title: WT1-HSC (0h) rep1

city: BOSTON

first: Jose

last: Cancelas

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: WT-1-18685

data_processing:
Reads were aligned with TopHat software, using  mm10 as the reference genome and Reads Per Kilobase of transcript per Million mapped reads (RPKM) as output.
To identify differentially expressed genes using default parameters moderated t-test, raw p-value cut-off of 0.05, and an expression cut-off of 1.5-fold using AltAnlayze v2.1.0 (developed at Cincinnati Children's Hospital Medical Center). The Gene ontology pathway analyses and heatmaps were generated using Altanalyze v2.1.0 software.
Assembly: mm10
Supplementary files format and content: excel files (expression values and group comparison statistics)

source_name: Bone Marrow

growth_protocol: WT and Connexin 43 knockout bone marrow HSC (Lin- /cKit+/Sca1+/CD48-/CD150+) were cultured in IMDM medium supplemented with 10% FBS, 100 IU/mL penicillin, 0.1 mg/ml streptomycin and 2mM L-glutamine, recombinant murine stem cell factor (rm-SCF, 50 ng/mL, Peprotech Inc) and recombinant mouse thrombopoietin (rm-TPO, 25 ng/mL, Peprotech Inc). The cells were analyzed after cell division (48 hours in culture).

extract_protocol:
Total RNA was extracted from WT and Connexin 43 knockout quiescent (0h) and dividing (48h) HSC (Lin- /cKit+/Sca1+/CD48-/CD150+) using RNeasy Mini Kit (QIAGEN) according to manufacturer's protocols. RNA quality and concentration were measured by Bioanalyzer 2100 using the RNA 6000 Nano Assay (Agilent Technologies).
RNA-seq libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2500 following the manufacturer's protocol. The concentration of the pool was optimized to acquire at least 25-30 million reads per sample using Paired-End Reads with a read length of 75 bps.

value: Bone Marrow

value: LT-HSC

value: WT

value: Quiescent (0 h)


title: FWT_C1

status: Public on Aug 19 2025

type: SRA

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

country: China

institute: Tongji University

description: Library name: FWT_C1

library_source: transcriptomic

data_processing:
Pair-end FASTQ files were mapped to the Mus_musculus.GRCm38.101 reference genomes, via using the HISAT2 package. Then, the FPKM values were calculated with StringTie and Ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html). Differential gene expression was analyzed using DESeq2, with genes having a P value ≤ 0.05 and absolute fold change ≥ 2 recognized as differentially expressed genes (DEGs). Heatmaps were generated, and Gene Ontology (GO) and KEGG pathway analyses were performed on DEGs using the OmicStudio tools at https://www.omicstudio.cn/tool. Gene set enrichment analysis (GSEA) was conducted using GSEA (v4.1.0) and MSigDB to identify gene sets involved in specific pathways.
Assembly: Mus_musculus.GRCm38.101
Supplementary files format and content: Excel file including FRKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: aorta

extract_protocol:
High-throughput mRNA sequencing was performed by the LC-Bio Technology co.ltd., (HangZhou, China). The quality of total RNAs was assessed by BioAnalyzer 2100 (Agilent Technologies).
RNA libraries were constructed with TruSeq Stranded Total RNA Library Prep kit (Illumina). Libraries were quality-controlled for size distribution and quantified with Qubit Fluorometer (Thermo Fisher Scientific). The libraries were sequenced on an Illumina HiSeq sequencer for 150-bp paired-end reads according to the manufacturer’s instructions.

tag: tissue

value: aorta

tag: genotype

tag: treatment

value: PBS


title: siCRY1, RPA, ChIP

city: Sevilla

first: Pablo

last: Huertas

address: Av.Americo Vespucio 24

country: Spain

institute: University of Sevilla

library_source: genomic

data_processing:
Raw sequencing files (fastq) quality was assessed using FastQC 0.12.0
Aligment to the reference human genome (version hg19) using bwa 0.7.17
Mapped sequences were sorted and indexed using samtools 1.19.2
Coverage of mapped reads in bigwig format was obtained using deepTools 3.5.3 bamCoverage
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: AsiSI-ER U2OS

growth_protocol: Low-glucose Dulbecco’s Modified Eagle Medium (DMEM) + 10% charcoal-stripped FBS

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10minutes at 37°C. Crosslinking reaction was quenched with 125mM glycine for 5minutes and cells were washed 3 times with PBS. Cell pellets were resuspended in 2.5mL lysis buffer A (5mM Pipes pH 8.0, 85mM KCl, 0.5% NP40, 1mM PMSF) supplemented with protease inhibitors and incubated for 10minutes on ice.
Libraries were amplified for N-1 cycles (being N the optimum Cq determined by qPCR reaction) using NEBNext High-Fidelity Polymerase (New England Biolabs, M0541). Libraries were purified with Sera-Mag Select Beads (GE Healthcare, 29343052)

treatment_protocol: 300 nM 4-OHT for 4h

tag: cell line

value: AsiSI-ER U2OS

tag: cell type

value: Bone epithelium

tag: chip antibody

value: RPA32 (Abcam Cat#ab2175, RRID:AB_302873)


city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

country: USA

institute: Harvard Medical School

description:
Library name: I36H2_spleen_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40

source_name: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

extract_protocol:
Single-cell suspensions of spleens and lymph nodes were prepared by mechanical disruption, followed by ACK-lysing buffer. For tissue preparations, siIEL were prepared by excision of Peyer’s patches and removal of luminal contents. Then the entire tissue section was cut longitudinally, then cut laterally into 1 cm pieces, which were then incubated at 37°C for 30 minutes in Hanks’ balanced salt solution with 2.4 mg ml−1 of Hepes, 2.1 mg ml−1 of sodium bicarbonate, 8% bovine growth serum and 0.154 mg ml−1 of DTE (EMD Millipore). After collecting the siIEL sample, RPMI with 1.2 mg ml−1 of Hepes, 292 µg ml−1 of L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% FBS and 100 U ml−1 of collagenase (Worthington) was added to the SI pieces at 37°C for 30 minutes for siLPL isolation. The SG and lung were cut into small pieces then incubated with shaking at 37°C for 30 minutes (SG) or 1 hour (lung) in the same RPMI-collagenase solution as listed previously for the siLPL. Prostate tissue was dissected from the bladder and seminal vesicles, cut into small pieces, the incubated shaking at 37°C for 30 minutes in the same RPMI-collagenase solution as listed previously. Bone marrow was isolated by harvesting the femurs and tibias and pushing out the bone marrow with a syringe. Lymphocytes from non-lymphoid tissues were further enriched using a 44%/67% Percoll density gradient. Cells were incubated with FC block and stained with Live/Dead, CD3, CD45.2 and CD45.1 on ice prior to sorting.
Libraries were prepared according to the 10x Genomics 5'v2 protocol for GEX, VDJ, and FBC

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

tag: prep description

value: mechanical dissociation alone

tag: organ

value: spleen

tag: organ uberon_id

tag: t specificity

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

tag: gating strategy

value: CD45+ CD3e+

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells

tag: batch


title: AK cells, rep2

city: taipei

first: Tai-Lung

last: Cha

state: taipei

address: 11490 No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114, Taiwan (R.O.

department: National Institute of Cancer Research

country: Taiwan

institute: National Defense Medical Center

description:
Library name: Smaple 20
Column name in ACHN_LL_raw_counts.txt :AK_rep2

data_processing:
RNAseq:RNA-seq data were aligned to the UCSC reference genome using Bowtie2 (v2.4.5). The human genome (GRCh37/hg19) and mouse genome (GRCm38/mm10) assemblies from the UCSC Genome Browser were used as references. Aligned reads were processed with SAMtools (v1.3) to generate a read count table for each gene.
ATACsaq: Reads were mapped to the human genome (hg19) and mouse genome (mm10) using Bowtie2. PCR duplicates were removed using Picard Tools. For peak calling, biological replicates were merged and processed using MACS2. Peaks from all replicates were further merged using SAMtools. Variance-stabilizing transformation and principal component analysis (PCA) were performed using SeqMonk, based on the DESeq2 model. Visualization of ATAC-seq signals across specific genes was performed using the Integrative Genomics Viewer (IGV).
Assembly: hg19 and mm10
Supplementary files format and content: text files inculed raw counts for each sample
Supplementary files format and content: csv files include FPKM value for each sample

source_name: kidney

growth_protocol: Cell lines were cultured in media recommended by the American Type Culture Collection (ATCC) and maintained at 37°C in a humidified incubator with 5% CO₂. Bone marrow cells were isolated from mouse femurs and tibias by PBS flushing, followed by red blood cell lysis with Tris-ammonium chloride. Cells were filtered through a 70-μm strainer and cultured in RPMI-1640 supplemented with 10% heat-inactivated FBS. For stimulation, cells were seeded at 0.5 × 10⁶ cells/ml with 20 ng/ml M-CSF. Fresh cytokine-containing medium was added on day 2, and cells were collected over a 5-day period.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN). RNA-seq libraries were prepared from pretreated RNA using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. For ATAC-seq, 1×10⁶ cells were collected, washed with PBS, and lysed in cold ATAC RSB lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1%Tween-20, and 0.01% digitonin). Nuclei were washed with ATAC RSB containing 0.1% Tween-20 and resuspended in transposition mix containing Tn5 transposase (Illumina). Transposition was carried out at 37°C for 30 min with shaking at 300 rpm. DNA was purified using the Qiagen MinElute PCR Purification Kit and libraries were amplified using NEBNext PCR master mix (NEB).
RNA-seq libraries were quantified using Qubit (Invitrogen), denatured to single-stranded DNA, loaded onto Illumina flow cells, amplified by in situ cluster generation, and sequenced for 150 cycles on an Illumina HiSeq 2500 platform following the manufacturer's instructions. ATAC-seq libraries were sequenced on an Illumina NextSeq 550 system using paired-end reads.

tag: tissue

value: kidney

tag: cell line

value: AK

tag: cell type

value: human renal carcinoma cell

tag: genotype

value: wild-type

tag: treatment

value: no treatment (wild-type, differing metastatic potential)


title: FKO_T2

description: Library name: FKO_T2

value: aorta

value: Ang-II/BAPN


description:
Library name: I36H2_spleen_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: CITE-seq

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE


title: AK cells, rep1

description:
Library name: Smaple 19
Column name in ACHN_LL_raw_counts.txt :AK_rep1

tag: tissue


title: siCRY1, CtIP, ChIP

tag: cell line

value: AsiSI-ER U2OS

value: Bone epithelium

tag: chip antibody

value: CtIP 14.1 (Active Motif Cat# 61141, RRID:AB_2714164)


title: I36H1_spleen_allT_mouse0126_TCR

description:
Library name: I36H1_spleen_allT_mouse0126_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

data_processing:
The demultiplexing, barcode process and gene/ ADT/ hash counts were generated using Cellranger software v7.0.0.
TCRab contig annotations were generating using the cellranger vdj function from Cellranger software v7.0.0. The contigs generated were then mapped to with IMGT, and TRA and TRB chains put back together to create a summary table.
GEX and FBC libraries were processed using Seurat, where RNA, ADT QC was performed, a long with HTO demultiplexing to assign each cell a sample
Assembly: mm10
Supplementary files format and content: Cellranger output files: IGT36_cells.tsv, IGT36_matrix_rna.mtx, genes.tsv, IGT36_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT36.
Supplementary files format and content: Cellranger output files: IGT36_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT36
Supplementary files format and content: Cellranger output files: IGT38_cells.tsv, IGT38_matrix_rna.mtx, genes.tsv, IGT38_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT38.
Supplementary files format and content: Cellranger output files: IGT38_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT38
Supplementary files format and content: Cellranger output files: IGT40_cells.tsv, IGT40_matrix_rna.mtx, genes.tsv, IGT40_matrix_protein.mtx, proteins.tsv,  - Processed data from GEX, ADT and HTO libraries for IGT40.
Supplementary files format and content: Cellranger output files: IGT40_summary_table.csv - Mapped TCR contigs with TCR gene annotations for VDJ library of IGT40
Library strategy: TCR-seq

value: spleen

value: wt

tag: jax

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

tag: gating strategy

value: CD45+ CD3e+

tag: cell type

value: T cells

tag: batch


title: ACHN cells, rep2

description:
Library name: Smaple 18
Column name in ACHN_LL_raw_counts.txt :ACHN_rep2

value: kidney

value: ACHN

value: human renal carcinoma cell

tag: genotype

value: wild-type

tag: treatment

value: no treatment (parental ACHN)


title: FKO_T1

description: Library name: FKO_T1

value: aorta

value: Ang-II/BAPN


title: siNT, RPA, ChIP

value: RPA32 (Abcam Cat# ab2175, RRID:AB_302873)


title: siNT, CtIP, ChIP

value: AsiSI-ER U2OS

value: CtIP 14.1 (Active Motif Cat# 61141, RRID:AB 2714164)


title: I36H1_spleen_allT_mouse0126_GEX

description:
Library name: I36H1_spleen_allT_mouse0126_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: male

value: FALSE


title: ACHN cells, rep1

description:
Library name: Smaple 17
Column name in ACHN_LL_raw_counts.txt :ACHN_rep1

tag: tissue

tag: cell line


title: I36H1_spleen_allT_mouse0126_FBC

description:
Library name: I36H1_spleen_allT_mouse0126_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: spleen

value: wt

tag: Sex

tag: age weeks

tag: pool of_mice

tag: jax

tag: prep description

value: mechanical dissociation alone

tag: organ

tag: organ uberon_id

tag: target cells

value: all T

value: CD45+ CD3e+

value: T cells


title: FKO_C2

description: Library name: FKO_C2

value: aorta

tag: genotype

tag: treatment

value: PBS


title: FKO_C3

description: Library name: FKO_C3


title: U937 cells, biol rep 2

city: Heidelberg

first: Fu

last: Xu

address: INF 280

country: Germany

institute: DKFZ

data_processing:
DKFZ One Touch Pipeline (OTP), RNA-seq workflow version 1.3.0 with Roddy version 3.5.8 or 3.5.9
Reads were aligned using STAR version 2.5.3a 31. Duplicate marking was performed using Sambamba version 0.6.5 32. FeatureCounts of the Subread package version 1.5.1 35 was used for gene specific quantification of reads. Gene annotation: GENCODE version 19 in the strand-specific counting mode.
Assembly: hg19
Supplementary files format and content: text files include raw count values per sample

extract_protocol:
RNA was extracted from cells or tissues using TRIZOL (Thermo Fisher Scientific) following manufacturer’s instructions. DNase treatment was performed for 30 minutes at 37oC and DNase was removed via phenol-chloroform extraction. rRNA-depleted RNA was used to generate the RNA-sequencing libraries using NEB Ultra II directional kit (New England Biolabs).
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol.

tag: cell type

value: Leukaemia cell line


title: U937 cells, biol rep 3


title: FKO_C1

description: Library name: FKO_C1


title: Sum159 ITGB low clone 3 control

city: Cambridge

first: Jingwei

last: Zhang

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

data_processing:
The Illumina 50bp long single-end reads were mapped with STAR(version 2.7.1a), using index files created with the gene annotation from Ensemble human hg38 version 93 with the ‘--sjdbOverhang 49’ option, and reads corresponding to the second read strand aligned with RNA were assigned to features.
Assembly: hg38
Supplementary files format and content: tab delimited text with raw counts for each sample

molecule: polyA RNA

growth_protocol: The cancer cells harvested from lungs of mice were cultured in Ham's F-12 medium supplemented with 5% inactivated fetal bovine serum (FBS), 5 μg/mL insulin, 1 μg/mL hydrocortisone, and 1% penicillin/streptomycin at 37℃ in a 5% CO2 incubator.

extract_protocol:
RNA was extracted and purified with RNeasy Micro Kit (Qiagen).
Libraries were prepared for RNA-Seq using Roche Diagnostics KAPA mRNA HyperPrep Kit, according to manufacturer’s directions. Briefly, total RNA (0.1-1 ug) is enriched for polyadenylated sequences using oligo-dT magnetic bead capture. The enriched mRNA fraction is then fragmented, and first-strand cDNA is generated using random primers.Strand specificity is achievedduring second-strand cDNA synthesis by replacing dTTP with dUTP, which quenches the second strand during amplification. The resulting cDNA is A-Tailed and ligated with indexed adapters. Finally, the library is amplified using a DNA Polymerase which cannot incorporate past dUTPs, effectively quenching the second strand during PCR.

treatment_protocol: Mice transplanted with Sum159low-1 cells were treated with bleomycin through trachea, or Sum159low-1 cells and LM2 cells were co-injected into the lungs of mice. At the end point of the experiment, lungs were harvested and dissociated into cell suspension.

value: ITGB4 low


title: U937 cells, biol rep 1


title: BMM cells, MYADM knockout, rep2

description:
Library name: Smaple 16
Column name in BMM_raw_counts.txt :BMM_KO_rep2

source_name: bone marrow

value: bone marrow

value: mouse bone marrow-derived monocyte

value: MYADM knockout

value: bone marrow-derived monocytes from MYADM knockout mice


title: Sum159 ITGB low clone 1 induced by LM2

value: induced by LM2


description:
Library name: I36H10_LNmediastinal_LCMVarm_D7_allT_P14_SMARTA_mouse0127_FBC
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

value: P14 and SMARTA > wt

value: male

tag: infection agent

value: LCMV armstrong

tag: infection dose

value: 2?ó10E5 PFU

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

value: mediastinal lymph node

tag: t specificity

value: P14, SMARTA

value: all T including P14 and SMARTA

tag: gating strategy

tag: sample comments

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

tag: batch


title: BMM cells, MYADM knockout, rep1

description:
Library name: Smaple 15
Column name in BMM_raw_counts.txt :BMM_KO_rep1

tag: tissue

value: bone marrow

value: mouse bone marrow-derived monocyte


title: SCC25 cells, biol rep 3

tag: cell line

value: HNSCC


title: SCC25 cells, biol rep 2


title: Sum159 ITGB low clone 1 control

tag: genotype

value: ITGB4 low


title: YSCH_01_2

first: Hanqiang

last: Jin

address: Pujian Road No.160

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

description: Library name: SAMPLES4

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRch38
Supplementary files format and content: tab - delimited text file includes raw counts for each Sample

source_name: bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone

value: Osteosarcoma cell line


title: Sum159 ITGB low clone 1 beomycin treated

tag: treatment

value: bleomycin treated


title: BMM cells, wild type, rep1

description:
Library name: Smaple 13
Column name in BMM_raw_counts.txt :BMM_WT_rep1

tag: cell type

value: wild-type

value: bone marrow-derived monocytes from wild-type mice


title: Vehicle_2

description: Library name: SAMPLES3


title: Sum159 ITGB4 high cells

value: ITGB4 high


title: Sum159 ITGB low clone 3 induced by LM2

value: induced by LM2


title: 4T1 cells, shRhoA, rep3

description:
Library name: Smaple 12
Column name in 4T1_raw_counts.txt :4T1_shRhoA_23B_rep3

source_name: mammary gland

value: mammary gland

value: mouse mammary carcinoma cell

value: RhoA knockdown

value: RhoA knockdown (shRhoA)


title: H143B_YSCH01

description: Library name: SAMPLES2


title: 4T1 cells, shRhoA, rep2

description:
Library name: Smaple 11
Column name in 4T1_raw_counts.txt :4T1_shRhoA_23B_rep2


title: RPMI-8226 cells, biol rep 2

value: B lymphocyte


title: no rRNA depletion

first: Jiří

last: Koubek

address: INF 345

department: ZMBH

institute: Heidelberg University

description: Library name: mouse-no-depletion

data_processing:
demultiplexed libraries were trimmed via cutadapt to remove universal linkers
unique molecular identifiers were extracted
rRNA sequences were removed by alignment against known rRNA
rRNA-depleted reads were aligned to corresponding genome
Assembly: E.coli GCA_000499485.1, yeast GCA_000146045.2, mouse GRCm39, GCA_000001635.9, human GRCh38p10, GCA_000001405.25
Supplementary files format and content: hdf5 files contain p-site assigned reads
Library strategy: Ribo-Seq

source_name: brain

extract_protocol:
total RNA was extracted via phenol:chlorophorm extraction
libraries were prepared according to Ingolia et al (2009) and by a method described within the accompanying manuscript

value: brain


description:
Library name: I36H10_LNmediastinal_LCMVarm_D7_allT_P14_SMARTA_mouse0127_TCR
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: immgent igt_10xlane_id

value: TRUE

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

value: Goldrath

tag: organism name

tag: strain

tag: genetics

value: P14 and SMARTA > wt

tag: Sex

value: male

tag: age weeks

tag: pool of_mice

value: FALSE

tag: jax

value: LCMV armstrong

value: 2?ó10E5 PFU

tag: prep description

value: anti-CD45 IV injection before tissue harvest, mechanical dissociation alone

tag: organ

value: mediastinal lymph node

tag: organ uberon_id

value: P14, SMARTA

tag: target cells

value: all T including P14 and SMARTA

value: CD45+ CD3e+

value: 100x10E3 SMARTA (male, CD45.1.2) and 50x10E3 P14 (male, CD45.1), intravenous, 1 day before infection

value: T cells


title: 4T1 cells, shRhoA, rep1

description:
Library name: Smaple 10
Column name in 4T1_raw_counts.txt :4T1_shRhoA_23B_rep1

tag: tissue

value: mammary gland

value: mouse mammary carcinoma cell

value: RhoA knockdown

value: RhoA knockdown (shRhoA)


description:
Library name: I36H10_LNmediastinal_LCMVarm_D7_allT_P14_SMARTA_mouse0127_GEX
Two separate 10x lanes of 10 individually hashed samples: Control_spleen, Bone.Marrow.LCMV.D7, IEL.LCMV.D7, LPL.LCMV.D7, Lung.Draining.LN, Lung.LCMV.D7, Mesenteric.LN.LCMV.D7, Prostate.LCMV.D7, Salivary.LCMV.d7, Spleen.LCMV.D7.M

value: siIEL, siLPL, prostate, SG, lung, bone marrow, spleen, mesenteric lymph nodes, mediastinal lymph nodes

tag: hashtag number

tag: condition detailed_organ

tag: cite seq

value: TRUE

tag: exp name

value: Pan organ and time course analysis of T cells in acute LCMV (armstrong) infection (day 7)

tag: lab

value: Goldrath

tag: infection agent

tag: infection dose

tag: t specificity

tag: gating strategy

tag: sample comments

tag: batch


title: Flow-sorted immune cells under CR infection in Small Intestine, 10x single-cell RNAseq, Gene Expression

city: Hangzhou

first: Heping

state: Zhejiang

address: 18 Shilongshan Road

institute: Westlake University

description:
Library name: sc10xCD4T.ILC3.SI_CR7d.AhrCKO.GEX
10x Genomics

data_processing:
sn/scRNA-seq: 10x Genomics Cellranger v7.0.0 was used to process fastq files and generate matrix files. Downstream normalization, filtering and clustering were done using Seurat v4.1.1 in R v4.1.3/ Rstudio.
Assembly: mm10
Supplementary files format and content: sn/scRNAseq: Cellranger output expression matrix files and feature barcode setting files packaged in tar.gz; final seurat object in rds file.
Library strategy: sn/scRNAseq: HTO hashtags + Gene Expression

source_name: Small intestine

growth_protocol: All mice were housed in specific-pathogen-free conditions with the Institutional Animal Care and Use Committee Guidelines of Westlake University

extract_protocol:
Flow-sorted GFP+ nuclei were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and 3’-end Library Kits by 10X Genomics,following the manufacturer’s protocol
Flow-sorted ILCs and Th cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and 3’-end Library Kits by 10X Genomics,following the manufacturer’s protocol
The nuclei/ cells were partitioned into the GemCode instrument.The products were subjected to reverse transcription, emulsion breaking, cDNA amplification, and sample index attachment (10×Genomics). Libraries were pair-end (150+ 150 bp)

treatment_protocol: Mice were fasted for 12-16 hours and then orally gavage with 200 μl of PBS containing 2×109 C. rodentium colony-forming units (CFU). Mice were euthanized 7 days post-infection for analysis.

value: Small intestine

tag: cell type

value: ILCs and Th cells

tag: genotype

value: Actl6b-Cre-Ahr-flox, CKO and CTL

tag: strain

tag: Sex

value: Female

tag: age

value: 8 weeks

tag: treatment

value: 2×109 C. rodentium infection 7days


title: PC-9 cells, biol rep 3

tag: cell line

value: Lung cancer line


title: 4T1 cells, shMYADM#2, rep3

description:
Library name: Smaple 9
Column name in 4T1_raw_counts.txt :4T1_shMY_256_rep3

tag: tissue

value: MYADM knockdown

value: MYADM knockdown (shMYADM)


title: BMM cells, wild type, rep2

description:
Library name: Smaple 14
Column name in BMM_raw_counts.txt :BMM_WT_rep2

value: bone marrow

value: mouse bone marrow-derived monocyte

value: wild-type

value: bone marrow-derived monocytes from wild-type mice


title: Flow-sorted immune cells under CR infection in Small Intestine, 10x single-cell RNAseq, HTO Hashtags

description:
Library name: sc10xCD4T.ILC3.SI_CR7d.AhrCKO.FB
10x Genomics

library_source: other

molecule: other


title: Enteric Neurons under CR infection in Colon, 10x single-nucleus RNAseq, Gene Expression

description:
Library name: sn10xENC.LI_CR7d.AhrCKO.GEX
10x Genomics

source_name: Colon

value: Colon

value: Enteric neurons

value: Actl6b-Cre-Ahr-flox-Sun1GFP, CKO and CTL

value: Male


title: EPSCs_NT1220_Rep.1

city: Cheongju

first: Lian

last: Cai

state: Chungcheongbuk-do

address: 1 Chungdae-ro, Seowon-gu

country: South Korea

institute: Chungbuk national university

description:
Library name: Sample 5
Column name in Raw_Counts_All_Samples.txt: EPSCs_NT1220_Rep.1

data_processing:
cutadapt v 2.8
Sequence reads were trimmed for adoptor sequence, parameter : quality-cutoff (20), minimum-length (50)
STAR v 2.7.1a
Filtered reads were mapped to the reference genome related to the species.
parameter : outFilterType (BySJout), outFilterMultimapNmax (20), alignSJoverhangMin (8), alignSJDBoverhangMin (1), outFilterMismatchNmax (999), outFilterMismatchNoverLmax (0.04), alignIntronMin (20), alignIntronMax (1000000), alignMatesGapMax (1000000)
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Sus scrofa

source_name: EPSCs

extract_protocol:
RNA was harvested using RNAiso Plus reagent (TaKaRa Bio Inc., Otsu, Japan), 10ng total RNA was used for constrction of RNA sequecing labraries.
Libraries were constructed for 151bp paired-end sequencing using a SMARTer Stranded Total RNA-Seq Kit V2-Pico Input (Takara Bio, Inc.) following manufacturer's protocols

value: EPSCs

value: Pluripotent stem cells


title: 4T1 cells, shMYADM#2, rep2

description:
Library name: Smaple 8
Column name in 4T1_raw_counts.txt :4T1_shMY_256_rep2

value: mammary gland

value: mouse mammary carcinoma cell


title: PC-9 cells, biol rep 1


title: PC-9 cells, biol rep 2


title: cas9 rRNA depletion

description: Library name: mouse-cas9-depletion

value: brain


title: Enteric Neurons under CR infection in Colon, 10x single-nucleus RNAseq, HTO Hashtags

description:
Library name: sn10xENC.LI_CR7d.AhrCKO.FB
10x Genomics

value: 8 weeks

value: 2×109 C. rodentium infection 7days


title: iPSCs_Rep.1

description:
Library name: Sample 3
Column name in Raw_Counts_All_Samples.txt: iPSCs_Rep.1

source_name: iPSCs

value: iPSCs


title: 4T1 cells, shMYADM#1, rep3

description:
Library name: Smaple 6
Column name in 4T1_raw_counts.txt :4T1_shMY_255_rep3

value: MYADM knockdown

value: MYADM knockdown (shMYADM)


title: RPMI-8226 cells, biol rep 1

value: B lymphocyte


title: 4T1 cells, shMYADM#1, rep2

description:
Library name: Smaple 5
Column name in 4T1_raw_counts.txt :4T1_shMY_255_rep2


title: SCC25 cells, biol rep 1

value: HNSCC


title: NT_BL_Day7_Rep.2

description:
Library name: Sample 2
Column name in Raw_Counts_All_Samples.txt: NT_BL_Day7_Rep.2

source_name: Pre-implantation Embryos

value: Pre-implantation Embryos


title: EPSCs_NT1220_Rep.2

description:
Library name: Sample 6
Column name in Raw_Counts_All_Samples.txt: EPSCs_NT1220_Rep.2


title: OPM2 cells, biol rep 2

value: multiple myeloma


title: Enteric Neurons at steady state in Small Intestine, 10x single-nucleus RNAseq, Gene Expression

description:
Library name: sn10xENC.SI_Stst.AhrCKO.GEX
10x Genomics

value: Small intestine

value: Enteric neurons

value: Steady state


title: RPMI-8226 cells, biol rep 3


title: 4T1 cells, shMYADM#2, rep1

description:
Library name: Smaple 7
Column name in 4T1_raw_counts.txt :4T1_shMY_256_rep1


title: Enteric Neurons at steady state in Small Intestine, 10x single-nucleus RNAseq, HTO Hashtags

description:
Library name: sn10xENC.SI_Stst.AhrCKO.FB
10x Genomics

value: Actl6b-Cre-Ahr-flox-Sun1GFP, CKO and CTL

value: Male


title: NT_BL_Day7_Rep.1

description:
Library name: Sample 1
Column name in Raw_Counts_All_Samples.txt: NT_BL_Day7_Rep.1


title: 4T1 cells, shMYADM#1, rep1

description:
Library name: Smaple 4
Column name in 4T1_raw_counts.txt :4T1_shMY_255_rep1

value: mammary gland


title: Enteric Neurons under CR infection in Small Intestine, 10x single-nucleus RNAseq, Gene Expression

description:
Library name: sn10xENC.SI_CR7d.AhrCKO.GEX
10x Genomics


title: H143B_Vehicle

description: Library name: SAMPLES1

value: bone

value: Osteosarcoma cell line


title: iPSCs_Rep.2

description:
Library name: Sample 4
Column name in Raw_Counts_All_Samples.txt: iPSCs_Rep.2

value: Pluripotent stem cells


title: OPM2 cells, biol rep 3


title: OCI-AML3 cells, biol rep 3

value: Leukaemia cell line


title: Thyroid gland, PD16, Cyanamid, replicate7

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
Quality control and preprocessing of data were performed by GenomEast (France).
The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI).
The second reads were aligned to the Rattus niorvegicus reference transcriptome from the UCSC website (release rn6) using BWA version 0.7.4.4 with the parameter “-l 24”
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Thyroid gland

growth_protocol: Pregnant Sprague-Dawley (Crl:CD(SD)) rats (breeder Charles River Europe, distributor SCANBUR, Denmark) were delivered on gestation day (GD) 3 of pregnancy to the BioFacility at the Technical University of Denmark. Nulliparous rats with approximate body weights of 240 ± 30 g were time-mated, with day of plug detection denoted GD1. On GD4 dams were weighed and randomly assigned a treatment group. Animals were kept at environmentally controlled conditions of 55 ± 5% humidity, 21 ± 1˚C, 50 times airchange/h, and reverse light/dark cycles of 12 h. Acidified tap water and a standard diet of Altromin 1314 (soy and alfalfa-free, Altromin GmbH, Lage, Germany) were given ad libitum. Pups were weighed, sexed and counted on the day of birth (PD1). At PD16 two male pups/litter were anesthetized by CO2/O2 and killed by decapitation.

extract_protocol:
Thyroid glands (n = 8, 2 male pups per litter) were dissected from the trachea and frozen in liquid nitrogen. Samples were stored at –80 ˚C until further analysis. Total RNA isolation was performed using a RNeasy Micro Kit following manufacturer’s protocol with the DNase step included (Qiagen, Germany). RNA quantity, quality, and purity was determined by a combination of a Nano-drop-1000 spectrophotometer (ND-1000, Fisher Scientific) and an Agilent 2100 Bioanalyzer System (Agilent Technologies, CA, USA). Samples with RNA integrity (RIN)-score > 6.8 were used. RNA samples were diluted to 25 ng/µL, and stored at -80 ˚C.
The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Illumina, #FC-131-1024) following the manufacturer’s recommendations.

treatment_protocol: Treatment started on GD7 and continued to tissue collection on PD16 with daily doses of MBI (10 and 20 mg/kg bw/day), amitrole (25 and 50 mg/kg bw/day) and cyanamide (7 and 15/11.25 mg/kg bw/day) administered by oral gavage (2 mL/kg bw, corn oil (Sigma-Aldrich)) in the morning. A vehicle control group was also included. No treatment was given on the day of birth. From GD16 the cyanamide dose was reduced from 15 to 11.25 mg/kg bw/d due to reduced dam weight gain. The high doses were selected for further analysis as part of this study, namely 10 mg/kg bodyweight (bw)/d) MBI (high dose group lost due to severe reproductive toxicity), 50 mg/kg bw/d amitrole and15/11.25 mg/kg bw/d cyanamide.

value: Sprague-Dawley

value: Thyroid gland

value: male

tag: developmental stage

tag: exposure

value: Cyanamide


title: Thyroid gland, PD16, Cyanamid, replicate6


title: Enteric Neurons under CR infection in Small Intestine, 10x single-nucleus RNAseq, HTO Hashtags

description:
Library name: sn10xENC.SI_CR7d.AhrCKO.FB
10x Genomics

value: 8 weeks

value: 2×109 C. rodentium infection 7days


title: OCI-AML3 cells, biol rep 2


title: 4T1 cells, shContral, rep2

description:
Library name: Smaple 2
Column name in 4T1_raw_counts.txt :4T1_shCtrl_rep2

value: mouse mammary carcinoma cell

value: wild-type

value: shRNA control


title: KPC tumor, ICB and CA4948 treatment, biological replicate 3

city: Stanford

first: Daniel

last: Delitto

address: 257 Campus Dr

institute: Stanford University

description: Samples were actually sequenced with the Singular Genomics G4 sequencer (https://singulargenomics.com/g4/)

data_processing:
For the KPC collagen gel characterization studies and tumors from Col1a1CreERT2 MyD88fl/fl mice and control mice comparison studies, fastqs were aligned using 10x Genomics Cloud Analysis using cellranger-7.1.0 with the mm10-2020-A transcriptome. The hashtag oligo (HTO) data were normalized using the centered log-ratio method. Cells were demultiplexed using the HTODemux function in Seurat, and cells were classified based on the maximum HTO ID.  For the ICB and CA-4948 treatment studies, fastqs were aligned using 10x Genomics Cloud Analysis using cellranger-8.0.1 with the GRCm39-2024-A transcriptome.
Assembly: GRCm39-2024-A
Supplementary files format and content: raw_feature_bc_matrix.h5 output from cellranger

source_name: KPC collagen gel tumor

extract_protocol:
Single-cell suspensions were prepared using the Mouse Tumor Dissociation Kit (Miltenyi Biotec) from mouse pancreatic tumors. Cells were frozen in Bambanker (NIPPON Genetics) and stored in -80°C until sequenced. Once ready, cells were quickly thawed in a 37°C bath and transferred into a 15 ml conical tube with 4 ml 1% BSA in PBS (Sigma-Aldrich). The resuspended cells were filtered using a MACS™ 30 µm filter (Miltenyi Biotec) and centrifuged at 300 RCF for 5 minutes at 6°C. Supernatant was removed from the cells with care taken not to disturb the pellet, and the cells were then resuspended in 1% BSA in PBS, with volumes adjusted depending on the pellet size. Cells were quantified using a fluorescent cell counter with 1:1 trypan blue (Bio-Rad) and 1:1 AO/PI viability assay (DeNovix).
For the KPC collagen gel characterization studies and tumors from Col1a1CreERT2 MyD88fl/fl mice and control mice comparison studies, cells from each individual sample were labeled separately with TotalSeq™-B hashtag antibodies (BioLegend). Target input cell range was 700-1200 cells/µl with a target cell recovery of 10,000 cells. Library preparation was performed using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 and sequenced at the Stanford Functional Genomics Facility on the Illumina NovaSeq 6000.  Target input cell range was 1300-1600 cells/µl with a target cell recovery of 20,000 cells. Library preparation was performed using Chromium GEM-X Single Cell 5’ Reagent Kits v3 (10x Genomics), per manufacturer’s protocol. Library conversion was then done with Singular Genomics Library Compatibility Kit (Singular Genomics), and libraries were sequenced on the Singular Genomics G4 sequencer, using 100 cycle F3 flow cells (Singular Genomics), with two lanes per library at 28/90 paired end.

value: KPC collagen gel tumor

value: KPC

value: All cells


title: 4T1 cells, shContral, rep3

description:
Library name: Smaple 3
Column name in 4T1_raw_counts.txt :4T1_shCtrl_rep3

value: mammary gland


title: Thyroid gland, PD16, Cyanamid, replicate5


title: OCI-AML3 cells, biol rep 1


title: 4T1 cells, shContral, rep1

description:
Library name: Smaple 1
Column name in 4T1_raw_counts.txt :4T1_shCtrl_rep1


title: OCI-AML2 cells, biol rep 3


title: Thyroid gland, PD16, Cyanamid, replicate4


title: KPC tumor, ICB and CA4948 treatment, biological replicate 2


title: OPM2 cells, biol rep 1

value: multiple myeloma


title: KPC tumor, ICB and CA4948 treatment, biological replicate 1


title: RNA_KO_9

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

data_processing:
The RNA-seq samples were mapped against the mm10 mouse genome assembly using TopHat(Trapnell et al., 2009) with the option –g 1 to discard those reads that could not be uniquely mapped in just one region.
DESeq2(Love et al., 2014) was run to quantify the expression of every annotated transcript using the RefSeq(O’Leary et al., 2016) catalogue of exons and to identify each set of differentially expressed genes.
Assembly: mm10
Supplementary files format and content: RPKMs calculated by DESeq2 (columns ordered by samples WT10,WT11, WT3, WT13, KO6, KO11, KO4, KO9)

source_name: posterior part of the tailbud of 4-5 somite-matched E8.5 embryos

growth_protocol: E8.5 embryos were collected and dissected in PBS. The second half of the tail bud, including the presomitic mesoderm, was placed in 350 µl of RLT buffer with B-mercaptoethanol (RNeasy Micro kit, Qiagen) and stored at -80 ºC

extract_protocol:
RNA extraction was performed using the RNeasy kit (Qiagen, 74134) according to the manufacturer’s instructions.
Libraries were prepared according to Illumina instructions.
RNA-seq (Smart-Seq 2)

value: EPOP KO


title: OCI-AML2 cells, biol rep 2


title: OCI-AML2 cells, biol rep 1


title: KPC tumor, ICB only treatment, biological replicate 3


title: KPC tumor, ICB only treatment, biological replicate 2


title: RNA_KO_4

value: posterior part of the tailbud of 4-5 somite-matched E8.5 embryos


title: Thyroid gland, PD16, Cyanamid, replicate2


title: RNA_KO_6


title: Thyroid gland, PD16, Cyanamid, replicate3


title: KPC tumor, ICB only treatment, biological replicate 1


title: Thyroid gland, PD16, Amitrol, replicate7

value: Amitrole


title: Normal human epdermal melanocytes, biol rep 2

source_name: NHEM

value: NHEM

value: Primary healthy melanocyte


title: RNA_WT_13

value: WT


title: Thyroid gland, PD16, Cyanamid, replicate1

value: Sprague-Dawley

value: Thyroid gland

value: male

value: Cyanamide


title: Thyroid gland, PD16, Amitrol, replicate6


title: Normal human epdermal melanocytes, biol rep 1


title: RNA_WT_3


title: Thyroid gland, PD16, Amitrol, replicate5


title: RNA_WT_11


title: RNA_KO_11


title: KPC tumor, control treatment, biological replicate 1


title: Normal human epdermal keratinocytes, biol rep 2

source_name: NHEK

value: NHEK

value: Primary healthy keratinocyte


title: RNA_WT_10


title: KPC tumors in control mice, set 2

description: Library name: Control2

data_processing:
For the KPC collagen gel characterization studies and tumors from Col1a1CreERT2 MyD88fl/fl mice and control mice comparison studies, fastqs were aligned using 10x Genomics Cloud Analysis using cellranger-7.1.0 with the mm10-2020-A transcriptome. The hashtag oligo (HTO) data were normalized using the centered log-ratio method. Cells were demultiplexed using the HTODemux function in Seurat, and cells were classified based on the maximum HTO ID.  For the ICB and CA-4948 treatment studies, fastqs were aligned using 10x Genomics Cloud Analysis using cellranger-8.0.1 with the GRCm39-2024-A transcriptome.
Assembly: mm10-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5 output from cellranger

value: KPC collagen gel tumor


title: Thyroid gland, PD16, Amitrol, replicate3


title: Normal human epdermal melanocytes, biol rep 3


title: Thyroid gland, PD16, Amitrol, replicate4


title: Jurkat_shDMAP1_3

city: Jupiter

first: Susana

middle: T

last: Valente

state: FL

address: 130 Scripps Way

department: Immunology and Microbiology

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
shRNAmir Replicate 2
639-8

data_processing:
FastQC
Pseudoalignment by Salmon v 0.14.1 using the --validateMappings flag using a decoy-aware index of the GRCh38 transcriptome with the HIV-R7/E-/GFP or HIVGKO transcript added to the end.
The resulting quantification files were read into R (version 4.2.3) using the tximport function from the R package tximport (1.26.1)
Differential expression analysis was done using edgeR.
Raw counts were converted to a DGEList object using DGEList(), lowly expressed transcripts were removed using filterByExpr() and normalization factors were calculated using calcNormFactors().  Normalized counts were converted to log2 counts per million using cpm() and fit to the contrast of interest using lmFit().  Differential expression values were calculated using eBayes(trend=TRUE) and summarized with topTable().
Assembly: GRCh38 transcriptome with the HIV-R7/E-/GFP or HIVGKO transcript added to the end as an extra transcript
Supplementary files format and content: Salmon quantification files in a .sf format

source_name: Jurkat cells

growth_protocol: For primary CD4+ T cells: Human PBMCs from 3 healthy donors were obtained from Buffy coats by density centrifugation and CD4+ T cells isolated by negative selection. Cells were then activated with 1:2 ratio with Dynabeads™ Human T-Activator in the presence of 6 ng/ml IL-2, 36 ng/ml IL-7 and 36 ng/ml IL-15. The cells were cultured in RPMI 1640 media supplemented with 1xMEM vitamin solution, 1xNEAA, 1x Sodium Pyruvate , 1xPen/Strep/L-glut, 0.01M HEPES pH 8.0, 1xL-Asp/L-Arg/Folic acid mix (house-made), and 10% FBS. Jurkat and J-Lat 10.6 cells were maintained in RPMI 1640 supplemented with 2.0 mM L-glutamine/100 U/ml penicillin/100 µg/ml streptomycin and 10% heat-inactivated FBS (complete RPMI) and cultured at 37°C and 5% CO2.

extract_protocol:
For primary CD4+ T cells: total RNA was isolated using RNeasy Micro kit which includes an on column DNase treatment. For Jurkat and J-Lat 10.6 cells: Total RNA was extracted from cells using the Qiagen RNeasy kit. RNA was DNase treated using the TURBO DNA-freeTM kit.
For primary CD4+ T cells: Two days post activation of primary CD4+ T cells, non-tissue culture treated 24-well plates were coated with RetroNectin (RN) overnight at 4˚C (RetroNectin® Recombinant Human Fibronectin Fragment). RN was removed, plates washed w

treatment_protocol: For primary CD4+ T cells: Two days post activation of primary CD4+ T cells, non-tissue culture treated 24-well plates were coated with RetroNectin (RN) overnight at 4˚C (RetroNectin® Recombinant Human Fibronectin Fragment). RN was removed, plates washed with PBS and then blocked with sterile 2% BSA in PBS for 30 min at room temperature. Plates were washed with PBS and then GaLV-pseudotyped LMPd was loaded onto the RN (2,000 x g, 2 h at 32˚C). Unbound virus was washed off with PBS and 5x10^5 activated T cells were added at a density of 1x10^6/ml on top of the LMPd-coated plates, concentrated HIVGKO was added on top and centrifuged at 2000 x g for 5 mins to facilitate attachment to the virus and RN, then placed in an incubator overnight. The next day, cells were detatched from the RN and maintained at 1.5x10^6/ml for 9 days in T cell media prior to FACS isolation for RNA-seq analysis. For Jurkat and J-Lat 10.6 cells: cells were transduced with an MOI of 0.3 of LMPd shRNAmirs (two independent shRNAmirs per gene were used as biological replicates). Two days post transduction, transduced cells were FACS isolated and cultured for a further seven days before RNA was extracted.

value: Jurkat cells


title: Thyroid gland, PD16, Amitrol, replicate2


title: MOLM13 cells, biol rep 3

value: Leukaemia cell line


title: KPC tumors in control mice, set 1

description: Library name: Control1

value: KPC

value: All cells


title: Jurkat_shDMAP1_2

description:
shRNAmir Replicate 1
639-7


title: MOLM13 cells, biol rep 2


title: KPC tumor, control treatment, biological replicate 3


title: KPC tumors in Col1a1CreERT2 MyD88fl/fl mice

description: Library name: Experiment


title: Thyroid gland, PD16, Amitrol, replicate1


title: Jurkat_shEP400_4

description:
shRNAmir Replicate 2
639-6


title: Jurkat_shEP400_2

description:
shRNAmir Replicate 1
639-5


title: Thyroid gland, PD16, MBI, replicate7

value: 2-mercaptobenzimidazole (MBI)


title: Normal human epdermal keratinocytes, biol rep 3


title: MOLM13 cells, biol rep 1


title: ChIL-seq sample for Hnf4a in iHepC, replicate 2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: Library name: iHepC_Hnf4a_2

data_processing:
library strategy: Chromatin Integration Labeling sequencing (ChIL-seq)
Raw data are trimmed and removed PCR duplicates using fastp (v 0.23.4).
The sequence reads were aligned to a mouse reference genome (Ensemble mm10) using hisat2 (v2.0.5).
Peaks for Hnf4a are called by MACS2 (v2.2.9.1).
Assembly: mm10
Supplementary files format and content: Peak files (BED format)

source_name: Embryo

growth_protocol: MEFs are incubated in MEF medium [Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS), 2 mM l-glutamine (Nacalai Tesque), and penicillin/streptomycin (Nacalai Tesque)], and the reprogrammed cells derived from MEFs (iHepCs) are incubated in hepato-medium. This medium comprises a 1:1 mixture of DMEM and F-12 medium (Nacalai Tesque), supplemented with 10% FBS, 1 μg/ml insulin (Wako), 100 nM dexamethasone (Sigma–Aldrich), 10 mM nicotinamide (Sigma–Aldrich), 2 mM l-glutamine, 50 mM β-mercaptoethanol (Nacalai Tesque), penicillin/streptomycin, 20 ng/ml hepatocyte growth factor (PeproTech), and 20 ng/ml epidermal growth factor (Sigma–Aldrich).

extract_protocol:
ChIL-seq was performed following a modified protocol of the original ChIL-seq (PMID: 30532068). 10,000 cells were plated on typeⅠcollagen coated 96-well plates and let to attach for 16 h in culture. Cells were then fixed with 1% formaldehyde in PBS for 5 min and permeabilized with 1% Triton X-100 in PBS for 20 min.
Samples were incubated in 10% Blocking One-P (Nacalai Tesque) in PBS with anti-Hnf4α mAb (Cell Signaling Technology; #3113) for 6 h at room temperature, washed three times in PBS and then incubated at 4℃ overnight in 10% Blocking One-P in PBS containing 500 mM NaCl and the ChIL probe at 2 μg/ml. After washing in PBS, samples were incubated in 50 µl Tn5 solution [50 mM HEPES-KOH (pH 7.2), 0.1 M NaCl, 0.1 mM EDTA, 1 mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol] containing 0.5 µl Tn5 transposase (given by Dr. Yasuyuki Ohkawa) for 10 min at room temperature. Tn5-MEDS-B oligo (2 µM) was then added at 0.5 µl per well in 1× dialysis buffer [50 mM HEPES-KOH (pH 7.2), 0.1 M NaCl, 0.1 mM EDTA, 1 mM dithiothreitol, 0.1% Triton X-100 and 10% glycerol] and incubated for 60 min at room temperature. Samples were then washed in 1× dialysis buffer and three times in PBS, incubated in 100 µl 1× TAPS-DMF buffer [10 mM TAPS-NaOH (pH 8.5), 5 mM MgCl2 and 10% N,N-dimethylformamide] for 1 h at 37℃, and washed at three times in PBS. To stop the Tn5 reaction, cells were incubated in 100 µl 0.2% SDS for 10 min at room temperature. After washing at three times in PBS, samples were incubated in 50 µl reaction mixture [200 U T4 DNA ligase (New England Biolabs), and 1.5 U T4 DNA polymerase (New England Biolabs), in 1× T4 DNA ligase reaction buffer containing 0.1 mM dNTP] for 30 min at room temperature. After discarding the solution, 100 µl 0.2% SDS were added to remove DNA-bound enzymes, followed by incubation for 10 min at room temperature and three washes in PBS. In situ transcription was then carried out using T7 RNA polymerase (200 U per well; Ambion) for 20 h at 37 ℃. The samples were treated with DNase I (2.5 U per well; Thermo Fisher Scientific) for 30 min at 37℃ and RNA was extracted using a RNAClean XP beads (Beckman Coulter). Purified RNA was reverse-transcribed with SMARTScribe reverse transcriptase (Takara) following the manufacturer’s instructions and the resulting cDNA was amplified by SeqAmp DNA Polymerase (Takara) by 14 cycles. After amplification, small fragments (<150 bp) were removed and large size of fragments (>600 bp) were removed using AMPure XP beads (Beckman Coulter). The amplified DNA was purified using AMPure XP beads and the quality of the libraries was assessed using a Bioanalyzer 2100 (Agilent Technologies). Samples were paired-end sequenced at PE100 on an Illumina NovaSeq 6000 platform. As detailed described in previous report (PMID: 30532068).

treatment_protocol: Following the reported protocol (PMID: 21716291), iHepC was induced by using a retroviral vector to forcibly express Foxa2 and Hnf4a in MEFs.

value: Embryo

value: Fibroblast


title: ChIL-seq sample for Hnf4a in iHepC, replicate 1

description: Library name: iHepC_Hnf4a_1


title: Jurkat_shCD19_4

description:
shRNAmir Replicate 2
639-4


title: Kasumi-1 cells, biol rep 3


title: Thyroid gland, PD16, MBI, replicate6


title: Kasumi-1 cells, biol rep 2


title: Normal human epdermal keratinocytes, biol rep 1


title: Jurkat_shCD19_3

description:
shRNAmir Replicate 1
639-3


title: Embryo , Lmo3 Positive, replicate 3, scRNAseq

city: Beijing

first: xi

last: rongwen

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

institute: National Institute of Biological Sciences, Beijing

description: 10× Genomics

data_processing:
CellRanger V3.0.3 for  reads alignment, filtering, barcode counting, and UMI counting
Seurat V4.3.0 for downstream analysis
Assembly: mm10
Supplementary files format and content: Table-separated values files and matrix files

extract_protocol:
For samples from E12.5 to E19.5, isolated intestinal samples were washed in cold Dulbecco’s phosphate-buffered saline (DPBS, Gibco, C14190500CP) to remove intestinal contents. The E19.5d tissues were opened longitudinally and sliced into small fragments for the following digestion. The embryonic (E12.5d, E13.5d, E14.5d, and E15.5d) tissues were directly pooled into the tube with collagenase I (Gibco, 17100-017) and elastase (Sigma, E2058) to perform digestion at room temperature to obtain cell mixture. The cell mixture was then passed through a 40-µm filter to obtain the single-cell suspension. The obtained single-cell suspension was centrifuged at 300g for 10 min, and incubated with ACK lysis buffer (Gibco, A10492-01) for 1 min on the ice. Another centrifugation at 300g for 10 min was performed and the supernatant was removed. The final fraction was mixed in suitable DPBS with 0.05% BSA and Propidium Iodide. For Lmo3_E19.5 samples, small intestines were collected at E19.5, minced into small pieces, and processed in a solution composed of DNaseI (Merk, 10104159001), and Y27632 (R&D Sytems, 1254/50 ,5000X) in TrypLE (Gibco, 12605-010) for about 15min in 37℃ on 150rpm shaker. The remaining tissues were further digested in digestion buffer containing 1.2mg/ml Collagenase (Sigma, C2139-1G), 1mg/ml Dispase II (Gibco, 17105041), 0.1mg/ml DNase I, and Y27632 in Hank’s balanced salt solution (HBSS. Gibco 14170-112) for 20min in 37℃, 150rpm shaker. Tissues were resuspended every 6min through pipetting. The reaction was stopped by adding 3-volume of wash buffer containing 5% FBS (Gibco, 16000-044), Gentamicin / Amphotericin (Gibco, 50-0640, 500X), Penicillin / Streptomycin B (Gibco, 15140-122,100X), HEPES (Sigma, H0887-100ML,100X), Y27632 in F12 culture medium (Gibco, 11765-054). The lysates were passed through 70-μm filters, centrifuged at 300g for 8 min, and resuspended in the wash buffer. 1ml ACK lysis buffer was added to remove the red blood cells on ice for 4min. The remaining cells were washed twice with wash buffer and filtered again with 40-μm Millipore. The final fraction was resuspended into the wash buffer with 1ug/ml DAPI.
Cell suspensions with at least 80% cell viability were diluted to the appropriate concentration and loaded on a 10x Genomics Chromium Single Cell Controller (Pleasanton, CA) with a target of about 5000 cells per sample. Single-cell library preparation was completed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2 strictly following the manufacturer’s protocol.

value: Small intestine

value: 120mg/kg tamoxifen was injected each day for three days (E13.5-E15.5) intraperitoneally


title: Thyroid gland, PD16, MBI, replicate5


title: Jurkat_shCD8B_3

description:
shRNAmir Replicate 2
639-2


title: Thyroid gland, PD16, MBI, replicate4


title: Embryo , Lmo3 Positive, replicate 1, scRNAseq

description: 10× Genomics


title: Embryo , Lmo3 Positive, replicate 2, scRNAseq

description: 10× Genomics


title: Kasumi-1 cells, biol rep 1


title: FaDu cells, biol rep 3

source_name: FaDu

value: FaDu

value: HNSCC


title: Thyroid gland, PD16, MBI, replicate3

value: Sprague-Dawley

value: Thyroid gland


title: Jurkat_shCD8B_1

description:
shRNAmir Replicate 1
639-1


title: FaDu cells, biol rep 2


title: Thyroid gland, PD16, MBI, replicate2

value: male


title: FaDu cells, biol rep 1


title: Thyroid gland, PD16, MBI, replicate1


title: J_Lat_10_6_shDMAP1_3

description:
shRNAmir Replicate 2
583_8

source_name: J-Lat 10.6 cells

value: J-Lat 10.6 cells


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D3, BiolRep2

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

description:
Library name: 14-D3-siChst7-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

data_processing:
Fastq reads were mapped to mm10 with HISAT2.
The counts table was generated with subread featurecounts. DESeq23 in R was used for differential expression analysis.
DESeq2 in R was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: This is a raw counts matrix without normalization

growth_protocol: The cells were cultured in plates precoated with 0.1% gelatin (Stem Cell Technologies, #7903) and maintained in Fibroblast Culture Medium consisting of DMEM (Corning, #10-013-CV), 10% fetal bovine serum (FBS; VWR, #89510-186), and 1% antibiotic-antimycotic solution (Gibco, #15240062) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
On day 0 post-siRNA knockdown, day 1 post-MGT overexpression, and day 3 post-MGT overexpression, RNA was extracted from the cells using the Zymo Research Quick-RNA MircoPrep Kit (#R1051) following the manufacturer’s recommendations.Cells were pooled from 40 wells per sample for each biological replicate.
Library preparation was performed by the La Jolla Institute for Immunology Next Gen Sequencing core using NEB poly-A kit mRNA-seq Library Prep following the manufacturer’s recommendations.

treatment_protocol: One day prior to siRNA transfection (day −1), cells were detached by addition of 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, and then washed in FCM, centrifuged, and resuspended in Induced-CM Reprogramming Medium (iCRM), consisting of DMEM, 20% Medium 199 (Gibco, #11150-059), 10% FBS, and 1% A/A. Cells were plated in 384-well plates at 1000 cells/well and transfected with siChst7 or siControl. The next day (day 0), 1 μg/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in iCRM was added to the cells to induce MGT expression. Samples harvested at D0 did not receive Doxy treatment.

value: mouse embryonic fibroblasts

value: Cardiomyocyte transdifferentiation

tag: time

value: Day 3 (post-MGT)


title: Thyroid gland, PD16, Ctrl, replicate8

value: Control


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D3, BiolRep3

description:
Library name: 18-D3-MGT-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

value: siControl


title: KPC tumor, control treatment, biological replicate 2

value: KPC collagen gel tumor

value: KPC

value: All cells


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D3, BiolRep3

description:
Library name: 15-D3-siChst7-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: Cal33 cells, biol rep 2


title: Thyroid gland, PD16, Ctrl, replicate7


title: J_Lat_10_6_shDMAP1_2

description:
shRNAmir Replicate 1
583_7


title: Cal33 cells, biol rep 3


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D3, BiolRep2

description:
Library name: 17-D3-MGT-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: Thyroid gland, PD16, Ctrl, replicate6


title: Cal33 cells, biol rep 1


title: J_Lat_10_6_shCD19_4

description:
shRNAmir Replicate 2
583_4


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D3, BiolRep1

description:
Library name: 16-D3-MGT-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D1, BiolRep3

description:
Library name: 9-D1-siChst7-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

value: Day 1 (post-MGT)


title: A549 cells, biol rep 3

value: Lung cancer line


title: Thyroid gland, PD16, Ctrl, replicate5


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D1, BiolRep2

description:
Library name: 8-D1-siChst7-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: J_Lat_10_6_shCD19_3

description:
shRNAmir Replicate 1
583_3


title: A549 cells, biol rep 2


title: J_Lat_10_6_shCD8B_3

description:
shRNAmir Replicate 2
583_2


title: J_Lat_10_6_shEP400_4

description:
shRNAmir Replicate 2
583_6


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D1, BiolRep1

description:
Library name: 7-D1-siChst7-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: J_Lat_10_6_shCD8B_1

description:
shRNAmir Replicate 1
583_1


title: Thyroid gland, PD16, Ctrl, replicate4


title: A375 cells, biol rep 3

value: melanoma cell line


title: A549 cells, biol rep 1


title: Thyroid gland, PD16, Ctrl, replicate2


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep3

description:
Library name: 12-D1-MGT-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: J-Lat 10.6, input, shDMAP1,unstimulated, Rep1

data_processing:
FASTQC
Read trimming with trim_galore (--paired --length 24 --stringency 3)
Align with bowtie2 (-p 16 --no-mixed --no-discordant -1)
Removed duplicates with samtools
Peaks were called with macs2 (callpeak  --broad -f BAMPE -g hs -q 0.05 -B)
For visualization, bam files for replicates were merged using samtools, deepTools was used to convert BAM files to bedgraph format (bamCoverage), and and then the bdg files were normalized across samples to library size prior to conversion to bigwig format (bedGraphToBigWig).
Assembly: custom genome GRCh38 with HIV-R7/E-/GFP inserted into chromosome 9 at position 136,468,578, shifting the remaining chromosome 9 by 10,200 bp (the length of the HIV insertion), including a repeat of the “ACAAA” sequence in the SEC16A intron that became duplicated upon HIV integration
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak

growth_protocol: J-Lat 10.6 cells were maintained in RPMI 1640 supplemented with 2.0 mM L-glutamine/100 U/ml penicillin/100 µg/ml streptomycin and 10% heat-inactivated FBS (complete RPMI) and cultured at 37°C and 5% CO2.

extract_protocol:
Native ChIP was performed using MNase to fragment chromatin to mono-to pentanucleosomes sizes.
ChIP DNA libraries for next-generation sequencing on the Illumina platform were constructed based on the protocol of NEB Next Ultra II DNA Library Prep Kit (#E7103, NEB) using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, # E6440S)

treatment_protocol: Cells were transduced with the indicated shRNAs in pMKO.1-puro. Two days post transduction cells were selected with 4 µg/ml puromycin for one week, after which cells were collected for Native ChIP-seq

value: Unstimulated


title: Thyroid gland, PD16, Ctrl, replicate1


title: Thyroid gland, PD16, Ctrl, replicate3


title: J_Lat_10_6_shEP400_2

description:
shRNAmir Replicate 1
583_5


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D3, BiolRep1

description:
Library name: 13-D3-siChst7-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep2

description:
Library name: 11-D1-MGT-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: PBS_5.2

first: Angela

last: Galdamez

state: California

address: 450 Jane Stanford Way

description: Library name: PBS-5.2

data_processing:
Sequencing data was aligned to Mus_musculus_GCF_000001635.27_GRCm39 using the HISAT2 alignment program (v2.0.4)
Gene expression and normalized reads (in FPKM) were quantified using RSEM software (v1.2.18)
Differential expression analysis between control and drug-treated groups, along with the statistical significance, was determined using the DESeq2 package (v1.4.5)
Sequencing saturation-Perl script is used for sequencing saturation analysis.
Assembly: Integrative Genomics Viewer genome (IGV) browser to view the reads align to the genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: excel file includes FPKM values for each sample

source_name: Retina

growth_protocol: Salubrinal (10 μM), ISRIB (10 μM), Ceapin-A7 (10 μM), AA147 (10 μM) and Tunicamycin (10 μM) were all dissolved in sterile-filtered saline with 0.05-0.1% dimethyl sulfoxide. 1 μL of each drug was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle. For control, 1 μL of saline containing 0.05-0.1% of DMSO was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle.

extract_protocol:
DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing preperation - Stranded mRNA library
RNA-Seq

treatment_protocol: Cornea and lens were removed and retina was harvested using Rneasy miniplus kit (Quagen)/ >2ug of total RNA eas used for the construction of sequencing libarieis.

value: Retina

value: WT

value: PBS


title: J-Lat 10.6, input, shEP400,unstimulated, Rep1


title: PBS_4.2

description: Library name: PBS-4.2


title: A375 cells, biol rep 2


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep1

description:
Library name: 10-D1-MGT-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: J-Lat 10.6, RNAPII, ChIP, shEP400, TNFa, Rep1

description:
686_6
shEP400_TNF_n_of_2_NORMsort.bw

tag: chip antibody

value: RNA polymerase II (Millipore, #05-623)

value: TNFa stimulated


title: A2058 cells, biol rep 3


title: PBS_3.2

description: Library name: PBS-3.2


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D0, BiolRep3

description:
Library name: 3-D0-siChst7-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

value: mouse embryonic fibroblasts

value: Day 0 (prior to MGT)


title: A2058 cells, biol rep 2


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D0, BiolRep2

description:
Library name: 2-D0-siChst7-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

value: Cardiomyocyte transdifferentiation


title: A2058 cells, biol rep 1


title: J-Lat 10.6, RNAPII, ChIP, shDMAP1, TNFa, Rep1

description:
686_5
shDMAP1_TNF_n_of_2_NORMsort.bw

value: J-Lat 10.6 cells


title: A375 cells, biol rep 1


title: J-Lat 10.6, RNAPII, ChIP, shCD8B, TNFa, Rep1

description:
686_4
shCD8B_TNF_n_of_2_NORMsort.bw


title: PBS_1.2

description: Library name: PBS-1.2


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D0, BiolRep3

description:
Library name: 6-D0-MGT-3
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample

value: siControl


title: chr1:241498239 T/C variant reporter cells, GFP positive cells, replicate 3

city: Bethesda

first: Pedro

middle: Jorge

last: Batista

address: 37 Convent Dr

institute: NCI

description:
Library name: variant_reporter_cells_GFP_positivecells_3
Column name in normalized counts matches sample name

data_processing:
Reads for each sample were trimmed for adapters and low-quality bases using cutadapt 5.0 using the -q10 -m 20 -g CGAAACACCG parameters.
Mapping, counting and normalization of counts was performed with MAGeCK 0.5.9.5
Assembly: Reads aligned to sgRNA library sequence
Supplementary files format and content: tab delimited text file contains normalized counts for each samples
Library strategy: CRISPR Screen

source_name: T-REx 293 cell line

growth_protocol: T-Rex 293 cell were cultured in DMEM supplemented with 10% fetal bovine serum, 1% glutamax, and 1% PenStrep. Cells were grown in a humidified incubator at 37 °C in the presence 5% CO2 and were split every 2-3 days at approximately 80% confluency.

extract_protocol:
After sorting, cells were pelleted at 400xg for 4 min at room temperaure and frozen at -20°C. DNA was isolated using the QIAamp DNA Blood Mini Kit (Qiagen; 51106), following manufacturers protocol and concentrated using Zymo DNA Clean & Concentrator-5 kit (Zymo; D4014), following manufacturers protocol. Samples were eluted 2x with 12 µl of Zymo elution buffer.
The first step PCR was performed with up to 250 ng of DNA using 2x Q5 hot start polymerase (NEB M0494), 2.5 µl 10 µM of pooled forward oligos, 2.5 µl 10 µM of reverse oligo that targets sequence on Lenti-CRISPR-V2, and 0.5 µl 25x sybr green (Thermo Fisher Scientific S7563) in 50 µl reactions. If a sample had more than 250 ng of DNA, multiple PCRs per sample were set up to amplify the entirety of DNA from that sample. PCR was run on a light cycler (QuantStudio3 by Thermo Fisher Scientific) with the following parameters 98C for 30s; [98C for 10s; 61C for 20s; 72C for 15s] x 40. Amplification was tracked and PCRs were stoped 2 to 3 cycles after exponential increase. After first step PCR, PCR products were cleaned using 1X Ampure XP beads (Beckman A63881). If multiple PCRs were performed per sample, those PCRs were pooled. The beads were mixed the pooled PCRs, incubated for 10 minutes at room temperature, washed 2 x 30 sec with 75% EtOH, dried for 5 minutes, and resuspended and eluted in 30 µl H2O. Products were quantified by Qubit™ dsDNA HS Assay Kit (Q32854). Second step PCRs were performed on the entirety of product from the first step PCRs, split into multiple PCRs with a maximum of 20 ng template for each. PCRs were performed with a common forward oligo, and specific barcoded reverse oligos (Supplemental Table 4. This second PCR was performed with Q5 hot start polymerase (NEB M0494), 1 µl 10 µM of forward oligo, 1 µl 10 µM of reverse oligo and 20 ng of DNA with the following parameters: 98C for 30s; [98C for 10s; 61C for 20s; 72C for 15s] x 5. The multiple PCRs performed per sample were pooled and cleaned again using 1X Ampure XP beads following the same protocol as above but eluted in 22 µl and were submitted for Tape Station analysis DNA 1000 regular sensitivity. The barcoded PCR products were then pooled into equimolar pools, grouped by sample type, and purified on a non denaturing 10% polyacrylamide gel as previously described 10 (38328795). After gel purification samples were cleaned on Zymo DNA columns and submitted again for Tape Station analysis DNA 1000 regular sensitivity. The final three samples were pooled at equimolar amounts and sequenced with a MiSeq Nano kit.

treatment_protocol: Variant reporter cells were plated in 4x15 cm dishes at 2.5 million cells. One plate was used for counting, and the remaining cells infected at MOI < 0.3 to achieve at least 500 cells per sgRNA. The following day cells carrying sgRNAs were selected for with 3 µg/mL puromycin. Cells were selected and expanded for 6 days. 100K cells were collected as the pre-sort fraction and around 13 million cells resuspended in (2% FBS in PBS) for FACS sorting. GFP positive cells were sorted with a FACS Aria (BD Biosciences) in the CCR/LGI Flow Cytometry Core.

value: T-REx 293 cell line

value: GFP reporter for splicing

value: FACS sorted GFP positive cells


title: RNA-iMGT-Myh6-eGFP-MEFs, siChst7, D0, BiolRep1

description:
Library name: 1-D0-siChst7-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: CeapinA7-5

description: Library name: CeapinA7-5

extract_protocol:
Cornea and lens were removed and retina was harvested using Rneasy miniplus kit (Quagen)/ >2ug of total RNA eas used for the construction of sequencing libarieis.
DNBSEQ Eukaryotic Strand-specific Transcriptome Resequencing preperation - Stranded mRNA library

treatment_protocol: Salubrinal (10 μM), ISRIB (10 μM), Ceapin-A7 (10 μM), AA147 (10 μM) and Tunicamycin (10 μM) were all dissolved in sterile-filtered saline with 0.05-0.1% dimethyl sulfoxide. 1 μL of each drug was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle. For control, 1 μL of saline containing 0.05-0.1% of DMSO was administored into both eyes via intravitreal injection using 33-gauge Hamilton syringe needle.


title: CeapinA7-4

description: Library name: CeapinA7-4


title: chr1:241498239 T/C variant reporter cells, GFP positive cells, replicate 1

description:
Library name: variant_reporter_cells_GFP_positivecells_1
Column name in normalized counts matches sample name


title: J-Lat 10.6, RNAPII, ChIP, shEP400, unstimulated, Rep1

description:
686_3
shEP400_NS_n_of_2_NORMsort.bw


title: chr1:241498239 T/C variant reporter cells, GFP positive cells, replicate 2

description:
Library name: variant_reporter_cells_GFP_positivecells_2
Column name in normalized counts matches sample name


title: J-Lat 10.6, RNAPII, ChIP, shCD8B, unstimulated, Rep1

description:
686_1
shCD8B_NS_n_of_2_NORMsort.bw


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D0, BiolRep1

description:
Library name: 4-D0-MGT-1
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: J-Lat 10.6, input, shCD8B,unstimulated, Rep1


title: RNA-iMGT-Myh6-eGFP-MEFs, siControl, D0, BiolRep2

description:
Library name: 5-D0-MGT-2
NEB poly-A kit mRNA-seq Library Prep; 30M reads/sample


title: CeapinA7-3

description: Library name: CeapinA7-3


title: CeapinA7-2

description: Library name: CeapinA7-2


title: J-Lat 10.6, input, TNFa, Rep2

description:
660-10
input_TNF_n_of_2_NORMsort.bw


title: chr1:241498239 T/C variant reporter cells, before sort, replicate 2

description:
Library name: variant_reporter_cells_beforeSort_2
Column name in normalized counts matches sample name

value: unsorted cells


title: chr1:241498239 T/C variant reporter cells, before sort, replicate 3

description:
Library name: variant_reporter_cells_beforeSort_3
Column name in normalized counts matches sample name


title: 10dpi-gall-neighboring tomato root tissues-Control

city: Knoxville

first: Hewezi

last: Tarek

state: TN

address: 2621 Morgan Circle

institute: niversity of Tennessee, Knoxvile

description:
Library name: Toma-10dpi-NR
10X genomics

data_processing:
The raw scRNA-seq data was analyzed using Cell Ranger 7.2.0 (https://www.10xgenomics.com/support/software/cell-ranger/downloads).
Assembly: Tomato (Solanum lycopersicum), SL3.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Solanum lycopersicum

source_name: 1 cm of gall-neighboring root tissues

growth_protocol: All experiments described in this study were conducted using the nematode susceptible tomato (Solanum lycopersicum) cultivar Heinz 1706. The plants were cultivated in controlled growth chambers maintained at 26°C with a 16-hour light and 8-hour dark photoperiod 65% humidity.

extract_protocol:
Frozen tissue samples from tomato root were transferred to SeqMatic LLC (Fremont, CA, USA) in dry ice for nuclei isolation, library preparation, and sequencing. Frozen tissue was carefully transferred to a gentleMACS M tube that was filled with 5 ml of Honda buffer (2.5% Ficoll 400, 5% Dextran T40, 0.4 M sucrose, 10 mM MgCl2, 1 µM DTT, 0.5% Triton X-100, 1 tablet/50 ml cOmplete Protease Inhibitor Cocktail (Roche), 0.4 U µl−1, Protector RNase Inhibitor (Sigma-Aldrich), 25 mM Tris-HCl, pH 7.4). This buffer composition enables efficient lysis of cell membranes while keeping the nuclear membranes intact. The M tubes were placed onto a gentleMACS Dissociator, where a specific program was executed at 4°C to disrupt the tissue and release the nuclei. The resulting suspension was filtered through a 70-µm strainer and centrifuged at 700 g for 10 min at 4°C. Finally, the pellet was resuspended carefully in 500 µl Honda buffer and filtered through a 30-µm strainer.
scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 following the manufacturer protocol (Manual part CG000315, Rev E; 10x Genomics). Library quality was validated using an Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library composition and size). Preliminary spike-in sequencing was performed and samples were pooled to equal read counts. Final library concentration was confirmed using qPCR on a Roche LightCycler 96.

treatment_protocol: Meloidogyne incognita infection

value: 1 cm of gall-neighboring root tissues

value: Non-infected


title: J-Lat 10.6, input, unstimulated, Rep2

description:
660-9
input_NS_n_of_2_NORMsort.bw


title: 5dpi-gall-neighboring tomato root tissues-Control

description:
Library name: Toma-5dpi-NR
10X genomics


title: chr1:241498239 T/C variant reporter cells, before sort, replicate 1

description:
Library name: variant_reporter_cells_beforeSort_1
Column name in normalized counts matches sample name


title: PBS_2.2

description: Library name: PBS-2.2


title: J-Lat 10.6, H3K27Ac, ChIP, TNFa, Rep2

description:
660-8
H3K27Ac_TNF_n_of_2_NORMsort.bw
H3K27Ac_TNF_n_of_2_MACS2__peaks.broadPeak

value: H3K27ac (Active motif , #39085)

value: Unstimulated


title: ATAC-iMGT-Myh6-eGFP-MEFs, siChst7, D1, BiolRep2

description:
Library name: d1_siChst7_2_atac
Active MOTIF ATAC-seq pre #105320; 50M reads/sample

data_processing:
Fastq files containing raw reads were mapped with Bowtie to the mm10 genome.
Bam files were sorted and indexed with Samtools before MACS3 peak calling.
Bedtools was used for comparing accessible regions in different samples.
Peaks were annotated with HOMER.
Assembly: mm10
Supplementary files format and content: These are bed files with the peaks listed

extract_protocol:
At Day 1 post-MGT overexpression, cells were harvested and frozen in 90% FBS with 10% DMSO using a controlled-rate freezing container (Mr. Frosty) at –80C. Approximately 250,000 cells were used per condition. Some cells were reserved for RNA extraction and sample validation.
Assay for Transposase-Accessible Chromatin (ATAC) was performed using the Active Motif ATAC-seq Kit (#53150) according to the manufacturer’s instructions. Following thawing, cells were lysed, and nuclei were subjected to Tn5 transposase-mediated tagmentation as described in the kit protocol. DNA clean up, library preparation and indexing were performed using reagents provided in the Active Motif kit. Final libraries were sequenced on the Element Biosciences AVITI platform with paired-end, 2×75 bp reads, targeting approximately 50 million reads per sample.

treatment_protocol: One day prior to siRNA transfection (day −1), cells were detached by addition of 0.25% trypsin-EDTA (Thermo Fisher, #25200056) for 3 min at 37°C, and then washed in FCM, centrifuged, and resuspended in Induced-CM Reprogramming Medium (iCRM), consisting of DMEM, 20% Medium 199 (Gibco, #11150-059), 10% FBS, and 1% A/A. Cells were plated in 10cm plates at 500,000 cells/plate and transfected with siChst7 or siControl. The next day (day 0), 1 μg/mL doxycycline hydrochloride (Dox; Sigma, #D3072) diluted in iCRM was added to the cells to induce MGT expression.

value: Day 1 (post-MGT)


title: AA147-5

description: Library name: AA147-5

value: Retina

value: WT


title: J-Lat 10.6, H3K27Ac, ChIP, unstimulated, Rep2

description:
660-7
H3K27Ac_NS_n_of_2_NORMsort.bw
H3K27Ac_NS_n_of_2_MACS2__peaks.broadPeak

value: TNFa stimulated


title: J-Lat 10.6, RNAPII, ChIP, shDMAP1, unstimulated, Rep1

description:
686_2
shDMAP1_NS_n_of_2_NORMsort.bw

value: RNA polymerase II (Millipore, #05-623)


title: HepG2 siDDX55 replicate 3 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Biophysics

institute: University of Pennsylvania

description: Library name: C_siDDX55_3

data_processing:
Cutadapt was used to remove adapter sequences and polyA or polyT sequences.
Trimmed reads were aligned to the genome using STAR (v2.6.1a) with the following parameters --outFilterType BySJout --outFilterMultimapNmax 200 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6   --seedPerWindowNmax 10 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1
Uniquely mapped reads were used to generate bigwig coverage files for each strand. To call clusters, read coverage was for all samples was combined and polyA site (PAS) clusters were defined as continuous regions with more than 10 reads covering every position and more than 20 reads overall in the merged samples. The site of cleavage and polyadenylation was defined as the single nucleotide with highest coverage across merged samples. In the case of a tie, the 3’ most position was used.
Assembly: hg38
Supplementary files format and content: tab seperated file containing the read cluster boundaries, single position of highest coverage, and read counts for each sample.
Supplementary files format and content: bigwig files for forward and reverse strand containing all unique reads for each sample.

molecule: cytoplasmic RNA

growth_protocol: Low passage HepG2 cells were grown on 10 cm plates to 75% confluency in 10 mL DMEM+10% FBS

extract_protocol:
Cells were lysed on ice for 5 minutes in 10mM Tris-HCl pH 8.0, 0.32 sucrose, 3mM CaCl2,  2mM MgCl2, 0.1mM EDTA 0.1% NP40 1mM DTT plus 0.04U/ul RNasin. Total RNA was extracted using TRIzol following the manufacturer's protocol. For fractionation samples, low speed centrifugation was used to separate the fractions with the supernatant added to TRIzol for cytoplasmic and pellet lysed in TRIzol for nuclear fractions.
RNA quality for all samples and fractions was verified using a BioAnlyzer. Further QC and library preparation using QuantSeq Rev V2 (Lexogen) was carried out by Lexogen and subjected to single end, stranded sequencing.

treatment_protocol: Cells were treated with 120 pmol of DDX55 siRNA or non-targeting pool (NTP) siRNA  with 25 uL RNAiMAX with forward transfection protocol using Opti-MEM. Cells were harvested 45-50 hours post transfection and resuspended in 2 mL DPBS for RNA and protein extraction

value: hepatocellular carcinoma

value: siRNA targeting DDX55


title: ATAC-iMGT-Myh6-eGFP-MEFs, siChst7, D1, BiolRep1

description:
Library name: d1_siChst7_1_atac
Active MOTIF ATAC-seq pre #105320; 50M reads/sample

value: mouse embryonic fibroblasts

value: Cardiomyocyte transdifferentiation


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep2

description:
Library name: d1_siControl_2_atac
Active MOTIF ATAC-seq pre #105320; 50M reads/sample

value: siControl


title: HepG2 siDDX55 replicate 2 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

description: Library name: C_siDDX55_2


title: J-Lat 10.6, DMAP1, ChIP, TNFa, Rep2

description:
660-6
DMAP1_TNF_n_of_2_NORMsort.bw
DMAP1_TNF_n_of_2_MACS2__peaks.broadPeak

value: J-Lat 10.6 cells

value: DMAP1 (Thermo Fisher Scientific, #10411-1-AP)


title: HepG2 siDDX55 replicate 1 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

description: Library name: C_siDDX55_1


title: AA147-3

description: Library name: AA147-3


title: J-Lat 10.6, p400, ChIP, TNFa, Rep2

description:
660-4
P400_TNF_n_of_2_NORMsort.bw
P400_TNF_n_of_2_MACS2__peaks.broadPeak


title: Input Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (Input)

city: Vienna

first: Vikas

last: Shukla

state: Vienna

address: Dr.Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: TH40

data_processing:
Reads were trimmed with Trim Galore with options --stringency 1  --length 5 --paired
Trimmed reads were aligned to reference genome MpTak1v7.1 using bowtie2 with --sensitive option
Aligned SAM files were converted to sorted BAM files using samtools
Aligned sorted BAM files for ChIP and Iput samples were used to create BigWig files using deeptools like this: bamCompare -b1 ${test_bam} -b2 ${control_bam} -o ${out}.bw -p max
Assembly: https://marchantia.info/data/MpTak1_v7.1/
Supplementary files format and content: BigWig file containing ChIP signal normalized to input

organism: Marchantia polymorpha

source_name: 14d thalli

growth_protocol: Plants were cultured on half-strength Gamborg’s B5 medium solidified with 1% (w/v) agar under continuous white light at 22°C

extract_protocol:
Two-week-old thalli started from gemmae of M. polymorpha Tak-1 wild type were collected and cross-linked using 1% formaldehyde in 1× PBS under vacuum on ice for 10 min. The cross-linking reaction was quenched by adding 2 M glycine to achieve a final concentration of 0.125 M under vacuum on ice for 10 min. Excess solution was removed from cross-linked tissue by blotting with paper towels. Cross-linked tissue was then snap frozen in liquid nitrogen and ground to a fine powder using mortar and pestle. The powder was transferred into a 50-ml plastic tube and suspended in 40 ml of MP1 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 0.4 M sucrose, 2% (w/v) PVP-10, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 6 mM EGTA, 1× cOmplete protease inhibitor cocktail). Suspended samples were then filtered twice through one layer of Miracloth, once through a 40 μm nylon mesh, and twice through a 10 μm nylon mesh. Filtered samples were centrifuged at 3000 × g at 4°C for 10 min, and the supernatant was discarded. The pellet was washed using 15 ml of MP2 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 0.25 M sucrose, 10 mM MgCl2, 10 mM 2-mercaptoethanol, 0.2% Triton-X 100, 1× cOmplete protease inhibitor cocktail) three times. The final pellet was then resuspended in 5 ml of MP3 buffer (10 mM MES-KOH buffer pH 5.3, 10 mM NaCl, 10 mM KCl, 1.7 M sucrose, 2 mM MgCl2, 10 mM 2-mercaptoethanol, 1× cOmplete protease inhibitor cocktail) and centrifuged at 16 000 × g at 4°C for 1 h. After centrifugation, the supernatant was discarded, and the pellet was resuspended in 900 μl of covaris buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris–HCl pH 8.0, 1× cOmplete protease inhibitor cocktail). The resuspended pellet containing the chromatin fraction was fragmented using a Covaris E220 High-Performance Focused Ultrasonicator for 15 min at 4°C (duty factor, 5.0; peak incident power, 140.0; cycles per burst, 200) in a 1-ml Covaris milliTUBE. Sheared chromatin was centrifuged at 20 000 × g at 4°C for 10 min, and the supernatant was transferred into a new 5-ml tube and diluted by adding 2.7 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton-X-100, 1.2 mM EDTA, 16.7mM Tris-HCl pH 8.0, 167 mM NaCl). Diluted chromatin was cleared by incubating with proteinA/G beads (Thermo Fisher Scientific, Waltham, MA, USA) at 20 rpm spinning at 4°C for 1 h. Beads were removed by magnetic racks and precleared chromatin was separated into five tubes and incubated with 1 μg of specific antibodies for histone H2A variants () at 20 rpm spinning at 4°C overnight. Chromatin bound by antibodies was collected by incubating with protein A/G beads for 3 h. The beads were collected by magnetic racks and washed twice with a low salt wash buffer (20 mM Tris–HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a high salt wash buffer (20 mM Tris–HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100 and 0.1% SDS), once with a LiCl wash buffer (10 mM Tris–HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL CA-630 and 0.1% sodium deoxycholate), and twice with a TE buffer (10 mM Tris–HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted using 500 μl elution buffer (1% SDS and 0.1 M NaHCO3) at 65°C for 15 min. To reverse cross-link, eluted DNA was mixed with 51 μl of reverse cross-link buffer (40 mM Tris–HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg ml−1 proteinase K; Thermo Fisher Scientific) and incubated at 45°C for 3 h and then at 65°C for 16 h. After cross-link reversal, DNA was treated with 10 μg of RNase A (Thermo Fisher Scientific), incubated at room temperature for 30 min and purified using the MinElute PCR purification kit (Qiagen).
ChIP-seq library was generated from ChIPed DNAs using Ovation® Ultralow Library Systems V2 (Tecan, Männedorf, Switzerland).

value: 14d thalli

value: Mpez1,Mpknox2 double mutant


title: ATAC-iMGT-Myh6-eGFP-MEFs, siControl, D1, BiolRep1

description:
Library name: d1_siControl_1_atac
Active MOTIF ATAC-seq pre #105320; 50M reads/sample


title: AA147-4

description: Library name: AA147-4


title: HepG2 siControl replicate 3 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

description: Library name: C_siNTP_3

value: siRNA non-targeting pool


title: AA147-2

description: Library name: AA147-2


title: Input Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (Input)

description: Library name: TH39


title: Tunicamycin-5

description: Library name: Tunicamycin-5

value: Tunicamycin


title: J-Lat 10.6, DMAP1, ChIP, unstimulated, Rep2

description:
660-5
DMAP1_NS_n_of_2_NORMsort.bw
DMAP1_NS_n_of_2_MACS2__peaks.broadPeak


title: CeapinA7-1

description: Library name: CeapinA7-1


title: HepG2 siControl replicate 1 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

description: Library name: C_siNTP_1


title: J-Lat 10.6, RNAPII, ChIP, TNFa, Rep2

description:
660-2
PolII_TNF_n_of_2_NORMsort.bw
PolII_TNF_n_of_2_MACS2__peaks.broadPeak

value: Unstimulated


title: H3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

description: Library name: TH38


title: HepG2 siDDX55 replicate 3 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siDDX55_3


title: Tunicamycin-4

description: Library name: Tunicamycin-4


title: J-Lat 10.6, RNAPII, ChIP, unstimulated, Rep2

description:
660-1
PolII_NS_n_of_2_NORMsort.bw
PolII_NS_n_of_2_MACS2__peaks.broadPeak


title: H3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH37


title: J-Lat 10.6, input, TNFa, Rep1

description:
644-20
input_TNF_n_of_2_NORMsort.bw


title: Tunicamycin-3

description: Library name: Tunicamycin-3


title: HepG2 siDDX55 replicate 1 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siDDX55_1


title: Tunicamycin-1

description: Library name: Tunicamycin-1


title: H2AKUb ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH35


title: J-Lat 10.6, input, unstimulated, Rep1

description:
644-19
input_NS_n_of_2_NORMsort.bw


title: HepG2 siDDX55 replicate 2 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siDDX55_2


title: H2AKUb ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

description: Library name: TH36


title: J-Lat 10.6, H3K27Ac, ChIP, TNFa, Rep1

description:
644-18
H3K27Ac_TNF_n_of_2_NORMsort.bw
H3K27Ac_TNF_n_of_2_MACS2__peaks.broadPeak

value: H3K27ac (Active motif , #39085)


title: H3K4me3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

description: Library name: TH34


title: Tunicamycin-2

description: Library name: Tunicamycin-2

value: Retina


title: HepG2 siControl replicate 2 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siNTP_2


title: HepG2 siControl replicate 2 QuantSeq Rev V2 3'end seq of cytoplasmic RNA

description: Library name: C_siNTP_2


title: J-Lat 10.6, H3K27Ac, ChIP, unstimulated, Rep1

description:
644-17
H3K27Ac_NS_n_of_2_NORMsort.bw
H3K27Ac_NS_n_of_2_MACS2__peaks.broadPeak


title: H3K4me3 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH33


title: H3K9me1 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

description: Library name: TH32


title: J-Lat 10.6, DMAP1, ChIP, TNFa, Rep1

description:
644-16
DMAP1_TNF_n_of_2_NORMsort.bw
DMAP1_TNF_n_of_2_MACS2__peaks.broadPeak


title: PBS-3

description: Library name: PBS-3

value: WT

value: PBS


title: HepG2 siControl replicate 1 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siNTP_1


title: HepG2 siDDX55 replicate 3 QuantSeq Rev V2 3'end seq of whole cell RNA

description: Library name: WC_siDDX55_3


title: H3K9me1 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH31


title: HepG2 siDDX55 replicate 2 QuantSeq Rev V2 3'end seq of whole cell RNA

description: Library name: WC_siDDX55_2


title: PBS-4

description: Library name: PBS-4


title: J-Lat 10.6, p400, ChIP, TNFa, Rep1

description:
644-14
P400_TNF_n_of_2_NORMsort.bw
P400_TNF_n_of_2_MACS2__peaks.broadPeak

value: TNFa stimulated


title: PBS-2

description: Library name: PBS-2


title: AA147-1

description: Library name: AA147-1


title: H3K27me1 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep2 (ChIP)

description: Library name: TH30


title: HepG2 siControl replicate 3 QuantSeq Rev V2 3'end seq of nuclear RNA

description: Library name: N_siNTP_3

value: hepatocellular carcinoma


title: PBS-5

description: Library name: PBS-5


title: HepG2 siDDX55 replicate 1 QuantSeq Rev V2 3'end seq of whole cell RNA

description: Library name: WC_siDDX55_1

value: siRNA targeting DDX55


title: J-Lat 10.6, DMAP1, ChIP, unstimulated, Rep1

description:
644-15
DMAP1_NS_n_of_2_NORMsort.bw
DMAP1_NS_n_of_2_MACS2__peaks.broadPeak


title: H3K27me1 ChIP-seq in Mpez1,Mpknox2 double mutant, 14d thalli, biol rep1 (ChIP)

description: Library name: TH29