title: IFN14_24months_cd34pos_GoT-ChA

description:
Library name: IFN14_24months_cd34pos_GoT-ChA
GoT-ChA

data_processing:
10x data was processed using Cell Ranger 1 and v6.1.2 using default parameters. RNA reads were aligned to the human referece genome. Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x RNA-seq dataATAC-seq 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-CALR genes and those matching no gene below a supporting read threshold.
CUT&RUN data were down-sampled to have same number of reads across all conditions within the sample replicate to account for difference in sequencing depth. Among the down-sampled reads, low-quality reads were filtered out using Trimmomatic, resulting reads were aligned with hg38 genome with Bowtie2, and PCR duplicates were removed with SAMtools with a previously described workflow. Aligned reads were then used for peak calling with MACS3 with a q-value threshold of 0.01 and reads from IgG antibody as the control. SPI1 over-enrichment in the called peaks was confirmed with Simple Enrichment Analysis (SEA, v5.5.5). Overlapping peaks between replicates of the same condition were kept for further processing. The peaks were processed with multiBamSummary function from deepTools to obtain counts matrix per sample for downstream analysis.
Genotyping data processing was performed according to the previously published instructions and available Gotcha R package. Briefly, initial FASTQ files were filtered based on base quality scores, and the Fastqsplit function was used to split FASTQ files for subsequent parallel computing. Mutations were determined via the BatchMutationCalling function, which identifies reads that are correctly primed, calculates the counts of reads per cell for each specified genotype (i.e., WT, JAK2-V617F).
Assembly: GRCh38
Supplementary files format and content: Processed 10X data is matrix table of gene/peak counts per cell for each sample
Supplementary files format and content: Output matrices processed from genotyping data have two columns: barcodes (BC) and Genotype

extract_protocol:
GoT-IM Extraction Protocol: Cryopreserved bone marrow mononuclear cells approved by the Institutional Review Board of Weill Cornell Medicine were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, Miltenyi Biotec) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. To eliminate experimental batch effects, cells were labelled simultaneously with hashing antibodies with time-point-identifying barcodes using Hashtag Antibodies 1, 2 or 3 (TotalSeq-A, clone LNH-94, Biolegend) for GoT-IM. To link cell identities to expression of cell surface proteins, cells were also incubated with CITE-seq antibodies according to manufacturer protocol (TotalSeq-A, Biolegend). Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Genotyping of Transcriptomes (GoT) was performed by adapting the 10x Genomics platform. FACS-sorted CD34+ cells for each time-point from the same individual were pooled, targeting a total of 10,000-15,000 cells.  GoT-ATAC Extraction Protocol: Cryopreserved bone marrow mononuclear cells were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, MACS) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Nuclei were isolated from DAPI-, CD34+ cells according to 10x Genomics Demonstrated Low Cell Input Nuclei Isolation protocol. Lysis buffer was prepared following manufacturer’s recommendations and then split into aliquots for each serial sample. Either TotalSeq-A Anti-Nuclei Pore Complex Proteins Hashtag 9 or 10 Antibody (1uL at 1:5 dilution; BioLegend) was added to each aliquot of lysis buffer. Low-input nuclei isolation was otherwise performed following manufacturer’s recommendations. Subsequently, nuclei from each time-point were counted and pooled together at approximately equal proportions. For IFN03, additional nuclei from the IFNa-treated sample were available to be run on a separate lane.  RFX3-OE Extraction Protocol: Cells from frozen umbilical cord blood mononuclear cells were thawed rapidly at 37°C, red blood cell lysis was performed using ACK Lysis Buffer, then centrifuged, and cell pellet was resuspended in cold MACS buffer. Cells were centrifuged at 300g for 5min at 4°C, and resuspended in cold MACs buffer at a concentration of 1x10^7 cells/mL. CD34+ cells were then isolated with the EasySep™ Human CD34 Positive Selection Kit II (StemCell Technologies #17856) according to manufacturer’s protocol. After isolation, cells were counted and plated in 96-well round-bottom plates (Falcon) in StemSpan™ SFEM II media (StemCell Technologies) with StemSpan™ CD34+ Expansion Supplement (StemCell Technologies) and 1% Pen/Strep. After 24 hours in culture, cells were spun down and resuspended in minimal media consisting of StemSpan StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement, 1% Pen/Strep, 10μM prostaglandin E2 (StemCell Technologies #72192) and 100ng/μl poloxamer 407 (Millipore Sigma P2164030). Cells were split into 2 technical replicates each for untransduced condition, mCherry-control vector transduction, and RFX3-OE vector transduction. Lentivirus or PBS control was added at an MOI of 100, spinoculated at 300g, 32°C for 1 hour, and cells were incubated in same lentivirus-containing media for 24 hours at 37°C before resuspension in fresh media consisting of StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement and 1% Pen/Strep. After 48 hours of incubation, cells were stained with CD34-APC antibody (1:50). Cells were then FACS isolated for the CD34+ population in the untransduced condition and the CD34+ mCherry+ populations in the RFX3-OE and mCherrycontrol conditions. Three independent transduction experiments were completed with new units of umbilical cord blood cells. Untransduced, mCherry-Control, and RFX3-OE CD34+ cells were stained with Cell Hashing antibodies (HTO TotalSeq-A, BioLegend) for 30 min at 4°C. Cells were then washed with FACs Buffer three times, pooled, and counted for loading. scRNA-sequencing was then performed using the 10x 3’ v3.1 platform according to manufacturer’s protocol. HTO demultiplexing and downstream analyses such as differential gene expression and gene set enrichment were performed as in GoT-IM for CD34+ bone marrow samples. scRNA-seq experiment was completed on one replicate of three independent transduction experiments.  CUT&RUN Extraction Protocol: UT7 cell lines expressing MPL (thrombopoietin receptor) and either the mutant CALR (type 1, L367Tfs*46) or wildtype CALR transgene (93) were seeded in 10cm plates in DMEM supplemented with 10% FBS (Thomas Scientific) and 5 ng/ml GM-CSF (Miltenyi-Biotec). Cells were treated with 0.1μg/ml Recombinant Human IFN-alpha2a (RC217-14) or PBS-1X control for 24hrs. After treatment, cells were washed 1x with PBS and collected for use with the CUTANA™ CUT&RUN assay (EpiCypher) according to the manufacturer’s protocol. 0.5μg of anti-human rabbit monoclonal PU.1 antibody (ab76543) and IgG antibody (ab172730) were used in the assay.
GoT-IM Library Construction Protocol: The standard 10x Genomics Chromium 3′ (v.3.1 chemistry) was implemented according to the manufacturer’s recommendations up to the cDNA amplification step (10X Genomics, Pleasanton, CA). After cDNA amplification and SPRI cleanup, 10x scRNA-seq and ADT/HTO libraries were generated as recommended. A portion of the cDNA was used for somatic genotyping. Briefly, to capture the somatic genotypes of cells, cDNA was amplified with a locus-specific amplification (10 PCR cycles), using the generic forward SI-PCR primer and a following locus-specific reverse primer for the CALR mutations. The amplified locus-specific cDNAs are then cleaned using SPRI purification to remove unincorporated primers. Finally, the targeted amplicon libraries are generated through a PCR performed with a P5 generic forward PCR primer together with an RPI-x primer. The targeted amplicon libraries were spiked into the remainder of the gene expression and immunophenotyping libraries to be sequenced together on a NovaSeq (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 8 cycles for i7 sample index and 8 cycles for i5 sample index.  GoT-ATAC Library Construction Protocol: Single-nucleus gene expression (GEX) and chromatin accessibility libraries were constructed from the pooled nuclei according to the Chromium Next GEM Single Cell Multiome User Guide (10X Genomics). Genotyping libraries targeting the CALR mutant transcripts were constructed from the remaining amplified cDNA, similar to the original GoT method. The re-amplified sample was purified and concentrated via 0.7X SPRI cleanup, eluting it into 10uL Buffer EB. To pre-enrich the CALR mutation locus, a gene-specific PCR was performed with 3uL of cleaned re-amplified cDNA and Partial Read 1 and gene-specific primers. CALR locus-specific amplification was then performed with 3uL of cleaned gene-specific amplified cDNA and SI-PCR and loci-specific Primers. A 0.7X SPRI cleanup was performed, and cDNA was eluted into 11uL Buffer EB. Finally, to construct the targeted amplicon library, loci-amplified cDNA was mixed with P5 Generic and RPIx indexing primers and amplified. The constructed library was cleaned via 0.8X SPRI cleanup and eluted into 12uL Buffer EB. At the cDNA amplification stage of the Chromium Next GEM Single Cell Multiome protocol, supernatant from the 0.6X size selection was retained and was used to generate the hashing libraries as per HTO protocol25 with the following modification. For the hashing library construction step, the PCR reaction was prepared with 0.65uL of 10uM SI-PCR primer, 0.65uL of 10uM TruSeq DNA D7xx_s primer, 11.25uL cleaned supernatant and 12.5 uL Kapa HiFI HotStart Ready Mix (Roche, Basel, Switzerland). Hashing, gene expression, and genotyping libraries were pooled and sequenced together on a NovaSeq (Illumina).  Genotyping for JAK2-mutated samples (IFN14, IFN15): Nuclei were processed according to the 10x Genomics Chromium Next GEM Single-Cell ATAC v2 Kit guidelines, with several modifications specific to the GoT-ChA protocol. 1 µl of 22.5 µM GoT–ChA primer mix was added to the barcoding reaction mixture, containing the locus-specific primers GoT–ChA_R1N and GoT–ChA_Rev (primer sequences in Supplementary Table 32). During the post-GEM incubation clean-up, 45.5 µl of elution solution I was used to elute the SPRIselect bead reaction, and 5 µl was used for GoT-ChA library generation. GoT-ChA libraries were generated according to the published protocol.

value: Polycythemia vera


title: IFN12_cd34neg_10x

status: Public on Jul 07 2026

type: SRA

city: New York

first: Anna

middle: S.

last: Nam

state: New York

address: Weiss Research Building, Floor 11

department: Pathology and Laboratory Medicine

country: USA

institute: Weill Cornell Medicine

description: 10x genomics

library_source: other

data_processing:
10x data was processed using Cell Ranger 1 and v6.1.2 using default parameters. RNA reads were aligned to the human referece genome.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x RNA-seq dataATAC-seq 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-CALR genes and those matching no gene below a supporting read threshold.
CUT&RUN data were down-sampled to have same number of reads across all conditions within the sample replicate to account for difference in sequencing depth. Among the down-sampled reads, low-quality reads were filtered out using Trimmomatic, resulting reads were aligned with hg38 genome with Bowtie2, and PCR duplicates were removed with SAMtools with a previously described workflow. Aligned reads were then used for peak calling with MACS3 with a q-value threshold of 0.01 and reads from IgG antibody as the control. SPI1 over-enrichment in the called peaks was confirmed with Simple Enrichment Analysis (SEA, v5.5.5). Overlapping peaks between replicates of the same condition were kept for further processing. The peaks were processed with multiBamSummary function from deepTools to obtain counts matrix per sample for downstream analysis.
Differential peak enrichment analysis was run between conditions (MUT vs WT and IFN⍺-treated vs control) using DESEQ2 for distal PU.1 peaks. Differential peaks in each condition were centered around SPI1 motif and motif enrichment was performed for regions +/- 250 bp from SPI1 motif using HOMER (v.4.1.1). Differential ranking between each motif two conditions was calculated.
Assembly: GRCh38
Supplementary files format and content: Processed 10X data is matrix table of gene/peak counts per cell for each sample
Supplementary files format and content: Output matrices processed from genotyping data have two columns: barcodes (BC) and Genotype
Library strategy: GEX+ADT+HTO

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
GoT-IM Extraction Protocol: Cryopreserved bone marrow mononuclear cells approved by the Institutional Review Board of Weill Cornell Medicine were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, Miltenyi Biotec) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. To eliminate experimental batch effects, cells were labelled simultaneously with hashing antibodies with time-point-identifying barcodes using Hashtag Antibodies 1, 2 or 3 (TotalSeq-A, clone LNH-94, Biolegend) for GoT-IM. To link cell identities to expression of cell surface proteins, cells were also incubated with CITE-seq antibodies according to manufacturer protocol (TotalSeq-A, Biolegend). Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Genotyping of Transcriptomes (GoT) was performed by adapting the 10x Genomics platform. FACS-sorted CD34+ cells for each time-point from the same individual were pooled, targeting a total of 10,000-15,000 cells.
GoT-ATAC Extraction Protocol: Cryopreserved bone marrow mononuclear cells were thawed and stained using standard procedures with the surface antibody CD34-PE (clone AC136, dilution 1:50, MACS) and DAPI (Sigma-Aldrich), according to manufacturer’s protocol. Cells were subsequently sorted for DAPI−, CD34+ cells using BD Influx at the Weill Cornell Medicine flow cytometry core. Nuclei were isolated from DAPI-, CD34+ cells according to 10x Genomics Demonstrated Low Cell Input Nuclei Isolation protocol. Lysis buffer was prepared following manufacturer’s recommendations and then split into aliquots for each serial sample. Either TotalSeq-A Anti-Nuclei Pore Complex Proteins Hashtag 9 or 10 Antibody (1uL at 1:5 dilution; BioLegend) was added to each aliquot of lysis buffer. Low-input nuclei isolation was otherwise performed following manufacturer’s recommendations. Subsequently, nuclei from each time-point were counted and pooled together at approximately equal proportions. For IFN03, additional nuclei from the IFNa-treated sample were available to be run on a separate lane.
RFX3-OE Extraction Protocol: Cells from frozen umbilical cord blood mononuclear cells were thawed rapidly at 37°C, red blood cell lysis was performed using ACK Lysis Buffer, then centrifuged, and cell pellet was resuspended in cold MACS buffer. Cells were centrifuged at 300g for 5min at 4°C, and resuspended in cold MACs buffer at a concentration of 1x10^7 cells/mL. CD34+ cells were then isolated with the EasySep™ Human CD34 Positive Selection Kit II (StemCell Technologies #17856) according to manufacturer’s protocol. After isolation, cells were counted and plated in 96-well round-bottom plates (Falcon) in StemSpan™ SFEM II media (StemCell Technologies) with StemSpan™ CD34+ Expansion Supplement (StemCell Technologies) and 1% Pen/Strep. After 24 hours in culture, cells were spun down and resuspended in minimal media consisting of StemSpan StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement, 1% Pen/Strep, 10μM prostaglandin E2 (StemCell Technologies #72192) and 100ng/μl poloxamer 407 (Millipore Sigma P2164030). Cells were split into 2 technical replicates each for untransduced condition, mCherry-control vector transduction, and RFX3-OE vector transduction. Lentivirus or PBS control was added at an MOI of 100, spinoculated at 300g, 32°C for 1 hour, and cells were incubated in same lentivirus-containing media for 24 hours at 37°C before resuspension in fresh media consisting of StemSpan™ SFEM II media with StemSpan™ CD34+ Expansion Supplement and 1% Pen/Strep. After 48 hours of incubation, cells were stained with CD34-APC antibody (1:50). Cells were then FACS isolated for the CD34+ population in the untransduced condition and the CD34+ mCherry+ populations in the RFX3-OE and mCherrycontrol conditions. Three independent transduction experiments were completed with new units of umbilical cord blood cells. Untransduced, mCherry-Control, and RFX3-OE CD34+ cells were stained with Cell Hashing antibodies (HTO TotalSeq-A, BioLegend) for 30 min at 4°C. Cells were then washed with FACs Buffer three times, pooled, and counted for loading. scRNA-sequencing was then performed using the 10x 3’ v3.1 platform according to manufacturer’s protocol. HTO demultiplexing and downstream analyses such as differential gene expression and gene set enrichment were performed as in GoT-IM for CD34+ bone marrow samples. scRNA-seq experiment was completed on one replicate of three independent transduction experiments.
CUT&RUN Extraction Protocol: UT7 cell lines expressing MPL (thrombopoietin receptor) and either the mutant CALR (type 1, L367Tfs*46) or wildtype CALR transgene (93) were seeded in 10cm plates in DMEM supplemented with 10% FBS (Thomas Scientific) and 5 ng/ml GM-CSF (Miltenyi-Biotec). Cells were treated with 0.1μg/ml Recombinant Human IFN-alpha2a (RC217-14) or PBS-1X control for 24hrs. After treatment, cells were washed 1x with PBS and collected for use with the CUTANA™ CUT&RUN assay (EpiCypher) according to the manufacturer’s protocol. 0.5μg of anti-human rabbit monoclonal PU.1 antibody (ab76543) and IgG antibody (ab172730) were used in the assay.
GoT-IM Library Construction Protocol: The standard 10x Genomics Chromium 3′ (v.3.1 chemistry) was implemented according to the manufacturer’s recommendations up to the cDNA amplification step (10X Genomics, Pleasanton, CA). After cDNA amplification and SPRI cleanup, 10x scRNA-seq and ADT/HTO libraries were generated as recommended. A portion of the cDNA was used for somatic genotyping. Briefly, to capture the somatic genotypes of cells, cDNA was amplified with a locus-specific amplification (10 PCR cycles), using the generic forward SI-PCR primer and a following locus-specific reverse primer for the CALR mutations. The amplified locus-specific cDNAs are then cleaned using SPRI purification to remove unincorporated primers. Finally, the targeted amplicon libraries are generated through a PCR performed with a P5 generic forward PCR primer together with an RPI-x primer. The targeted amplicon libraries were spiked into the remainder of the gene expression and immunophenotyping libraries to be sequenced together on a NovaSeq (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 8 cycles for i7 sample index and 8 cycles for i5 sample index.
GoT-IM Library Construction Protocol: The standard 10x Genomics Chromium 3′ (v.3.1 chemistry) was implemented according to the manufacturer’s recommendations up to the cDNA amplification step (10X Genomics, Pleasanton, CA). After cDNA amplification and SPRI cleanup, 10x scRNA-seq and ADT/HTO libraries were generated as recommended. A portion of the cDNA was used for somatic genotyping. Briefly, to capture the somatic genotypes of cells, cDNA was amplified with a locus-specific amplification (10 PCR cycles), using the generic forward SI-PCR primer and a following locus-specific reverse primer for the CALR mutations. The amplified locus-specific cDNAs are then cleaned using SPRI purification to remove unincorporated primers. Finally, the targeted amplicon libraries are generated through a PCR performed with a P5 generic forward PCR primer together with an RPI-x primer. The targeted amplicon libraries were spiked into the remainder of the gene expression and immunophenotyping libraries to be sequenced together on a NovaSeq (Illumina, San Diego, CA). The cycle settings were as follows: 28 cycles for Read 1, 90 cycles for Read 2, 8 cycles for i7 sample index and 8 cycles for i5 sample index.
GoT-ATAC Library Construction Protocol: Single-nucleus gene expression (GEX) and chromatin accessibility libraries were constructed from the pooled nuclei according to the Chromium Next GEM Single Cell Multiome User Guide (10X Genomics). Genotyping libraries targeting the CALR mutant transcripts were constructed from the remaining amplified cDNA, similar to the original GoT method. For each PCR, 12.5uL Kapa HiFI HotStart Ready Mix was mixed with 0.75uL of 10uM forward primer, 0.75uL of 10uM reverse primer, 3uL cDNA and nuclease-free water for a total reaction volume of 25uL. In the first PCR, 3uL cDNA was re-amplified with Partial TSO and Partial Read 1 primers, using the following PCR condition: 98°C for 3min; 3 cycles of 98°C for 15sec, 67°C for 20sec and 72°C for 1min; 72°C for 1min. The re-amplified sample was purified and concentrated via 0.7X SPRI cleanup, eluting it into 10uL Buffer EB. To pre-enrich the CALR mutation locus, a gene-specific PCR was performed with 3uL of cleaned re-amplified cDNA and Partial Read 1 and gene-specific primers. The following PCR condition was used: 98°C for 3min; 11 cycles of 98°C for 20sec, 60°C for 20sec, and 72°C for 2min; 72°C for 2min. After 0.7X SPRI cleanup, cDNA was eluted into 10uL Buffer EB. CALR locus-specific amplification was then performed with 3uL of cleaned gene-specific amplified cDNA and SI-PCR and loci-specific Primers, using the PCR condition: 98°C for 3min; 11 cycles of 98°C for 20sec, 60°C for 20sec, and 72°C for 2min; 72°C for 2min. A 0.7X SPRI cleanup was performed, and cDNA was eluted into 11uL Buffer EB. Finally, to construct the targeted amplicon library, loci-amplified cDNA was mixed with P5 Generic and RPIx indexing primers and amplified with the PCR condition: 98°C for 3min; 5 cycles of 98°C for 15sec, 60°C for 20sec, and 72°C for 1min; 72°C for 1min. The constructed library was cleaned via 0.8X SPRI cleanup and eluted into 12uL Buffer EB. At the cDNA amplification stage of the Chromium Next GEM Single Cell Multiome protocol, supernatant from the 0.6X size selection was retained and was used to generate the hashing libraries as per HTO protocol25 with the following modification. For the hashing library construction step, the PCR reaction was prepared with 0.65uL of 10uM SI-PCR primer, 0.65uL of 10uM TruSeq DNA D7xx_s primer, 11.25uL cleaned supernatant and 12.5 uL Kapa HiFI HotStart Ready Mix (Roche, Basel, Switzerland). Hashing, gene expression and genotyping libraries were pooled and sequenced together on a NovaSeq (Illumina) with cycle settings: 28 cycles for Read 1, 90 cycles for Read 2, 10 cycles for i7 sample index and 10 cycles for i5 sample index. The ATAC library was sequenced separately on a NovaSeq, with cycle settings: 50 cycles for Read 1 and Read 2, 8 cycles for i7 sample index and 24 cycles for i5 sample index. Single-cell RNA-seq (10X) with targeted amplification of a mutation of interest.

tag: tissue

value: Bone marrow

tag: cell type

tag: disease state

value: Essential thrombocythemia

tag: treatment

value: IFNa

tag: library type

value: GEX+ADT+HTO


title: A66_Y_Zfp219_Tterm_2

city: Boston

first: Alex Chang-Yu

last: Chen

state: MA

address: 149 13th Street, 7th floor, Room 7103

department: Krantz Family Center for Cancer Research

institute: Massachusetts General Hospital

description:
Library name: A66_Y_Zfp219_Tterm_2
Y_Zfp219_Tterm

library_source: genomic

data_processing:
Raw fastq files were downloaded from Illumina BaseSpace. Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:30 CROP:35. Trimmed reads were aligned to mm10 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000. Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed. Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3.1) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix. Normalization and differential expression were performed using DESeq2 (v 1.28.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts

molecule: genomic DNA

organism: Mus musculus

source_name: B16-OVA Tumor

extract_protocol:
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

tag: gene knockout

tag: cell state

value: terminally exhausted


title: duodenum male low-dose exposure rep3

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: OCSPP

institute: US EPA

description: Library name: D_11

library_source: transcriptomic

data_processing:
RNA-seq data quality was assessed using FASTQC (v0.12.1) and summarized with MultiQC (v1.28)
PCR duplicates were removed by deduplicating sequencing reads with UMI-tools (v1.1.5)
Low-quality bases were trimmed using Cutadapt (v4.9) and Trim Galore (v0.6.10)
The cleaned reads were then aligned to the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1) using STAR (v2.7.11b)
Quantification of transcript abundance was performed with Salmon (v1.10.3)
Assembly: the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcrit level generated by salmon  (*.gene_counts.tsv )
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcript level generated by salmon  (*.transcript_counts.tsv )

molecule: polyA RNA

organism: Rattus norvegicus

source_name: duodenum

growth_protocol: Rats were fed a standard rodent chow

extract_protocol:
A 50% (v/v) solution of Antifoam A (cat. no. A5633; Sigma, St. Louis, MO) was prepared in propylene glycol (cat. no. W294004; Sigma St. Louis, MO). The solution was vortexed prior to use. Homogenization buffer was prepared by adding 10 µl of β-mercaptoethanol (cat no. 0482, VWR, Radnor, PA) and 60 µl antifoam solution per milliliter of Buffer RLT Plus (Qiagen, Germantown, MD).
Prior to homogenization, large tissue samples were broken into smaller pieces using a mortar and pestle cooled with liquid nitrogen (LN2). Several of the resulting pieces (each approximately 3–5 mm) were then pulverized together to produce the final sample. For homogenization, 400 µl of buffer was added to a 3 ml, flat-bottom polystyrene tube (Globe Scientific, Mahwah, NJ). The tube was placed into a CoolRack CF15 (Corning Inc., Corning, NY) cooled with LN2. A cooled 30 µl plastic scoop was used to transfer pulverized tissue to the tube. The target mass of tissue was 50 µg, although the actual mass varied due to the need to work quickly and differences in the sizes of the pulverized samples.
The tube was placed on ice, and 600 µl of ice-cold homogenization buffer was added to the sample. The sample was homogenized using a model 985-370 TissueTearor rotor-stator homogenizer with a 7 mm probe (BioSpec Products, Bartlesville, OK) until no remnants of intact tissue were visible. If the homogenate appeared significantly darker than other samples, suggesting an excess of tissue, additional buffer was added until the color of the sample was similar to that of the other samples. Homogenates were stored at -80 °C until used for RNA isolation. The homogenizer was rinsed between samples within a treatment by running it at the highest speed for 30 s in three changes of deionized water. Between treatments, the rotor and stator were disassembled and cleaned with a polyester test tube brush before rinsing in water.
For RNA isolation, homogenized samples were removed from the freezer and placed on ice to thaw. The samples were vortexed, and 100 µl of the homogenate was transferred to the well of a 96-well round bottom plate (Caplugs Evergreen, Buffalo, NY). RNA was isolated using the MagMAX-96 Total RNA Isolation Kit (Fisher Scientific, Hampton, NH) according to the manufacturer’s protocol, except for the substitution of RLT Plus buffer for the lysis/binding solution as described above.
Isolated RNA was quantified on a Synergy HTX plate reader using a Take3 microvolume plate (Agilent, Santa Clara, CA). The integrity of the RNA was analyzed on an Agilent TapeStation using RNA Screen Tapes and reagents (Agilent, Santa Clara, CA). Concentrations of samples ranged from 75 to 470 ng/µl. RNA integrity numbers (RIN) ranged from 8.0 to 10.0; nearly 90% of samples had a RIN higher than 9.0.
Isolated RNA was next used to prepare RNA-Seq libraries. Samples were blocked so that about eight samples of each tissue and treatment combination were included in one of two plates. RNA was normalized to 25 ng/uL with nuclease-free water (Ambion, USA). 250 ng total RNA (10 uL of normalized RNA) was input into mRNA purification with magnetic beads using a PolyA Selection Module (Lexogen, USA). Purified mRNA was then used directly in CORALL mRNA-Seq V2 library preparation with set A unique dual indexes (UDIs). Each batch was checked by qPCR to determine the appropriate number of PCR cycles for library amplification with Add-On PCR V2 kit (Lexogen, USA), SYBR Green (ThermoFisher, USA), and a QuantStudio 6 Flex real-time PCR instrument (ThermoFisher, USA). After final PCR amplification, libraries were quantified with Quant-iT PicoGreen (ThermoFisher, USA). The distribution of library size was checked by TapeStation D1000 assay (Agilent, USA). The average library size was 508 – 517 bp. Samples below 1 ng/uL were re-amplified.

value: duodenum

tag: strain

value: Sprague-Dawley

tag: developmental stage

value: adult

tag: genotype

value: WT

value: Male-Low Dose/5mg/kg

tag: batch

value: Batch 1


title: CAL27,control siRNA,rep1

city: Stanford

first: Namyoung

last: Jung

state: CA

address: 269 Campus Dr. CCSR Room 2150

department: Medicine

institute: Stanford University

data_processing:
Sequencing data alignment, quality check, PCR duplicate removal, peak calling, blacklisted region removal, IDR peak filtration and signal track generation were performed through the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes peak coordinates and counts

growth_protocol: CAL27 human squamous cell carcinoma cells were obtained from ATCC (CRL-2095) and cultured in DMEM F:12 (ThermoFisher) supplemented with 10% FBS. SCC-13 human squamous cell carcinoma cells were obtained from J.G.Rheinwald, Dana-Farber/Harvard Cancer Center as a generous gift and cultured in Keratinocyte-SFM (ThermoFisher) supplemented with 25 ug/ml BPE, 0.2ng/ml EGF (GIBCO, Thermofisher) and 0.3mM CaCl2 (Sigma-Aldrich). Primary human keratinocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Keratinocytes were cultured in 1:1 Keratinocyte-SFM (ThermoFisher) and Medium 154 (ThermoFisher) supplemented with HKGS (ThermoFisher). Keratinocytes were induced to differentiate by the addition of 1.2mM calcium for 3 days at full confluence.

extract_protocol:
55,000 viable cells were pelleted and resuspended in 50 uL of ATAC resuspension buffer (RSB) with 0.1% Igepal CA-630 (NP-40), 0.1% Tween-20, and 0.01% digitonin (Promega, G9441). After 3 minutes on ice, 1 mL of ATAC RSB with 0.1% Tween-20 was added, tubes were inverted, and nuclei pelleted by centrifugation at 500 RCF for 10 minutes at 4C. Supernatant was carefully removed and the nuclei pellet was resuspended in 50 uL of transposition mixture (25 uL TD buffer, 2.5 uL of TDE1 (Illumina, 20034197), 16.5 uL PBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (Zymo, D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
ATAC-seq libraries were generated on two biological replicates for each group following Omni-ATAC protocol

treatment_protocol: Dharmacon siStable siRNA was designed to target PAN-p63 with the sequences as follows: sense (5’-CGACAGUCUUGUACAAUUUUU-3’) and antisense (5’-AAAUUGUACAAGACUGUCGUU-3’) or FOXK1 with si1 sense (5’-GAACGGAAAGCAUGCGGUU-3’), antisense (5’-AACCGCAUGCUUUCCGUUC-3’) and si2 sense (5'-GCAGUGUACCUUCCGGUUU-3’) and antisense (5’-AAACCGGAAGGUACACUGC-3’). 1-1.5nmol of siRNA was electroporated into 1 million keratinocytes and 2 million SCC cells using the human keratinocyte Nucleofector kit (Lonza) according to the manufacturer’s protocol. After 24 hours, fresh media was added to the cells and cells were subsequentially seeded for differentiation after 48 h transfection or maintained at subconfluence. The negative control was the ON-TARGET Smart pool negative control (Horizon, D-001810-10-20).

tag: cell line

value: Squamous cell carcinoma


title: A66_Y_Zfp219_Tterm_1

description:
Library name: A66_Y_Zfp219_Tterm_1
Y_Zfp219_Tterm


title: IFN11_cd34neg_10x

description: 10x genomics


title: A66_Y_Zfp219_Tprog_2

description:
Library name: A66_Y_Zfp219_Tprog_2
Y_Zfp219_Tprog

value: progenitor exhausted


title: IFN09_cd34neg_10x

description: 10x genomics


title: duodenum male low-dose exposure rep2

description: Library name: D_10

value: Batch 2


title: ATACseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep3

city: Beijing

first: xi

last: rongwen

address: No. 7 Science Park Road, zhongguancun Life Science Park, Changping District,

country: China

institute: National Institute of Biological Sciences, Beijing

description: Library name: Psc-Su(z)2-XL26-Marcm-Rep3

data_processing:
For RNAseq data,the samples were subsequently sequenced by Illumina Hiseq-2500 system with 50 bp read length
For ATACseq data, the samples were subsequently sequenced by Illumina Hiseq-2500 system with paired-end 150 bp read length.
reads are aligned to Fly genome with STAR-aligner, and gene counts were summarized with featureCounts.
Clean reads were mapped to reference genome by Bowtie2 (2.3.5.1) aligner with ‘--very-sensitive’ parameter. Duplicated reads were removed by picard MarkDuplicates function. Multi-mapped reads and reads in blacklist regions were also discarded separately by using samtools (v1.7) and bedtools (v2.30.0). Bam files were imported to iDEAR (https://bitbucket.org/juanlmateo/idear/src/master/) to identify the positively and negatively enriched regions with respect to the control sample. Significantly changed regions were annotated using annotatePeaks.pl function from Homer. bw files generated from bam files by deeptools.
Assembly: BDGP6
Supplementary files format and content: tab-delimited text file includes raw counts for each RNAseq sample
Supplementary files format and content: bigwig

organism: Drosophila melanogaster

source_name: midgut

extract_protocol:
For RNAseq, after collecting midgut epithelial cells by FACS, we used a series of RNA isolation and amplification kits to satisfy the mount of mRNA for RNA-seq. RNA isolation was performed according to manufacturer’s instruction (Arcturus PicoPure TM RNA isolation kit, Thermofisher, 12204-1). For ATACseq, midgut epithelial cells were collected by FACS. After centrifugation, the pelleted cells were treated by ATAC lysis buffer and centrifuged again to isolate nucleus. Then the tranposase Tn5 was used to cut opened regions on the chromosome and add a defined adaptor to these DNA fragments.
For RNAseq, synthesis of cDNA complementary strands, double-stranded DNA purification, in vitro transcription of DNA into aRNA, and aRNA purification were carried out by Arcturus RiboAmp PLUS RNA Amplification kit (Thermofisher, RA7016), Arcturus cDNA Purification kit (Thermofisher, RA7011) and In-Vitro Transcription kit (Thermofisher, RA7009) respectively.
For ATACseq, the tagmented DNA were purified and then amplified by PCR to construct library for next-generation sequencing.

value: midgut

value: intestinal epithelial cells

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL82

value: mutant


title: ATACseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep2

description: Library name: Psc-Su(z)2-XL26-Marcm-Rep2

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL81


title: duodenum male low-dose exposure rep1

description: Library name: D_09


title: IFN08_cd34neg_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia

value: IFNa

value: GEX+ADT+HTO


title: A66_Y_Zfp219_Tprog_1

description:
Library name: A66_Y_Zfp219_Tprog_1
Y_Zfp219_Tprog

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells


title: ATACseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep1

description: Library name: Psc-Su(z)2-XL26-Marcm-Rep1

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL80


title: A66_Y_OTC_Ttran_3

description:
Library name: A66_Y_OTC_Ttran_3
Y_OTC_Ttran

value: OTC control

value: transitory, effector-like


title: IFN05_cd34neg_10x

description: 10x genomics


title: ATACseq, intestinal stem cells, Pc-RNAi-Rep3

description: Library name: Pc-RNAi-Rep3

value: intestinal stem cells

value: esgts>PcRNAi

value: RNAi


title: duodenum male control rep7

description: Library name: D_07

value: duodenum

value: Sprague-Dawley

value: adult

value: WT

value: Male-Vehicle Control

value: Batch 2


title: duodenum male control rep8

description: Library name: D_08

value: Batch 3


title: RNA-seq_Differentiated KC,p63 siRNA,rep2

data_processing:
Single-end reads were aligned using STAR aligner (2.5.4b) using GENCODE v19 gene annotation in hg19 with default settings.
To obtain raw expected read counts, RSEM (1.3.0) was used, and these raw counts were subjected to differential expression analysis with DESeq2 (1.26.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes expected counts from RSEM for each sample

source_name: Primary keratinocyte

extract_protocol:
Cells were harvested and pellets were flash frozen on dry ice. RNA was extracted using the RNeasy Mini Kit (QIAGEN).
RNA-seq libraries were generated on two biological replicates for each group using the Lexogen Quant-seq 3’ mRNA -seq Library Prep Kit FWD (Lexogen) according to the manufacturer’s protocol. The libraries were sequenced as single-end 1X101bp reads on an Illumina HiSeq2000 or 1X150bp reads on an Illumina NovaSeq 6000 instrument.

value: Primary keratinocyte

value: Normal keratinocyte

value: p63 knockdown

value: Keratinocyte differentiation day3


title: duodenum male control rep6

description: Library name: D_06


title: IFN02_cd34neg_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia

value: IFNa

value: GEX+ADT+HTO


title: ATACseq, intestinal stem cells, Pc-RNAi-Rep2

description: Library name: Pc-RNAi-Rep2

value: midgut

value: intestinal stem cells

value: esgts>PcRNAi


title: A66_Y_OTC_Ttran_2

description:
Library name: A66_Y_OTC_Ttran_2
Y_OTC_Ttran

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: OTC control

value: transitory, effector-like


title: IFN01_cd34neg_10x

description: 10x genomics


title: duodenum male control rep5

description: Library name: D_05

value: duodenum

value: Sprague-Dawley

value: adult

value: WT

value: Male-Vehicle Control

value: Batch 1


title: A66_Y_OTC_Ttran_1

description:
Library name: A66_Y_OTC_Ttran_1
Y_OTC_Ttran


title: ATACseq, intestinal stem cells, Pc-RNAi-Rep1

description: Library name: Pc-RNAi-Rep1

value: RNAi


title: IFN10_cd34pos_Genotyping

description: Ironthrone-GoT

data_processing:
10x data was processed using Cell Ranger 1 and v6.1.2 using default parameters. RNA reads were aligned to the human referece genome.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, 5) Analyze reads with CB that are also observed in the 10x RNA-seq dataATAC-seq 6) Collapse networks of closely related UMIs within CBs to correct for sequencing error, 7) Matching of CB/UMI pairs found in 10x scRNA-seq data, discarding those matching non-CALR genes and those matching no gene below a supporting read threshold.
CUT&RUN data were down-sampled to have same number of reads across all conditions within the sample replicate to account for difference in sequencing depth. Among the down-sampled reads, low-quality reads were filtered out using Trimmomatic, resulting reads were aligned with hg38 genome with Bowtie2, and PCR duplicates were removed with SAMtools with a previously described workflow. Aligned reads were then used for peak calling with MACS3 with a q-value threshold of 0.01 and reads from IgG antibody as the control. SPI1 over-enrichment in the called peaks was confirmed with Simple Enrichment Analysis (SEA, v5.5.5). Overlapping peaks between replicates of the same condition were kept for further processing. The peaks were processed with multiBamSummary function from deepTools to obtain counts matrix per sample for downstream analysis.
Differential peak enrichment analysis was run between conditions (MUT vs WT and IFN⍺-treated vs control) using DESEQ2 for distal PU.1 peaks. Differential peaks in each condition were centered around SPI1 motif and motif enrichment was performed for regions +/- 250 bp from SPI1 motif using HOMER (v.4.1.1). Differential ranking between each motif two conditions was calculated.
Assembly: GRCh38
Supplementary files format and content: Processed 10X data is matrix table of gene/peak counts per cell for each sample
Supplementary files format and content: Output matrices processed from genotyping data have two columns: barcodes (BC) and Genotype
Library strategy: Ironthrone-GoT

value: Bone marrow

value: Essential thrombocythemia

value: Ironthrone-GoT


title: A66_Y_OTC_Tterm_3

description:
Library name: A66_Y_OTC_Tterm_3
Y_OTC_Tterm

value: terminally exhausted


title: duodenum male control rep4

description: Library name: D_04


title: A66_Y_OTC_Tterm_2

description:
Library name: A66_Y_OTC_Tterm_2
Y_OTC_Tterm


title: IFN10_cd34pos_10x

description: 10x genomics

value: IFNa

value: GEX+ADT+HTO


title: ATACseq, intestinal stem cells, control-Rep3

description: Library name: esg-rep3

value: midgut

value: intestinal stem cells

value: esgts>GFP

value: control


title: duodenum male control rep3

description: Library name: D_03

value: duodenum


title: ATACseq, intestinal stem cells, control-Rep2

description: Library name: esg-rep2


title: IFN09_cd34pos_Genotyping

description: Ironthrone-GoT


title: A66_Y_OTC_Tterm_1

description:
Library name: A66_Y_OTC_Tterm_1
Y_OTC_Tterm

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: OTC control


title: ATACseq, intestinal stem cells, control-Rep1

description: Library name: esg-rep1


title: duodenum male control rep2

description: Library name: D_02

value: Sprague-Dawley

value: adult

value: WT

value: Male-Vehicle Control

value: Batch 2


title: A66_Y_OTC_Tprog_2

description:
Library name: A66_Y_OTC_Tprog_2
Y_OTC_Tprog

value: progenitor exhausted


title: IFN09_cd34pos_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia


title: duodenum male control rep1

description: Library name: D_01


title: IFN08_cd34pos_Genotyping

description: Ironthrone-GoT

value: IFNa

value: Ironthrone-GoT


title: A66_Y_OTC_Tprog_1

description:
Library name: A66_Y_OTC_Tprog_1
Y_OTC_Tprog


title: ATACseq, intestinal stem cells, E(z)-RNAi-Rep3

description: Library name: E(z)-RNAi-Rep3

value: midgut

value: intestinal stem cells

value: esgts>E(z)RNAi

value: RNAi


title: liver female high-dose exposure rep6

description: Library name: L_48

source_name: liver

value: liver

value: Female-High Dose/50mg/kg


title: ATACseq, intestinal stem cells, E(z)-RNAi-Rep2

description: Library name: E(z)-RNAi-Rep2


title: IFN08_cd34pos_10x

description: 10x genomics

value: GEX+ADT+HTO


title: liver female high-dose exposure rep5

description: Library name: L_46

value: Sprague-Dawley


title: ATACseq, intestinal stem cells, E(z)-RNAi-Rep1

description: Library name: E(z)-RNAi-Rep1


title: IFN07_cd34pos_Genotyping

description: Ironthrone-GoT


title: A66_Y_Dusp5_Ttran_3

description:
Library name: A66_Y_Dusp5_Ttran_3
Y_Dusp5_Ttran

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: transitory, effector-like


title: A66_Y_Dusp5_Ttran_2

description:
Library name: A66_Y_Dusp5_Ttran_2
Y_Dusp5_Ttran


title: liver female high-dose exposure rep4

description: Library name: L_45

value: adult

value: WT

value: Batch 3


title: RNAseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep3

description:
Library name: Psc-Su(z)2-mut-Rep3
column name in gene-expression-matrix-from-featurecounts.txt: Psc_Suz2_mut_Rep3

value: intestinal epithelial cells

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL82

value: mutant


title: IFN07_cd34pos_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia

value: IFNa


title: A66_Y_Dusp5_Ttran_1

description:
Library name: A66_Y_Dusp5_Ttran_1
Y_Dusp5_Ttran


title: IFN06_cd34pos_Genotyping

description: Ironthrone-GoT

value: Ironthrone-GoT


title: liver female high-dose exposure rep3

description: Library name: L_44

value: liver

value: Batch 2


title: A66_Y_Dusp5_Tterm_3

description:
Library name: A66_Y_Dusp5_Tterm_3
Y_Dusp5_Tterm

value: terminally exhausted


title: liver female high-dose exposure rep2

description: Library name: L_42

value: Sprague-Dawley

value: Female-High Dose/50mg/kg


title: RNAseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep2

description:
Library name: Psc-Su(z)2-mut-Rep2
column name in gene-expression-matrix-from-featurecounts.txt: Psc_Suz2_mut_Rep2

value: midgut

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL81


title: RNAseq, intestinal epithelial cells, Psc-Su(z)2-XL26 mutant-Rep1

description:
Library name: Psc-Su(z)2-mut-Rep1
column name in gene-expression-matrix-from-featurecounts.txt: Psc_Suz2_mut_Rep1

value: hs-flp, tubulin>GFP; Psc-Su(z)2XL26 FRT 42D, tublin>GAL80


title: A66_Y_Dusp5_Tterm_2

description:
Library name: A66_Y_Dusp5_Tterm_2
Y_Dusp5_Tterm

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells


title: liver female high-dose exposure rep1

description: Library name: L_41

value: adult

value: WT

value: Batch 1


title: IFN06_cd34pos_10x

description: 10x genomics

value: Bone marrow

value: GEX+ADT+HTO


title: RNAseq, intestinal epithelial cells, Notch55e11 mutant-Rep3

description:
Library name: Notch55e11-Rep3
column name in gene-expression-matrix-from-featurecounts.txt: Notch_55e11_Rep3

value: intestinal epithelial cells

value: hs-flp, N55e11 FRT 19A, tubulin>GAL82; actin>GFP

value: mutant


title: A66_Y_Dusp5_Tterm_1

description:
Library name: A66_Y_Dusp5_Tterm_1
Y_Dusp5_Tterm


title: IFN05_cd34pos_Genotyping

description: Ironthrone-GoT

value: Essential thrombocythemia

value: IFNa

value: Ironthrone-GoT


title: liver female low-dose exposure rep8

description: Library name: L_40

value: liver

value: Sprague-Dawley

value: Female-Low Dose/5mg/kg


title: RNAseq, intestinal epithelial cells, Notch55e11 mutant-Rep2

description:
Library name: Notch55e11-Rep2
column name in gene-expression-matrix-from-featurecounts.txt: Notch_55e11_Rep2

value: midgut

value: hs-flp, N55e11 FRT 19A, tubulin>GAL81; actin>GFP


title: IFN05_cd34pos_10x

description: 10x genomics


title: A66_Y_Dusp5_Tprog_2

description:
Library name: A66_Y_Dusp5_Tprog_2
Y_Dusp5_Tprog

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: progenitor exhausted


title: liver female low-dose exposure rep7

description: Library name: L_39

value: adult

value: WT

value: Batch 2


title: RNAseq, intestinal epithelial cells, Notch55e11 mutant-Rep1

description:
Library name: Notch55e11-Rep1
column name in gene-expression-matrix-from-featurecounts.txt: Notch_55e11_Rep1

value: intestinal epithelial cells

value: hs-flp, N55e11 FRT 19A, tubulin>GAL80; actin>GFP


title: IFN04_cd34pos_Genotyping

description: Ironthrone-GoT

value: Bone marrow


title: A66_Y_Dusp5_Tprog_1

description:
Library name: A66_Y_Dusp5_Tprog_1
Y_Dusp5_Tprog


title: liver female low-dose exposure rep6

description: Library name: L_38


title: A66_A_Zfp219_Ttran_2

description:
Library name: A66_A_Zfp219_Ttran_2
A_Zfp219_Ttran

value: transitory, effector-like


title: IFN04_cd34pos_10x

description: 10x genomics

value: Essential thrombocythemia

value: IFNa

value: GEX+ADT+HTO


title: RNAseq, intestinal stem cells, control-Rep3

description:
Library name: esg-control-Rep3
column name in gene-expression-matrix-from-featurecounts.txt: esg_control_Rep3

value: intestinal stem cells

value: esgts>GFP

value: control


title: RNAseq, intestinal stem cells, control-Rep2

description:
Library name: esg-control-Rep2
column name in gene-expression-matrix-from-featurecounts.txt: esg_control_Rep2

value: midgut


title: IFN03_cd34pos_Genotyping

description: Ironthrone-GoT

value: Ironthrone-GoT


title: liver female low-dose exposure rep5

description: Library name: L_37

value: liver

value: Sprague-Dawley

value: Female-Low Dose/5mg/kg

value: Batch 1


title: liver female low-dose exposure rep4

description: Library name: L_36

value: adult

value: WT


title: A66_A_Zfp219_Ttran_1

description:
Library name: A66_A_Zfp219_Ttran_1
A_Zfp219_Ttran

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells


title: RNAseq, intestinal stem cells, control-Rep1

description:
Library name: esg-control-Rep1
column name in gene-expression-matrix-from-featurecounts.txt: esg_control_Rep1


title: A66_A_Zfp219_Tterm_2

description:
Library name: A66_A_Zfp219_Tterm_2
A_Zfp219_Tterm

value: terminally exhausted


title: RNAseq, intestinal epithelial cells, dome468 mutant-Rep3

description:
Library name: dome468-Rep3
column name in gene-expression-matrix-from-featurecounts.txt: dome468_Rep3

value: intestinal epithelial cells

value: hs-flp, dome468 FRT 19A, tubulin>GAL82; actin>GFP

value: mutant


title: liver female low-dose exposure rep3

description: Library name: L_35


title: IFN03_cd34pos_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia

value: IFNa

value: GEX+ADT+HTO


title: IFN02_cd34pos_Genotyping

description: Ironthrone-GoT

value: Ironthrone-GoT


title: A66_A_Zfp219_Tterm_1

description:
Library name: A66_A_Zfp219_Tterm_1
A_Zfp219_Tterm


title: RNAseq, intestinal epithelial cells, dome468 mutant-Rep2

description:
Library name: dome468-Rep2
column name in gene-expression-matrix-from-featurecounts.txt: dome468_Rep2

value: midgut

value: hs-flp, dome468 FRT 19A, tubulin>GAL81; actin>GFP


title: liver female low-dose exposure rep2

description: Library name: L_34

value: liver

value: Sprague-Dawley

value: Female-Low Dose/5mg/kg

value: Batch 2


title: HiChIP_SCC13,p63 siRNA,rep1

data_processing:
Paired-end reads were aligned to the hg19 using HiC-Pro with default parameters.
To identify HiChIP peaks , hichipper was applied to the filtered reads using (EACH,ALL) setting. The HiC-Pro valid interactions and hichipper identified peaks were used to identify statistically significant loops using FitHiChIP with default parameters except for the following parameters: MappSize = 500, BINSIZE = 10000, QVALUE = 0.01, UseP2PBackground = 0.
Union of the significant loop list was generated and used for downstream differential loop analysis. The raw counts of all samples from FitHiChIP pipeline were processed with DESeq2 to identify differential loop between control siRNA treated and PAN-p63 siRNA treated samples.
Assembly: hg19
Supplementary files format and content: tab-delimited text file (output from FitHiChIP)
Library strategy: HiChIP-seq

extract_protocol:
The HiChIP protocol was performed  as previously described (Mumbach et al., 2016) using  H3K27ac antibody  (Abcam, ab4729) with the following modifications. Samples were sheared using a Covaris E220 using the following parameters: Fill Level = 10, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 4 minutes and then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C. We used 7.5 ug of antibody to H3K27ac and captured the chromatin-antibody complex with 60 uL Protein A beads (Thermo Fisher). Qubit quantification following ChIP ranged from 125-150 ng. The amount of Tn5 used and number of PCR cycles performed were based on the post-ChIP Qubit amounts.
HiChIP samples were size selected by PAGE purification (200-800 bp) .

tag: chip antibody

value: H3K27ac Abcam, ab472

value: Squamous cell carcinoma

value: p63 knockdown


title: liver female low-dose exposure rep1

description: Library name: L_33

value: adult

value: WT


title: A66_A_Zfp219_Ttad_2

description:
Library name: A66_A_Zfp219_Ttad_2
A_Zfp219_Ttad

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: age-associated dysfunctional


title: IFN02_cd34pos_10x

description: 10x genomics

value: Bone marrow

value: Essential thrombocythemia

value: IFNa


title: A66_A_Zfp219_Ttad_1

description:
Library name: A66_A_Zfp219_Ttad_1
A_Zfp219_Ttad


title: RNAseq, intestinal epithelial cells, dome468 mutant-Rep1

description:
Library name: dome468-Rep1
column name in gene-expression-matrix-from-featurecounts.txt: dome468_Rep1

value: midgut

value: intestinal epithelial cells

value: hs-flp, dome468 FRT 19A, tubulin>GAL80; actin>GFP

value: mutant


title: IFN01_cd34pos_Genotyping

description: Ironthrone-GoT

value: Ironthrone-GoT


title: liver female control rep8

description: Library name: L_32

value: liver

value: Sprague-Dawley

value: Female-Vehicle Control

value: Batch 1


title: NHA_ChIPseq_PPARD_RA_24h_rep2

first: Evgeny

last: Deforzh

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

description: Library name: Sample 32

data_processing:
Low-quality reads (MAPQ<=30) were filtered out.
The remaining reads were alignedusing Bowtie2 (v2.5.3) with default end-to-end sensitive parameters.
PCR duplicates were removed from the aligned BAM files using SAMtools (rmdup, v1.13.7).
aligned BAM files were converted to BigWig format using deepTools (v3.5.0) bamCoverage without additional scaling or normalization
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig

source_name: NHA

growth_protocol: GBM8 were maintained as neurospheres in serum-free Neurobasal medium (Gibco) supplemented with: B-27 Plus and N-2 supplements (Gibco), 3 mM GlutaMAX (Gibco), 20 ng/mL recombinant human FGF2 and EGF (Sigma-Aldrich), 2 μg/mL heparin (Sigma-Aldrich), 50 units/mL penicillin/streptomycin (Gibco). Normal human astrocytes, immortalized via E6/E7 and hTERT expression (a generous gift from Dr. Yukihiko Sonoda), served as non-malignant controls. These cells were cultured in Astrocyte Medium (ScienCell, Cat# 1801) according to the manufacturer’s instructions.

extract_protocol:
DNA was recovered using the Monarch PCR and DNA Cell Cleanup Kit (NEB, #T1030L).
Library Preparation and Sequencing ChIP-seq libraries were constructed from purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, #E7546S).

treatment_protocol: Glioma stem cells (GSCs) and normal human astrocytes (NHAs) were seeded in 6-well plates and transfected with 500 ng of both vectors using Lipofectamine 2000 (Thermo Fisher Scientific) according to the manufacturer’s protocol. NHA cells were treated with All trans retinoic acid (SigmaAldrich,  R2500-25MG) diluted in DMSO according to manufacturer's protocol. Cross-linked NHA cells were incubated with Proteinase K (Thermo Scientific, EO0491) for 48 hours

value: NHA

value: immortalized human astrocytes


title: NHA_ChIPseq_PPARD_RA_24h_rep1

description: Library name: Sample 31

value: WT


title: IFN01_cd34pos_10x

description: 10x genomics

value: GEX+ADT+HTO


title: liver female control rep7

description: Library name: L_31

value: adult

value: Batch 2


title: A66_A_Zfp219_Tprog_2

description:
Library name: A66_A_Zfp219_Tprog_2
A_Zfp219_Tprog

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: progenitor exhausted


title: MicroC, IAA

city: Tokyo

first: Shoin

last: Tei

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
The sequenced reads were aligned to hg38 with bwa mem in “-5SP -T0 -t16” parameters. Identification of ligation junctions, sorting of reads, removal of PCR duplication and generation of pairs files were performed with pairtools (version 0.3.0). From the pairs files, matrix files were made by Juicer (version 1.22.01) at 5k, 2k and 1k resolution.
Chromatin loops were identified using Juicer Tools HiCCUPS and Mustache at 5k, 2k and 1k resolution. Loops called by HiCCUPS and Mustache at various resolutions were combined to generate a set of Micro-C loops. TADs were identified using Juicer Tools Arrowhead at 25k resolution.
Assembly: hg38
Supplementary files format and content: Hic files generated by Juicer (version 1.22.01)

source_name: Colorectal carcinoma

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium containing 10% FBS, penicillin, and streptomycin solution (Wako) at 37 C with 5% CO2.

extract_protocol:
HCT116 cells were dissociated into single cells with TrypLE Express (Thermo Fischer Scientific) and washed with PBS once. The washed cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min. After washing with PBS, the cells were crosslinked with 3 mM DSG (Thermo Fisher) for 40 min and quenched with 400 mM glycine for 5 min. The crosslinked cells were washed with PBS and frozen in aliquots of 5 x 106 cells. Frozen cells were resuspended in Micro-C Buffer #1 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 1 mM CaCl2, 0.2% NP-40, 1x cOmplete EDTA-free (Roche)) and incubated on ice for 20 min. Cells were collected by centrifugation and resuspended with Micro-C Buffer #1 again. The treatment with MNase (NEB) at 37 C for 10 min fragmented chromatin. The reaction was stopped by EDTA and incubation at 65C for 10 min. The chromatin was collected by centrifugation and washed with Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2). To generate 5’ overhangs, the ychromatin was resuspended with 50 μl end-repair mix (5 μl of 10 x NEBuffer 2.1, 2 μl of 100 mM ATP, 2.5 μl of 100 mM DTT, 8 μl of Large Klenow Fragment (NEB), 2 μl of T4 Polynucleotide Kinase (NEB).) and incubated at 37 C for 15 min. The DNA overhangs were filled with biotinylated nucleotides by addition of 100 μl Fill-in master mix (10 μl of 1 mM biotin-14-dATP (JBS), 10 μl of 1 mM biotin-11-dCTP (JBS), 1 μl of 10 mM dGTP (Thermo Fisher), 1 μl of 10 mM dTTP (Thermo Fisher), 10 μl of 10x NEBuffer 2.1). After incubation at 65 C for 20 min, the reaction was stopped by EDTA. The chromatin was collected with centrifugation and washed with 1x Ligase Reaction Buffer (NEB). For proximity ligation, the chromatin was resuspended with 500 μl Micro-C ligase mix (50 μl of 10x NEB Ligase buffer, 2.5 μl of 200x BSA (NEB), 5 μl of NEB T4 Ligase (NEB)) and incubated at RT form 2.5-3 h. For removal of biotin-dNTP from un-ligated ends, collected chromatin by centrifugation was resuspended with 100 μl of exonuclease mix (1x NEBuffer 1 (NEB) and 2 μl of 100 U/μl NEB Exonuclease III (NEB)) and incubate at 37C for 15 minutes. For deproteination and reverse crosslinking, 15 μl of Proteinase K (50 mg/mL) and 13 μl of 10% SDS (Invitrogen) were added and incubated at 55 C for 2h and at 65 C overnight. Ligated DNA was purified with QIAquick PCR purification kit (QIAGEN) and eluted in 110 μl of EB. Size selection of DNA was performed by AMPure XP beads (Beckman Coulter). 40 μl of beads were added to each reaction and incubated for 5 min. Using a magnetic stand, the clear solution was transferred to a fresh tube, and 20 μl of beads were added. After incubation for 5 min, the supernatant was removed, and beads were washed with 70 % ethanol without mixing. Beads were left to dry for 5 min and DNA was eluted with 50 μl of EB. For biotin pull-down, we used Dynabeads™ MyOne™ Streptavidin C1 beads. 5 μl beads were washed twice with 300 μl 1x Tween Washing Buffer (1x TWB; 5 mM Tris-HCl (pH 7.5), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and suspended in 150 μl 2x Binding Buffer (2x BB; 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2 M NaCl). 100 μl H2O and 150 μl washed beads in 2x Binding Buffer were added to the sample and incubated rotation at RT for 20 min. Beads were washed with 1x TWB twice and with EB once.
End repair and adaptor ligation was performed on beads using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol. Then, beads were washed with 1x TWB twice and with EB once and resuspended with 15 μl of EB. DNA was amplified by PCR and DNA purification was performed using NEBNext Ultra II DNA Library Prep Kit, NEBNext® Multiplex Oligos for Illumina and AMPure XP beads following the manufacturer’s instructions.

treatment_protocol: Treatment with 0.5 mM indole-3-acetic acid (IAA, SIGMA) for 3h was performed to deplete Rad21.

value: Colorectal carcinoma

value: Auxin


title: liver female control rep6

description: Library name: L_30


title: NHA_ChIPseq_Input_RA_24h

description: Library name: Sample 30


title: MicroC, control

value: DMSO


title: A66_A_Zfp219_Tprog_1

description:
Library name: A66_A_Zfp219_Tprog_1
A_Zfp219_Tprog


title: A66_A_OTC_Ttran_2

description:
Library name: A66_A_OTC_Ttran_2
A_OTC_Ttran

value: OTC control

value: transitory, effector-like


title: liver female control rep5

description: Library name: L_29

value: liver

value: Sprague-Dawley


title: Non-treated egtB:Tn cells replicate 3

city: Fresno

first: Mamta

last: Rawat

address: 2555 E. San Ramon Ave. MS S/B 73

department: Biology

institute: California State University, Fresno

description:
Library name: BT egtB- 2
SE5983_SA52163_S29

data_processing:
We used fastp with default settings to automatically remove any adapters and trim low quality bases (Q<15) from the ends of reads . Reads were mapped to the reference genome for B. thailandensis E64 (RefSeq GCA_000012365.1) using HISAT2 . Transcript assembly and quantification were performed using StringTie. (v2.2.1) -e and -B options to enable reference-based transcript abundance estimation.
To generate count matrices for differential expression analysis, we used the prepDE.py3 script provided by the StringTie suite. This script extracted transcript- and gene-level read counts by parsing coverage values from each sample’s GTF file and computing estimated counts as coverage × transcript length / average read length (default read length = 75 bp). The resulting count matrices were used as input for downstream analyses in DESeq2. Genes with at least 10 total mapped reads across all samples were retained for differential expression analysis
Quality control and sample clustering were performed using variance-stabilized data transformed with DESeq2’s vst() function. A combination of hierarchical clustering (sample distance heatmap), Principal Component Analysis (PCA), and 3D multidimensional scaling (MDS) plots was used to evaluate sample similarity. One of the three B. thailandensis gshA1 mutant replicates clustered more closely with the wild-type samples on the heatmap and PCA (Fig. S1). It also had lower pairwise R² values (e.g., Rep1 vs Rep3: 0.885) and Rep1 and Rep2 (R² = 0.904) compared to Rep2 vs Rep3 (R² = 0.975).
Based on these data, the replicate was excluded from downstream differential expression analysis. For upregulated genes, genes demonstrating greater than or equal to 1 log2FC (two-fold increase) with an adjusted p value P <0.05 were considered for analysis. For downregulated genes, genes demonstrating less than or equal to -1 log2FC (two-fold decrease) with an adjusted p value P <0.05 were considered for analysis.
Assembly: RefSeq GCA_000012365.1
Supplementary files format and content: raw_counts.csv contains the raw counts for each set of aligned reads for each individual sample.
Supplementary files format and content: BT_processed.xlsx contains an excel file containing both version of the available gene IDs, gene description, log2FC of the mutants compared to the wildtype strain, and the adjusted p-value. There are three different sheets in the file, one for each mutant vs wildtype.

organism: Burkholderia thailandensis

growth_protocol: Burkholderia thailandensis was grown in TSB and collected at mid-logarithmic phase (OD600 0.4 - 0.6) grown while shaken at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to manufacturer instructions with the following exception: samples were lysed by bead-beating using a BeadBlaster 24 (Benchmark Scientific). To remove ribosomal RNAs, high-quality total RNA was processed using Illumina’s Ribo-Zero Bacteria kit (Illumina, San Diego, CA).
cDNA libraries were generated with rRNA depleted mRNA using the KAPA RNA Hyper Plus Kit (Roche, Indianapolis, IN) following the manufacturer’s instructions

treatment_protocol: No treatments were applied, rather a comparison between the wildtype and transposon mutated strain were compared.

value: whole-cell

value: 37C, shaken, logrithmic growth


title: NHA_ChIPseq_PPARD_RA_12h_rep2

description: Library name: Sample 29

value: NHA

value: immortalized human astrocytes


title: A66_A_OTC_Ttran_1

description:
Library name: A66_A_OTC_Ttran_1
A_OTC_Ttran


title: liver female control rep4

description: Library name: L_28

value: WT

value: Female-Vehicle Control


title: Non-treated gshA2:Tn cells replicate 3

description:
Library name: BT gshA2- 1
SE5983_SA52168_S34


title: A66_A_OTC_Tterm_2

description:
Library name: A66_A_OTC_Tterm_2
A_OTC_Tterm

value: terminally exhausted


title: liver female control rep3

description: Library name: L_27

value: adult

value: Batch 2


title: NHA_ChIPseq_PPARD_RA_12h_rep1

description: Library name: Sample 28


title: Non-treated gshA1:Tn cells replicate 3

description:
Library name: BT gshA1- 2
SE5983_SA52166_S32


title: NHA_ChIPseq_Input_RA_12h

description: Library name: Sample 27


title: liver female control rep2

description: Library name: L_26

value: Batch 1


title: A66_A_OTC_Tterm_1

description:
Library name: A66_A_OTC_Tterm_1
A_OTC_Tterm

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells


title: NHA_ChIPseq_PPARD_DMSO_rep2

description: Library name: Sample 26


title: Non-treated wildtype cells replicate 3

description:
Library name: BT wildtype 2
SE5983_SA52160_S26

value: wild-type


title: liver female control rep1

description: Library name: L_25


title: A66_A_OTC_Ttad_2

description:
Library name: A66_A_OTC_Ttad_2
A_OTC_Ttad

value: OTC control

value: age-associated dysfunctional


title: Non-treated egtB:Tn cells replicate 2

description:
BT egtB- 3
raw_counts.txt
BT_processed.xlsx
SE5983_SA52164_S30

source_name: whole bacterial cell

value: whole bacterial cell

tag: growth condition

value: 37C, shaken, logarithmic growth


title: NHA_ChIPseq_PPARD_DMSO_rep1

description: Library name: Sample 25


title: A66_A_OTC_Ttad_1

description:
Library name: A66_A_OTC_Ttad_1
A_OTC_Ttad


title: liver male high-dose exposure rep8

description: Library name: L_24

value: liver

value: Sprague-Dawley

value: Male-High Dose/50mg/kg


title: Non-treated egtB:Tn cells replicate 1

description:
BT egtB- 1
raw_counts.txt
BT_processed.xlsx
SE5983_SA52162_S28


title: A66_A_OTC_Tprog_2

description:
Library name: A66_A_OTC_Tprog_2
A_OTC_Tprog

value: progenitor exhausted


title: NHA_ChIPseq_Input_DMSO

description: Library name: Sample 24

value: NHA

value: immortalized human astrocytes

value: WT


title: liver male high-dose exposure rep7

description: Library name: L_23

value: adult

value: Batch 3


title: NHA_ChIPseq_H3K27Me3_before_CRISPRi_rep2

description: Library name: Sample 23


title: Non-treated gshA2:Tn cells replicate 2

description:
BT gshA2- 3
raw_counts.txt
BT_processed.xlsx
SE5983_SA52170_S36


title: liver male high-dose exposure rep6

description: Library name: L_22

value: Batch 2


title: NHA_ChIPseq_H3K27Me3_before_CRISPRi_rep1

description: Library name: Sample 22


title: Non-treated gshA2:Tn cells replicate 1

description:
BT gshA2- 2
raw_counts.txt
BT_processed.xlsx
SE5983_SA52169_S35


title: A66_A_OTC_Tprog_1

description:
Library name: A66_A_OTC_Tprog_1
A_OTC_Tprog

value: B16-OVA Tumor


title: A66_A_Dusp5_Ttran_2

description:
Library name: A66_A_Dusp5_Ttran_2
A_Dusp5_Ttran

value: Cas9 OT-1 CD8+ T cells

value: transitory, effector-like


title: liver male high-dose exposure rep5

description: Library name: L_21


title: NHA_ChIPseq_H3K27AC_before_CRISPRi_rep_2

description: Library name: Sample 21


title: Non-treated gshA1:Tn cells replicate 2

description:
BT gshA1- 3
raw_counts.txt
BT_processed.xlsx
SE5983_SA52167_S33


title: A66_A_Dusp5_Ttran_1

description:
Library name: A66_A_Dusp5_Ttran_1
A_Dusp5_Ttran


title: liver male high-dose exposure rep4

description: Library name: L_20


title: Non-treated wildtype cells replicate 2

description:
BT wildtype 3
raw_counts.txt
BT_processed.xlsx
SE5983_SA52161_S27

value: wild-type


title: liver male high-dose exposure rep3

description: Library name: L_19

value: Batch 1


title: A66_A_Dusp5_Tterm_1

description:
Library name: A66_A_Dusp5_Tterm_1
A_Dusp5_Tterm

value: terminally exhausted


title: NHA_ChIPseq_H3K27Me3_after_CRISPRi_rep2

description: Library name: Sample 18


title: A66_A_Dusp5_Ttad_2

description:
Library name: A66_A_Dusp5_Ttad_2
A_Dusp5_Ttad

value: age-associated dysfunctional


title: liver male high-dose exposure rep1

description: Library name: L_17

value: liver


title: NHA_ChIPseq_H3K27Me3_after_CRISPRi_rep1

description: Library name: Sample 17


title: Mycosis fungoides patient 16 plaque skin lesion CosMx SMI

type: RNA

city: Seoul

first: Myoung Eun

last: Choi

address: Song-pa gu

country: South Korea

institute: Asan medical center

description: CosMx SMI profiling of MF plaque stage skin, patient 16

hyb_protocol: In situ hybridization was performed on FFPE sections according to the NanoString CosMx SMI protocol. Probe hybridization, ligation, and fluorescence imaging were performed on the CosMx SMI instrument.

scan_protocol: Fluorescence imaging was performed on the NanoString CosMx SMI instrument. Multiple fields of view (FOVs) were acquired per tissue section. Transcript detection and cell segmentation were performed using NanoString AtoMx software.

data_processing:
Raw transcript counts were processed using NanoString AtoMx software. Cell segmentation was performed using DAPI and morphology marker channels. Downstream analysis including quality control, normalization (SCTransform), dimensionality reduction, and cell type annotation was performed in R using Seurat v5. Cells passing QC filters (nCount_RNA > 0, qcFlagsRNACounts = Pass) were retained for analysis.
Raw transcript counts per cell per gene

source_name: skin biopsy

label_protocol: RNA targets were detected using the NanoString CosMx 980-plex RNA panel with fluorescently labeled probes according to the manufacturer's protocol (NanoString Technologies).

growth_protocol: N/A - clinical biopsy specimens

extract_protocol: Skin punch biopsies from patients with mycosis fungoides were formalin-fixed and paraffin-embedded (FFPE). FFPE sections (5 um) were prepared for CosMx SMI profiling according to the NanoString CosMx SMI FFPE sample preparation protocol.

treatment_protocol: N/A - clinical biopsy specimens

tag: disease

value: mycosis fungoides

value: skin

tag: disease stage

value: plaque

tag: patient id


title: liver male low-dose exposure rep8

description: Library name: L_16

tag: tissue

value: Sprague-Dawley

value: Male-Low Dose/5mg/kg


title: A66_A_Dusp5_Ttad_1

description:
Library name: A66_A_Dusp5_Ttad_1
A_Dusp5_Ttad

tag: cell type


title: NHA_ChIPseq_H3K27AC_after_CRISPRi_rep_2

description: Library name: Sample 16

value: NHA

value: immortalized human astrocytes

value: WT


title: Mycosis fungoides patient 15 plaque skin lesion CosMx SMI

description: CosMx SMI profiling of MF plaque stage skin, patient 15


title: liver male low-dose exposure rep7

description: Library name: L_15

value: adult

value: Batch 2


title: A66_A_Dusp5_Tprog_1

description:
Library name: A66_A_Dusp5_Tprog_1
A_Dusp5_Tprog

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: progenitor exhausted


title: NHA_ChIPseq_H3K27AC_after_CRISPRi_rep_1

description: Library name: Sample 15


title: liver male low-dose exposure rep6

description: Library name: L_14


title: Mycosis fungoides patient 13 plaque skin lesion CosMx SMI

description: CosMx SMI profiling of MF plaque stage skin, patient 13


title: scPerturb_AgedtdLN1

description:
Library name: scPerturb_AgedtdLN1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Gzipped files include 10x format single cell gene expression matrices, including barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, and protospacer_calls_per_cell.csv

extract_protocol:
Fifteen days after tumor inoculation, ametrine⁺ CD45.1 Cas9⁺ OT-1 CD8⁺ T cells were isolated from tumors and tumor-draining lymph nodes (tdLNs) of young and aged mice using a BD FACSAria™ Fusion sorter. Sorted cells from independent mice were pooled into two biological replicates per group, counted, and loaded onto a Chromium Controller (10x Genomics) for a target recovery of 10,000 single cells per run. Libraries were prepared with the 10x Single Cell 5′ Reagent Kits v2 (Dual Index) and Feature Barcode technology for CRISPR screening, following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq X or NextSeq 1000/2000 system using 100-cycle kits with paired-end reads.
Library was performed according to the manufacter’s instructions (10x Single Cell 5′ Reagent Kits v2, CG00511 RevD, 10x Genomics).

value: tdLN, B16-OVA Tumor


title: NHA_ChIPseq_Input_after_CRISPRi

description: Library name: Sample 14


title: liver male low-dose exposure rep5

description: Library name: L_13

value: Batch 3


title: GBM8_ChIPseq_PPARD_rep2

description: Library name: Sample 13

value: low-passage glioma-initiating stem-like cells


title: liver male low-dose exposure rep4

description: Library name: L_12

value: liver

value: Batch 1


title: Mycosis fungoides patient 11 plaque skin lesion CosMx SMI

description: CosMx SMI profiling of MF plaque stage skin, patient 11

value: mycosis fungoides

value: skin


title: scPerturb_YoungtdLN1

description:
Library name: scPerturb_YoungtdLN1
10x Genomics


title: liver male low-dose exposure rep3

description: Library name: L_11

value: Sprague-Dawley


title: GBM8_ChIPseq_Input

description: Library name: Sample 11


title: Mycosis fungoides patient 10 plaque skin lesion CosMx SMI

description: CosMx SMI profiling of MF plaque stage skin, patient 10

value: plaque


title: PETCC2610, DOX+PeptideE, rep3

city: Wuhu

first: Yu

last: Du

address: No. 8, Yinhe Avenue, Fanchang Economic Development Zone, Fanchang District

institute: Nourse Centre for Pet Nutrition

description: Library name: DOX_taiE3

data_processing:
Raw sequencing reads (FASTQ format) were quality-controlled using FastQC (v0.11.9). Low-quality reads and adapter sequences were trimmed using fastp (v0.19.5) with default parameters.
Assembly: Felis catus reference genome assembly F.catus_Fca126_mat1.0 (GCF_018350175.1)
Supplementary files format and content: Processed data are provided as a tab-delimited text file containing the gene expression count matrix for all six samples. Columns include gene ID, gene name, gene description, and raw read counts for each sample (DOX1, DOX2, DOX3, DOX_taiE1, DOX_taiE2, DOX_taiE3).

organism: Felis catus

source_name: kidney

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (TIANGEN; Cat. No. DP424) according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated by agarose gel electrophoresis and Agilent 5300 (RIN > 6.5).
mRNA was enriched from total RNA using Oligo(dT)-coated magnetic beads. The enriched mRNA was fragmented into approximately 300 bp fragments using fragmentation buffer. First-strand cDNA was synthesized using random primers and reverse transcriptase, followed by second-strand cDNA synthesis to generate double-stranded cDNA. The cDNA products were end-repaired, A-tailed, and ligated with sequencing adaptors. The adaptor-ligated products were purified and size-selected, followed by PCR amplification to enrich the final library. Library quality was assessed, and sequencing was performed on the Illumina NovaSeq 6000 platform (paired-end 150 bp).

value: kidney

value: PETCC 2610

value: DOX+PeptideE


title: liver male low-dose exposure rep2

description: Library name: L_10

value: adult

value: WT

value: Male-Low Dose/5mg/kg


title: GBM8_ChIPseq_H3K27Me3_before_CRISPRi_rep2

description: Library name: Sample 10


title: NHA_ChIPseq_H3K27AC_before_CRISPRi_rep_1

description: Library name: Sample 20

value: NHA

value: immortalized human astrocytes


title: liver male low-dose exposure rep1

description: Library name: L_09

value: Batch 2


title: GBM8_ChIPseq_H3K27Me3_before_CRISPRi_rep1

description: Library name: Sample 9


title: GBM8_ChIPseq_H3K27Ac_before_CRISPRi_rep2

description: Library name: Sample 8


title: Mycosis fungoides patient 7 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 7

value: patch


title: ChIPseq, RPB1, aux, flav, 0

data_processing:
Sequenced reads were aligned to hg38 and mm10 using bowtie (version 1.2.3) with “-n2-m1” parameters. The removal of redundant reads and the normalization of the read number for each sample were performed with parse2wig (version 3.7.2). For peak-calling, we used drompa_peakcall (version 3.7.2) in “PC_SHARP” mode, and for visualization, we used drompa+ PC_SHARP (version 1.17.2) and deeptools (version 3.5.1.)
Assembly: hg38
Supplementary files format and content: BigWig files generated by parse2wig (version 3.7.2)

extract_protocol:
HCT116 and C2C12 cells were crosslinked with 1% formaldehyde for 10 min, quenched with 125 mM glycine for 5 min, and washed with PBS. After collection by centrifugation, the fixed cells were frozen and stored at -80 C. The thawed cells resuspended with LB1 Buffer (50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton-X, 1 mM PMSF, 10 mM DTT, 1x cOmplete EDTA-free (Roche)) and incubated on ice for 10 min. After collection by centrifugation, the pellet was resuspended with LB2 Buffer (20 mM Tris-HCl (pH7.5), 200 mM NaCl, 1 mM EDTA, 1 mM PMSF, 1x cOmplete EDTA-free) and incubated on ice for 10 min. After centrifugation, the pellet was resuspended with LB3 Buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Na-Deoxycholate, 0.1 % SDS, 1x cOmplete EDTA-free) and incubated on ice for 10 min. Then, we repeated the centrifugation and resuspension with LB3 Buffer. For shearing chromatin, sonication was performed for 12 sec 6 times with amplitude setting at 17 % of the maximum amplitude using Sonifier 250D. Between each cycle, chromatin was collected by centrifugation. After the step of sonication, cell debris was removed by centrifugation at 19000 g for 15 min. 50 μl of Dynabeads Protein A or Dynabeads Protein G (Invitrogen) was washed with 5 mg/ml BSA/PBS twice and resuspended with BSA/PBS. 4 μg antibody was added to the beads, and the mixture was rotated for 3 h at 4 C. The beads was washed with BSA/PBS twice and with LB3 Buffer once and resuspended with LB3 Buffer. Chromatin from HCT116 and from C2C12 cells were mixed and incubated with antibody beads for 14 h at 4 C. The beads was washed with LB3 Buffer once, with LB3 High Buffer ( 20 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1 mM EDTA, 1 % Triton-X, 0.1 % Na-Deoxycholate, 0.1 % SDS) twice, with RIPA wash Buffer (50 mM HEPES-KOH (pH 7.4), 0.25 M LiCl, 1 mM EDTA, 0.5 % Na-Deoxycholate, 1 % NP-40) 3 times and with TE50 Buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA) once. Chromatin bound to beads was eluted with Elution Buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1 % SDS). The eluates were incubated at 65 °C for 6 h to reverse crosslinks and then treated with RNaseA and then with proteinase K. The samples were purified with QIAquick PCR purification kit (QIAGEN).  Methods Mol Biol, 2017. 1515: p. 257-271).
The library for sequencing was prepared with NEBNext DNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

value: Colorectal carcinoma

value: Flavopiridol,Auxin


title: PETCC2610, DOX, rep3

description: Library name: DOX3

value: DOX


title: liver male control rep7

description: Library name: L_07

value: liver

value: Male-Vehicle Control


title: GBM8_ChIPseq_H3K27Ac_before_CRISPRi_rep1

description: Library name: Sample 7

value: low-passage glioma-initiating stem-like cells


title: Mycosis fungoides patient 6 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 6

value: mycosis fungoides

value: skin


title: Mycosis fungoides patient 8 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 8


title: GBM8_ChIPseq_Input_before_CRISPRi

description: Library name: Sample 6


title: Y/Ti_2

city: Miami

first: xiaomin

last: cai

state: Florida

address: Rosenstiel Medical Science Building 1600 NW, 10th Ave.

institute: University of Miami

description: Library name: J2

data_processing:
Raw FASTQ files were processed in a Linux (Ubuntu 22.04) environment. Reads were aligned to the Mus musculus GRCm38 reference genome using HISAT2. Gene-level read counts were generated using featureCounts with the GENCODE vM25 annotation (gencode.vM25.annotation.gtf).
Assembly: Mus musculus GRCm38
Supplementary files format and content: The processed data file is a gene-level raw count matrix generated by featureCounts.

source_name: mouse knee joint tissue

extract_protocol:
For the first set, total RNA was extracted from mouse knee joint cartilage tissue using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. For the second and third sets, total RNA was extracted from mouse knee joint tissues using a modified Trizol/RNeasy. Knee tissues were cryogenically homogenized using stainless steel beads, lysed in TRIzol reagent, treated with Proteinase K, subjected to chloroform extraction, and purified using RNeasy spin columns (Qiagen).
For the first set, Sequencing libraries were then prepared according to the manufacturer’s protocol and sequenced by Innomics Inc. on the DNBSEQ platform using paired-end 100-bp reads.  For the second and third sets, Sequencing libraries were prepared according to the manufacturer’s protocol and sequenced by Admera Health, LLC on an Illumina platform using paired-end 150-bp reads.

value: mouse knee joint tissue


title: Mycosis fungoides patient 5 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 5


title: PETCC2610, DOX, rep1

description: Library name: DOX1

value: kidney

value: PETCC 2610


title: liver male control rep5

description: Library name: L_05

value: Sprague-Dawley

value: adult

value: WT


title: GBM8_ChIPseq_H3K27Me3_after_CRISPRi_rep2

description: Library name: Sample 5


title: Mycosis fungoides patient 4 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 4


title: A66_A_Dusp5_Tterm_2

description:
Library name: A66_A_Dusp5_Tterm_2
A_Dusp5_Tterm

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

value: terminally exhausted


title: Non-treated gshA1:Tn cells replicate 1

description:
BT gshA1- 1
raw_counts.txt
BT_processed.xlsx
SE5983_SA52165_S31

value: whole bacterial cell

value: 37C, shaken, logarithmic growth


title: NHA_ChIPseq_Input_before_CRISPRi

description: Library name: Sample 19

value: NHA

value: immortalized human astrocytes


title: PETCC2610, DOX, rep2

description: Library name: DOX2

value: DOX


title: liver male high-dose exposure rep2

description: Library name: L_18

value: liver

value: Male-High Dose/50mg/kg

value: Batch 2


title: Non-treated wildtype cells replicate 1

description:
BT wildtype 1
raw_counts.txt
BT_processed.xlsx
SE5983_SA52159_S25

value: wild-type


title: liver male control rep6

description: Library name: L_06

value: Male-Vehicle Control

value: Batch 3


title: LN, DC, KP, CD11c_IRF4, ADT

city: Paris

first: Nathan

last: Vaudiau

address: 25 rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

description:
Library name: LN_DC_KP_CD11c_IRF4_ADT
10x genomics
Antibody-derived oligonucleotide (ADT)
LN_DC_feature_reference.csv
LN_DC_KP_CD11c_IRF4_barcodes.tsv.gz
LN_DC_KP_CD11c_IRF4_features.tsv.gz
LN_DC_KP_CD11c_IRF4_matrix.mtx.gz

data_processing:
Raw sequencing reads were processed using the 10x Genomics software Cellranger. To obtain a cell count matrix, reads were mapped to the mouse mm10 reference genome. scRNA-seq analysis was performed using Seurat v4. For each dataset, cells with low genes per cell or with a high percentage of mitochondrial genes were removed from downstream analyses. Following data QC we obtained 4421 cells from the lungs KP CD8+ T cells dataset, 1404 cells for the tdLN KP WT CD8+ T cells dataset, 3340 cells for the tdLN KP CD11cIRF4 CD8+ T cells dataset, 2076 cells for the tdLN KP WT CD11c+MHCII+ cells dataset and 3150 cells for the tdLN KP CD11cIRF4 CD11c+MHCII+ cells dataset. RNA and ADT expression were normalized separately using the default Seurat LogNormalize and Centered Log Ratio (CLR) approaches, respectively. Top 2000 most variable genes were then determined by applying a VST (Variance Stabilizing Transformation). Datasets were analyzed separately or were integrated together before analysis. For integration, top 2000 most variable genes across datasets were used as anchors with the LogNormalize method. Dimensionality reduction was performed using PCA and the top informative principle components were determined after visualization with an elbow plot and dimensional reduction heatmaps, and used for the non-linear dimensionality reduction technique UMAP. Louvain clustering of the data was performed across a range of resolution parameters visualized using a clustree. Cluster of cells with low number of genes and in which no T lymphocyte cell identifying genes could be detected were not considered in the analysis. Subsequent analyses were performed using Seurat default parameters.
Assembly: mm10
Supplementary files format and content: Cellranger output files: Tab-separated values and matrix files
Supplementary files format and content: For ADT data: feature_reference.csv files
Library strategy: CITE-seq

molecule: protein

source_name: Lymph node

extract_protocol:
The droplet-based approach of 10X Genomics platform was used to perform scRNA-seq. For each scRNA-seq sample, cell suspension from three individual mice were pooled and sorted in PBS containing 0,04%BSA.
10 000 cells were loaded on a Chromium Controller using the Chromium Next GEM Single Cell 3 Reagent Kits v3.1 according to manufacturer instructions.

treatment_protocol: In this project, we have worked in the KP (KRASG12D; p53-/-) model of murine lung cancer. 14 days after intravenous injection of the KP cell line, CD8+ T cells or CD11c+MHCII+ cells were stained with CITE-Seq antibodies then sorted by flow cytometry from pooled lungs or lymph nodes of 3 C57BL/6J mice before scRNA-seq analysis.Single cells were isolated using a 10X Chromium droplet-based approach and sequenced.

value: Lymph node

value: KP

value: CD11c+MHCII+ cells

value: CD11ccre x Irf4fl/fl

tag: age

value: 8-12 weeks

value: ADT

tag: adt

value: TotalSeq-B0201 anti-mouse CD103, TotalSeq-B0422  anti-mouse SIRPa, TotalSeq-B0568 anti-mouse XCR1, TotalSeq-B0565 anti-mouse MerTK, TotalSeq-B0563 anti-mouse CX3CR1, TotalSeq-B0566 anti-mouse MGL2


title: liver male control rep4

description: Library name: L_04

value: Sprague-Dawley

value: adult

value: WT

tag: treatment


title: Mycosis fungoides patient 3 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 3

value: mycosis fungoides

value: skin

value: patch


title: GBM8_ChIPseq_H3K27Me3_after_CRISPRi_rep1

description: Library name: Sample 4

value: low-passage glioma-initiating stem-like cells


title: A66_A_Dusp5_Tprog_2

description:
Library name: A66_A_Dusp5_Tprog_2
A_Dusp5_Tprog

value: B16-OVA Tumor

value: Cas9 OT-1 CD8+ T cells

tag: gene knockout

value: progenitor exhausted


title: liver male control rep3

description: Library name: L_03

value: liver

value: Male-Vehicle Control

value: Batch 2


title: LN, DC, KP, WT, ADT

description:
Library name: LN_DC_KP_WT_ADT
10x genomics
Antibody-derived oligonucleotide (ADT)
LN_DC_feature_reference.csv
LN_DC_KP_WT_barcodes.tsv.gz
LN_DC_KP_WT_features.tsv.gz
LN_DC_KP_WT_matrix.mtx.gz

value: Lymph node

value: KP

value: CD11c+MHCII+ cells

tag: library type


title: Mycosis fungoides patient 2 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 2


title: GBM8_ChIPseq_H3K27Ac_after_CRISPRi_rep2

description: Library name: Sample 3


title: Mycosis fungoides patient 14 plaque skin lesion CosMx SMI

description: CosMx SMI profiling of MF plaque stage skin, patient 14

value: plaque


title: liver male control rep2

description: Library name: L_02

tag: strain

value: Sprague-Dawley

value: Batch 1


title: GBM8_ChIPseq_H3K27Ac_after_CRISPRi_rep1

description: Library name: Sample 2

value: WT


title: LN, DC, KP, CD11c_IRF4, RNA

description:
Library name: LN_DC_KP_CD11c_IRF4_RNA
10x genomics
RNA

data_processing:
Raw sequencing reads were processed using the 10x Genomics software Cellranger. To obtain a cell count matrix, reads were mapped to the mouse mm10 reference genome. scRNA-seq analysis was performed using Seurat v4. For each dataset, cells with low genes per cell or with a high percentage of mitochondrial genes were removed from downstream analyses. Following data QC we obtained 4421 cells from the lungs KP CD8+ T cells dataset, 1404 cells for the tdLN KP WT CD8+ T cells dataset, 3340 cells for the tdLN KP CD11cIRF4 CD8+ T cells dataset, 2076 cells for the tdLN KP WT CD11c+MHCII+ cells dataset and 3150 cells for the tdLN KP CD11cIRF4 CD11c+MHCII+ cells dataset. RNA and ADT expression were normalized separately using the default Seurat LogNormalize and Centered Log Ratio (CLR) approaches, respectively. Top 2000 most variable genes were then determined by applying a VST (Variance Stabilizing Transformation). Datasets were analyzed separately or were integrated together before analysis. For integration, top 2000 most variable genes across datasets were used as anchors with the LogNormalize method. Dimensionality reduction was performed using PCA and the top informative principle components were determined after visualization with an elbow plot and dimensional reduction heatmaps, and used for the non-linear dimensionality reduction technique UMAP. Louvain clustering of the data was performed across a range of resolution parameters visualized using a clustree. Cluster of cells with low number of genes and in which no T lymphocyte cell identifying genes could be detected were not considered in the analysis. Subsequent analyses were performed using Seurat default parameters.
Assembly: mm10
Supplementary files format and content: Cellranger output files: Tab-separated values and matrix files
Supplementary files format and content: For ADT data: feature_reference.csv files

value: CD11ccre x Irf4fl/fl

value: 8-12 weeks

value: RNA


title: Mycosis fungoides patient 1 patch skin lesion CosMx SMI

description: CosMx SMI profiling of MF patch stage skin, patient 1

value: mycosis fungoides

value: skin

value: patch


title: LN, DC, KP, WT, RNA

description:
Library name: LN_DC_KP_WT_RNA
10x genomics
RNA


title: GBM8_ChIPseq_Input_after_CRISPRi

description: Library name: Sample 1

value: low-passage glioma-initiating stem-like cells


title: Zebra finch Gonadal culture timecourse, DIV10 replicate 1

status: Public on Jul 06 2026

first: Matthew

middle: T

last: Biegler

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: zT10_r1
ZF_Gonad_timecourse_fcCounts.csv

data_processing:
Quality control analysis was performed using similar approaches in our previous study28. Briefly, raw sequencing data, was aligned to either the zebra finch, chicken, or mouse reference genome (depending on the sample) using CellRanger (v6.0.1). The DIV150 chicken dataset was also aligned to a concatenated chicken and mouse assembly for competitive mapping. Subsequent processing steps (quality controls and barcode trimming) were performed using R (v4.4.1) with soupX (v1.5.2), Seurat (v5.1.0), and DoubletFinder (v2.0.4).
For bulk RNA sequencing data,, gonadal and blood culture samples (see Table S11 from the associated study) were aligned to the bTaegut1.4.pri reference genome using HiSAT2 (v2.2.1) and analyzed with DESeq2 using a standard pipeline.
Assembly: Zebra Finch - bTaeGut1.4.pri: GCF_003957565.2 with custom GTF
Supplementary files format and content: ZF_Gonad_timecourse_fcCounts.csv contains assigned gene counts for all timecourse samples.

organism: Taeniopygia guttata

source_name: primary cell culture

growth_protocol: Gonadal cultures from HH28 zebra finch and chicken embryos were generated as previously described9,27, incubated at 37°C and 5% CO2 in a Heracell VIOS 160i incubator (Thermo Scientific). Cell culture media recipes used are available in Table S16 of the associated manuscript.  For the primary culture pool, forty embryos (unsexed male and female) were pooled and dissociated at 37°C with 0.05% trypsin (zebra finch: 5min; chicken: 15min) and equally split across multiple wells of a 12-well plate (zebra finch = 8 wells; chicken = 12 wells). For the non-adherent fraction, the supernatant was collected from all wells after briefly swirling the plate and pelleted at 300xg for 5min. For the adherent cells, wells were washed twice with HBSS and dissociated with 0.05% trypsin for 5min, neutralized in PGC media, and pelleted at 300xg for 5min. For each fraction, half of the pellets were taken for DIV3 samples, while the remaining cells were resuspended in fresh PGC media and incubated in 4-6 wells until DIV6.

extract_protocol:
RNA was extracted from cell pellets using RNA micro kit (QIAGEN, Cat. # 74034), reverse transcribed using SuperScript Reverse Transcriptase II (Invitrogen, Cat. # 18064014), and PCR amplified for 16 cycles with KAPA Hi-Fi HotStart ReadyMix (KAPA Biosystems, Cat. #KK2601).
Bulk RNA Sequencing libraries were prepared using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, Cat. #E7805S) before being sent to Novogene Corporation, Inc. (Sacramento, CA, USA) for sequencing on an Illumina HiSeq 4000.

treatment_protocol: At designated time points, non-adherent cells were pelleted at 250xg for 3min.

tag: Sex

value: pooled male and female

value: primary cell culture

tag: days in_vitro

value: 10 days in vitro

value: embryonic gonadal cell cultures (HH28)

value: C


title: liver male control rep1

description: Library name: L_01

data_processing:
RNA-seq data quality was assessed using FASTQC (v0.12.1) and summarized with MultiQC (v1.28)
PCR duplicates were removed by deduplicating sequencing reads with UMI-tools (v1.1.5)
Low-quality bases were trimmed using Cutadapt (v4.9) and Trim Galore (v0.6.10)
The cleaned reads were then aligned to the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1) using STAR (v2.7.11b)
Quantification of transcript abundance was performed with Salmon (v1.10.3)
Assembly: the Rattus norvegicus genome assembly (mRatBN7.2; GCA_036323735.1
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcrit level generated by salmon  (*.gene_counts.tsv )
Supplementary files format and content: A tab-delimited matrix table with  raw read counts at the  transcript level generated by salmon  (*.transcript_counts.tsv )

value: liver

tag: developmental stage

value: adult

tag: genotype

value: Male-Vehicle Control

tag: batch


title: Zebra finch Gonadal culture timecourse, DIV10 replicate 2

description:
Library name: zT10_r2
ZF_Gonad_timecourse_fcCounts.csv

tag: cell line


title: Zebra finch Gonadal culture timecourse, DIV9 replicate 2

description:
Library name: zT9_r2
ZF_Gonad_timecourse_fcCounts.csv

value: 9 days in vitro