title: UV_treatment_rep3

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

institute: Gregor Mendel Institute

description:
Assembly_UV.gtf
UV_assembly_RawCounts_UV_samples.txt

data_processing:
Raw reads (fastq files) were processed (trimmed) using TrimGalore V0.11.8
Reads were mapped using STAR V2.7.1a with the following options: twopassMode Basic, outFilterMultimapNmax 10, alignIntronMax 10000, alignMatesGapMax 6000
Mapped reads were pooled and transcriptomes were assembled using Stringtie Version 2.1.5 with the following options: rf, m = 200, c = 1, s = 2, j = 2.5, f = 0.5 and a = 15 with strand-specific awareness. This was performed separately for Zeocin treated/mock samples and UV-C treated/mock samples resulting in 2 transcriptome assembly files: Assembly_Zeo.gtf and Assembly_UV.gtf
The assembled transcriptome file was then annotated using gffcompare program with the Araport11 annotation Version 0.12.1
For each gene in transcriptome assemblies assembly_UV.gtf and Assebmly_Zeo.gtf, reads were counted using FeatureCounts from Subread package (Version 2.0.1) summarized in: UV_assembly_RawCounts_UV_samples.txt and Zeo_assembly_RawCounts_Zeo_samples.txt
Assembly: TAIR10
Supplementary files format and content: Assembly_UV.gtf file contains the final transcriptome assembly for UV treatment and mock samples
Supplementary files format and content: Assembly_Zeo.gtf file contains the final transcriptome assembly for Zeocin treatment and mock samples
Supplementary files format and content: Zeo_assembly_RawCounts_Zeo_samples.txt contains raw read counts for each gene from Assembly_Zeo.gtf and each of the Zeo mock/treatment samples
Supplementary files format and content: UV_assembly_RawCounts_UV_samples.txt contains raw read counts for each gene from Assembly_UV.gtf and each of the UV-C mock/treatment samples

organism: Arabidopsis thaliana

source_name: Seedlings 15d old

growth_protocol: A.thaliana (Col-0 line) seedlings grown in vitro for 15 days

extract_protocol:
RNA was extracted with TRI reagent
Ribosomal depletion followed byt NEBNext Ultra Directional RNA library Prep

treatment_protocol: Exposure to zeocin (200 microg/ml zeocin for 3 h) or UV-C (8 kJ/m2)

value: Seedlings 15d old

value: Columbia (Col-0)

value: UV-C


title: C11

status: Public on Jul 14 2023

type: SRA

city: Milwaukee

first: Satoshi

last: Shimada

state: WI

address: 8701 Watertown plank road

department: Physiology

country: USA

institute: Medical College of Wisconsin

library_source: transcriptomic

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction: The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly:  ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: all_compare.xls

molecule: polyA RNA

organism: Rattus norvegicus

extract_protocol:
RNA were extracted from snap frozen tissues by Trizol reagent and cleaned up by RNAeasy MinElute Cleanup kit (Qiagen)
mRNA library preparation (polyA enrichment) (Novogene, Plant and Animal Eukaryptic mRNA-seq with reference (WBI-quantification)

tag: strain

value: Sprague-Dawley

tag: tissue

value: Right kidney cortex

tag: treatment


title: UV_treatment_rep2

city: Vienna

country: Austria

molecule: total RNA

tag: genotype


title: BM-MSC-1

city: Seongnam

first: Hyun-Ju

last: An

state: --- Select One ---

address: Seongnam-si, 13496

country: South Korea

institute: CHA university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Homo sapiens

source_name: mesenchymal stem cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: cell type

value: mesenchymal stem cells

value: non differentiation

tag: time

value: Day 0


title: UV_treatment_rep1


title: ATAC-seq CD8+ T cells, Tim3+, AC484-treated, Replicate B

city: Cambridge

first: Robert

last: Manguso

state: MA

address: 415 Main Street

institute: Broad Institute

library_source: genomic

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.20.0)
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
Trimmed reads were aligned to mm10 using Bowtie2 (v2.5.0)
Outputs (.sam) from Bowtie2 were converted to bam files and sorted using samtools (v1.6)
PCR duplicates were marked using picard MarkDuplicates (v2.27.5)
Peaks were called using macs2 (v2.2.7.1) on combined bam files for each sample condition with a q-value threshold of 0.01
Outputs (.narrowPeak) from each condition were merged to form a single peak universe
Using bedtools (v2.30.0), the single peak universe was sorted, overlapping peaks were merged, and peaks within blacklisted regions of the mm10 genome were removed
For each biological replicate, the number of reads intersecting each of the single universe peaks was quantified to form a counts matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: genomic DNA

organism: Mus musculus

source_name: Subcutaneous tumours

extract_protocol:
Subcutaneous B16 tumours were implanted on the back mice. On day 19 after tumours were injected, tumors were collected, weighed and chpped before chemical and mechanical digestions with Tumour Dissociation Kit II (Myltenyi) and gentleMACS DIssociator (Myltenyi) using the m-TDK-1 program. Immune cells were isolated by density centrifugation with Lympholyte (Cederlane Labs) followed by positive selection for CD8a+ cells (Myltenyi). CD8+ cells were pooled into samples from 5-11 tumours, depending on cell counte recovered. Live cells were sorted into Tim3+ and Slamf6+ populations with two pooled samples per treatment condition.
Libraries were constructed by incubating 15,000 Slamf6+ or 31,000 Tim3+ cells with transposition mix, which contains 2x TD Buffer, Tn5 Transposase and 1% digitonin, at 1,000 cells/uL for 30 minutes at 37 C with agitation at 1000 RPM. DNA was purified using Qiagen MinElute Reaction Kit. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Subcutaneous tumours

tag: cell line

value: B16 melanoma

value: CD8 + Tim3 +


title: BM-MSC-2


title: C10


title: ATAC-seq CD8+ T cells, Slamf6+, AC484-treated, Replicate B

value: CD8 + Slamf6 +


title: ATAC-seq CD8+ T cells, Tim3+, AC484-treated, Replicate A


title: C9


title: ATAC-seq CD8+ T cells, Slamf6+, AC484-treated, Replicate A


title: Fetal-MSC-1


title: ATAC-seq CD8+ T cells, Tim3+, a-PD1-treated, Replicate B


title: UV_mock_rep2

value: Mock


title: C8


title: L1T3 tumor trt.4B

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Data was aligned using STAR against hg19 genome with Ensemble transcriptome information. RSEM was used for estimation of raw counts
Assembly: hg19
Supplementary files format and content: Raw counts for all genes

source_name: L1T3 tumor

extract_protocol:
RNA was extracted from the cells using the RNeasy kit (Qiagen, 74106)
Lexoge QUANTSEQ

treatment_protocol: L1T3 tumors treated in mouse xenografts with L-NMMA ((NG-methyl L-arginine) 25 mg/kg) or vehicle control

value: L1T3 tumor

value: Kaposi's Sarcoma (KS)

tag: tumor id

value: L-NMMA treated


title: UV_mock_rep1


title: C7


title: Zeo_treatment_rep5

description:
Assembly_zeo.gtf
Zeo_assembly_RawCounts_Zeo_samples.txt

value: Zeocin


title: L1T3 tumor trt.2E


title: UV_mock_rep3

value: Seedlings 15d old


title: C12


title: C6


title: ATAC-seq CD8+ T cells, Slamf6+, a-PD1-treated, Replicate B


title: L1T3 tumor unt.3B

value: untreated


title: C5

source_name: CLS

value: LS


title: L1T3 tumor unt.1A


title: C4

value: Sprague-Dawley


title: ATAC-seq CD8+ T cells, Tim3+, a-PD1-treated, Replicate A


title: Fetal-MSC-2


title: Zeo_treatment_rep4

value: Columbia (Col-0)


title: Zeo_treatment_rep2


title: C3

value: Right kidney cortex


title: ATAC-seq CD8+ T cells, Slamf6+, a-PD1-treated, Replicate A


title: ATAC-seq CD8+ T cells, Tim3+, Untreated, Replicate B


title: ATAC-seq CD8+ T cells, Slamf6+, Untreated, Replicate B


title: Mouse/human library mix 72hrs SGC0946 K562 cells -ChIP H3k79me2

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
H3K79me2 ChIP from mouse/human mixed cells
Custom targeted epigenetic library

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
The RSA algorithm was used to rank the genes for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Supplementary files format and content: Guide Counts file
Library strategy: CRISPR-seq

source_name: CML

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 2mM Glutamax, 100IU/ml Penicillin, 100 ug/ml Streptomycin and 10%HI-FCS in 5% CO2 37degrees.

extract_protocol:
Genomic DNA was extracted using Blood and tissue genomic DNA kit, Qiagen
One-step PCR was performed, containing adaptors for Illumina sequencing.

treatment_protocol: K562 and MLLAF9 Cas9 cells (100x10^6 per cell line) were infected with the pooled lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. ~ 100x10^6 cells were fixed/sonicated and ChIP performed at day 6 (H3K4me3) and day 9 (H3K79me2).

tag: time point

tag: chip antibody


title: Mouse/human library mix 96hrs SGC0946 K562 cells -ChIP H3k79me2


title: C2


title: Zeo_treatment_rep1


title: Zeo_mock_rep5


title: ATAC-seq CD8+ T Cells, Tim3+, Untreated, Replicate A


title: Mouse/human library mix 48hrs SGC0946 K562 cells -ChIP H3k79me2


title: C1


title: ATAC-seq CD8+ T Cells, Slamf6+, Untreated, Replicate A


title: Zeo_mock_rep4


title: Mouse/human library mix 24hrs SGC0946 K562 cells -ChIP H3k79me2


title: IP_og2.3

city: shanghai

first: li

last: peng

country: China

institute: PSC

data_processing:
cleaned the paired-end reads by Trimmomatic
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters
Mapped reads with low mapping quality (MAPQ < 30) or multiple positions on the genome were identified and removed by SAMtools (version 1.3)
Enriched peaks were identified by MACS (version 1.4) with default parameters.
The target genes of each peak were annotated by annotatePeak function in ChIPseeker package
The visualization of the average read coverage over gene body and additional 1.5kb up- and down-stream of the TSS and TES was performed by deepTools6 (version 2.4.1).
The statistical test of the overlap between two gene lists was performed by GeneOverlap7 package.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

source_name: Total seedlings

growth_protocol: seedlings grown in half-strength MS media

extract_protocol:
Nuclei were extracted from10-d-old WT or ogdh seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with Magna ChIP A/G kit (Millipore)
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

treatment_protocol: no

tag: developmental stage

value: 10-day-old seedlings

value: Total seedlings

value: ogdh double (og2)

tag: ecotype

value: anti-H3K27me3 (07-449, Sigma-Aldrich)


title: KPC, aPD-1, Replicate 5

description: 10X Genomics 3'v2 chemistry; raw fastqs from each separate flow cell and lane are included, but included processed files are concatonated across replicate flow cells

library_source: transcriptomic single cell

data_processing:
Cellranger v5.0.1 mkfastq command to convert bcl files to fastq files and to demultiplex fastq files
Cellranger v5.0.1 count command to generate raw and filtered count matrices
Supplementary files format and content: Assembly: mm10
Supplementary files format and content: Hierarchical data file (.h5)

source_name: melanoma subcutaneous tumor

extract_protocol:
Subcutaneous B16 tumours were implanted on the back mice. On day 13 after tumours were injected, tumors were collected, weighed and chpped before chemical and mechanical digestions with Tumour Dissociation Kit II (Myltenyi) and gentleMACS DIssociator (Myltenyi) using the m-TDK-1 program. Immune cells were isolated by density centrifugation with Lympholyte (Cederlane Labs) followed by positive selection for CD45+ cells (Myltenyi)
Library was performed according to the manufacter’s instructions (single cell 5’ v1 protocol or 5' v2.2 protocol, 10x Genomics).

value: melanoma subcutaneous tumor

value: KPC

value: CD45+ immune cells


title: Zeo_mock_rep3

value: Mock


title: Zeo_treatment_rep3


title: IP_og2.2


title: Mouse/human library mix DMSO K562 cells - ChIP H3K79me2


title: Zeo_mock_rep2


title: Mouse/human library mix 96hrs SGC0946 K562 cells

description:
SGC0946 treatment in Human library K562 cells then mixed with DMSO treated mouse library K562 cells
Custom targeted epigenetic library


title: KPC, aPD-1, Replicate 4


title: KPC, aPD-1, Replicate 2


title: Mouse/human library mix 72hrs SGC0946 K562 cells


title: Mouse/human library mix 48hrs SGC0946 K562 cells


title: ntESC, B6D2F1, female, line2

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description: TruSeq standed mRNA

data_processing:
Low quality reads and adapters were removed with fastp (0.22.0).
Retained reads were aligned to the reference mouse genome (GRCm38) using HISAT2 (2.2.1).
Read count data was obtained with StringTie (2.1.7).
The count data was normalized to CPM values with EdgeR.
Assembly: GRCm38
Supplementary files format and content: Counts_Data, Normalized_Data

organism: Mus musculus domesticus

growth_protocol: NtESCs were established and maintained by 2i/LIF method on feeder. Cells were cultured at 37C at 5% CO2

extract_protocol: Total RNA was extracted by RNeasy Mini Kit. The library was prepared with TruSeq standed mRNA Library Prep Kit.

value: ntESC

value: SCNT

tag: Sex

value: female


title: IP_WT.3

value: WT


title: IP_WT.2


title: KPC, aPD-1, Replicate 1


title: KPC, aPD-1, Replicate 3


title: ntESC, B6D2F1, male, line3

description: TruSeq standed mRNA

value: male


title: Mouse/human library mix 24hrs SGC0946 K562 cells


title: MEF, B6D2F1

description: TruSeq standed mRNA

value: MEF


title: Mouse/human library mix DMSO K562 cells

description:
mix of human and mouse sgRNA lirbaries expressed in k562 cells
Custom targeted epigenetic library


title: KPC, A484, Replicate 6


title: IP_WT.1


title: KPC, A484, Replicate 5


title: Input_og2.3


title: human library K562 cells

description:
human sgRNA library
Custom targeted epigenetic library


title: Mouse library K562 cells

description:
mouse sgRNA library
Custom targeted epigenetic library


title: Input_og2.2


title: KPC, A484, Replicate 4


title: IP_og2.1


title: Zeo_mock_rep1

value: Seedlings 15d old


title: Input_og2.1


title: KPC, A484, Replicate 3


title: RBBP5 KO - Pol II ChIP-seq

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
K562 ChIP-seq reads were aligned to the GRCh37.73 ensembl genome assembly using BWA. MLLAF9 ChIP-seq reads were aligned to the Mm10 genome assembly using BWA.
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Peak calling was performed using MACS2.
Genome_build: GRCh37.73 and Mm10
Supplementary_files_format_and_content: Bed files

extract_protocol:
ChIP DNA was purified using qiagen PCR clean up columns
Library prep was performed on ChIP DNA using rubicon kit

treatment_protocol: K562 and MLLAF9 Cas9 cells (10x10^6 per cell line) were infected with lentiviral sgRNA libraries at a multiplicity of infection of 0.3. Infected cells were selected with 2ug/ml puromycin for 72hrs, commencing 48hrs after transduction. ~ 100x10^6 cells were fixed/sonicated and ChIP performed at indicated timepoints from approx- 20-30 million cells per ChIP

value: RBBP5 KO - 6 days

tag: antibody

value: Pol II ab CTD4H8 3692628 05-623 Millipore


title: Input_WT.3

value: 10-day-old seedlings


title: stim_D110

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

institute: Keio University

data_processing:
Illumina NovaSeq 6000 was used for base calling.
The raw data was stored in FASTQ format. Trimming, mapping and acquiring read count data were performed by Trim-galore, Hisat2, and Htseq-count.
Assembly: hg38
Supplementary files format and content: txt files

source_name: CD8+T cells

growth_protocol: For stimulation, human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked with the transmembrane and cytoplasmic domain of CD8a as well as CD80 (K562-OKT3/CD80) at day 0. Unstimulated T cells were maintained in the presence of human IL-7 (10 ng/mL).

extract_protocol:
T cells were collected at day 0 or day 3.  CD8+ naïve T cells (CD8+CD45+CCR7+), CD8+ unstimulated T cells cultured in the presence of IL-7 (CD8+CD45+CCR7+), and stimulated CD8+ T cells (CD8+) were isolated by flow cytometry and RNA was extracted.
RNA libraries were prepared for sequencing using SMART-Seq HT kit.

value: CD8+T cells

tag: donor

value: stimulated and cultured in the presence of IL-2 and IL-15 for 3 days


title: stim_0309


title: IL7_D110

value: IL-7 for 3 days


title: KPC, A484, Replicate 1

value: melanoma subcutaneous tumor


title: KPC, A484, Replicate 2

value: KPC


title: IL7_0309


title: Input_WT.2

value: Total seedlings


title: RBBP5 KO - H3K4me3 ChIP-seq

value: H3K4me3 Rb Ab ab8580 GR3264490-1 Abcam


title: Input_WT.1


title: KPC, Vehicle, Replicate 5

value: CD45+ immune cells

value: Vehicle


title: control guide - H3K4me3 ChIP-seq

value: Control guide - 6 days


title: d0_D110


title: ESC, B6D2F1

description: TruSeq standed mRNA

value: ESC

value: WT


title: cKO_RP319

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP319

data_processing:
For gene expression profiling the reads were sorted into individual libraries based on the barcodes and mapped either to the mouse or human transcriptome (Ensembl release 102) with STAR v2.7.10a and then the corresponding BAM files were processed by salmon v1.8.0 (salmon quant with options -l A  --validateMappings --gcBias)(Patro et al., 2017). The DESeq function of DESeq2_1.34.0 bioconductor package (Love et al., 2014) was used to obtain log2 fold changes of gene expression and the adjusted p-values. Log2 fold change of 1 and adjusted p-value 0.05 was used as a threshold for statistical significance.
Ribosome profiling libraries were mapped to rRNAs and the remaining fraction of reads was aligned by STAR v2.7.10a (--alignEndsType EndToEnd) either to the mouse or human genome (Ensembl release 102). Metagene analysis of the ribosome fragments phasing was done by metagene count function of the plastid package v0.6.1. RiboCode toolkit v1.2.13 was used to detect longest translated ORFs (-l yes). Count tables of the longest translated ORFs for further differential translation efficiency analysis were made by ORFcount program from the RiboCode toolkit. First and last 10 translated codons were masked from counting (-f 10 -l 10). Hidden noise was inferred by sva bioconductor package and 2 surrogate variables (SV1 and SV2) were included into model. Differential translational efficiency analysis was done by DESeq function from DESeq2 bioconductor package with the following parameters specified: test=”LRT”, reduced = ~SV1 + SV2 + assay + condition. Model design was as follows: ~SV1 + SV2 + assay + condition + assay:condition.
Assembly: Ensembl release 102
Supplementary files format and content: RNA-seq and ribosome profiling supplementary files contain tables with DESeq2-specific differential gene expression parameters (baseMean, log2 fold change, adjusted p-value, etc.).

source_name: Liver

growth_protocol: The Cmtr1 floxed mouse was generated at the Transgenic Mouse Facility of University of Geneva, while the Cmtr1 and Cmtr2 knockout models were generated by the Knockout Mouse Project (KOMP). The Alb-CreERT2 mouse  specifically expresses using the Albumin (Alb) promoter the tamoxifen-inducible CreERT2 in hepatocytes. As described by the authors , a cassette consisting of an IRES with coding sequence for Cre-ERT2 was inserted (knock-in) downstream of the stop codon, in the 3′ UTR of the serum albumin (Alb) gene. The Alb-CreERT2 mouse was a gift from David Gatfield, University of Lausanne, Switzerland. The Cmtr1loxP/loxP mice were crossed with Alb-CreERT2KI/KI mice. In another cross, the Cmtr1+/- mice were crossed with the Alb-CreERT2KI/KI mice. Using the these lines we prepared the conditional knockouts (cKO) (Cmtr1loxP/- ; Alb-CreERT2KI/+ mice) and control (Cmtr1loxP/+; Alb-CreERT2KI/+) animals.

extract_protocol:
HAP1 cell pellets were directly mixed with the TRIzol reagent (Invitrogen, Cat. No. 15596026), flash frozen and kept at -70°C. They were then processed according to the manufacture’s protocol. To remove genomic DNA, approximately 10 µg of the extracted RNA was treated with TurboDNase (Invitrogen, Cat. No. AM2238) for 30 minutes and then cleaned by RNA Clean and Concentrator kit (Zymo Research, Cat. No. R1017). For total RNA purification from mouse livers we used multiple biological replicates (n=4) of mouse liver from control (Cmtr1loxP/+; Alb-Cre-ERT2) and Cmtr1 cKO (Cmtr1loxP/-; Alb-Cre-ERT2) animals after tamoxifen injections. Approximately 0.5 g tissue was taken and placed in a 50 mL conical tube (Sarstedt, Cat. No. 62.547.254) with 5 mL of extraction buffer. [Preparation of the extraction buffer: 250 g guanidium thiocyanate (ITW Reagents, Cat. No. A1107), 17.6 mL sodium citrate, 0.75 M, pH 7.0 (Sigma-Aldrich, Cat. No. C8532) and 320 mL water were mixed at 60°C. Add 1/10 volume of sodium acetate, 2 M, pH 4.0 (Merck, Cat. No. 1.06268 ); 1/100 volume β-mercaptoethanol (Sigma, M3148), before use.] Homogenize using a douncer (Kinematica AG, Cat. No. PT 2500E) in the 50 ml conical tube for 20 s until no fragments are left, and then add 5 mL phenol-H2O, mix well and stand on ice. Add 2 mL chloroform (VWR, Cat. No. 8.22265.2500 ): isoamyl alcohol (Merck, Cat. No. W205702 ) (49:1), mix well, stand on ice for 15 min, and transfer all the solution to a 15 mL TPP centrifuge tube (Thermo Fisher, Cat. No. 91016). Spin down for 20 min at 4000 rpm at 4°C, transfer the upper phase (approximately 5 ml) to a new 15 mL TPP tube. Then add 1 volume (~5ml) of phenol-chloroform: isoamyl alcohol (48:2) mix. Shake well to mix. Spin down for 15 min at 4000 rpm at 4°C, transfer upper phase (approximately 4 ml) to a new 15 mL TPP tube. Add 4 mL isopropanol to precipitate the nucleic acids, and leave it at −20°C for 25 min. After this, spin down at 5000rpm, 15min at 4°C, remove all the solution, and completely dry the tube by keeping it up-side down on a tissue to remove all the liquid. Add 6 mL 4M lithium chloride (Merck, Cat. No. 1.05679) to resuspend the precipitate. The volume used depends on the size of the pellet. Shake till the pellet completely dissolves. Note that the pellet contains DNA along with the RNA. Leave on ice for 5 min, and spin down at 4500 rpm for 15 min at 4°C, remove all the solution and dry the tube completely. Add 7 mL 75% ethanol to resuspend the precipitate and leave it at room temperature for 10 min. Spin down at 4500 rpm for 15 min, remove all the solution and dry the tube completely with a tissue. A pellet will be visible if the amount of RNA is abundant.. Add 75% ethanol and keep sample on ice or at -20°C for longer time. Repeat the 75% ethanol step once again. And dry the tubes at room temperature for 45min by keeping them open. Dissolve the RNA precipitation with ~700 ul DEPC treated water to a proper concentration. Dissolve RNA by gently pipetting. After a short spin, measure concentration and transfer RNA into a new 1.5ml tube. Store it under -80°C.
RNA-seq library: Library preparation for embryos form the heterozygous (HET) Cmtr1+/- crosses (n=4) was performed at the Genomics Core Facility (GeneCore, EMBL Heidelberg) using 50 ng (for E6.5 embryos) and 200 ng (for E7.5 embryos) of total RNA with stranded rRNAminus RNAseq protocol and sequenced on NextSeq 500, HI, 75SE (85SE). Library preparation and sequencing of a second batch of embryos from the heterozygous (HET) Cmtr1+/- crosses or Cmtr2+/- crosses was performed at iGE3 facility at the University of Geneva. We used 50 ng (for E6.5 embryos) and 200 ng (for E7.5 embryos) of total RNA for the Smarter Ribodepletion kit. The prepared libraries were sequenced on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva). Libraries were prepared with total RNA (500 ng) from human HAP1 WT and CMTR1 KO (n=4) cells at the Genomics Core Facility (GeneCore, EMBL Heidelberg) sequencing facility using the stranded rRNAminus RNAseq protocol and sequenced on the HiSeq2000. Ribosome profiling: ribosome protected fragments (RPFs) were size-selected (25-34 nt) by electrophoresis using a 15% TBE-Urea polyacrylamide gel electrophoresis (PAGE) and two RNA markers, 25-mer (OP-RNA25) and 34-mer (OP-RNA34) (Table S1). After dephosphorylation with T4 Polynucleotide Kinase (NEB, #M0201S) the adapter Linker-1 (OP-RNA45) was ligated to the 3′ end of the RPF using T4 RNA Ligase 2 (NEB, #M0242S). The ligated products were purified using 10% TBE-Urea PAGE. Ribosomal RNA was removed using RiboCop rRNA Depletion Kit V2 H/M/R (Lexogen #144) for mouse liver samples or using the Ribo-Zero Plus rRNA Depletion kit (Illumina, #20040892) for HAP1 cell samples. The adapter Linker-1 was used for priming reverse transcription (RT) with the RT primer Ni-Ni-9 (OP27) using ProtoScript® II Reverse Transcriptase (NEB, #M0368S). RT products were purified using 10% TBE-Urea PAGE. The cDNA was circularized with CircLigase™ II ssDNA Ligase (Epicentre, #CL9021K). The final libraries were generated by PCR using forward index primer NI-N-2 (OP28) and reverse index primers. Amplified libraries were purified using 8% TBE-PAGE and analyzed with TapeStation. Libraries were sequenced on an Illumina HiSeq 4000, single-reads, 1x 50 bp, 8 libraries in a pool.

tag: type

value: ribosome profiling

tag: age

value: cKO (input)


title: cKO_RP320

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP320


title: Rpb1 KO Guide1 - H3K27ac ChIP-seq

value: PolII guide 1 6 days


title: Rpb1 KO Guide2 - H3K27ac ChIP-seq

value: Pol II guide 2 6 days


title: d0_0309


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS1_SF4

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
ChIP-seq: Reads were aligned with bowtie 1.2.50. Genes (N=6,481) with pausing site and TES annotation were obtained from a previously published study. FeatureCounts 2.0.1.52 was used to calculate the total mapped reads from Pol II ChIP-seq. BamCoverage in deeptools 3.1.1.53 was used to extend ChIP-seq reads to 150bp. Log2FC of ChIP-seq was calculated using bigwigCompare in deeptools with the following nondefault options: binSize 10, pseudocount 0.1.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: DLD1 human cells were purchased from ATCC (CCL-221) and cultured in DMEM (Corning, #10013CV) supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
DLD1 cells were crosslinked with 15ml 1% PFA (ThermoFisher, #28908) in PBS on 15cm plates for 10 minutes at RT and quenched by the addition of 2ml 2.5M glycine followed by shaking for 5 minutes. Crosslinked cells were collected by scraping. Chromatin sonication was performed for 10 minutes using a Covaris E200 set to 10% duty factor, 200 cycles per burst, and 140 peak intensity power.
Eluted DNA was purified with the QIAquick PCR Purification Kit (Qiagen, #28106), and libraries were prepared using the KAPA HTP library preparation kit (Roche, #07961901001) for sequencing on the NovaSeq 6000

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: KPC, Vehicle, Replicate 3

tag: strain


title: cKO_RP318

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP318


title: KPC, Vehicle, Replicate 4

tag: tissue


title: KPC, Vehicle, Replicate 2

tag: treatment


title: cKO_RP317

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP317

tag: genotype


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-MS1_SF4

tag: cell type


title: KPC, Vehicle, Replicate 1


title: Control guide-H3K27ac ChIP-seq


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS1_F4


title: WT_RP324

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP324

value: control (input)


title: Rpb1 KO Guide 2- H3K4me3 ChIP-seq


title: AR control guide - Pol II ChIP-seq

value: Pol II ab CTD4H8 3692628 05-623 Millipore


title: B16F10,  aPD-1 + GVAX, Replicate 5

value: melanoma subcutaneous tumor

value: aPD-1 + GVAX


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS0_F4


title: WT_RP323

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP323


title: Rpb1 KO guide 1 - H3K4me3 ChIP-seq

value: Pol II guide 1 6 days

value: H3K4me3 Rb Ab ab8580 GR3264490-1 Abcam


title: Control guide- H3K4me3 ChIP-seq


title: WT_RP322

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP322


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-MS1_F4


title: B16F10,  aPD-1 + GVAX, Replicate 2

value: CD45+ immune cells


title: Rpb1 KO guide2 -Pol II ChIP-seq


title: ChIPseq_48hDox_3hdBET6_Pol2CST_TetOEGFP_NCIH2009

source_name: lung

value: lung

value: lung adenocarcinoma


title: WT_RP321

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP321


title: Rpb1 KO guide1 -Pol II ChIP-seq


title: B16F10,  aPD-1 + GVAX, Replicate 1


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOdBD_F2


title: B16F10, A484 + GVAX, Replicate 4

value: A484 + GVAX


title: control guide - Pol II ChIP-seq

value: Control guide - 6 days


title: B16F10, A484 + GVAX, Replicate 3


title: K562 Pol II screen conrol

description: Custom targeted epigenetic library

data_processing:
Library strategy: CRISPR-seq
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with fastx clipper or cutadapt
Trimmed reads were aligned to the reference sgRNA library with bowtie2
After filtering to remove multi-aligning reads, the read counts were computed for each sgRNA.
The RSA algorithm was used to rank the genes for which targeting sgRNA were significantly enriched in the sorted populations compared to the control unsorted populations grown in parallel.
Supplementary_files_format_and_content: Guide Counts file

value: day 6


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-TetOdCTM

value: Dox


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-TetO4S


title: K562 Pol II CRISPR-ChIP day 6

description: Custom targeted epigenetic library


title: cKO_RP119

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP119

value: ribosome profiling

value: cKO (footprints)


title: cKO_RP118

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP118


title: K562 H3K4me3 CRISPR-ChIP day 6

description: Custom targeted epigenetic library


title: B16F10,  aPD-1 + GVAX, Replicate 3


title: cKO_RP117

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP117


title: WT_RP124

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP124

value: control (footprints)


title: K562 screen conrol

description: Custom targeted epigenetic library


title: B16F10, Vehicle + GVAX, Replicate 4

value: Vehicle + GVAX


title: B16F10, Vehicle + GVAX, Replicate 3


title: 29323

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCh37 assembly using the gene, transcript, and exon features of Ensembl (release 70) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Genome_build: GRCh37
Supplementary_files_format_and_content: comma seperated file includes RSEM expected read count values for each sample

extract_protocol:
Viable splenic hCD45+ cells from leukemic mice were sorted after continuous treatment with imetelstat or vehicle control.
RNA was isolated from a maximum of 0.5 x 106 cells using the Qiagen RNeasy Micro kit according to the manufacturer's instructions. Replicates were taken from at least 2 different experiments. RNA samples were quantitated using the Nanodrop Spectrophotometer (Thermo Fischer Scientific) and the Qubit Fluorometer using the Qubit RNA HS Assay Kit (Molecular Probes) according to the manufacturer's recommendations. RNA integrity was confirmed using the RNA 6000 PICO Kit (Agilent Technologies) with analysis using the Agilent 2100 Bioanalyser (Agilent Technologies). Total RNA (100 _g) was used for NGS and prepared according to the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, NEB; Cat# E7770S). Briefly, following mRNA isolation, fragmentation and priming, first and second strand cDNA were synthesised. The double-stranded cDNA was purified, A-tailed and ligated to adaptors. Following purification, the adaptor ligated DNA was enriched by PCR, purified and assessed for quality using the High Sensitivity DNA Kit (Agilent) on the Agilent 2100 Bioanalyser. Libraries were sequenced using a High output, single-end, 75 cycle (version 2) sequencing kit on the Illumina Nextseq 550 platform.

value: hCD45+ cells from AML PDX

value: spleen

value: imetelstat


title: cKO_RP120

description:
Cmtr1-/loxP; AlbCreERT2+/-
RP120


title: B16F10, Vehicle + GVAX, Replicate 2

value: melanoma subcutaneous tumor


title: Si-FASN_2

city: Hangzhou

first: shuying

last: shen

state: Zhejiang

address: 3 East Qingchun Road

department: Department of Orthopaedic Surgery

institute: Sir Run Run Shaw Hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances
Essentially, differential expression analysis was performed using the DESeq2/DEGseq[6]/edgeR/Limm/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: articular sample

extract_protocol:
Total RNA was extracted from the cell using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara)
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA

value: articular sample

value: chondrocyte

value: Primary generation chondrocyte

value: wild type

value: FASN SiRNA transfection


title: Si-NC_3

value: Negetive SiRNA transfection


title: Si-FASN_1


title: 28023


title: Si-NC_2


title: WT_RP121

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP121


title: Si-FASN_3


title: 25716

value: vehicle


title: B16F10, A484 + GVAX, Replicate 1

value: CD45+ immune cells

value: A484 + GVAX


title: B16F10, A484 + GVAX, Replicate 2


title: Si-NC_1


title: B16F10, Vehicle + GVAX, Replicate 1


title: 28613


title: B16, AC484, Replicate 14

data_processing:
MIXCR was used to perform QC and reconstruct raw reads to quantifiable amino-acid level clonotypes
Assembly: mm10
Supplementary files format and content: bulk_df.csv
Library strategy: TCR-Seq

source_name: melanoma tumour

extract_protocol:
Subcutaneous B16 tumours were implanted on the back mice. On day 12, 100 ug of tissue was harvested from each tumour and stored in RNAlater at -80C. RNA was extracted using Tiissue Lyser II Homogenizer (Qiagen) and RNEasy Mini Kit (Qiagen) according to manufacturer's instructions.
Complete V(D)J variable regions of TCR transcripts were captured using the SMARTer Mouse TCR a/b Profilinf Kit (Takara) according to manufacturer's instructions.

value: melanoma tumour

value: B16F10 melanoma

value: bulk tumour

value: WT


title: B16, AC484, Replicate 15


title: 28326

value: hCD45+ cells from AML PDX


title: E7_5_Cmtr2_KO4b

description:
Cmtr2-/-
MD_KO4

source_name: Embryo

value: gene expression profiling

value: KO


title: WT_RP123

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP123

value: ribosome profiling

value: control (footprints)


title: MALBAC_GM12878_rep4

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description: MALBAC

data_processing:
The raw sequencing data of MALBAC was preprocessed as previously described. Firstly, UMI-tools (v1.1.1) was used to extract the cell barcodes in read 2 and attached them to the read name of matched read 1, and a whitelist containing 96 cell barcodes were used to filter the reads. Next, fastp (v0.20.1) was used to perform quality control with default parameters and the output ‘clean’ fastq files were mapped to GRCh38 reference with ‘bwa mem’ (v 0.7.17-r1188), and only alignments with MAPQ > 30 were retained for downstream analysis. We also used picard MarkDuplicates (v2.23.6) to remove PCR duplicates. After that, we attached the cell barcodes in read name into the bam tag ‘CB’ with local python scripts (using the simplesam module) and split bam into single cells with bamtools (v2.5.1). The demultiplexed bam files of each cell were then used to calculate the copy number ratios by Control-FREEC (v11.6) in 1 Mb resolution with recommended parameters.
Assembly: GRh38
Supplementary files format and content: CNV ratio calculated by Control-freec at 1 Mb resolution for each cell
Library strategy: MALBAC

growth_protocol: GM12878 (HG001) cell line and GM24385 (HG002) cell line were cultured in RPMI-1640 (Gibco; 11875093) supplemented with 15%fetal bovine serum (FBS,Gibco,cat#26140079) and Penicillin/Streptomycin (PS; Gibco, cat#15140122). K562 cell line was cultured in RPMI-1640 supplemented with 10% FBS and 1% PS. COLO320DM cell line was cultured RPMI-1640 supplemented with 10% FBS and 1% PS. Wild-type V6.5 murine embryonic stem cells (mESCs) were cultured on 0.25% gelatin-coated 6-well plate in Dulbecco’s modified eagle’s medium (DMEM/F-12, Gibco, cat#11320033) containing 15%FBS,1%Glutamax(Gibco, cat#35050061),0.1mM 2-mercaptoethanol (Gibco, cat#21985023),1%MEM nonessential amino acids(Gibco, cat#11140050),1%nuleoside (Millipore, cat#ES-008-D), 1%PS and 10000× 107 units/ml Leukemia Inhibitory Factor (LIF; Millipore, cat#ESG1107). The other male mouse ES cell line (named F15) was cultured in serum-free 2i/LIF medium, with in equal volume of DMEM (DMEM/F-12, Gibco; 11320033) and Neurobasal Medium (Gibco; 131 21103049) maintained in 2i (3 μM CHIR99021 and 1 μM PD0325901), LIF (1 000 U/ml), as previously described. These cell lines were all cultured at 37 ˚C with 5% CO2.

extract_protocol:
Resuspended ligated nuclei pellets in 200μL 0.25%BSA in PBS each tube and added 0.2μL 1000×DAPI for sorting nuclei. Single nucleus was flow sorted into each well of 96-well plate containing 2 μL lysis buffer(0.04 μL 1M Tris-HCl (pH 8.0),0.08μL 500 mM NaCl,0.03μL10% Triton X-100 (Sigma), 0.0004μL 0.5 M EDTA,0.05μL 20mg/mL QIAGEN protease). And then to decrosslinking and digest, incubated at 50°C, 3h; 70°C, 20 min; 68°C, 45 min; 4°C pause. After digesting, 96-well plates were stored at −80 ˚C.
A single cell was flow sorted into each well of 96-well plate containing 2.5 μL lysis buffer (0.25 μL 100 mM Tris-EDTA, 0.075μL 10% Triton X-100, 0.05μL 1 M KCL, 0.125μL 20mg/mL QIAGEN protease). And then incubated at 50°C for 3h; inactivate the protease at 70℃ for 30 min; 4°C pause. After digestion, we added 15μl amplification mixture (1.5μL 10×Thermopol buffer, 0.6μL 2.5 mM dNTP, 0.2μL 100 mM MgSO4, 0.5μL 10 μM GAT-N5-3G primer, 0.5μL 10 μM GAT-N5-3T primer, 0.5μL 2 U/μl DeepVentR (exo-) polymerase; New England BioLabs, M0259L ) into each tube containing lysed single cell, and performed quasilinear pre-amplification: 95℃, 3 min; then 11 cycles of 4°C for the 50s, 10°C for 50s, 20°C for 50s, 30°C for 50s, 40°C for 45s, 50°C for 45s, 65°C for 4min, 95°C for 20s, 58°C for 20s. And then added 15μl similar amplification mixture within GAT-8nt-barcode-primer, the products were then exponentially amplified for 12 cycles of 95°C for the 20s, 58°C for 30s,72°C for 3min, and finally 72°C for 5 minutes. After amplification, we pooled products with different barcodes together and then purified them with DNA Clean & concentration-5 kit (Zymo Research, D4014) with 5× binding buffer. cDNA products were further used to construct of libraries for next-generation sequencing as the previous report

value: lymphoblast cell


title: E7_5_Cmtr2_KO3b

description:
Cmtr2-/-
MD_KO3


title: MALBAC_GM12878_rep3

description: MALBAC


title: B16, AC484, Replicate 13


title: 28716

value: spleen


title: WT_RP122

description:
Cmtr1+/loxP; AlbCreERT2+/-
RP122


title: E7_5_Cmtr2_KO2

description:
Cmtr2-/-
MD_KO2


title: MALBAC_GM12878_rep2

description: MALBAC


title: 28323

value: imetelstat


title: B16, AC484, Replicate 11


title: E7_5_Cmtr2_KO6b

description:
Cmtr2-/-
MD_KO5


title: MALBAC_GM12878_rep1

description: MALBAC


title: B16, AC484, Replicate 10


title: 28011


title: E7_5_Cmtr2_WT5b

description:
Cmtr2+/+
MD_WT5


title: B16, AC484, Replicate 9


title: 28012


title: E7_5_Cmtr2_WT4b

description:
Cmtr2+/+
MD_WT4


title: HCT116 cells, control, biol rep3

city: Chengdu

first: haiyan

last: ren

address: ren min nan lu san duan 17 hao

institute: sichuan univerisity

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (v1.15) software
The filtered reads were mapping to the reference genome using HISAT2 v2.0.5 fraction: 0.8)
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
we mapped all the genes to Terms in the Gene Ontology database and calculated the numbers of differentially enriched genes in each Term. Using topGO to perform GO enrichment analysis on the differential genes, calculate P-value by hypergeometric distribution method (the standard of significant enrichment is P-value <0.05), and find the GO term with significantly enriched differential genes to determine the main biological functions performed by differential genes. ClusterProfiler (3.4.4) software was used to carry out the enrichment analysis of the KEGG pathway of differential genes, focusing on the significant enrichment pathway with P-value <0.05.
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa (GRCh38.98)
Supplementary files format and content: files include FPKM values for each Sample

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  with 5% CO2 at 37°C

extract_protocol:
HCT116 RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies). 3µg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: colon

value: epithelial cell


title: 26722


title: B16, AC484, Replicate 8


title: HCT116 cells, NleE, biol rep3

value: NleE overexpression


title: 25722


title: B16, AC484, Replicate 12


title: B16, AC484, Replicate 7


title: E7_5_Cmtr2_WT2b

description:
Cmtr2+/+
MD_WT2


title: E7_5_Cmtr2_WT1b

description:
Cmtr2+/+
MD_WT1


title: E6_5_Cmtr2_50_KO

description:
Cmtr2-/-
MD_KO5


title: E7_5_Cmtr2_KO1b

description:
Cmtr2-/-
MD_KO1


title: B16, AC484, Replicate 5


title: 29713

value: vehicle


title: HCT116 cells, NleE, biol rep2


title: HCT116 cells, NleE, biol rep1


title: HCT116 cells, control, biol rep2


title: HCT116 cells, control, biol rep1


title: E7_5_Cmtr2_WT3b

description:
Cmtr2+/+
MD_WT3


title: E6_5_Cmtr2_46_KO

description:
Cmtr2-/-
MD_KO4


title: B16, AC484, Replicate 4


title: 28625


title: RNAseq_48hDox_24hH2O_BRD4G3-GFP_rep2

data_processing:
ChIP-seq: Reads were aligned with bowtie 1.2.50. Genes (N=6,481) with pausing site and TES annotation were obtained from a previously published study. FeatureCounts 2.0.1.52 was used to calculate the total mapped reads from Pol II ChIP-seq. BamCoverage in deeptools 3.1.1.53 was used to extend ChIP-seq reads to 150bp. Log2FC of ChIP-seq was calculated using bigwigCompare in deeptools with the following nondefault options: binSize 10, pseudocount 0.1.
RNA-seq:  Reads were aligned using STAR v.2.5.2 and quantified with HTSeq v.2.0.2. Read counts were corrected for technical differences and normalized between samples with R package RUVseq.  Differential gene expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: counts table

extract_protocol:
ChIP-seq: DLD1 cells were crosslinked with 15ml 1% PFA (ThermoFisher, #28908) in PBS on 15cm plates for 10 minutes at RT and quenched by the addition of 2ml 2.5M glycine followed by shaking for 5 minutes. Crosslinked cells were collected by scraping. Chromatin sonication was performed for 10 minutes using a Covaris E200 set to 10% duty factor, 200 cycles per burst, and 140 peak intensity power.
ChIP-seq: Eluted DNA was purified with the QIAquick PCR Purification Kit (Qiagen, #28106), and libraries were prepared using the KAPA HTP library preparation kit (Roche, #07961901001) for sequencing on the NovaSeq 6000
RNA-seq: Total RNAs from 6-well plate were extracted using the RNeasy mini kit from Qiagen (Qiagen, #74106).
RNA-seq: mRNAs were enriched using a NEBNext poly(A) mRNA magnetic isolation module (NEB, #E7490L). RNA libraries were prepared using NEBNext Ultra II Directional RNA library preparation kit (NEB, #E7760L) and sequenced on the Illumina NovaSeq 6000.

value: colorectal carcinoma


title: 29312


title: RNAseq_48hDox_24hH2O_BRD4G3-GFP_rep1


title: 28314


title: 29725


title: B16, AC484, Replicate 2

value: melanoma tumour


title: B16, AC484, Replicate 3

value: B16F10 melanoma


title: E6_5_Cmtr2_42_KO

description:
Cmtr2-/-
MD_KO3


title: E6_5_Cmtr2_39_KO

description:
Cmtr2-/-
MD_KO2


title: B16, AC484, Replicate 6

value: bulk tumour


title: RNAseq_48hDox_24hAux_BRD4G3-GFP_rep2

value: Dox,Aux


title: 26715

value: hCD45+ cells from AML PDX


title: RNAseq_48hDox_24hAux_BRD4G3-GFP_rep1


title: B16, AC484, Replicate 1

value: WT


title: E6_5_Cmtr2_66_WT

description:
Cmtr2+/+
MD_WT5

value: gene expression profiling


title: E6_5_Cmtr2_35_KO

description:
Cmtr2-/-
MD_KO1

value: KO


title: 28726


title: E6_5_Cmtr2_64_WT

description:
Cmtr2+/+
MD_WT4


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4FL_rep2


title: 29726


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4dCTM_rep2


title: E6_5_Cmtr2_63_WT

description:
Cmtr2+/+
MD_WT3


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4FL_rep1


title: B16, aPD-1, Replicate 14


title: 26723


title: B16, aPD-1, Replicate 13


title: 29324


title: E6_5_Cmtr2_62_WT

description:
Cmtr2+/+
MD_WT2


title: B16, aPD-1, Replicate 15


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4dCTM_rep1


title: E6_5_Cmtr2_33_WT

description:
Cmtr2+/+
MD_WT1


title: 25721


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4dBD_rep2


title: 28722


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4dBD_rep1


title: 28626


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4C2_rep2


title: B16, aPD-1, Replicate 9


title: 29316


title: MiDo11

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo11_cKO_D22_b2

value: Day22 expt-2ndbatch

value: cKO


title: RNAseq_48hDox_24hAux_BRD4G3-BRD4C2_rep1


title: MiDo10

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo10_cKO_D22_b2


title: B16, aPD-1, Replicate 12


title: B16, aPD-1, Replicate 8


title: MiDo16

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDi16_ctrl_D22_b2

value: control


title: 25715

value: spleen


title: 28713


title: 28611


title: B16, aPD-1, Replicate 6


title: MiDo15

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo15_ctrl_D22_b2


title: B16, aPD-1, Replicate 7


title: ChIPseq_input_48hDox_TetO-GFP_BRD4G3

value: colon

value: Dox


title: B16, aPD-1, Replicate 11


title: B16, aPD-1, Replicate 10


title: MiDo9

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo9_cKO_D22_b2


title: MiDo14

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo14_ctrl_D22_b2


title: B16, aPD-1, Replicate 5


title: ChIPseq_input_48hDox_3hH2O_BRD4G3-GFP


title: 28022

value: imetelstat


title: ChIPseq_input_48hDox_3hDMSO_TetOEGFP_NCIH2009

value: lung

value: lung adenocarcinoma

value: Dox,DMSO


title: MiDo30

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo30_ctrl_D22_b2


title: B16, aPD-1, Replicate 4

value: melanoma tumour

value: B16F10 melanoma


title: 28311

value: vehicle


title: MiDo4

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo4_cKO_D6_b2

value: Day6 expt-2ndbatch


title: ChIPseq_input_48hDox_3hAux_BRD4G3-TetOdBD

value: colorectal carcinoma

value: Dox,Aux


title: MiDo3

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo3_cKO_D6_b2

value: gene expression profiling


title: B16, aPD-1, Replicate 3

value: bulk tumour

value: WT


title: ChIPseq_input_48hDox_3hH2O_BRD4G3-MS1


title: ChIPseq_input_48hDox_3hAux_BRD4G3-MS1


title: B16, aPD-1, Replicate 2


title: ChIPseq_input_48hDox_3hAux_BRD4G3-MS0


title: 26711

value: hCD45+ cells from AML PDX


title: 29714

value: spleen


title: MiDo2

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo2_cKO_D6_b2

value: cKO


title: RCH11

extract_protocol:
Viable hCD3- hCD45+ bone marrow cells were sorted from AML patients.
RNA was isolated from a maximum of 0.5 x 106 cells using the Qiagen RNeasy Micro kit according to the manufacturer's instructions. Replicates were taken from at least 2 different experiments. RNA samples were quantitated using the Nanodrop Spectrophotometer (Thermo Fischer Scientific) and the Qubit Fluorometer using the Qubit RNA HS Assay Kit (Molecular Probes) according to the manufacturer's recommendations. RNA integrity was confirmed using the RNA 6000 PICO Kit (Agilent Technologies) with analysis using the Agilent 2100 Bioanalyser (Agilent Technologies). Total RNA (100 _g) was used for NGS and prepared according to the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, NEB; Cat# E7770S). Briefly, following mRNA isolation, fragmentation and priming, first and second strand cDNA were synthesised. The double-stranded cDNA was purified, A-tailed and ligated to adaptors. Following purification, the adaptor ligated DNA was enriched by PCR, purified and assessed for quality using the High Sensitivity DNA Kit (Agilent) on the Agilent 2100 Bioanalyser. Libraries were sequenced using a High output, single-end, 75 cycle (version 2) sequencing kit on the Illumina Nextseq 550 platform.

value: hCD3- hCD45+ bone marrow cells

value: bone marrow

value: no treatment


title: MiDo28

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo28_cKO_D6_b2


title: R41B


title: B16, Vehicle, Replicate 14

value: Vehicle


title: ChIPseq_input_48hDox_3hAux_BRD4G3-GFP

value: colon


title: ChIPseq_input_48hDox_3hAux_BRD4G3-FL


title: B16, aPD-1, Replicate 1

value: melanoma tumour


title: B16, Vehicle, Replicate 13

value: B16F10 melanoma


title: ChIPseq_input_48hDox_3hAux_BRD4G3-delBD


title: U16


title: MiDo27

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo27_cKO_D6_b2


title: MiDo1

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo1_cKO_D6_b2


title: B16, Vehicle, Replicate 12


title: MiDo13

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo13_cKO_D6_b2


title: R68


title: ChIPseq_input_48hDox_2hAux_3hDMSO_BRD4G3-MS1

value: Dox,Aux,DMSO


title: MiDo12

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo12_cKO_D6_b2

value: Day6 expt-2ndbatch


title: R65


title: R64


title: MiDo8

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo8_ctrl_D6_b2

value: control


title: R55


title: B16, Vehicle, Replicate 9


title: B16, Vehicle, Replicate 10


title: ChIPseq_input_3hDMSO_BRD4IAA7G3

value: colorectal carcinoma

value: DMSO


title: B16, Vehicle, Replicate 8

value: bulk tumour


title: MiDo7

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo7_ctrl_D6_b2

value: gene expression profiling


title: R47


title: ChIPseq_input_3hDMSO_BRD4G3


title: MiDo6

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo6_ctrl_D6_b2


title: ChIPseq_input_3hAux_BRD4G3

value: Aux


title: B16, Vehicle, Replicate 11

value: WT


title: B16, Vehicle, Replicate 7


title: R40


title: ChIPseq_input_0hAux_BRD4IAA7G3


title: MiDo5

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo5_ctrl_D6_b2


title: B16, Vehicle, Replicate 6


title: MiDo29

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo29_cKO_D2_b2

value: Day2 expt-2ndbatch

value: cKO


title: R37

value: hCD3- hCD45+ bone marrow cells

value: bone marrow


title: ChIPseq_5hAux_Pol2CST_BRD4IAA7G3


title: ChIPseq_48hDox_TetO-GFP_Ser2P_BRD4G3

value: Dox


title: R58

value: no treatment


title: B16, Vehicle, Replicate 4

value: melanoma tumour

value: Vehicle


title: U18


title: ChIPseq_48hDox_TetO-GFP_CCNT1CST_BRD4G3

value: colon


title: MiDo17

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo17_cKO_D2_b2


title: MiDo18

description:
Cmtr1-/loxP; AlbCreERT2+/-
MiDo18_cKO_D2_b2


title: MiDo26

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo26_ctrl_D2_b2


title: R56


title: R52


title: ChIPseq_48hDox_TetO-dCTM_Ser2P_BRD4G3


title: B16, Vehicle, Replicate 3

value: B16F10 melanoma


title: ChIPseq_48hDox_TetO-dCTM_CCNT1CST_BRD4G3


title: B16, Vehicle, Replicate 1


title: B16, Vehicle, Replicate 5


title: MiDo25

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo25_ctrl_D2_b2

value: control


title: ChIPseq_48hDox_TetO-4S_Ser2P_BRD4G3

value: colorectal carcinoma


title: MiDo22

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo22_ctrl_D2_b2


title: B16, Vehicle, Replicate 2


title: ChIPseq_48hDox_TetO-4S_CCNT1CST_BRD4G3


title: MiDo21

description:
Cmtr1+/loxP; AlbCreERT2+/-
MiDo21_ctrl_D2_b2


title: R48


title: R38


title: E16_hom2, replicate 2, scRNAseq

city: Solna

first: Emma

middle: R

last: Andersson

state: Not required for this country

address: Solnav. 9, BioMedicum

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
Demultiplexing, quality control, raw data, gene expression data counts were performed using CellRanger v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger), by the BEA and SciLife core facilities. Matrices were further processed and analyzed with R (version 4.1.2) in R Studio. Prior to transformation into Seurat Objects, matrices were precleared using SoupX (https://github.com/constantAmateur/SoupX) with default settings of setContaminationFraction parameter (sc) for the P3, and (sc, 0.13) for the E16.5 stages. All bioinformatic analyses was performed using Seurat pipeline, doublet removal with scDblFinder (https://github.com/plger/scDblFinder), QC cutoffs for E16.5 datasets were nFeature_RNA > 500 & nFeature_RNA < 7000 & percent.mt < 10, for P3 a range of nFeature_RNA > 300-500 & nFeature_RNA < 4500-6000 & percent.mt < 10 were used, followed by SCT based integration of the E16.5 and P3 Jag1+/+, Jag1Ndr/+, and Jag1Ndr/ Ndr datasets 13. In total, 183,542 cells passed through the cross-contamination adjustment, quality control filtering and doublet removal in each of the duplicates per genotype and stage, analyzed in Seurat (https://satijalab.org/seurat/). A mean of 1520 genes, 6703 reads, and 3.0% of mitochondrial mRNA content were detected per cell.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Embryo stage was determined based on the presence of vaginal plug, the morning after breeding initiation, noon of day of plug was considered as E0.5. All embryos at E16.5 and P3 pups from the Jag1Ndr/+ x Jag1Ndr/+ breeding were sacrificed by decapitation, their livers (and spleens at P3) dissected out and placed in 12- or 24-well plates with ice-cold DPBS on ice unless stated otherwise. In case of P3 pups we further determined the sex based on pigmentation of the scrotum. Material for genotyping was collected (tail or limb tissue) and processed for genotyping using TaqMan probe (Thermo Fisher) yielding results in 3 hours (P3 Jag1Ndr/Ndr pups were identified based on the presence of jaundice and random Jag1Ndr/+ and Jag1+/+ controls genotypes were confirmed afterwards). The tissue was kept in ice-cold DPBS for 30min before being transferred into 5ml FACS tubes with 1.5 ml LDM + 0.5 ml of TrypLE Express (E16.5) or 2ml LDM (P3 stage), pipetted 5x through sterile wide-bore blue tip (E16.5) or transfer pipettes (P3) and incubated at 37°C/5min in a water bath (inverting each tube after 2-3 minutes). After the 5 min incubation, we disrupted the tissue further by gentle pipetting of the tissue 10x using a filtered 1 ml tip, followed by an additional round of incubation at 37°C/5min in a water bath (inverting each tube after 2-3 minutes). The enzymatic digestion was terminated by addition of 1.5 ml of WB16-E/ WBP3-E and additional mechanical disruption of the remaining tissue by pipetting each sample 20x using filtered 1 ml wide-bore blue pipette tip. We immediately poured the suspension through 70 µm filters into FACS tubes, rinsed the filter once with 0.5 ml WB16/WBP3, and passed the filtered suspension through a 40 µm strainer, each sample into two 2 ml Eppi tubes.  The duplicates of E16.5/P3 samples were centrifuged at 100g for 5mins at 5°C. Each supernatant was transferred to two new tubes, while the pellets were resuspended in 200 μl of Dead Cell Removal MicroBead suspension in Binding buffer and the resuspended pellets were further incubated for 5min at RT. In the meantime, the supernatant from the previous step was centrifuged at 250g for 5min at 5°C. The new supernatant was discarded, and the corresponding pellets were mixed with 200 μl of Dead Cell Removal MicroBeads with the previous cell suspension in Binding buffer. The mixture was incubated for 10min at RT. After the incubation 300 μl 1× Binding Buffer was added to the cell suspension to obtain a final volume of 500 μl, suitable for magnetic separation with MS columns. The separation was done based on the manufacturer’s recommendations. Briefly, we rinsed the columns with 500 μl of 1× Binding Buffer, applied the cell suspension onto the column, and collected the flowthrough containing unlabeled cells (living cells). Columns were further washed three more times with 500μl of 1× Binding Buffer, flowthrough collected and 20 μl filter sterile 10% BSA was added to the purified cells. Resulting samples were divided in two, whereof 250 μl was used for scRNAseq, following the 10x Genomics® Single Cell Protocol, and the remainder was used for the FACS as described below.  The duplicate P3 samples were centrifuged at 100g for 5min at 5°C, and supernatants were transferred to new tubes. The pelleted cells from each duplicate were pooled and resuspended in 1.5 ml of the WBP3-E buffer and transferred to a new 2 ml tube. In the meantime, the supernatants from the previous step were centrifuged at 250g for 5min at 5°C. The supernatants were discarded, and the corresponding pelleted cells were resuspended in 0.5 ml of the WBP3-E buffer and added to the resuspended cells obtained from the first centrifugation. The full sample cell suspensions (now in 2 ml of WBP3-E buffer) were then transferred into a new protein lo-bind tube through 40 μl cell strainer to remove any remaining cell debris or large clumps. We then determined the cell concentration using a Countess® II Quantification to calculate the appropriate volume for the subsequent resuspension to obtain the target concentrations of ~1200cells/μl as recommended by the 10x Genomics® Single Cell Protocol. Buffers: E16.5 - Wash Buffer (WB16-E) 1% BSA in HBSS, filter sterile (0.22 µm), Wash Buffer (WB16) 1% BSA, 1mM EDTA, HBSS, filter sterile (0.22 µm).P3 - Wash Buffer (WBP3-E) 1% FCS in HBSS, filter sterile (0.22 µm), Wash Buffer (WBP3) 1% FCS, 1mM EDTA, HBSS, filter sterile (0.22 µm).
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR, and the appropriated-sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: multiple

value: liver

value: embryonic day E16.5


title: E16_hom1, replicate 1, scRNAseq

description: 10x Genomics


title: ChIPseq_48hDox_3hH2O_Ser2P_BRD4G3-MS1


title: E16_het2, replicate 2, scRNAseq

description: 10x Genomics


title: ChIPseq_48hDox_3hH2O_Ser2P_BRD4G3-GFP


title: R16


title: E16_het1, replicate 1, scRNAseq

description: 10x Genomics


title: E16_wt2, replicate 2, scRNAseq

description: 10x Genomics


title: E16_wt1, replicate 1, scRNAseq

description: 10x Genomics


title: R23


title: U17


title: R44


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-TetOEGFP


title: R45


title: ChIPseq_48hDox_3hH2O_Pol2CST_BRD4G3-MS1_F6


title: ChIPseq_48hDox_3hH2O_CCNT1_BRD4G3-MS1


title: ChIPseq_48hDox_3hDMSO_Pol2CST_TetOEGFP_NCIH2009

value: lung

value: lung adenocarcinoma

value: Dox,DMSO


title: P3_wt2, replicate 2, scRNAseq

description: 10x Genomics

value: postnatal day 3


title: ChIPseq_48hDox_3hDMSO_Pol2CST_BRD4G3-TetOEGFP


title: P3_wt1, replicate 1, scRNAseq

description: 10x Genomics


title: R43

value: hCD3- hCD45+ bone marrow cells


title: R42

value: bone marrow


title: Patient 12

type: RNA

city: Sendai

first: Kazusa

last: Miyahara

address: Seiryo-machi 2-1

institute: Tohoku University

hyb_protocol: The biotinylated cRNA were hybridized to Human 6v2 Expression BeadChips (Illumina, San Diego, CA, USA).  日野案）The biotinylated cRNA were hybridized to Human 6v2 Expression BeadChips (Illumina, San Diego, CA, USA). The BeadChips were then labeled with streptavidin–Cy3 (GE Healthcare, Chicago, IL, USA).

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensity (SI) of each bead was measured and normalized using average normalization by BeadStudio software Ver. 3.1 (Illumina).

source_name: occipital lobe

label_protocol: The BeadChips were  labeled with streptavidin–Cy3 (GE Healthcare, Chicago, IL, USA).  日野案）Biotinylated cRNA was prepared by using the Ambion Illumina RNA Ampliﬁcation Kit (Ambion, Austin, TX, USA).

extract_protocol: Biotinylated cRNA was prepared by using the Ambion Illumina RNA Ampliﬁcation Kit (Ambion, Austin, TX, USA).  日野案）Total RNA was isolated by using an AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA, USA), and genomic DNA in the RNA samples was digested by RNase-free DNase I.

value: occipital lobe

tag: disease

value: schizophrenia


title: R46

value: no treatment


title: EDOX3

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

country: Canada

institute: McGill University

description: processed data for EDOX3 in EDOXvsWTDOX_DEG.xls, column W

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base calling).
Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5. RNA-seq Adapter information: NEBNext® UltraTM RNA Library Prep Kit RNA 5' Adapter(5'Adaptor) 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT RNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index) 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
STAR software is used to alignment for RNA-seq sequencing data analysis
Assembly: mm10
Supplementary files format and content: .xls format includes raw counts and comparison between differentially expressed genes across EDOX vs WTDOX groups.

source_name: Mammary gland

growth_protocol: Epithelial cells were harvested from the mammary glands of 8-12-week-old MIC mice and grown as organoids as described previously. Roughly 10,000 mammary epithelial cells were cultured in 8-well chambers in the organotypic medium consisted of Epicult-B mouse medium (Stem Cell Technologies, 05610), knockout serum replacement (Gibco, 10828010), penicillin/streptomycin, 10 ng/mL EGF, 25 μg/mL insulin (Sigma, 10156), and 1 μg/mL hydrocorticone for 6 days to allow formation of acinar structures.

extract_protocol:
Mammary organoids were collected after 8 days of doxycycline induction and lysed for RNA purification using a commercial total RNA Purification kit (Favorgen, Cat# FATRK 011-2).
mRNA was purified using poly-T oligo-attached magnetic beads and fragmented randomly by addition of fragmentation buffer. First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  The final library was prepared by PCR amplification and purification of PCR products using AMPure XP beads.

treatment_protocol: Doxycycline was added to growth media for 8 days, with media changes every 48hrs.

value: FVB/N

value: Female

value: Mammary gland

value: Primary Mammary epithelial cells

value: MIC/Conditional Ezh2 KO

value: Doxycyline (2µg/ml) for 8 days


title: Patient 13


title: ChIPseq_48hDox_3hdBET6_Pol2CST_TetOdBD_NCIH2009

tag: cell line


title: EDOX2

description: processed data for EDOX2 in EDOXvsWTDOX_DEG.xls, column V


title: R36


title: Patient 11


title: Patient 10


title: Patient 11 replicate

description: replication


title: ChIPseq_48hDox_3hdBET6_Pol2CST_BRD4G3-TetOEGFP

value: colon

value: colorectal carcinoma


title: Patient 9


title: U5


title: ChIPseq_48hDox_3hdBET6_Pol2CST_BRD4G3-TetOdBD


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-pBZ197

value: Dox,Aux


title: R6


title: WTDOX3

description: processed data for WTDOX3 in EDOXvsWTDOX_DEG.xls, column Z

value: MIC/Wild-type


title: R7


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-pBZ196


title: WTDOX1

description: processed data for WTDOX1 in EDOXvsWTDOX_DEG.xls, column X


title: U9


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-MS7


title: Input2_D

data_processing:
Data quality was assessed using FastQC
Sequence reads were trimmed using Trimmomatic as follows: (1) Discard the reads with low quality (proportion of low quality bases larger than 50%); (2) Discard the reads with N ratio (unsure base) larger than 15%; (3) Discard the reads with adaptor at the 5’-end; (4) Discard the reads without adaptor and inserted fragment at the 3’-end; (5) Trim the adapter sequence at the 3’-end; (6) Discard the reads whose length are less than 18nt after trimming.
Trimmed sequence reads were mapped to GrCM38/mm10 using BWA
Peaks were called using MACS2 software (Yong Zhang, Tao Liu et al., 2008) using a threshold q value of 0.05
BAM files were generated for each sample and visualized using IGV
Assembly: GrCM38/mm10
Supplementary files format and content: bigwig files

source_name: mammary glands

growth_protocol: Epithelial cells were harvested from the mammary glands of 8-12-week-old MIC mice and grown as organoids. Roughly 10,000 mammary epithelial cells were cultured in 8-well chambers in the organotypic medium consisted of Epicult-B mouse medium (Stem Cell Technologies, 05610), knockout serum replacement (Gibco, 10828010), penicillin/streptomycin, 10 ng/mL EGF, 25 μg/mL insulin (Sigma, 10156), and 1 μg/mL hydrocorticone for 6 days to allow formation of acinar structures. Subsequently, doxycycline was added to growth media either in the presence or absence of drug treatments for 8 days, with media changes every 48hrs.

extract_protocol:
ChIP assays were performed using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling, Cat#9003) based on the manufacturer’s instructions.
The libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S/#E7103S), according to the manufacturer's instructions. Library construction protocol & strategy: (1) The DNA fragments are repaired, dA-tailed. (2) The DNA fragments with A tail are ligated to sequencing adaptors. (3) The final DNA library is obtained by size selection and PCR amplification.

treatment_protocol: EZH2wt/wt MIC organoids were treated with doxycycline for 8 days prior to fixation and crosslinking with 1% formaldehyde for 10 min. Chromatin fragmentation was achieved by micrococcal nuclease treatment, and modified histones were immunoprecipitated using an H3K27me3 antibody (Cell signaling, Cat#9733) and ChIP Grade magnetic beads.

value: mammary glands

value: Established from mammary epithelial cells

value: epithelial cells

value: Treat with doxycycline for 8 days


title: Patient 8

value: occipital lobe


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-MS6


title: U4

value: hCD3- hCD45+ bone marrow cells

value: bone marrow


title: EDOX1

description: processed data for EDOX1 in EDOXvsWTDOX_DEG.xls, column U

value: FVB/N


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-MS2


title: OT1_2_S49

city: Aurora

first: Ross

middle: M

last: Kedl

state: CO

address: 12800 E. 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: Naive OT-I T cells

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq converter (version 2.17) without adapter trimming.
Nextera TruSight adapters were trimmed with skewer (version 0.2.2).
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl version 84.
Reads mapping to each gene of the Ensembl 90 annotation were counted with the featureCounts program from the Subread software package (v1.6.2).
Statistical comparisons were conducted using the EdgeR package (version 3.24.3) for the R statistical software (version 3.6).
Assembly: GRCm38 (incl. “random” contigs)
Supplementary files format and content: tpm_all-samples_annotated.xlsx:transcripts per million (Ensembl 90 mouse annotation) for each sample as a matrix in microsoft excel file format (.xlsx)

source_name: spleen

extract_protocol:
Transferred OT-1 T cells were isolated using FACS sorting for CD45.1+ CD8+ cells. Total RNA was isolated using the RNAEasy micro kit (Qiagen).
Poly(A) selection was performed, and all samples were sequenced using ultralow protocols.

value: spleen

value: Naive CD8+ T cell

value: OT-I

tag: recipient

tag: day

value: day 0


title: OT1_1_S48

description: Naive OT-I T cells


title: WTDOX2

description: processed data for WTDOX2 in EDOXvsWTDOX_DEG.xls, column Y

value: Female

value: Mammary gland

value: Primary Mammary epithelial cells

value: Doxycyline (2µg/ml) for 8 days


title: Patient 7

value: schizophrenia


title: Patient 5 replicate

description: replication


title: DOX2_IP

value: mammary glands


title: Patient 5


title: Patient 4 replicate

description: replication


title: Patient 6


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-MS1

value: colon

value: colorectal carcinoma

value: Dox,Aux

tag: chip antibody


title: DOX1_IP

value: Established from mammary epithelial cells

value: epithelial cells

value: Treat with doxycycline for 8 days


title: OT1_3_S50

description: Naive OT-I T cells


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-MS0


title: Patient 4

value: occipital lobe


title: DSS-treated colon mucosa, experimental day 18

first: Cambrian

middle: Yangshao

last: Liu

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina software was used for basecalling.
Transcript abundances were obtained from cellranger 3.0.0 using default options.
Downstream analyses were primarily performed using monocle3. Count matrices were loaded from the cellranger quantification. Cells from a separate experiment (GSE168033) profiling the anorectal junction were added in as a separate batch (Batch B). Cells with fewer than 100 UMI counts were filtered out. All samples were merged into a CellDataSet object. Batch correction was performed with a nearest-neighbors technique. Squamous cells were filtered out of the dataset.
The count matrix was normalized by the per-cell count total and subsequently log-transformed (preprocess_cds() and reduce_dimension() function defaults). The top 50 principal components were used for dimensional reduction and uniform manifold approximation and projection (UMAP). Clustering of cells was performed using the leiden algorithm with automatic detection of the resolution (cluster_cells() function defaults). Trajectories were computed using the defaults of the learn_graph() function.
Analysis scripts are available at: https://github.com/stalepig/2021-stem-cell-clonality
Assembly: mm10
Supplementary files format and content: Sparse Matrix (mtx) file of merged UMI counts with each row representing a gene and each column a cell barcode, can be read into R with readMM function in the Matrix package
Supplementary files format and content: Tab-delimited text (txt) files providing gene names (row data) or cell clustering and sample information (column data), matched to the sparse Matrix file

source_name: colonic mucosa

growth_protocol: Each sample is derived from mucosal tissue pooled from colons of 3-8 mice. Mice were ordered from Jackson Laboratory. At 8 wks-old, they were either dissected (for the no-injury or "day 0" control sample) or treated with 3% DSS for 6 days (for DSS samples). Mice treated with DSS were dissected at either 6, 7, 9, 11, 12, 16, 18, 19, or 23 days after their first day of exposure to DSS. Il10-/- mice were purchased from Jackson Laboratory and maintained in a specific pathogen-free animal facility for approximately 8 months; these mice were dissected at approximately 10 months-old. Colitis in Il10-/- mice was confirmed with measurements of fecal lipocalin levels that were found to be elevated.

extract_protocol:
Colons were dissected, manually stripped of myenteric layers, and enzymatically digested in Liberase TM/DNAse I. Dissociated tissue was strained through 70 and 40-micron filters, and the resulting single-cell suspension was treated with a red blood cell lysis buffer. Dead cells were removed using a magnetic separation kit with antibodies targeted against annexin V. The purified suspension was either frozen in 90% fetal bovine serum supplemented with 10% dimethyl sulfoxide (Batch A), or directly submitted (Batch C) for single-cell analysis and library prep via the 10X Genomics Chromium platform.
Samples in Batch A were thawed and processed on the same day, representing a single batch run. Samples in Batch C were directly processed after cell isolation, representing a separate batch run. Cells were washed with PBS and pre-loading viability was confirmed to exceed 75%. Cells were run on the Chromium (10X Genomics) platform for single-cell lysis, reverse transcription, barcoding, and library preparation. Paired-end sequencing of 3' transcript ends was performed on a novaSeq machine (Illumina).

tag: injury

value: 3% DSS (treated for 6 days)

value: WT

tag: inflammation

value: Inflamed

value: ~2 months

tag: batch

value: C


title: Input1_D


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-GFP


title: DSS-treated colon mucosa, experimental day 11


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-delCTM


title: WT_LM_3_run1

description: Transferred WT OT-I T cells recovered from WT recipient day 4 post infection with Listeria monocytogenes expressing ovalbumin

value: spleen

value: CD8+ T cell

value: OT-I

value: listeria monocytogenes ova infection

value: day 4


title: WT_VV_1_run1

description: Transferred WT OT-I T cells recovered from WT recipient day 4 post infection with vaccinia virus expressing ova peptide

value: vaccinia ova infection


title: IL27RKO_Vaccine_2_run1

description: Transferred IL27R KO OT-I T cells recovered from WT recipient day 3 post immunization with poly IC and anti CD40 and ovalbumin

value: IL27R KO OT-I

value: ova poly IC anti-CD40 immunization

value: day 3


title: IL27RKO_Vaccine_3_run1


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-FL

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: DSS-treated colon mucosa, experimental day 7

growth_protocol:
Each sample is derived from mucosal tissue pooled from colons of 3-8 mice. Mice were ordered from Jackson Laboratory. At 8 wks-old, they were either dissected (for the no-injury or "day 0" control sample) or treated with 3% DSS for 6 days (for DSS samples). Mice treated with DSS were dissected at either 6, 7, 9, 11, 12, 16, 18, 19, or 23 days after their first day of exposure to DSS. Il10-/- mice were purchased from Jackson Laboratory and maintained in a specific pathogen-free animal facility for approximately 8 months; these mice were dissected at approximately 10 months-old. Colitis in Il10-/- mice was confirmed with measurements of fecal lipocalin levels that were found to be elevated.
Each sample is derived from mucosal tissue pooled from colons of 3-8 mice. Mice were ordered from Jackson Laboratory. At 8 wks-old, they were either dissected (for the no-injury or "day 0" control sample) or treated with 3% DSS for 6 days (for DSS samples). Mice treated with DSS were dissected at either 6, 7, 9, 11, 12, 16, 18, 19, or 23 days after their first day of exposure to DSS. Il10-/- mice were purchased from Jackson Laboratory and maintained in a specific pathogen-free animal facility for approximately 8 months; these mice were dissected at approximately 10 months-old. Colitis in Il10-/- mice was confirmed with measurements of fecal lipocalin levels that were found to be elevated.

extract_protocol:
Colons were dissected, manually stripped of myenteric layers, and enzymatically digested in Liberase TM/DNAse I. Dissociated tissue was strained through 70 and 40-micron filters, and the resulting single-cell suspension was treated with a red blood cell lysis buffer. Dead cells were removed using a magnetic separation kit with antibodies targeted against annexin V. The purified suspension was either frozen in 90% fetal bovine serum supplemented with 10% dimethyl sulfoxide (Batch A), or directly submitted (Batch C) for single-cell analysis and library prep via the 10X Genomics Chromium platform.
Samples in Batch A were thawed and processed on the same day, representing a single batch run. Samples in Batch C were directly processed after cell isolation, representing a separate batch run. Cells were washed with PBS and pre-loading viability was confirmed to exceed 75%. Cells were run on the Chromium (10X Genomics) platform for single-cell lysis, reverse transcription, barcoding, and library preparation. Paired-end sequencing of 3' transcript ends was performed on a novaSeq machine (Illumina).
Colons were dissected, manually stripped of myenteric layers, and enzymatically digested in Liberase TM/DNAse I. Dissociated tissue was strained through 70 and 40-micron filters, and the resulting single-cell suspension was treated with a red blood cell lysis buffer. Dead cells were removed using a magnetic separation kit with antibodies targeted against annexin V. The purified suspension was either frozen in 90% fetal bovine serum supplemented with 10% dimethyl sulfoxide (Batch A), or directly submitted (Batch C) for single-cell analysis and library prep via the 10X Genomics Chromium platform.
Samples in Batch A were thawed and processed on the same day, representing a single batch run. Samples in Batch C were directly processed after cell isolation, representing a separate batch run. Cells were washed with PBS and pre-loading viability was confirmed to exceed 75%. Cells were run on the Chromium (10X Genomics) platform for single-cell lysis, reverse transcription, barcoding, and library preparation. Paired-end sequencing of 3' transcript ends was performed on a novaSeq machine (Illumina).

value: 3% DSS (treated for 6 days)


title: Dendritic cells Wild type WNV sNS1 + poly(I:C) Rep 3

city: Hannover

first: Imke

last: Steffen

address: Buenteweg 17

country: Germany

institute: University of Veterinary Medicine Hannover

description: Rep 3

data_processing:
Quality control of the sequenced raw FASTQ files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm39. Gene abundance was also determined by STAR.
Genes with a maximum read count <10 in all samples were removed before further analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene in each sample

source_name: Bone marrow

growth_protocol: Primary murine bone marrow-derived dendritic cells (BMDCs) were obtained from tibia and femur bone marrows of C57BL/6 mice and cultured in Iscove's modified Dulbecco's medium (IMDM, PAN-Biotech) supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% granulocyte-macrophage colony stimulating factor (GM-CSF,  Miltenyi Biotech) supernatant derived from X63 cells. Medium was exchanged every 48h and BMDCs were used after 8 days

extract_protocol:
RNA was isolated BMDCs either untreated, poly(I:C) stimulated, or TBEV sNS1 or WNV sNS1 treated before poly(I:C) stimulation. RNA was extracted using Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDCs were pre-treated with 10 µg/ml TBEV or WNV sNS1 for 16 h and stimulated with 25 µg/ml poly(I:C) for 24 h.

value: Bone marrow

value: Dendritic cells

value: Wild type

value: WNV sNS1 + poly(I:C)


title: IL15KO_Vaccine_2_run1

description: Transferred WT OT-I T cells recovered from IL-15 KO recipient day 3 post immunization with poly IC and anti CD40 and ovalbumin

value: spleen


title: ChIPseq_48hDox_3hAux_Ser2P_BRD4G3-delBD


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOFL


title: Dendritic cells Wild type WNV sNS1 + poly(I:C) Rep 2

description: Rep 2


title: Patient 3

value: occipital lobe

value: schizophrenia


title: WT_LM_1_run1

value: CD8+ T cell

value: OT-I

value: listeria monocytogenes ova infection


title: Dendritic cells Wild type WNV sNS1 + poly(I:C) Rep 1

description: Rep 1


title: Patient 2


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOEGFP


title: Dendritic cells Wild type TBEV sNS1 + poly(I:C) Rep 3

description: Rep 3

value: TBEV sNS1 + poly(I:C)


title: WT_Vaccine_4_run1

description: Transferred WT OT-I T cells recovered from WT recipient day 3 post immunization with poly IC and anti CD40 and ovalbumin

value: ova poly IC anti-CD40 immunization


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOdN


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOdET


title: WT_VV_2_run1

value: vaccinia ova infection

value: day 4


title: Patient 1


title: WT_Vaccine_3_run1

value: day 3


title: Patient 3 replicate

description: replication


title: Dendritic cells Wild type TBEV sNS1 + poly(I:C) Rep 1

description: Rep 1


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOdCTM

value: colon

value: colorectal carcinoma

value: Dox,Aux


title: Dendritic cells Wild type Poly(I:C) Rep 3

description: Rep 3

value: Bone marrow

value: Dendritic cells


title: WT_Vaccine_2_run1


title: ChIPseq_input_48hDox_2hAux_3hdCDK9_BRD4G3-MS1


title: NoRx_11

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Rhesus Macaque Genome Array. GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics script FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 scanner with 7G upgrade

data_processing: Data from .CEL files were uploaded to the Bioconductor for further analysis and normalized using RMA (‘simpleaffy’ package). Resulting fluorescent intensities were normalized to account for batch effects using the ‘sva’ package.

label: biotin

organism: Macaca mulatta

source_name: CD3 Transcripts

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3’IVT Plus protocol from 70-85 ng total RNA.

extract_protocol: CD3 T cells were lysed in RLT Buffer and total RNA was isolated using the RNAEasy kit per manufacturers instructions.

treatment_protocol: Cohorts of NHP received either an allogeneic or autologous HCT. Allogeneic HCT recipients received various immunoprophylactic treatments for prevention of GVHD. CD3 T cells were sorted by FACS from peripheral blood at various timepoints in the post transplant period and from healthy controls.

tag: tag

tag: hct

value: YES

tag: survival

tag: dayposthct

tag: sample group

value: NoRx


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOdBD_F3

tag: tissue


title: NoRx_10


title: WT_LM_2_run1

value: spleen

tag: treatment


title: Dendritic cells Wild type Poly(I:C) Rep 2

description: Rep 2

tag: genotype

value: Wild type


title: Patient 1 replicate

description: replication

value: occipital lobe

value: schizophrenia


title: NoRx_9


title: IL15KO_Vaccine_1_run1

tag: cell type

value: CD8+ T cell

value: OT-I


title: Dendritic cells Wild type TBEV sNS1 + poly(I:C) Rep 2

description: Rep 2

value: TBEV sNS1 + poly(I:C)


title: NoRx_8


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOC2


title: Dendritic cells Wild type untreated Rep 3

description: Rep 3

value: untreated


title: IL27RKO_Vaccine_1_run1

value: IL27R KO OT-I

value: ova poly IC anti-CD40 immunization


title: Dendritic cells Wild type untreated Rep 2

description: Rep 2


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOC1

value: colon


title: WT_VV_3_run1

value: vaccinia ova infection

value: day 4


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetO4S

value: colorectal carcinoma

value: Dox,Aux


title: NoRx_5

value: YES


title: NoRx_7

value: NoRx


title: NoRx_6


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-TetOC3


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-pBZ196


title: Dendritic cells Wild type untreated Rep 1

description: Rep 1

value: Bone marrow

value: Dendritic cells


title: IL15KO_Vaccine_3_run1

value: spleen

value: C57BL/6 IL15 KO

value: day 3


title: Dendritic cells Wild type Poly(I:C) Rep 1

description: Rep 1

value: Wild type


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS7


title: Inhbe KO, HFD diet, epididymal adipose, biol rep8

city: Tarrytown

first: Yuanqi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: Sample 101

data_processing:
OmicSoft Aligner Version 4 (OSA4) Benchmark
sequence reads were trimmed for adaptor sequence/low-quality sequence using OSA benchmark (parameter-trim by quality score is 2)
trimmed sequence reads were mapped to GenomeReference Mouse.mm10.regn, genemodel regn20150724 using OSA4 benchwork(parameters - Fixed penalty is 3, Indel penalty is 2)
read count extraction and normalization were performed using OSA4 benchmark
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

extract_protocol: mRNA-seq libraries were generated using KAPA® mRNA HyperPrep Kit (Roche Sequencing.) Starting material was 500 ng RNA and fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM xGen Dual Index UMI Adapters (Integrated DNA Technologies) and amplified using 14 PCR cycles. In addition to the vendor-indicated post-library amplification clean up step, another 0.65X SPRI bead clean up was performed to enrich for larger sized fragments for optimized sequencing. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 76 cycle, paired-end sequencing recipe targeting 25 million paired reads per library.

tag: strain

tag: Sex

value: male

tag: diet

value: HFD

value: KO


title: WT_Vaccine_1_run1

value: CD8+ T cell

value: OT-I

tag: recipient

value: ova poly IC anti-CD40 immunization

tag: day


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS6

value: colon

tag: cell line

tag: chip antibody


title: NoRx_4

tag: batch


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS4

value: colorectal carcinoma


title: NoRx_3

tag: tag


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS3

value: Dox,Aux


title: Inhbe KO, HFD diet, epididymal adipose, biol rep6

description: Sample 99


title: NoRx_2

tag: hct

value: YES


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS2


title: Inhbe KO, HFD diet, epididymal adipose, biol rep3

description: Sample 96


title: ChIPseq_48hDox_3hAux_Pol2CST_BRD4G3-MS1_F6


title: E6_IFN-r1_H3K27ac Sample

city: Vancouver

first: Wilfred

last: Jefferies

state: BC

address: 2260 Oak st

department: Vancouver Prostate Centre

institute: University of British Columbia

description: IFNr1_H3K27ac_vs_input_peaks.narrowPeak.named.bed

data_processing:
We aligned reads to reference genome mm10 with BWA aligner (v0.7.17)
H3k27ac peaks were called with MACS2 v2.1.2 (Zhang et al 2008) with FDR cutoff 0.01 (-f BAMPE). Input samples were used as control background
Genome_build: mm10
Supplementary_files_format_and_content: peak were were in BED format ( chromosome, start, end, peakname)

growth_protocol: 1x10^6 A9 cells were plated onto a 6 well plate in two mL of DMEM media.

extract_protocol: The cells were pelleted at 500g for 6 minutes at 4C. Cells were put into Chip-seq lysis buffer (provided by Dr.Martin Hirst lab) (Confidential) and mixed up and down three times before being placed immediately in liquid nitrogen for 15-20 seconds. Cells were then immediately transferred to dry ice and stored in the -80C until they were ready for transport. Cells were transported to Dr.Martin Hirst’s lab on dry ice.

treatment_protocol: Twenty-four hours after seeding, cells were cultured at the optimum concentrations of Cannabigerol 0.055umol, or 5.832x10-6 nmol IFN gamma or 1% DMSO vehicle for 48 hours. Cells were harvested using trypsin, and were pelleted at 200g for 5 mins before being resuspended in PBS. Cell viability was determined using Trypan Blue dye (Catalog# 15250061, Gibco) and cell counting slides (Catalog#1450015, Biorad) with Biorad TC20 automated cell counter. Once the viability was above 90%, the cells were quantified and 130K live cells were transferred into a new tube

value: 5.832x10-6 nmol IFN gamma


title: Inhbe KO, HFD diet, epididymal adipose, biol rep7

description: Sample 100


title: NoRx_0

tag: survival

value: NoRx


title: Inhbe KO, HFD diet, epididymal adipose, biol rep2

description: Sample 95


title: KY1005.D15_3

tag: dayposthct


title: WT, HFD diet, epididymal adipose, biol rep8

description: Sample 93

value: WT


title: NoRx_1

tag: sample group


title: Inhbe KO, HFD diet, epididymal adipose, biol rep1

description: Sample 94

tag: tissue


title: Inhbe KO, HFD diet, epididymal adipose, biol rep5

description: Sample 98

tag: treatment


title: Inhbe KO, HFD diet, epididymal adipose, biol rep4

description: Sample 97

tag: genotype


title: E11_IFN-r1_input Sample


title: E4_cann1_H3K27ac Sample

description: cann1_H3K27ac_vs_input_peaks.narrowPeak.named.bed

value: Cannabigerol 0.055umol


title: WT, HFD diet, epididymal adipose, biol rep7

description: Sample 92


title: ChIPseq_48hDox_3hAux_DSHBGFP_BRD4G3-MS1

tag: cell type

value: DSHBGFP


title: KY1005.D15_2


title: WT, HFD diet, epididymal adipose, biol rep6

description: Sample 91

tag: strain


title: ChIPseq_07_48hDox_3hAux_Pol2CST_BRD4G3-MS0_SF4


title: KY1005.D15_1


title: Healthy.Control_70

value: NO


title: E10_cann1_input Sample


title: Healthy.Control_69


title: Healthy.Control_68


title: ChIPseq_48hDox_3hAux_DSHBGFP_BRD4G3-MS7


title: ChIPseq_48hDox_3hAux_DSHBGFP_BRD4G3-MS0


title: B7_DMSO_control_H3K27ac Sample

description: DMSO_H3K27ac_vs_input_peaks.narrowPeak.named.bed

value: 1percent DMSO


title: Healthy.Control_65


title: WT, HFD diet, epididymal adipose, biol rep5

description: Sample 90

tag: Sex

value: male


title: ChIPseq_48hDox_3hAux_DSHBGFP_BRD4G3-MS6


title: KY1005.D15_0


title: C4_DMSO_control_input Sample


title: ChIPseq_48hDox_3hAux_CCNT1_BRD4G3-MS1


title: WT, HFD diet, epididymal adipose, biol rep3

description: Sample 88

tag: diet

value: HFD


title: Healthy.Control_66


title: WT, HFD diet, epididymal adipose, biol rep1

description: Sample 86