title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_SC35_(231128_NK_hs_2089)

description: Testing compartment integrity. SC35-targeted SLAM-RT&Tag performed on untreated K562 cells without iodoacetamide.

value: untreated no IAA reaction


title: K562_untx_IgG_forSC35_SLAMRTTag_n2_(231128_NK_hs_2092)

status: Public on Mar 04 2025

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2

library_source: transcriptomic

data_processing:
1)Reads were aligned using SLAM-DUNK v0.4.3 to the UCSC hg19 genome using the default slamdunk all pipeline. Overall T>C conversion rate was calculated using SLAM-DUNK 'alleyoop rates -o summary' option.
2)Aligned reads were sorted using SAMtools 1.19.2 using samtools 'sort -n -o' option.
3)Sorted aligned reads were then processed using the bam2bakR pipeline. Processing was performed to the UCSC hg19 genome and used the GENCODE GRCh37.p13 v19 gene annotation. Default bam2bakR pipeline was used to generate tdf browser tracks and cB files for differential kinetic analysis.
Assembly: hg19
Supplementary files format and content: bigwig (.bw)
Supplementary files format and content: tar of tdf files
Library strategy: SLAMRT&Tag

molecule: total RNA

organism: Homo sapiens

extract_protocol:
K562 cells were cultured until they reached approximately 70% confluency. For RNA metabolic labeling, 100 µM s4U was added to the cell media for 4 hours. Cells were then collected by centrifugation at 300 g for 5 minutes and washed with 1x PBS. Nuclei were isolated by resuspending the cell pellets in NE1 buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, Roche Complete Protease Inhibitor Cocktail, 1 U/μL RNasin Ribonuclease Inhibitor) and incubating on ice for 10 minutes. The nuclei were centrifuged at 500 g for 8 minutes and resuspended in Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, Roche Complete Protease Inhibitor Cocktail, 1 U/μL RNasin Ribonuclease Inhibitor).  Next, 200,000 K562 nuclei were bound to 5 μL of ConA beads (Bangs Laboratories) for 10 minutes at room temperature. After removing the Wash Buffer, the nuclei were treated with 10 mM iodoacetamide in Wash Buffer and incubated for 1 hour at 37°C. The nuclei were then washed twice with Wash Buffer.  Subsequently, standard RT&Tag steps were followed starting from primary antibody incubation overnight. The detailed RT&Tag protocol can be found here: dx.doi.org/10.17504/protocols.io.x54v9jyjqg3e/v1.
Sequencing libraries were then amplified by mixing the nuclei suspension with 15 μL of 0.67% Triton X-100, 2 μL of 10 mM i7 primer, 2 μL of 10 mM i5 primer, and 25 μL of 2x NEBNext Master Mix (NEB). The following PCR conditions were used: 1) 58°C for 5 minutes, 2) 72°C for 5 minutes, 3) 98°C for 30 seconds, 4) 98°C for 10 seconds, 5) 60°C for 15 seconds, 6) Repeat steps 4-5 13 times, 7) 72°C for 2 minutes, 8) Hold at 4°C. The sequencing libraries were then purified using 0.8x HighPrep PCR Cleanup System (MagBio) beads according to the manufacturer’s instructions. Sequencing was performed using single-end 100 bp reads.

tag: cell line

tag: group

value: untreated

tag: antibody

value: IgG (Abcam ab172730)


title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_IgG_forSC35_(231128_NK_hs_2088)

description: Testing compartment integrity. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells without iodoacetamide.


title: K562_timecourse_4hs4U_SLAMRTTag_H3K27me_n3_(240318_NK_hs_2089)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3

value: 4h s4U treatment

value: H3K27me3 (Cell Signaling Technology CST9733)


title: K562_timecourse_2hs4U_SLAMRTTag_H3K27me_n3_(231128,240318_NK_hs_2087)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 2 hours, replicate 3

value: 2h s4U treatment


title: K562_timecourse_untx_SLAMRTTag_H3K27me_n3_(240318_NK_hs_2085)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: K562_timecourse_4hs4U_SLAMRTTag_IgG_n3_(240318_NK_hs_2088)

description: Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_timecourse_untx_SLAMRTTag_IgG_n3_(240318_NK_hs_2084)

description: Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: K562_compartment_integrity_untx_withIAA_SLAMRTTag_H3K27me3_(230802_NK_hs_2026)

description: Testing compartment integrity. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells with iodoacetamide.

value: untreated with IAA reaction


title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_H3K27me3_(230802_NK_hs_2023)

description: Testing compartment integrity. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells without iodoacetamide.


title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_IgG_forH3K27me3_(230802_NK_hs_2022)


title: K562_timecourse_4hs4U_SC35_SLAMRTTag_n1_(230703,231128_NK_hs_1923)

description: Optimization of s4U labeling time. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 1

value: SC35 (Abcam ab11826)


title: K562_4hs4U_H3K27me3_SLAMRTTag_n3_(230703,231128_NK_hs_1922)

description: H3K27me3-targeted RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_4hs4U_IgG_forH3K27me3_SLAMRTTag_n3_(230703,231128_NK_hs_1921)

description: IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 3


title: K562_timecourse_untx_SC35_SLAMRTTag_n1_(231128_NK_hs_1920)

description: Optimization of s4U labeling time. SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_untx_H3K27me3_SLAMRTTag_n3_(230703,231128_NK_hs_1919)

description: H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: K562_4hs4U_SC35_SLAMRTTag_n1_(230703,231128_NK_hs_1891)

description: SC35-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 1


title: K562_4hs4U_H3K27me3_SLAMRTTag_n1_(230703,231128_NK_hs_1890)

description: H3K27me3-targeted RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 1


title: K562_4hs4U_IgG_SLAMRTTag_n1_(230703,231128_NK_hs_1889)

description: IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 1


title: K562_untx_SC35_SLAMRTTag_n1_(231128_NK_hs_1888)

description: SC35-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_untx_H3K27me3_SLAMRTTag_n1_(231128_NK_hs_1887)

description: H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_untx_IgG_SLAMRTTag_n1_(231128_NK_hs_1886)

description: IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 1


title: K562_4hs4U_H3K27me3_SLAMRTTag_n2_(230309_NK_hs_1761)

description: H3K27me3-targeted RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 2


title: K562_4hs4U_IgG_forH3K27me3_SLAMRTTag_n2_(230309_NK_hs_1760)

description: IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 2


title: K562_untx_H3K27me3_SLAMRTTag_n2_(230309_NK_hs_1759)

description: H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2


title: K562_timecourse_untx_SLAMRTTag_H3K27me_n2_(230111,231128_NK_hs_1662)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2


title: K562_timecourse_24hs4U_SLAMRTTag_H3K27me_n1_(221214_NK_hs_1567)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 24 hours, replicate 1

value: 24h s4U treatment


title: K562_timecourse_8hs4U_SLAMRTTag_H3K27me_n2_(230111_NK_hs_1660)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 8 hours, replicate 2

value: 8h s4U treatment


title: K562_compartment_integrity_untx_withIAA_SLAMRTTag_IgG_forH3K27me3_(230802_NK_hs_2025)

description: Testing compartment integrity. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells with iodoacetamide.


title: K562_timecourse_4hs4U_SLAMRTTag_H3K27me_n2_(230111_NK_hs_1652)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 2


title: K562_timecourse_8hs4U_SLAMRTTag_H3K27me_n1_(221214_NK_hs_1564)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 8 hours, replicate 1


title: K562_timecourse_4hs4U_SLAMRTTag_H3K27me_n1_(221214_NK_hs_1561)

description: Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 1


title: K562_untx_IgG_forH3K27me3_SLAMRTTag_n2_(230309_NK_hs_1758)

description: IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 2


title: GSC 810- replicate2

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
*library strategy: Hi-ChIP
HiC-Pro pipeline (version 3.0.0) was used for processing paired-end files with default setting. Aligned filtered reads were assigned to MboI restriction fragments and valid read pairs (interactions) were used  for generating binned interaction matrices with Juicer-tools and loop calling at 10kb resolution with FitHiChIP (release 9.0) and coverage bias regression and “Peak2All” option active where peaks form ChIP-seq for each experiment were used as input alongside valid-pairs. Interactions with a distance of more than 10-kb between the start of both anchors and p-adjusted <0.05 were considered significant and called loops. For each loop we classified each anchor into ‘promoter’, if a TSS was present within the 10kb, ‘enhancer’, if there was a H3k27ac peak and no TSS and ‘X’, if none TSS and H3k27ac peak was present. Multi-connected anchors (n>=2) were considered as ‘hubs’ and hubs were annotated as ‘promoter’, ‘enhancer; and ‘X’ depending on the type of the multi-connected anchor.
Assembly: hg38
Supplementary files format and content: loops called with FitHiChIP after merging replicates per sample

molecule: genomic DNA

source_name: glioma-stem cell

growth_protocol: GSCs were cultured in Neurobasal medium A (NBE medium, Thermo Fisher Scientific) supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), human recombinant bFGF and EGF (25 ng/mL each, R&D Systems), heparin (2ng/ml, Sigma), Penicilin-Streptomycin solution (LifeTech), and L-glutamine (200 mM/100X. LifeTech). lt-NSCs were cultured in poly-L-ornithine and laminin coated plates with DMEM/F12 w/o HEPES supplemented with N2 (Gibco), insulin (SIgma),glucose (Sigma), human recombinant bFGF and EGF ( R&D Systems) and CHIR99021 (R&DSystems).

extract_protocol:
5M cells were collected, trypsinized and fixed with 1% formaldehyde
Hi-ChIP samples were prepared using the Arima-HiC+ kit (Arima, A101020) following manual's instructions with a few modifications. To improve the sonication efficiency, a modified lysis buffer was used containing 10 mM Tris pH 8, 1 mM EDTA and 0.5% SDS. Before overnight incubation with the antibody, the sample was diluted in a buffer to bring it back to the original composition of the Arima R1 buffer (10 mM Tris pH 8, 140 mM NaCl, 1 mM EDTA, 1% triton, 0.1% SDS, 0.1% sodium deoxycholate). Libraries were generated using the Swift Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, 21024) according to the manufacturer’s instructions and performing between 8 and 14 cycles of PCR amplification. The samples were quantified by Qubit and sent for Bioanalyzer to check the quality and final size of the library
Libraries were generated as described in the HiChIP protocol using the  Swift Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, 21024).

value: glioma-stem cell

tag: cell type

value: patient-derived glioma stem cells

tag: treatment

value: H3K27ac (active motif, 91193 )


title: PBMCs, TCR, 4wk post-CAR T, P23

city: Boston

first: Dimitra

last: Karagkouni

address: Brookline 330

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: Sample 116
10x Genomics

data_processing:
Cellranger v.4.0.0 for scRNA-seq data, cellranger v.4.0.0 V(D)J Annotation pipeline for scTCR-seq data
Assembly: hg38
Supplementary files format and content: Gene expression,  TCR sequences
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol: Library was performed according to the manufacter's indtructions. For each sample, 8,000-10,000 cells were loaded in one channel of a Chromium Chip K (10x Genomics, PN-1000286) and profiled using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, PN-1000263). Full-length paired α/β TCR libraries were obtained using the Chromium Single Cell V(D)J Enrichment Human T Cell (10x Genomics,  PN-1000252). cDNA, gene expression, and TCR libraries were assessed using the DNA High Sensitivity Bioanalyzer Chip (Agilent, 5067-4626).

tag: tissue

value: PBMC

value: CAR T

tag: time

value: 4wk post-CAR T


title: lt-NSC-replicate1

description: nsc.bedpe

value: long-term neural stem cells derived from hESC H9


title: GSC1206-replicate2


title: GSC 810- replicate1


title: lt-NSC-replicate2

description: nsc.bedpe


title: K562_untx_IgG_forH3K27me3_SLAMRTTag_n3_(231128_NK_hs_1918)

description: IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 3


title: GSC 728-replicate1

value: H3K27ac (Abcam, ab4729)


title: GSC 320-replicate2


title: GSC 320-replicate1


title: lt-NSC-replicate2_CHIP

description: nsc.bed

data_processing:
Paired-end reads were aligned to human genome (hg38 version) with bowtie2 (version 2.3.4.1) and ‘–local –very-sensitive-local’ option active. Picard tools, Samtools and Bedtools were used for filtering duplicate reads (‘MarkDuplicate’ option), low quality reads (MAPQ<20), chrM and blacklisted regions and converting files into sam, bam, bed bigWig format. All filtered reads were used to call both narrow and broad peaks with MACS2 and default options. All peaks within 147 bp (one nucleosome) were merged into one peak for each experiment and only common peak between replicates were considered as peaks in each experiment.
Assembly: hg38
Supplementary files format and content: bed files (chr/start/end)

extract_protocol:
5 million cells per replicate in each cell line were colelcted, tripzinyzed and crosslinked with 1% formaldehyde. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared  using the KAPA Hyper prep kit (KAPA Biosystems) following the manufacturer's instructions. 10-30ng of DNA was used as starting material. Libraries were amplified using 8 cycles and then size-selected to isolate 250-450bp fragments with the Agencourt Ampure XP beads.


title: GSC 810- replicate2_CHIP


title: lt-NSC-replicate1_CHIP

description: nsc.bed


title: GSC1206-replicate2_CHIP


title: GSC 810- replicate1_CHIP


title: GSC 728-replicate2_CHIP


title: GSC 728-replicate1_CHIP


title: CHIPSEQ_P65_Stimulated_CXCL-EC1_REP_2

city: Cambridge

first: Charles

last: O'Donnell

state: MA

address: 140 First Street, Suite 501

institute: Omega Therapeutics

description: Library name: CHIPSEQ_P65_Stimulated_CXCL-EC1_REP_2

data_processing:
Each library was sequenced targeting a depth of 30M raw reads/fragments. Illumina sequencing data in FASTQ format was collected and QCed using FASTQC. Illumina sequencing adaptors were trimmed using Trimmomatic to eliminate technical sources of ChIP-Seq bias. Trimmed reads were aligned to human genome hg19 using Bowtie2. Mapped reads in the BAM files were sorted and filtered to remove duplicate reads in the generated duplicated BAM files using Picard. was applied on filtered BAM files of individual ChIP samples to call ChIP peaks using FDR <0.05 against input control.
Assembly: hg19/GRCh37
Supplementary files format and content: Processed data represent MACS2 peaks in BED format filtered by q val < 0.05 relative to input control

source_name: lung

extract_protocol:
DNeasy Blood & Tissue Kit (69516; Qiagen)
500,000 cells were cross-linked in 1% formaldehyde for 15 minutes and quenched with 275 mM glycine prior to flash freezing and storage at -80C. Fixed cells were thawed in Cell Lysis Buffer (50 mM Tris HCl, 10 mM EDTA, 0.5% SDS) and HALT Protease Inhibitor (Thermo Fisher Scientific, Cat# 87786) and then processed via multi-modal shearing using a probe-based sonicator (QSonica) followed by the PIXUL acoustic Sonicator (Active Motif).  An input fraction was reserved, and cell lysates were transferred onto pre-loaded antibody-bead conjugates for immunoprecipitation overnight, rotating at 4oC. Beads were washed prior to on-bead tagmentation of chromatin using Tagment DNA Enzyme 1 (Illumina, Cat# 20034197). Samples were washed and PCR amplified for 12 cycles using HiFi MasterMix (New England Biolabs, Cat# M0541) and combinatorial i5/i7 primers derived from Mezger A, et al. The PCR protocol included an initial 5-minute 72 oC incubation for gap-filling and a 5-minute incubation at 95 oC, sufficient for cross-linking reversal. Final libraries were purified using SPRI beads (1X SPRISelect, Beckman Coulter, Cat# B23318), pooled at equimolar ratios, and sequenced on a NextSeq 2000 Sequencing System (Illumina) using a 2x50 PE strategy.

value: lung

value: fibroblast

tag: batch


title: lt-NSC-replicate2_INPUT

description: nsc.bed


title: GSC 320-replicate1_CHIP


title: GSC1206-replicate1


title: GSC1206-replicate2_INPUT


title: GSC1206-replicate1_INPUT


title: GSC 810- replicate2_INPUT


title: GSC 810- replicate1_INPUT


title: lt-NSC-replicate1_INPUT

description: nsc.bed


title: GSC 728-replicate2_INPUT


title: GSC 728-replicate2


title: GSC 728-replicate1_INPUT


title: GSC 320-replicate1_INPUT


title: lt-NSC-ATAC-seq-replicate2

data_processing:
Paired-end reads were aligned to human genome (hg38 version) with bowtie2 (version 2.3.4.1) and ‘–local –very-sensitive-local -I 10 -X 2000’ option active. Picard tools, Samtools and Bedtools were used for filtering duplicate reads (‘MarkDuplicate’ option), low quality reads (MAPQ<20), chrM and blacklisted regions and converting files into sam, bam, bed bigWig format. All filtered reads were corrected for Tn5 insertions per read – pair by shifting +4 bp or −5 bp from the positive and negative strands, respectively. All corrected – filtered reads were used to call both narrow and broad peaks with MACS2 and default options. All peaks within 147 bp (one nucleosome) were merged into one peak for each experiment and only common peak between replicates were considered as peaks in each experiment.
Assembly: hg38
Supplementary files format and content: bed files (chr/start/end)

source_name: long-term neural stem cells

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) . A total of 50.000 cells per sample were used as input.
In order to minimize PCR bias an aliquot of each ATAC-seq library was first subjected to five cycles of amplification to determine by quantitative PCR the suitable number of cycles required for optimal library amplification. Samples were then subjected to a dual size selection (0.55x–1.5x) using SPRIselect beads (Beckman Coulter, B23317). Fragment distribution of libraries was assessed with an Agilent Bioanalyzer

value: long-term neural stem cells


title: GSC 320-replicate2_INPUT


title: CHIPSEQ_P65_CXCL-EC1_E1_REP_1

description: Library name: CHIPSEQ_P65_CXCL-EC1_E1_REP_1


title: GSC1206-ATAC-seq-replicate2


title: lt-NSC-ATAC-seq-replicate1


title: GSC1206-ATAC-seq-replicate1


title: GSC1206-replicate1_CHIP


title: GSC 810- ATAC-seq-replicate1


title: GSC 728-ATAC-seq-replicate2


title: GSC 728-ATAC-seq-replicate1


title: GSC 320-ATAC-seq-replicate2


title: GSC 320-ATAC-seq-replicate1


title: GSC 320-replicate2_CHIP


title: lt-NSC-RNA-seq-replicate2

data_processing:
Paired-end read alignment to human genome (hg38 version) was performed with TopHat21 (version 2.11) with default setting and ‘-r 200 –mate-std-dev 100’ option. Samtools were used for filtering and sorting aligned reads before annotation to “Homo_sapiens.GRCh38.104” gene version with htseq-count and ‘-m intersection-nonempty’ option. Only protein-coding and long-non-coding RNA transcripts were used for annotation and downstream differential expression analysis was performed with R package DESeq where we set a log2 fold change of 1 and P-adjusted of <0.01 as a cut off for calling deferentially expressed genes. Average TPM values were calculated for all replicates and genes with TPM above 1 were considered as expressed.
Assembly: hg38 and Homo_sapiens.GRCh38.104.chr.gtf
Supplementary files format and content: raw counts per sample re submitted in tab delimited format

source_name: long-term neural stem cells derived from hESC H9

extract_protocol:
Total RNA was extracted with TRIzol (Life Technologies, cat. no. 15596018) following the manufacturer’s instructions
Libraries were generated using a Illumina TruSeq stranded total RNA kit (cat. no. 20020596) following the manufacturer's protocol.


title: lt-NSC-RNA-seq-replicate1


title: GSC1206-RNA-seq-replicate2

source_name: patient-derived glioma stem cells


title: GSC1206-RNA-seq-replicate1


title: GSC 810- RNA-seq-replicate2


title: GSC 728-RNA-seq-replicate2


title: GSC 728-RNA-seq-replicate1


title: GSC 320-RNA-seq-replicate2


title: GSC 320-RNA-seq-replicate1


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS60, rep1

city: Vancouver

first: Thomas

middle: F.

last: Nguyen

state: BC

address: 2350 Health Sciences Mall

country: Canada

institute: UBC Life Sciences Institute

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 60 mins of heat shock (rep1)

data_processing:
Reads were mapped to the mm10 genome using Bowtie2 v2.4.2 with the following parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --phred33 –I 10 –X 2000. The resulting SAM files were converted to BAM files using SAMtools v1.7.
BigWig coverage files were generated from the BAM files using deepTools v3.5.0 and normalization factors calculated by ChIPseqSpikeInFree (Jin et al., 2020). Biological replicates were merged using bigWigMerge.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured on 0.1% gelatin-coated plates in mESC media: KnockOut DMEM with 15% FBS, 0.1 mM MEM non-essential amino acids, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 100U/mL Penicillin, 100μg/mL Streptomycin, and 1000 units/ml of ESGRO Recombinant Mouse LIF Protein. mESCs were fed daily, cultured at 37°C in a 5% CO2 incubator, and passaged every 2 days by trypsinization.

extract_protocol:
CUT&Tag was performed on 100,000 cells with 1:10 diluted primary antibody, 1:100 diluted secondary antibody, and 1:20 diluted in house produced pA-Tn5. DNA was released from the cells with an overnight proteinase K digestion at 37C, followed by phenol-chloroform extraction.
Libraries were constructed using 21 µL of DNA, 2 µL Universal i5 primer (10 µM), 2 µL uniquely barcoded i7 primer, and 25 µL NEBNext HiFi 2x PCR Master mix. 12 cycles of PCR was used to amplify the CUT&Tag libraries, followed by DNA cleanup using SPRI beads.

treatment_protocol: For unconditioned cells, mESCs were subjected to a single round of heat shock at 42C for 0, 30 or 60 minutes. For preconditioned cells, mESCs were heat shocked for 1 hour at 42C, recovered at 37C for 24 hours, and subjected to heat shock for 0, 10, 30, or 60 minutes.

value: mouse embryonic stem cells

tag: genotype

value: HSF1 KO

tag: preconditioning

value: 1 hour at 42°C, recovered at 37°C for 24 hours

tag: heat shock

value: 60 minutes at 42°C


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS60, rep2

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 60 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS0, rep2

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 0 mins of heat shock (rep2)

value: unstressed


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS0, rep1

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 0 mins of heat shock (rep1)


title: GSC 810- ATAC-seq-replicate2


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS10, rep1

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 10 mins of heat shock (rep1)

value: 10 minutes at 42°C


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS30, rep1

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 30 mins of heat shock (rep1)

value: 30 minutes at 42°C


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS10, rep2

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 10 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS60, rep2

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 60 mins of heat shock (rep2)


title: PBMCs, TCR, 4wk post-CAR T, P13

description:
Library name: Sample 62
10x Genomics


title: PBMCs, TCR, Leukapheresis, P13

description:
Library name: Sample 60
10x Genomics

value: Leukapheresis


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS60, rep1

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 60 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS30, rep2

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 30 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS30, rep1

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 30 mins of heat shock (rep1)


title: PBMCs, TCR, Leukapheresis, P12

description:
Library name: Sample 54
10x Genomics


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS0, rep1

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 0 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, KO, unCond, HS0, rep2

description: Library name: Pol3 CUTnTag in HSF1KO unconditioned mESCs with 0 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS60, rep1

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 60 mins of heat shock (rep1)

value: wildtype


title: Vector_3_1

city: Bethesda

first: Peng

last: Jiang

state: Maryland

address: 41 Center Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
Library name: Vector_3_1
Tumor sample 3 with vector over expression

data_processing:
STAR 2.7.10b was used to align reads to the mm39 genome, and RSEM 1.3.3 was employed for read quantification.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes logTPM values for each sample.

molecule: polyA RNA

source_name: Tumor

extract_protocol:
RNA was extracted using TRIzol (Takara) in Dounce homogenizers. The RNA was subsequently separated, washed, and participated using chloroform, isopropanol, and 75% ethanol and eluted in RNase-free water.
RNA processing, quality control, library construction, and sequencing were performed by Novogene Co., Ltd using the NovaSeq 6000 Sequencing System (Illumina).

value: Tumor

value: Melanoma


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS30, rep2

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 30 mins of heat shock (rep2)


title: GSC 810- RNA-seq-replicate1

value: patient-derived glioma stem cells


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS10, rep2

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 10 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS30, rep1

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 30 mins of heat shock (rep1)


title: Vector_2_2

description:
Library name: Vector_2_2
The second half of tumor sample 2 with vector over expression


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS10, rep1

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 10 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS0, rep2

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 0 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, KO, preCond, HS30, rep2

description: Library name: Pol3 CUTnTag in HSF1KO preconditioned mESCs with 30 mins of heat shock (rep2)


title: Vector_1_2

description:
Library name: Vector_1_2
The second half of tumor sample 1 with vector over expression


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS0, rep1

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 0 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS60, rep2

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 60 mins of heat shock (rep2)


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS60, rep1

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 60 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS30, rep2

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 30 mins of heat shock (rep2)


title: Ly86_4

description:
Library name: Ly86_4
Tumor sample 4 with Ly86 over expression


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS30, rep1

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 30 mins of heat shock (rep1)


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS0, rep2

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 0 mins of heat shock (rep2)


title: Vector_1_1

description:
Library name: Vector_1_1
The first half of tumor sample 1 with vector over expression


title: Pol3 CUT&Tag, mESCs, WT, unCond, HS0, rep1

description: Library name: Pol3 CUTnTag in wildtype unconditioned mESCs with 0 mins of heat shock (rep1)


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.90 hr^-1 for 48 hours

city: Riverside

middle: Edward

last: Kuhlman

state: CA

address: 900 University Ave

department: Physics and Astronomy

institute: University of California Riverside

description: Library name: P90

data_processing:
Raw data (raw reads) of fastq format were first processed through fastp software. 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 downstream analyses were based on the clean data with high quality, with each sample including more than 80 x 106 reads.
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. featureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Assembly: hg38 Homo sapiens reference genome downloaded from NCBI
Supplementary files format and content: Excel file includes raw counts for each Sample

growth_protocol: cells were cultured in complete media containing 90% DMEM with high glucose (Gibco), 10% heat-inactivated FBS (Gibco), 200 mM L-glutamine (100X), 10 mM MEM nonessential amino acids (100X), 100 mM MEM sodium pyruvate (100X), and concentrated puromycin (Gibco).

extract_protocol:
Total RNA was extracted from HEK-293T cells using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions after 48 hours of the indicated treatment
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non-strand specific library or dUTP for strand specific library. For the non-strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: human embryonic kidney

value: WT

value: osmotic shock


title: Ly86_3_1

description:
Library name: Ly86_3_1
Tumor sample 3 with Ly86 over expression


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.72 hr^-1 for 48 hours

description: Library name: P72


title: Pol3 CUT&Tag, mESCs, WT, preCond, HS60, rep2

description: Library name: Pol3 CUTnTag in wildtype preconditioned mESCs with 60 mins of heat shock (rep2)


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.81 hr^-1 for 48 hours

description: Library name: P81


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.63 hr^-1 for 48 hours

description: Library name: P63


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.54 hr^-1 for 48 hours - replicate 2

description: Library name: P54-2


title: Ly86_2_1

description:
Library name: Ly86_2_1
Tumor sample 2 with Ly86 over expression


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.36 hr^-1 for 48 hours - replicate 2

description: Library name: P36-2


title: Ly86_1_1

description:
Library name: Ly86_1_1
The first half of tumor sample 1 with Ly86 over expression


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.45 hr^-1 for 48 hours

description: Library name: P45


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.54 hr^-1 for 48 hours - replicate 1

description: Library name: P54-1


title: Vector_2_1

description:
Library name: Vector_2_1
The first half of tumor sample 2 with vector over expression


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.36 hr^-1 for 48 hours - replicate 1

description: Library name: P36-1


title: PBMCs, TCR, 4wk post-CAR T, P10

description:
Library name: Sample 42
10x Genomics

value: PBMC

value: CAR T

value: 4wk post-CAR T


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.27 hr^-1 for 48 hours

description: Library name: P27


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.18 hr^-1 for 48 hours

description: Library name: P18


title: Continuous 40 mM sorbitol for 48 hours - replicate 2

description: Library name: C40mM-2


title: Sorbitol concentration oscillating between 0 - 40 mM at f = 0.09 hr^-1 for 48 hours

description: Library name: P09


title: CT3F_S12

city: Madison

first: Yixuan

last: Xie

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

description: Library name: CT3F_S12

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0
Assembly: Mouse mm10
Supplementary files format and content: Matrix file

source_name: larynx

extract_protocol:
Mouse larynges were collected from antibiotics treated (AB)and untreated (CT)  mice, and minced into 0.5 mm small pieces on a sterile petri dish under a dissection scope, then digested in a 1 ml modified dissociation solution for 40 min in a cold room (4 °C). We started from the dissociation protocol by Sekiguchi & Hauser (2019) and determined the optimal dissociation condition by optimizing the enzyme composition & concentration and dissociation temperature & time. Specifically, 1 ml of modified dissociation solution contained 5 mM CaCl2, 90 µl Accutase (Stem Cell Technologies, Cambridge, MA), 90 µl Accumax (Stem Cell Technologies, Cambridge, MA), 10 mg/ml Bacillus lichenformis protease (MilliporeSigma, Burlington, MA), and 125 U/ml DNase I (MilliporeSigma, Burlington, MA) dissolved in sterile calcium/magnesium-free PBS. Samples were gently triturated every 5 min using a wide-bore pipette tip during dissociation. After dissociation, cell suspension was filtered through 40 µm cell strainer to remove aggregates. Undigested cartilage was removed before cell straining to prevent clogging cell strainer and further impact dissociation efficiency. Dissociation was performed for each larynx separately. Single-cell suspensions from three larynges per mouse group were pooled as one sample (4 biological replicates per mouse group). Pooled suspensions were added to 5 ml Ca/Mg-free PBS supplemented with 10% FBS, filtered with a 40 µm cell strainer (MilliporeSigma, Burlington, MA), then centrifuged at 300 g, for 10 min, at 4°C.  Cell pellet was resuspended in 30 µl ACK lysing buffer (Lonza, Bend, OR) briefly to remove erythrocytes, following manufacture’s instruction.
ACK treated single cells were resuspended in 500 µl of Ca/Mg-free PBS supplemented with 2% FBS. Libraries were prepared according to Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Pleasanton, CA). Briefly, single cell suspensions were transported on ice to the University of Wisconsin-Madison Biotechnology Center, where cell concentration and viability were quantified on the Countess II (Thermo Fisher Scientific, Waltham, MA) using 0.4% Trypan Blue (Invitrogen, Carlsbad, CA). Cells were then partitioned into Gel Beads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 5′ adaptor and sample index attachment. Library preparation was performed to generate a single pool of cDNA containing both CT and AB samples to minimize batch effect between samples. Libraries were quantified using the Qubit High Sensitivity DNA Kit (Thermo Fisher Scientific, Waltham, MA), uniquely indexed, pooled, balanced for the number of estimated reads per cell with a MiSeq (Illumina, San Diego, CA) sequencing run, and subsequently sequenced on a NovaSeq S2 flowcell (Illumina, San Diego, CA) using a 150 x 150 bp sequencing reaction targeting > 60,000 reads/cell, yielding a calculated depth of over 100K mean reads per cell for samples of the first batch and over 70K mean reads per cell for samples of the second batch. MiSeq balancing run was quality controlled using calculations based on UMI-tools (99). Sequencing of the first batch of samples was performed first to serve as a pilot experiment for the second batch.

value: larynx

tag: Sex

value: F

value: control


title: CT3M_S9

description: Library name: CT3M_S9

value: M


title: Continuous 40 mM sorbitol for 48 hours - replicate 1

description: Library name: C40mM-1


title: negative control replicate 2

description: Library name: negative-2


title: Continuous 20 mM sorbitol for 48 hours - replicate 1

description: Library name: C20mM-1


title: negative control replicate 1

description: Library name: negative-1


title: CT2F_S11

description: Library name: CT2F_S11


title: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_SC35_(231128_NK_hs_2091)

description:
Library name: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_SC35
Testing compartment integrity. SC35-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours without iodoacetamide.

library_source: other

molecule: other

value: SC35 (Abcam ab11826)


title: CT1F_S10

description: Library name: CT1F_S10


title: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_IgG_forSC35_(231128_NK_hs_2090)

description:
Library name: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_IgG_forSC35
Testing compartment integrity. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours without iodoacetamide.

value: IgG (Abcam ab172730)


title: CT2M_S8

description: Library name: CT2M_S8


title: K562_timecourse_8hs4U_SLAMRTTag_H3K27me_n3_(240318_NK_hs_2091)

description:
Library name: K562_timecourse_8hs4U_SLAMRTTag_H3K27me_n3
Optimization of s4U labeling time. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 8 hours, replicate 3

value: H3K27me3 (Cell Signaling Technology CST9733)


title: AB3F_S6

description: Library name: AB3F_S6

value: antibiotics


title: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_H3K27me3_(241018,241028_NK_hs_2302)

description:
Library name: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_H3K27me3
Testing compartment integrity. H3K27me3-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours without iodoacetamide.


title: Ly86_1_2

description:
Library name: Ly86_1_2
The second half of tumor sample 1 with Ly86 over expression

value: Tumor


title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_H3K27me3_r2_(241018,241028_NK_hs_2299)

description:
Library name: K562_compartment_integrity_untx_noIAA_SLAMRTTag_H3K27me3_r2
Testing compartment integrity. H3K27me3-targeted SLAM-RT&Tag performed on untreated K562 cells without iodoacetamide.


title: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_IgG_forH3K27me3_(241018,241028_NK_hs_2301)

description:
Library name: K562_compartment_integrity_4hrs4U_noIAA_SLAMRTTag_IgG_forH3K27me3
Testing compartment integrity. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours without iodoacetamide.


title: K562_compartment_integrity_untx_noIAA_SLAMRTTag_IgG_forH3K27me3_r2_(241018_NK_hs_2298)

description:
Library name: K562_compartment_integrity_untx_noIAA_SLAMRTTag_IgG_forH3K27me3_r2
Testing compartment integrity. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells without iodoacetamide.


title: Continuous 20 mM sorbitol for 48 hours - replicate 2

description: Library name: C20mM-2


title: K562_timecourse_4hs4U_SLAMRTTag_IgG_n5_(230111_NK_hs_1651)

description:
Library name: K562_timecourse_4hs4U_SLAMRTTag_IgG_n5
Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on K562 cells treated with 100mM s4U for 4 hours, replicate 5


title: AB2F_S5

description: Library name: AB2F_S5


title: AB2M_S2

description: Library name: AB2M_S2


title: AB1F_S4

description: Library name: AB1F_S4


title: HEK293T_SON_RTTag_n6_(241018_NK_hs_2291)

description:
Library name: HEK293T_SON_RTTag_n6
SON-targeted RT&Tag performed on HEK293T cells, replicate 6

data_processing:
1. Adapter trimming of 100bp single-end reads was performed using Trim Galore 0.6.4_dev with parameters "-q 20 --length 20."
2. Trimmed reads were mapped to the Homo sapiens reference genome (hg19, UCSC) using HISAT2 2.1.0 with the parameter "--max-intronlen 30000."
4. BigWig files were generated using deepTools 3.3.1 bedCoverage with the parameter "--normalizeUsing CPM" (Supplementary file .bw).
Assembly: hg19
Supplementary files format and content: bigwig (.bw)
Library strategy: RTTag

extract_protocol:
The detailed RT&Tag protocol can be found here: dx.doi.org/10.17504/protocols.io.x54v9jyjqg3e/v1.
Sequencing libraries were then amplified by mixing the nuclei suspension with 15 μL of 0.67% Triton X-100, 2 μL of 10 mM i7 primer, 2 μL of 10 mM i5 primer, and 25 μL of 2x NEBNext Master Mix (NEB). The following PCR conditions were used: 1) 58°C for 5 minutes, 2) 72°C for 5 minutes, 3) 98°C for 30 seconds, 4) 98°C for 10 seconds, 5) 60°C for 15 seconds, 6) Repeat steps 4-5 13 times, 7) 72°C for 2 minutes, 8) Hold at 4°C. The sequencing libraries were then purified using 0.8x HighPrep PCR Cleanup System (MagBio) beads according to the manufacturer's instructions. Sequencing was performed using single-end 100 bp reads.

value: SON (Novus Biologicals NBP1-88706)


title: HEK293T_SRRM2_RTTag_n6_(241018_NK_hs_2292)

description:
Library name: HEK293T_SRRM2_RTTag_n6
SRRM2-targeted RT&Tag performed on HEK293T cells, replicate 6

value: SRRM2 (Thermo Scientific PA5-66827)


title: K562_timecourse_untx_SLAMRTTag_IgG_n5_(230111,231128_NK_hs_1661)

description:
Library name: K562_timecourse_untx_SLAMRTTag_IgG_n5
Optimization of s4U labeling time. IgG-targeted SLAM-RT&Tag performed on untreated K562 cells, replicate 5


title: HEK293T_SON_RTTag_n5_(240518,241018_NK_hs_2156)

description:
Library name: HEK293T_SON_RTTag_n5
SON-targeted RT&Tag performed on HEK293T cells, replicate 5


title: Pre-leukemic-sorted, mouse 7

city: Munich

first: Carolin

last: Prexler

address: Kölner Platz 1, Haus 11

department: School of Medicine and Health, Department of Pediatrics

country: Germany

institute: Technical University of Munich, TUM University Hospital

description: Library name: Pre-leukemic-sorted-7

data_processing:
Pre-processing: Raw ATAC-seq data were processed using the nf-core/atacseq pipeline (v2.1.2, https://nf-co.re/atacseq/2.1.2/). Quality control was performed with FastQC to assess metrics such as per-base quality scores, sequence content, and adapter contamination. Adapter trimming was automated with Trim Galore to excise unwanted sequences. Trimmed paired-end reads were aligned to the primary reference genome using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Peak calling: Open chromatin regions were identified using MACS2, a tool that detects significantly enriched read counts indicative of accessible genomic regions. Both narrow peaks and broad peaks (using the --broad option) were called, ensuring that regulatory elements were accurately mapped. These peak regions serve as the foundation for downstream analyses, including motif discovery and the assessment of chromatin dynamics.
Differential accessibility: A consensus peak count matrix was generated with each row corresponding to a peak region and each column to a sample. Differential accessibility analysis was then performed using DESeq2, which internally normalizes for library size via the median-of-ratios method. Minimal pre-filtering (retaining only peaks with at least 10 reads) and independent filtering were applied to enhance detection power. Peaks with an adjusted p-value below 0.05 were considered significantly differential, providing insights into the chromatin accessibility changes between experimental conditions.
Differential motif activity: Differential motif activity was evaluated to uncover regulatory factors underlying changes in chromatin accessibility between conditions. Using HOMER, we performed two complementary analyses: one based on the top 1000 peaks per sample (using qValue ranking) and another focusing on differentially accessible regions from pairwise comparisons. This dual approach allowed us to both scan for known transcription factor binding sites and discover novel motifs that are significantly enriched or depleted, thereby highlighting potential drivers of the observed chromatin dynamics.
The enrichment statistics (-10 log p-value and percentage of peaks with motif) for selected top motifs were visualized with dot plots (R package ggplot2_3.3.5). To visualise signal tracks at genomic regions of interest, the aligned BAM files (mm10 genome version) were converted to Homer tag directories (makeTagDirectory -fragLength 200, Homer/4.11 and samtools/1.12). Tag directories were then used to generate genome browser visualization files with makeMultiWigHub.pl.
Assembly: GRCh38
Supplementary files format and content: Peaks (bigWig format)

source_name: bone marrow

growth_protocol: Primary murine bone marrow cells were magnetically enriched for B220 positive cells and subsequently cultured on Mitomycin-C treated ST-2 feeder cells in the presence of IL-7 (Peprotech)

extract_protocol:
200,000 cells of each cell population analyzed were sort-purified and frozen in 90 % FCS and 10 % DMSO. Cryopreserved cells were sent to Active Motif to perform ATAC-seq. The cells were thawed in a 37°C water bath, slowly diluted with RPMI media, pelleted, washed with cold PBS, and tagmented with a Tn5 enzyme. Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the ATAC-Seq Kit (Active Motif).
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and the resultant libraries were purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using Qubit (Invitrogen) and TapeStation (Agilent). Final libraries were sequenced with PE50 sequencing on the Illumina platform.

tag: individual

value: Mouse 7

value: bone marrow

value: preleukemic population (pre-BII = B220+IgM/D-CD25+c-KIT+)

tag: disease

value: B acute lymphoblastic leukemia

value: Batch 1


title: HEK293T_IgG_RTTag_n5_(240518,241018_NK_hs_2153)

description:
Library name: HEK293T_IgG_RTTag_n5
IgG-targeted RT&Tag performed on HEK293T cells, replicate 5


title: AB3M_S3

description: Library name: AB3M_S3


title: Pre-leukemic-sorted, mouse 5

description: Library name: Pre-leukemic-sorted-5

value: Mouse 5


title: HEK293T_SRRM2_RTTag_n5_(240518,241018_NK_hs_2157)

description:
Library name: HEK293T_SRRM2_RTTag_n5
SRRM2-targeted RT&Tag performed on HEK293T cells, replicate 5


title: 241-Pax5-leukemic, B-cell leukemia, in vitro culture 2

description: Library name: 241-Pax5-leuk-2

value: Cell line 2

value: leukemic population (B220+CD19-IgM/D-)


title: HEK293T_SRRM2_RTTag_n4_(240518_NK_hs_2137)

description:
Library name: HEK293T_SRRM2_RTTag_n4
SRRM2-targeted RT&Tag performed on HEK293T cells, replicate 4


title: HEK293T_SON_RTTag_n4_(240518_NK_hs_2136)

description:
Library name: HEK293T_SON_RTTag_n4
SON-targeted RT&Tag performed on HEK293T cells, replicate 4


title: P_G9.FFPE skin.non-lesional.HCO

city: Graz

first: Theresa

last: Benezeder

address: Auenbruggerplatz 8

department: Department of Dermatology and Venereology

country: Austria

institute: Medical University of Graz

data_processing:
After a demultiplexing step, the FASTQ files were used for data analysis
The single-end raw sequencing data were imported into a private Galaxy (v23.0.1) instance running on the MedBioNode cluster from the Medical University Graz. After an initial quality control step was performed with FastQC (v0.73) and MultiQC (v1.11), the reads were trimmed with the Trimmomatic program (v0.38.1, minimum length 40 bp, and removing Illumina-specific adaptor sequences).
Reads were aligned against the reference genome GRCh38.p13 by using the Ensembl gene annotation Homo_sapiens.GRCh38.108.gtf with RNA STAR (v2.7.8a) in two-pass mode with standard settings, except for --outFilterType YES, --outFilterMismatchNoverLmax 0.05, --outFilterMultimapNmax 5, --alignSJoverhangMin 8 in the second pass, and HTSeq framework (v0.9.1) was used to generate count data.
Out of the 62,703 annotated genes, a total of 12,877 genes with a median count of >10 across all samples were retained for full statistical analysis.
Additionally, 4610 low count genes with either non-zero reads in 90% samples of any group or with non-zero reads in > 10 samples of the AGEP or GPP group were retained for explorative statistical analysis.
For differential gene expression the model Pat_sex + group with multiple test adjustment by Benjamini-Hochberg (BH) was used (cut-off adjusted p‑value < 0.05), since addition of Pat_sex was found to be significant for most differentially expressed genes (DEG).
Assembly: GRCh38.p13
Supplementary files format and content: counts_all_genes_all_samples_RNASeq_Benezeder_2024_AGEPGPP.txt: tab delimited text file with decimal separator = "," includes raw counts of all annotated genes for each sample
Supplementary files format and content: vst_12T_genes_RNASeq_Benezeder_2024_AGEPGPP.txt: tab delimited text file with decimal separator = "," includes DESeq2 normalized and vst transformed values of valid samples for 12,877 genes with median count >10
Supplementary files format and content: vst_4T_lowcount_genes_RNASeq_Benezeder_2024_AGEPGPP.txt: tab delimited text file with decimal separator = "," includes DESeq2 normalized and vst transformed values of valid samples for 4610 genes either non-zero reads in 90% samples of any group or with non-zero reads in > 10 samples of the AGEP or GPP group

source_name: skin

extract_protocol:
RNA was extracted from FFPE blocks using a Qiagen miRNeasy FFPE Kit with 15 min Proteinase K digestion (Qiagen, Hilden, Germany) as per the manufacturer's instructions
Library preparation was done using a QuantSeq 3'mRNA-Seq FWD Library Preparation Kit (Lexogen, Vienna, Austria) as per the manufacturer's instructions.

value: skin

tag: disease state

value: HCO

tag: tissue state

value: non-lesional

tag: disease state_full_name

value: healthy skin


title: HEK293T_IgG_RTTag_n4_(240518_NK_hs_2133)

description:
Library name: HEK293T_IgG_RTTag_n4
IgG-targeted RT&Tag performed on HEK293T cells, replicate 4

value: IgG (Abcam ab172730)


title: HEK293T_IgG_RTTag_n6_(241018_NK_hs_2288)

description:
Library name: HEK293T_IgG_RTTag_n6
IgG-targeted RT&Tag performed on HEK293T cells, replicate 6


title: P_G10.FFPE skin.non-lesional.HCO


title: 241-Pax5-leukemic, B-cell leukemia, in vitro culture 1

description: Library name: 241-Pax5-leuk-1

value: Cell line 1


title: P_G8.FFPE skin.non-lesional.HCO


title: AB1M_S1

description: Library name: AB1M_S1

value: larynx

value: M

value: antibiotics


title: TLR4ko CLP_3

city: Pittsburgh

first: Jie

last: Fan

address: 200 Lothrop Street

department: Department of Surgery

institute: University of Pittsburgh School of Medicine

description:
Library name: TLR4ko CLP_3
10x Genomics

data_processing:
We utilized Cell Ranger software (version 5.0.0) from 10x Genomics to demarcate cell barcodes and assign sequence reads to the corresponding genomic and transcriptomic profiles.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

extract_protocol:
Twenty-four hours post-surgery, all mice were euthanized and lung tissues were swiftly excised. Under sterile conditions, tissues were washed twice with ice-cold PBS supplemented with 0.04% BSA. Using sterile surgical scissors, the clean tissues were carefully minced into approximately 0.5 mm3 fragments and then placed in freshly prepared digestion solution. The digestion was conducted at 37°C for 30 minutes, with intermittent stirring every 10 minutes. The resulting cell suspension was filtered twice through a BD 70 μm cell strainer, followed by centrifugation at 4°C at 400 g for 5 minutes. The pellet was resuspended in an appropriate volume of medium, mixed with an equal volume of red blood cell lysis buffer, and incubated at 4°C for 5 minutes. Afterward, the sample was centrifuged at 400 g for 5 minutes, and the supernatant was discarded. The pellet was washed once with medium and centrifuged again at 400 g for 5 minutes. After discarding the supernatant, the sample was resuspended in 100 μl of medium. The freshly prepared single-cell suspension was adjusted to a concentration of 30,000 cells per sample.
Library construction followed the manufacturer's instructions for the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Catalog No. 000388).

value: lung


title: Pre-BII-WT, mouse 1

description: Library name: Pre-BII-WT-1

value: Mouse 1

value: bone marrow

value: WT

value: Healthy

value: Pilot experiment


title: D_B3_V1.FFPE skin.non-lesional.HCO


title: D_B4_V1.FFPE skin.non-lesional.HCO


title: P_G5.FFPE skin.non-lesional.HCO


title: D_B2_V1.FFPE skin.non-lesional.HCO


title: D_B1_V1.FFPE skin.non-lesional.HCO


title: TLR4ko CLP_2

description:
Library name: TLR4ko CLP_2
10x Genomics


title: P_E12.FFPE skin.lesional.ADR

value: ADR

value: lesional

value: adverse drug reaction


title: P_E11.FFPE skin.lesional.ADR

value: skin


title: Pre-BII-WT, mouse 2

description: Library name: Pre-BII-WT-2

value: Mouse 2

value: Batch 1


title: TLR4ko CLP_1

description:
Library name: TLR4ko CLP_1
10x Genomics


title: P_E9.FFPE skin.lesional.ADR


title: P_G6.FFPE skin.non-lesional.HCO

value: HCO

value: non-lesional

value: healthy skin


title: P_E5.FFPE skin.lesional.ADR


title: P_E8.FFPE skin.lesional.ADR


title: TLR4ko Sham_3

description:
Library name: TLR4ko Sham_3
10x Genomics

value: Sham


title: P_E6.FFPE skin.lesional.ADR


title: P_E7.FFPE skin.lesional.ADR


title: P_E4.FFPE skin.lesional.ADR


title: TLR4ko Sham_1

description:
Library name: TLR4ko Sham_1
10x Genomics


title: Liver, bulk RNA-seq, high-fat diet, HSC Plvap knockout, rep E

city: Odense M

first: Daniel

last: Hansen

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned using STAR v.2.7.8a to the mouse genome GRCm39 v.101
FeatureCounts (v.2.0) was employed for exon read counting
Quality of raw sequencing was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Assembly: GRCm39 v.101
Supplementary files format and content: Bulk RNA-seq data comparing 6 weeks western diet or high-fat diet fed Plvap knockout mice to littermate controls inclosed as txt.file

source_name: Liver

extract_protocol:
RNA was isolated using the Monarch® Total RNA Miniprep Kit (NEB #T2010S, New England BioLabs). Purified RNA was quantified using Qubit 3.0 Fluorometer and RNA quality was assessed using Fragment Analyzer 5200
NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, San Diego, CA)

treatment_protocol: Mice were given western diet with fructose in their drinking water or high-fat diet with normal drinking water for six weeks before fasted 12 hours over-night.

value: Liver

tag: line/strain

value: C57BL/6JBomTac, Male, Plvap Knockout

tag: fasting before_sac.

value: 12 hours o.n. before sac

value: Male

tag: tissue preservation

value: Snap frozen

value: High-Fat Diet


title: P_E1.FFPE skin.lesional.ADR


title: P_D7.FFPE skin.lesional.PSO

value: PSO

value: Psoriasis


title: P_D5.FFPE skin.lesional.PSO

value: lesional


title: P_D6.FFPE skin.lesional.PSO


title: P_E10.FFPE skin.lesional.ADR

value: ADR

value: adverse drug reaction


title: Liver, bulk RNA-seq, high-fat diet, HSC Plvap knockout, rep C


title: P_D2.FFPE skin.lesional.PSO

value: skin


title: P_D8.FFPE skin.lesional.PSO


title: P_D1.FFPE skin.lesional.PSO


title: P_E2.FFPE skin.lesional.ADR


title: P_D9.FFPE skin.lesional.PSO


title: Liver, bulk RNA-seq, high-fat diet, HSC Plvap knockout, rep B


title: TLR4ko Sham_4

description:
Library name: TLR4ko Sham_4
10x Genomics

value: lung


title: P_C14.FFPE skin.lesional.PPP

value: PPP

value: Palmoplantar Pustulosis


title: TLR4ko Sham_2

description:
Library name: TLR4ko Sham_2
10x Genomics


title: P_D4.FFPE skin.lesional.PSO


title: P_C10.FFPE skin.lesional.PPP


title: Liver, bulk RNA-seq, high-fat diet, littermate control, rep E

value: C57BL/6JBomTac, Male, Plvap Control


title: Liver, bulk RNA-seq, high-fat diet, HSC Plvap knockout, rep A


title: Liver, bulk RNA-seq, high-fat diet, littermate control, rep D


title: Liver, bulk RNA-seq, high-fat diet, HSC Plvap knockout, rep D


title: P_E3.FFPE skin.lesional.ADR


title: P_C8.FFPE skin.lesional.PPP


title: PBMCs, TCR, 4wk post-CAR T, P3

description:
Library name: Sample 12
10x Genomics

value: PBMC

value: CAR T

value: 4wk post-CAR T


title: P_C7.FFPE skin.lesional.PPP


title: P_D3.FFPE skin.lesional.PSO


title: Liver, bulk RNA-seq, high-fat diet, littermate control, rep C

value: Liver

value: 12 hours o.n. before sac


title: P_C5.FFPE skin.lesional.PPP


title: P_B54_V1.FFPE skin.lesional.GPP

value: GPP

value: Generalized Pustular Psoriasis


title: P_C4.FFPE skin.lesional.PPP


title: Liver, bulk RNA-seq, high-fat diet, littermate control, rep B

value: Male

value: Snap frozen

value: High-Fat Diet


title: Liver, bulk RNA-seq, high-fat diet, littermate control, rep A


title: P_C2.FFPE skin.lesional.PPP

value: lesional


title: P_B52_V1.FFPE skin.lesional.GPP


title: P_C9.FFPE skin.lesional.PPP


title: Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep D

value: C57BL/6JBomTac, Male, Plvap Knockout

value: Western Diet


title: Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep C


title: P_B51_V1.FFPE skin.lesional.GPP

value: skin


title: P_B50_V1.FFPE skin.lesional.GPP


title: Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep B


title: P_B47_V1.FFPE skin.lesional.GPP


title: P_B48_V1.FFPE skin.lesional.GPP


title: P_B46_V1.FFPE skin.lesional.GPP


title: P_C6.FFPE skin.lesional.PPP

value: PPP


title: Liver, bulk RNA-seq, western diet, HSC Plvap knockout, rep A


title: P_B45_V1.FFPE skin.lesional.GPP


title: P_B43_V1.FFPE skin.lesional.GPP


title: P_B44_V1.FFPE skin.lesional.GPP


title: Liver, bulk RNA-seq, western diet, littermate control, rep E


title: Liver, bulk RNA-seq, western diet, littermate control, rep D


title: Liver, bulk RNA-seq, western diet, littermate control, rep C


title: P_B40_V1.FFPE skin.lesional.GPP


title: P_B53_V1.FFPE skin.lesional.GPP


title: P_B42_V1.FFPE skin.lesional.GPP


title: P_B38_V1.FFPE skin.lesional.GPP


title: Liver, bulk RNA-seq, western diet, littermate control, rep A


title: FNA4

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

description: 10X genomics

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1) - note that any cell that contained TB genes was preserved (passed QC automatically); however, the human cell samples were of poor quality for the samples listed here - the data for the better quality samples are in GSE281148
Counts matrix and metadata of the final Seurat object are included.
Assembly: hg38 + HIV1 + TB
Supplementary files format and content: TBpath_counts_matrix.tar - the processed counts matrix for all the samples representing the pathology confirmed samples - so those in GSE281148 and those in this submission
Supplementary files format and content: TBpath_metadata.tar - the metadata

source_name: fine needle aspirate

extract_protocol:
The aspirate samples volumes are usually from ~0.1 to 0.2 ml and often contain substantial amounts of blood. The physician on-call obtained the samples, and washed one of the aspirates directly into a 6 ml heparinized blood draw tube containing 5 ml of ice cold complete RPMI cell culture medium. Cells were pelleted by centrifugation (5,000 rpm for 5 min.).  The supernatant was removed into bleach, and the pellet was re-suspended in 1 X RBC NH4Cl lysis buffer on ice and occasionally mixed gently for 3 min. Following centrifugation, the sample was resuspended in 1 ml of Accutase™ solution (Sigma-Aldrich) and incubated with occasional gentle mixing for another 2 min. on ice. Following centrifugation, the final cell pellet was gently re-suspended to a single cell suspension in 0.2 ml ice cold saline.  To this cell suspension, 1 ml of ice cold 100% methanol was added dropwise with constant mixing to fix and sterilize the sample for transport. A whole sample or aliquot of the MeOH fixed sample was centrifuged (600xg) the supernatant was discarded in medical waste, and the sample resuspended in PBS with 1% BSA, the sample was filtered through 70 and 40 micron FlowMI filters and submitted for 10X genomics sequencing.
Libraries were prepped according to the 10X Genomics scRNA-seq 3’ v3.1 Next GEM protocol, NovaSeq Reagent Kit v1.5_150x150 bp Sequencing.  All TB and HIV genes are listed with TB-'gene_name' and HIV1-'gene_name', respectively, in the counts matrix.

value: fine needle aspirate


title: Liver, bulk RNA-seq, western diet, littermate control, rep B

value: C57BL/6JBomTac, Male, Plvap Control


title: FNA20

description: 10X genomics


title: P_B37_V1.FFPE skin.lesional.GPP


title: P_B35_V1.FFPE skin.lesional.GPP


title: P_B49_V1.FFPE skin.lesional.GPP


title: P_B34_V1.FFPE skin.lesional.GPP


title: P_B33_V1.FFPE skin.lesional.GPP


title: P_B31_V1.FFPE skin.lesional.GPP


title: P_B32_V1.FFPE skin.lesional.GPP


title: P_B30_V1.FFPE skin.lesional.GPP


title: FNA20_m, replicate of FNA20

description:
20884X7
10X genomics

data_processing:
10x genomics Cell Ranger was used to process raw sequencing data, and produce counts
MEX data were further processed and merged with Seurat (4.1) - note that any cell that contained TB genes was preserved (passed QC automatically)
Counts matrix and metadata of the final Seurat object are included.
Assembly: hg38 + HIV1 + TB
Supplementary files format and content: counts_matrix.tar - the processed counts matrix
Supplementary files format and content: FNA_metadata.tar - the metadata


title: FNA21_m, replicate of FNA21

description:
20884X8
10X genomics


title: P_B39_V1.FFPE skin.lesional.GPP


title: FNA19_m, replicate of FNA19

description:
20884X6
10X genomics


title: P_B29_V1.FFPE skin.lesional.GPP


title: P_B27_V1.FFPE skin.lesional.GPP


title: P_B28_V1.FFPE skin.lesional.GPP


title: P_B41_V1.FFPE skin.lesional.GPP


title: P_B26_V1.FFPE skin.lesional.GPP


title: P_B24_V1.FFPE skin.lesional.GPP


title: P_B21_V1.FFPE skin.lesional.GPP


title: FNA15_m, replicate of FNA15

description:
20884X4
10X genomics


title: P_B20_V1.FFPE skin.lesional.GPP


title: P_B36_V1.FFPE skin.lesional.GPP


title: FNA14_m, replicate of FNA14

description:
20884X3
10X genomics


title: P_B16_V1.FFPE skin.lesional.GPP


title: FNA13_m, replicate of FNA13

description:
20884X2
10X genomics


title: FNA28

description:
20599X6
10X genomics


title: P_B25_V1.FFPE skin.lesional.GPP


title: P_B11_V1.FFPE skin.lesional.GPP


title: P_B9_V1.FFPE skin.lesional.GPP


title: P_B12_V1.FFPE skin.lesional.GPP


title: FNA27

description:
20599X5
10X genomics


title: FNA18_m, replicate of FNA 18

description:
20884X5
10X genomics


title: P_B2_V1.FFPE skin.lesional.GPP


title: P_B8_V1.FFPE skin.lesional.GPP


title: P_B4_V1.FFPE skin.lesional.GPP


title: P_B6_V1.FFPE skin.lesional.GPP


title: P_B5_V1.FFPE skin.lesional.GPP


title: FNA21

description:
20598X5
10X genomics


title: P_A54_V1.FFPE skin.lesional.AGEP

value: AGEP

value: Acute Generalized Exanthemtous Pustulosis


title: P_A52_V1.FFPE skin.lesional.AGEP


title: P_B3_V1.FFPE skin.lesional.GPP


title: FNA24

description:
20599X2
10X genomics


title: FNA25

description:
20599X3
10X genomics


title: P_B1_V1.FFPE skin.lesional.GPP


title: P_A55_V1.FFPE skin.lesional.AGEP


title: P_A51_V1.FFPE skin.lesional.AGEP


title: FNA22

description:
20598X6
10X genomics


title: P_A53_V1.FFPE skin.lesional.AGEP


title: P_A50_V1.FFPE skin.lesional.AGEP


title: FNA19

description:
20598X3
10X genomics


title: P_A49_V1.FFPE skin.lesional.AGEP


title: FNA18

description:
20598X2
10X genomics


title: P_A47_V1.FFPE skin.lesional.AGEP


title: P_A48_V1.FFPE skin.lesional.AGEP


title: P_A46_V1.FFPE skin.lesional.AGEP


title: FNA16

description:
20597X7
10X genomics


title: P_A45_V1.FFPE skin.lesional.AGEP


title: P_A41_V1.FFPE skin.lesional.AGEP


title: P_A44_V1.FFPE skin.lesional.AGEP


title: P_A42_V1.FFPE skin.lesional.AGEP


title: FNA15

description:
20597X6
10X genomics


title: P_A40_V1.FFPE skin.lesional.AGEP


title: FNA14

description:
20597X5
10X genomics


title: FNA13

description:
20597X4
10X genomics


title: P_A39_V1.FFPE skin.lesional.AGEP


title: FNA12

description:
20597X3
10X genomics


title: FNA11

description:
20597X2
10X genomics


title: P_A33_V1.FFPE skin.lesional.AGEP


title: P_A35_V1.FFPE skin.lesional.AGEP


title: P_A37_V1.FFPE skin.lesional.AGEP


title: P_A36_V1.FFPE skin.lesional.AGEP


title: P_A31_V1.FFPE skin.lesional.AGEP


title: P_A30_V1.FFPE skin.lesional.AGEP


title: P_A32_V1.FFPE skin.lesional.AGEP


title: P_A43_V1.FFPE skin.lesional.AGEP


title: FNA6

description:
19662X6
10X genomics


title: FNA10

description:
20597X1
10X genomics


title: P_A38_V1.FFPE skin.lesional.AGEP


title: FNA17

description:
20598X1
10X genomics


title: FNA0

description:
17557X2
10X genomics


title: P_A29_V1.FFPE skin.lesional.AGEP


title: P_A28_V1.FFPE skin.lesional.AGEP


title: P_A27_V1.FFPE skin.lesional.AGEP


title: UROtsa, ARID1A gRNA3 31

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

data_processing:
Paired-end reads were trimmed with Trimmomatic (v0.38) to remove adapter sequences and low-quality bases. Reads were cropped to a maximum length of 90bp to remove any remaining adapter sequence. Dovetailed alignment to the human reference genome (hg38) was done using Bowtie2 (v2.4.1), allowing a maximum insert size of 2000.
Duplicated and mitochondrial reads were discarded. The 5’ ends of the reads were shifted with deepTools alignmentSieve (v3.4.3), to match the center of the Tn5 binding site. Libraries were down-sampled to an equivalent size with Picard DownsampleSam (v2.10.6). Peak regions were then called for each sample using MACS2 (2.1.2) with parameters --nomodel --shift -100 --extsize 200. Peaks within ENCODE blacklisted regions were excluded.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: raw read count per peak in tab delimited file

source_name: UROtsa

growth_protocol: RPMI 1640 + 10% FCS + 1% Penicillin-Streptomycin-Glutamin. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
As in Corces et al (2017), Nature Methods. No DNAse treatment was performed.
As in Corces et al (2017), Nature Methods. PE, 2x100bp, 50M reads/sample

treatment_protocol: CRISPR/Cas9-mediated ARID1A knockout (KO) in 5 clones. NTC gRNA treatment in 5 control clones.

tag: cell line

value: UROtsa

value: ARID1A KO


title: P_A25_V1.FFPE skin.lesional.AGEP


title: P_A26_V1.FFPE skin.lesional.AGEP


title: P_A23_V1.FFPE skin.lesional.AGEP


title: P_A22_V1.FFPE skin.lesional.AGEP


title: Glycinergic neurons_m16

city: Shanghai

first: Lulu

last: Xu

address: No.500 Zhennan Raod

country: China

institute: TongJi university

description: Library name: M16

data_processing:
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, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. 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.
HTSeq v0.9.1 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: danio_rerio_Ensembl_97
Supplementary files format and content: FPKM values for each samples.

organism: Danio rerio

source_name: Glycinergic neurons

extract_protocol:
RNA was harvested using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc.)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell type

value: Glycinergic neurons

value: Tg (gly2:GFP)


title: UROtsa, ARID1A gRNA2 14


title: Glycinergic neurons_m11

description: Library name: M11


title: UROtsa, NTC10

value: WT


title: P_A18_V1.FFPE skin.lesional.AGEP

tag: tissue


title: Glycinergic neurons_m17

description: Library name: M17


title: Glycinergic neurons_m9

description: Library name: M9


title: P_A11_V1.FFPE skin.lesional.AGEP


title: P_A20_V1.FFPE skin.lesional.AGEP


title: UROtsa, ARID1A gRNA3 29


title: UROtsa, ARID1A gRNA3 13


title: UROtsa, NTC8


title: P_A17_V1.FFPE skin.lesional.AGEP


title: P_A10_V1.FFPE skin.lesional.AGEP


title: UROtsa, ARID1A gRNA3 5


title: UROtsa, NTC6


title: UROtsa, NTC4


title: Glycinergic neurons_m5

description: Library name: M5


title: P_A9_V1.FFPE skin.lesional.AGEP


title: P_A19_V1.FFPE skin.lesional.AGEP


title: P_A24_V1.FFPE skin.lesional.AGEP


title: UROtsa, NTC1


title: P_A34_V1.FFPE skin.lesional.AGEP


title: P_A8_V1.FFPE skin.lesional.AGEP


title: UROtsa,ARID1A gRNA3 31

data_processing:
Paired-end reads were trimmed with Trimmomatic (v0.38) to remove adapter content and bad quality bases. Reads were aligned to the human reference genome (hg38) and reads-per-gene were quantified using STAR (v2.5.2b).
Assembly: hg38
Supplementary files format and content: raw read count per gene in tab delimited file

growth_protocol: UROtsa & T24: RPMI 1640 + 10% FCS + 1% Penicillin-Streptomycin-Glutamin. For JMSU-1: as T24 + 3 µg/ml blasticidine. For HBLAK: CnT Prime. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
NucleoSpin Mini kit
Poly A Transcriptome (TruSeq), PE, 2x100bp, 60M reads, Spike-Ins (ERCC) for UROtsa

treatment_protocol: UROtsa & T24: CRISPR/Cas9-mediated ARID1A KO, HBLAK: siRNA-mediated ARID1A KD, JMSU-1: re-expression of ARID1A


title: Glycinergic neurons_m1

description: Library name: M1


title: P_A3_V1.FFPE skin.lesional.AGEP


title: UROtsa,ARID1A gRNA3 29


title: UROtsa,ARID1A gRNA3 5


title: P_A5_V1.FFPE skin.lesional.AGEP


title: Liver, HFD, Total Knock out, rep2

city: New Orleans

first: Chiung-Kuei

last: Huang

state: Louisiana

address: 1430 Tulane Ave

department: Department of Pathology and Laboratory Medicine

institute: Tulane University School of Medicine

description: Library name: HFD-TKO-2

data_processing:
Quality control (QC) assessment of sequence reads was performed using FastQC1 (v. 0.11.5) and reads were trimmed using Trimmomatic (v. 0.36)
Illumina adapters were removed using Trimmomatic ILLUMINACLIP parameters to allow for 2 mismatches, a 30 palindome clip threshold, and a simple clip threshold of 5, and a minimum adapter length of 6, and to keep both reads after trimming adapters ("ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:5:6:true”)
Additional quality trimming of reads was performed using Trimmomatic SLIDINGWINDOW to scan the reads in a 10-base wide sliding window and cutting when the average per-base quality dropped below 25 ("SLIDINGWINDOW:10:25 MINLEN:50").
Trimmonatic MINLEN was used to specify that reads should be at least 50 bases long (“MINLEN:50”)
Reads were also screened for evidence of human or bacterial contamination using FastQScreen3 (v. 0.11.3)
Assembly: Reads were aligned to mouse reference genome Ensembl GRCm38 release 89 using GMAP/GSNAP
Supplementary files format and content: Counts were generated using FeatureCounts (v. 1.5.3), such that at least 80% of bases in a read must overlap for read assignment, allowing for fractional counting of multi-mapped reads with each read to be assigned to more than one feature, and reversely strand-specific mapping of paired-end reads (featureCounts -p fracOverlap 0.8 -M -O --fraction -s 2)

source_name: Tet-1 whol body knockout fed with High fat diet for 16 weeks

extract_protocol:
RNA was extracted using QIAGEN RNeasy Mini Kit (50) kit following manufacturer's instructions
Samples were quantified on a NanoDrop ND-1000 instrument. Agarose electrophoresis was used to check the integrality of total RNA samples. 1~2μg total RNA of each sample was taken for RNA-seq library preparation. Briefly, mRNA was isolated from total RNA with NEBNext® Poly(A) mRNA Magnetic Isolation Module. Alternatively, rRNA is removed from the total RNA with a RiboZero Magnetic Gold Kit; The enriched mRNA or rRNA depleted RNA was used for RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The library preparation procedure included: 1.1 Fragmentation of the RNA molecules; 1.2 Reverse transcription to synthesis first strand cDNA; 1.3 Second strand cDNA synthesis incorporating dUTP; 1.4 End-repair and A-tailing of the double stranded cDNA; 1.5 Illumina compatible adapter ligation; 1.6 PCR amplification and purification for the final RNA-seq library. The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400~600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.

treatment_protocol: male WT and TET-1 whole body knockout were fed with high fat diet for 16 week

value: Hepatic Tissue

value: male

tag: strain

tag: treatment

value: HFD

tag: time

value: 16 weeks


title: Glycinergic neurons_m2

description: Library name: M2

tag: genotype


title: Liver, HFD, Wild type, rep3

description: Library name: HFD-WT-3

source_name: WT fed with High fat diet for 16 weeks


title: Liver, HFD, Total Knock out, rep1

description: Library name: HFD-TKO-1


title: UROtsa,NTC8


title: P_A1_V1.FFPE skin.lesional.AGEP

value: lesional


title: UROtsa,ARID1A gRNA3 13


title: Liver, HFD, Total Knock out, rep3

description: Library name: HFD-TKO-3


title: UROtsa,NTC6


title: K16CreER;RosatdTomato k16+ Vehicle

city: Beijing

first: Zhen

last: Qin

address: 22 Zhongguancun South Avenue

institute: Peking University

description: K16CreER;RosatdTomato k16+.txt

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.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: GRCh38,GRCm38
Supplementary files format and content: xlsx and txt files including FPKM values for each RNA-seq sample.

source_name: K16CreER;RosatdTomato k16+ Vehicle

extract_protocol:
extracting RNA after  isolated by flow cytometry
Total RNA was extracted using Trizol
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: K16+ tumor cells

value: Vehicle


title: WAP+ cell 3

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
WAP+ cell 3
Y6

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: whey acidic protein (WAP)+ cells

growth_protocol: The MMTV-Wnt-1 transgenic mouse model expresses the Wnt-1 transgene in the mammary epithelium under the control of the MMTV LTR, and develops widespread hyperplastic/dysplastic lesions in mammary glands starting by 4-6 weeks of age.  Precancerous lesions in this model contain multiple cell lineages including cells expressing genes encoding different keratins such as Krt5, 14, 8, and 6, as well as cells producing the whey acidic milk protein (WAP), which has been often associated with differentiated mammary epithelial cells.

extract_protocol:
Hundreds of cells for each sample were isolated by FACS using TVA antibody. Cell lysis, Reverse transcription and cDNA amplification was performed according to the manufacturer’s instructions of SMART-Seq v4 Ultra Low Input RNA Kit (Clontech). Amplified cDNA was purified using Agencourt AMPure XP Kit (Beckman Coulter).
The full-length cDNA output was processed with the Nextera Library Preparation Kit (Illumina) to prepare cDNA libraries for RNA-Seq experiments. All cDNA libraries were sequenced on a HiSeq 2500 (Illumina) platform. 100 bp paired end short reads were generated for subsequent Bioinformatics analysis.

value: MMTV-Wnt-1 transgenic mice

tag: background strain

value: mixture of FVB, SJL, and C57BL/6

value: mammary precancerous lesion

value: whey acidic protein (WAP)+ cells


title: Liver, HFD, Wild type, rep2

description: Library name: HFD-WT-2

tag: Sex


title: UROtsa,NTC10


title: Liver, HFD, Total Knock out, rep4

description: Library name: HFD-TKO-4


title: WAP+ cell 2

description:
WAP+ cell 2
Y5


title: UROtsa,NTC4


title: PDX #3 epcam+aldh- PTC209

description: PDX#3 epcam+aldh-.xls

source_name: PDX #3 epcam+aldh- PTC209

value: Epcam+ ALDH- tumor cells


title: Liver, HFD, Wild type, rep1

description: Library name: HFD-WT-1


title: P_A2_V1.FFPE skin.lesional.AGEP

value: skin

value: AGEP

value: Acute Generalized Exanthemtous Pustulosis


title: Glycinergic neurons_m6

description: Library name: M6

value: Glycinergic neurons

value: Tg (gly2:GFP)


title: PDX #3 epcam+aldh- Vehicle

description: PDX#3 epcam+aldh-.xls

source_name: PDX #3 epcam+aldh- Vehicle


title: Krt6a+ cell 3

description:
Krt6a+ cell 3
Y3

source_name: keratin 6a+ precancerous stem cells

value: keratin 6a+ precancerous stem cells


title: HBLAK,siARID1A7

source_name: HBLAK

value: HBLAK

value: siRNA ARID1A


title: HN6 ALDH PTC209

description: HN6 ALDH+.xlsx

source_name: HN6 ALDH PTC209

extract_protocol:
extracting RNA after  isolated by flow cytometry based on ALDEFLUOR analysis
Total RNA was extracted using Trizol
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

value: HN6 ALDH+ CSCs


title: HBLAK,siARID1A6


title: HN6 ALDH dmso

description: HN6 ALDH+.xlsx

source_name: HN6 ALDH dmso

value: DMSO


title: WAP+ cell 1

description:
WAP+ cell 1
Y4


title: HBLAK,siARID1A4


title: H3A110Ccup1F8*_SCEG3

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description:
Sample25_ACcup1-EG-3_S7
H3A110Ccup1F8*_SCEG3

data_processing:
FASTQ read 1 of the paired-end reads used for downstream analyses
Genomic alignment of FASTQ using HISAT2. Strand-specific alignment.
Assignment to open reading frames and counting using featureCounts. Strand-specific assignment.
Differential expression analysis performed with DESeq2
Assembly: sacCer3
Supplementary files format and content: csv

organism: Saccharomyces cerevisiae

source_name: whole yeast cells

growth_protocol: Cells were grown to 2-3 doublings before collection

extract_protocol:
RNA was extracted from whole yeast cells using hot acid phenol, followed by a further phenol-cholorform extraction and ethanol precipitation.
Prior to preparing RNA-seq libraries for Illumina NovaSeq sequencing, contaminating DNA was digested using Turbo DNase (Thermo Fisher). RNA quality was assessed by Agilent 2200 Tapestation. Stranded mRNA (Poly-A) libraries were constructed with automated NGS library construction and sequenced by UCLA Technology Center for Genomics & Bioinformatics

value: whole yeast cells

value: SCEG (oxidative medium)


title: H3A110Ccup1F8*_SCEG4

description:
Sample26_ACcup1-EG-4_S8
H3A110Ccup1F8*_SCEG4


title: UROtsa,ARID1A gRNA2 14

value: UROtsa

value: ARID1A KO


title: Krt6a+ cell 2

description:
Krt6a+ cell 2
Y2

value: MMTV-Wnt-1 transgenic mice

value: mixture of FVB, SJL, and C57BL/6

value: mammary precancerous lesion


title: H3A110Ccup1F8*_SCEG2

description:
Sample24_ACcup1-EG-2_S6
H3A110Ccup1F8*_SCEG2


title: H3A110Ccup1F8*_SCEG1

description:
Sample23_ACcup1-EG-1_S5
H3A110Ccup1F8*_SCEG1


title: K16CreER;RosatdTomato k16+ PTC209

description: K16CreER;RosatdTomato k16+.txt

source_name: K16CreER;RosatdTomato k16+ PTC209

value: K16+ tumor cells


title: Hepatocellularcarcinoma Rep3

city: Suwon-si

first: chanmo

last: yang

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu, Song Jae-gwan 207-5

department: Department of Pathology

country: South Korea

institute: Ajou University School of Medicine

description: Library name: H35

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Liver tumor tissue

growth_protocol: Primary liver tumor and normal tissues (cHCC-CCC, HCC, CCC) were collected from patients, fixed in formalin, embedded in paraffin (FFPE), and stored until processing.

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#015) standard protocols.

treatment_protocol: FFPE tumor samples were deparaffinized with xylene, rehydrated in ethanol, digested with Proteinase K, and processed for RNA extraction.

value: Liver tumor tissue

value: Patient-Derived Tumor Cells

value: Hepatocellularcarcinoma

value: WT


title: Cholangiocarcinoma Rep3

description: Library name: C3

value: Cholangiocarcinoma


title: Hepatocellularcarcinoma Rep2

description: Library name: H21


title: HBLAK,siNeg2

value: HBLAK


title: HBLAK,WT


title: Cholangiocarcinoma Rep2

description: Library name: C2


title: T24,ARID1A gRNA2 7


title: Cholangiocarcinoma Rep1

description: Library name: C1


title: UROtsa,NTC1


title: T24,ARID1A gRNA2 6


title: cup1F8*_SCEG3

description:
Sample21_cup1-EG-3_S3
cup1F8*_SCEG3


title: cup1F8*_SCEG4

description:
Sample22_cup1-EG-4_S4
cup1F8*_SCEG4


title: cHCC-CCC Notch Non-responsive Rep3

description: Library name: G3_5

value: Combined hepatocellular carcinoma and cholangiocarcinoma


title: HBLAK,siNeg3


title: Hepatocellularcarcinoma Rep1

description: Library name: H17


title: T24,ARID1A gRNA1 3


title: cHCC-CCC Notch Non-responsive Rep2

description: Library name: G3_2


title: cup1F8*_SCEG1

description:
Sample19_cup1-EG-1_S1
cup1F8*_SCEG1


title: T24,NTC5


title: cHCC-CCC Notch Non-responsive Rep1

description: Library name: G3_1


title: H3A110Cgsh1Δ_SCEG3

description:
Sample18_ACgsh1-EG-3_S19
H3A110Cgsh1Δ_SCEG3


title: T24,NTC4


title: T24,NTC2


title: H3A110Cgsh1Δ_SCEG2

description:
Sample17_ACgsh1-EG-2_S7
H3A110Cgsh1Δ_SCEG2


title: JMSU-1,ARID1A-reexpression18

value: ARID1A re-expression


title: cHCC-CCC Notch Responsive Rep3

description: Library name: G2_5


title: JMSU-1,ARID1A-reexpression17


title: H3A110Cgsh1Δ_SCEG1

description:
Sample16_ACgsh1-EG-1_S8
H3A110Cgsh1Δ_SCEG1


title: cHCC-CCC Notch Inactivated Rep3

description: Library name: G1_4


title: gsh1Δ_SCEG2

description:
Sample14_gsh1-EG-2_S16
gsh1Δ_SCEG2


title: cHCC-CCC Notch Responsive Rep2

description: Library name: G2_4


title: cHCC-CCC Notch Responsive Rep1

description: Library name: G2_3


title: JMSU-1,ARID1A-reexpression15


title: cHCC-CCC Notch Inactivated Rep2

description: Library name: G1_3


title: gsh1Δ_SCEG1

description:
Sample13_gsh1-EG-1_S14
gsh1Δ_SCEG1


title: E0771 Foxm1 knockout, sgRNA #3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files generated by cellranger.
Supplementary files format and content: tar.gz archive includes the tab-separated values files and matrix files generated by cellranger, in a folder format.

source_name: Mouse Mammary Carcinoma

growth_protocol: 250,000 E0771 control and Foxm1 knockout cells were injected into the mammary fat pad of 6-7 week old female C57BL6/J mice. Tumor growth was monitored and harvested at the end of the study.

extract_protocol:
E0771 Control, Foxm1 KO sg1, and Foxm1 KO sg3 tumors were harvested and digested with RPMI media containing 2% FBS, 1mg/ml Collagenase IV(Worthington, Cat #LS004188), and 20μg/ml DNAse I(Sigma, Cat #4536282001) at 37 degrees for 1 hr with shaking. Following tissue dissection, single cells were filtered using 40μm filter to remove residual clumps. 10 million cells were taken and dead cells were removed using the dead cell removal kit (Miltenyi Biotec; #130-090-101). Cells were then counted and loaded onto the 10X Chromium controller, targeting 10,000 cells for capture per well. Single-cell RNA sequencing  libraries were generated using the Chromium Single Cell 3’ Library & Gel Bead Kit V3.1 kit and 716 Chromium Single Cell 3’ Chips according to the manufacturer’s instructions (10X Genomics, 717 Pleasanton, CA).
10X Genomics Chromium X

value: Mouse Mammary Carcinoma

value: Foxm1 knockout sg3


title: cup1F8*_SCEG2

description:
Sample20_cup1-EG-2_S2
cup1F8*_SCEG2

value: whole yeast cells

value: SCEG (oxidative medium)


title: E0771 Foxm1 knockout, sgRNA #1

description: 10X Genomics

value: Foxm1 knockout sg1


title: cHCC-CCC Notch Inactivated Rep1

description: Library name: G1_2


title: H3A110C_SCEG3

description:
Sample12_AC-EG-3_S12
H3A110C_SCEG3


title: E0771 Control

description: 10X Genomics

value: Control


title: Normal liver tissue (Control) Rep3

description: Library name: N3_2

source_name: Normal liver tissue

value: Normal liver tissue

value: Patient-Derived Liver Cells

value: Normal hepatocyte


title: gsh1Δ_SCEG3

description:
Sample15_gsh1-EG-3_S20
gsh1Δ_SCEG3


title: JMSU-1,emptyvector1


title: JMSU-1,emptyvector4


title: JMSU-1,emptyvector2


title: H3A110C_SCEG2

description:
Sample11_AC-EG-2_S18
H3A110C_SCEG2


title: Liver, nuclei, snRNA-seq, chow diet, Plvap knockout, #C079

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
To perform the abovementioned steps the features mkfastq and count were run.
The raw count matrix is provided as an mtx.gz file along with gene and barcode names as tsv.gz files
Assembly: mm10

source_name: Liver , Plvaptm1.1Salm-Tg(Lrat-cre)1Rshw (B6.126(Cg))

extract_protocol:
Chromium Next GEM Single Cell 3´ GEM, Library and Gel Bead kit v.3.1 (10x Genomics)
Chromium Next GEM Single Cell 3´ GEM, Library and Gel Bead kit v.3.1 (10x Genomics)
single-nucleus RNA-seq

treatment_protocol: 18 weeks old male mice given chow diet. Mice were fasted 12 hours o.n. before sac.

value: Liver

value: Plvap knockout

value: 12 hours o.n. before sac

value: Male

value: Chow Diet