO using LCM

value: SD


title: D6.GAL36.SD6hr.56540

value: VLPO


title: stembase_DX_9hai_rep2

description: Gene expression data from stem base of DX line 9 h after dexamethasone treatment

source_name: stem base, DX line, 9hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_03_GFPpositive_TomatoNegative (RNA-seq)


title: E2.GAL10.SS9hr.56517

value: eGFP expressing galanin neurons


title: 14dM_2

description: 14 day kctd15 mutant larva replicate 2

source_name: 14 day kctd15 mutant larva

value: 14 day

value: larva


title: PulseChase_exp_uhrf1_fl_03_GFPnegative_TomatoPositive (RNA-seq)


title: D5.GAL32.SD3hr.56534


title: 14dM_3

description: 14 day kctd15 mutant larva replicate 3


title: D4.GAL59.SS12hr.56528


title: stembase_DX_6hai_rep2

description: Gene expression data from stem base of DX line 6 h after dexamethasone treatment

source_name: stem base, DX line, 6hour after dexamethasone treatment

value: stem base

value: cv Taichung 65, crl1 mutant


title: 14dWT_3

description: 14 day wildtype larva replicate 3

source_name: 14 day wildtype larva

value: wildtype


title: PulseChase_exp_uhrf1_fl_02_GFPpositive_TomatoNegative (RNA-seq)


title: 14dM_1

description: 14 day kctd15 mutant larva replicate 1

value: kctd15 mutant


title: D9.GAL23.0h.56555


title: PulseChase_exp_uhrf1_fl_02_GFPpositive_TomatoPositive (RNA-seq)


title: stembase_DXC_15hai_rep2

description: Gene expression data from stem base of DXC line 15 h after dexamethasone treatment

source_name: stem base, DXC line, 15hour after dexamethasone treatment

value: DXC


title: 14dWT_2

description: 14 day wildtype larva replicate 2


title: PulseChase_exp_uhrf1_fl_02_GFPnegative_TomatoPositive (RNA-seq)

source_name: ex-Foxp3 cells (Foxp3-GFP–tdTomato+)


title: stembase_DX_0hai_rep2

description: Gene expression data from stem base of DX line 0 h after dexamethasone treatment

source_name: stem base, DX line, 0hour after dexamethasone treatment


title: PulseChase_exp_uhrf1_fl_03_GFPpositive_TomatoPositive (RNA-seq)