title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2099

description: Library name: sample_2099


title: PBMCs, MS_11_t2 (scRNA-seq)

status: Public on May 27 2025

type: SRA

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

country: USA

institute: The University of Michigan

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of all samples , using 10X Cellranger v5.1.0 with default parameters.
Assembly: GRCh38-2020-A
Supplementary files format and content: raw read counts in gene-barcode matrix

molecule: total RNA

organism: Homo sapiens

source_name: Blood

growth_protocol: Cryopreserved PBMCs thawed for library preparation

extract_protocol:
10x Genomics Chromium Controller (gell bead emulsion formation and RNA capture)
Barcoded cDNA generation from bead-captured transcripts (10x Genomics Single-Cell Gene Expression Kit v3.1)

treatment_protocol: Samples were derived from people with CIS treated with atorvastatin or placebo

tag: tissue

value: Blood

tag: cell line

value: 6 month follow-up

tag: cell type

value: PBMC

tag: Sex

value: female

tag: age

value: 30 yo

tag: demographic information

value: NHW

tag: treatment

value: atorvastatin


title: genotype: CNAG_00000, librarydate: 2013-03-13, sample: 2113

city: St Louis

first: Chase

last: Mateusiak

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University, St Louis

description: Library name: sample_2113

library_source: transcriptomic

data_processing:
Reads were aligned with Novoalign (version 4.03.02) and quantified with HTSeq (0.9.1) using the FungiDB KN99 alpha genome sequence. Quality control ensued in two phases. In Phase I, custom scripts were used to verify the Crypto C. neoformans strain in each sample by calculating CDS coverage over putatively deleted genes and the corresponding selectable deletion cassette, ensuring that the former were absent and the latter present. Strains that passed this step were labeled as ‘passing’ if they contained at least 1e6 reads aligned to protein coding regions and less than 7% of all reads failed to align.
In Phase 2, we evaluated replicate agreement using the Regularized Log Expression (RLE). First, we used DESeq2 (version 1.34.0) to estimate the effect of the library date (the known batch effect). We removed the batch effect using the DESeq coefficients for the library dates such that the data was standardized to a single date, resulting in adjusted expression levels on a log2 normalized scale. To compute the RLE value for a given gene, the median expression level of that gene, across all samples in a replicate set, was subtracted from the expression level of that the gene in each sample. For each sample, we then calculated the interquartile range of the distribution of these RLE values across genes. If the interquartile range of RLEs of a given sample was greater than 1, indicating that more than half of genes deviated from their respective medians by a factor of 2 in adjusted count, the sample was considered an outlier and failed for replicate agreement.
Assembly: ASM221672v1
Supplementary files format and content: gzipped tab separated (tsv) raw counts and DESeq2 sizeFactor normalized counts

organism: Cryptococcus neoformans

growth_protocol: Strains were removed from -80C to YPD agar no more than 5 days before the experiment, grown at 30C for 2 nights , and a single colony was inoculated into 4 mL YPD and grown overnight  at 30C shaking at 230 rpm. One day before the experiment, 1 mL of the ON culture was inoculated into 100 mL YPD and grown as above. At the beginning of the experiment, this culture was spun down, washed in 25 mL PBS, and resuspended in 10 mL PBS. 2 x 10^8 cells were then inoculated into each of four T75 flasks containing preconditioned medium  and incubated under the conditions specified for the experiment. A single flask was harvested for each time point (30, 90, 180, and 1440 min after inoculation), with 1.5 mL of culture removed for imaging and the remaining 18.5 mL used for RNA-Seq. The latter was transferred into a tube on ice containing 2 mL RNA Stop solution (5% tris-saturated phenol in ethanol), the cells were sedimented (3000g, 5 min, 4C), supernatant fraction decanted, and the pellet was frozen in liquid nitrogen and stored at -80C. All flasks were prepared and then preconditioned for 24 hours at the designated temperature and pH concentration before use. Cultures were then inoculated as above and the T75 flasks (MIDSCI TP90076) incubated without rotation.

extract_protocol:
Frozen cell pellets were thawed on ice and 875m  TRIzol (Ambion 15-596-018) was added. Cells were then lysed with 750 ml 0.5mm silica-zirconia beads for 3 min in a Minibeadbeater (Biospec Products) and RNA isolated following the Trizol manufacturer’s protocol. Residual DNA was removed with the Turbo DNA-free Kit (Life Technologies AM1907) and polyA+ RNA isolated from ~1 mg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were constructed using the NEBNext Ultra Directional RNA Library Prep Kit from Illumina and samples were pooled at 10 nM. The pools were sequenced on a NextSeq 500 using the High75v2 kit as a 1x75 with 7bp Index1 and 6bp Index2 with 1% PhiX.  Fastq files were demultiplexed using the Illumina bcl2fastq2 allowing 1 bp mismatch.

value: yeast

tag: strain

tag: genotype

value: WT

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

tag: time

value: 90 min


title: Ift88; Pkd2 mutant-3

city: Birmingham

first: Bradley

last: Yoder

address: 1900 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

description:
Library name: double_3
10X Genomics

data_processing:
We processed the scRNA-seq FASTQ files using the 10X Genomics Cell Ranger (v9.0.0) cellranger multi pipeline.
Assembly: GRCm39
Supplementary files format and content: filtered gene-barcode matrix

organism: Mus musculus

source_name: Kidney

extract_protocol:
scRNA-seq analysis was performed on Pkd2 and DKO mutant kidneys at 16 and 26 weeks post-tamoxifen induction, respectively. Kidneys (n=3 per mutant group, n=1 per each control group, all females; 8 total mice) were isolated and processed using a modified cold-activated protease digestion. Birefly, kidneys were minced and digested in 1 ml of 2.5 mg/ml type II collagenase (Worthington, catalog no. LS004176), 7.5 mg/ml B. licheniformis cold-activated protease (Creative Enzymes, catalog no. NATE-0633), and 125 U/ml DNase in D-PBS for approximately 45 minutes at 12°C. After digestion, kidney tissues was individually passed through 70-µm cell-strainers (Falcon; BD Biosciences), yielding single-cell suspensions. Cells were centrifuged at 1300 rpm for 5 minutes at 4°C, resuspended in ACK red blood cell lysis buffer, and incubated at 37°C for 5 minutes. After 5 minutes, 10 ml of RPMI was added to each tube, cells were spun at 1300 rpm for 5 minutes at 4°C, and cells were resuspended in 1% BSA with FC blocking solution (1:200; BioXcell, catalog no. BE0307) for 30 minutes on ice. After blocking, cells were spun and incubated with CD45 (catalog nos. 12–0451, 30-F11; eBioscience) and Fixable Aqua Dead Cell Stain for 30 mins. After staining, cells were spun, washed with 1% BSA, and  ready for sorting.
About 30000 CD45+  cells from each samples were sorted via FACSAriaII sorter. After dilited to disired concentration, the single-cell suspensions were loaded onto the Chromium Controller (10x Genomics) to generate single-cell Gel Bead-in-Emulsions (GEMs) using the GEM-X Universal 3' Gene Expression v4 4-plex On-chip Multiplexing (OCM) kit, following manufacturer's protocols. Sequencing libraries were constructed from amplified cDNA and sequenced on an Illumina platform at a depth of 20,000 reads per cell. Data processing, including demultiplexing, alignment, and gene expression quantification was conducted (Cell Ranger pipeline, 10x Genomics, v3.1). Sequencing libraries were constructed from amplified cDNA and sequenced on an Illumina platform at a depth of 20,000 reads per cell. Data processing, including demultiplexing, alignment, and gene expression quantification was conducted (Cell Ranger pipeline, 10x Genomics, v3.1).

value: Kidney

value: Cre+ Ift88fl/fl ; Pkd2fl/fl

value: 26 weeks post tamoxifen induction


title: Ift88; Pkd2 mutant-2

description:
Library name: double_2
10X Genomics


title: genotype: CNAG_00000, librarydate: 2011-02-05, sample: 2029

description: Library name: sample_2029


title: FOXI2.D168V_455

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs). Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Cy3 signal was scanned to assess double-stranding efficiency and Alexa488 signal was scanned at multiple photomultiplier tube gain settings on a Molecular Devices GenePix 4400A microarray scanner.

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.

molecule: protein

source_name: in vitro trancription and translation

label_protocol: Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency; GST-tagged proteins were detected with Alexa488-labelled anti-GST antibody.

extract_protocol: GST fusion proteins were expressed by in vitro transcription and translation.

treatment_protocol: Reference alleles of human forkhead gene DNA-binding domains and flanks were obtained by commercial gene synthesis. Variants were generated by site-directed mutagenesis and Gateway cloned into pDEST15.

value: GST-tagged protein


title: PBMCs, MS_11_t1 (scRNA-seq)

description: 10X Genomics

value: baseline diagnosis


title: genotype: CNAG_00000, librarydate: 2011-02-05, sample: 2028

description: Library name: sample_2028


title: Ift88; Pkd2 mutant-1

description:
Library name: double_1
10X Genomics


title: Control-1

description:
Library name: CTL_pc2
10X Genomics

value: Cre- Pkd2fl/fl

value: 16 weeks post tamoxifen induction


title: PBMCs, MS_10_t2 (scRNA-seq)

description: 10X Genomics

value: Blood

value: 6 month follow-up

value: 37 yo

value: placebo


title: Pkd2 mutant-3

description:
Library name: pc2_3
10X Genomics

value: Cre+ Pkd2fl/fl


title: FOXI2.D168V_461


title: genotype: CNAG_00000, librarydate: 2013-10-08, sample: 1877

description: Library name: sample_1877


title: FOXI2.D168V_450


title: Control-2

description:
Library name: CTL_double
10X Genomics

value: Cre- Ift88fl/fl ; Pkd2fl/fl


title: FOXI2.D166V_461


title: PBMCs, MS_10_t1 (scRNA-seq)

description: 10X Genomics

value: PBMC

value: female

value: NHW


title: FOXI2.D169E_426


title: FOXI2.D169E_423


title: genotype: CNAG_00000, librarydate: 2013-10-08, sample: 1876

description: Library name: sample_1876

value: yeast

value: WT

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: Pkd2 mutant-2

description:
Library name: pc2_2
10X Genomics

value: Kidney


title: PBMCs, MS_9_t2 (scRNA-seq)

description: 10X Genomics

value: 33 yo

value: atorvastatin


title: FOXG1.S197I_460

value: GST-tagged protein


title: FOXI2.D166V_450


title: genotype: CNAG_00000, librarydate: 2013-10-08, sample: 1875

description: Library name: sample_1875


title: Pkd2 mutant-1

description:
Library name: pc2_1
10X Genomics

value: 16 weeks post tamoxifen induction


title: PBMCs, MS_9_t1 (scRNA-seq)

description: 10X Genomics

value: Blood

value: baseline diagnosis


title: FOXG1.ref_460


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1610

description: Library name: sample_1610


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1609

description: Library name: sample_1609


title: PBMCs, MS_8_t1 (scRNA-seq)

description: 10X Genomics

value: 27 yo


title: FOXG1.S197I_449


title: PBMCs, MS_8_t2 (scRNA-seq)

description: 10X Genomics

value: 6 month follow-up


title: optic nerve, obesogenic diet, sample #2

city: St. Louis

first: Nicole

last: Brossier

state: United States

address: 660 S. Euclid Ave Campus Box 8208

department: Pediatrics

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: tsv of all transcripts

molecule: polyA RNA

source_name: optic nerve

extract_protocol:
NucleoSpin RNA Plus XS kit (Takara Bio)
SMART-Seq mRNA kit (Takara Bio)

value: optic nerve

tag: diet

value: AIN-76A w/ 58% Fat Energy/Sucrose/Red

value: GFAP-Cre; Nf1-Flox/R681X


title: optic nerve, control diet, sample #3

value: PicoLab 5053*


title: PBMCs, MS_7_t1 (scRNA-seq)

description: 10X Genomics

value: PBMC

value: female

value: 39 yo

value: AI


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1608

description: Library name: sample_1608

value: yeast

value: WT

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: FOXG1.ref_449

value: GST-tagged protein


title: PBMCs, MS_7_t2 (scRNA-seq)

description: 10X Genomics

value: Blood

value: atorvastatin


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1597

description: Library name: sample_1597


title: optic nerve, control diet, sample #2


title: optic nerve, control diet, sample #1


title: PBMCs, LTNP_2_t2 (scRNA-seq)

description: 10X Genomics

value: male

value: 45 yo

value: NHW


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1596

description: Library name: sample_1596


title: FOXG1.R244H_449


title: FOXG1.R244H_460


title: FOXG1.R274Q_449


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1380

description: Library name: sample_1380


title: PBMCs, LTNP_2_t1 (scRNA-seq)

description: 10X Genomics

value: baseline diagnosis


title: optic nerve, obesogenic diet, sample #3

value: optic nerve

value: AIN-76A w/ 58% Fat Energy/Sucrose/Red

value: GFAP-Cre; Nf1-Flox/R681X


title: FOXG1.R244C_449


title: PAB-SC144 Pig 4

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

institute: University of Minnesota

description:
Library name: Sample 12
10x Genomics

data_processing:
cellranger-7.2.0
Assembly: Sscrofa10.2
Supplementary files format and content: Matrix files for analysis

organism: Sus scrofa domesticus

source_name: RV free wall

extract_protocol:
Nuclei were isolated from frozen RV samples and then subjected to flow cytometry to isolate pure nuclei fractions
RNA libraries from RNA-seq were prepared by the University of Minnesota Genomics center.

value: RV tissue

value: RV free wall

value: 10 weeks


title: FOXG1.R244C_460


title: FOXG1.R274Q_460


title: FOXG1.A188G_449


title: PAB-SC144 Pig 3

description:
Library name: Sample 11
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1379

description: Library name: sample_1379

value: yeast


title: genotype: CNAG_00000, librarydate: 2012-09-06, sample: 1598

description: Library name: sample_1598

value: WT


title: FOXG1.A188G_460


title: PAB-SC144 Pig 2

description:
Library name: Sample 10
10x Genomics


title: PBMCs, MS_6_t1 (scRNA-seq)

description: 10X Genomics

value: PBMC

value: female

value: 24 yo

value: placebo


title: PBMCs, MS_5_t2 (scRNA-seq)

description: 10X Genomics

value: Blood

value: 6 month follow-up

value: 42 yo

value: atorvastatin


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1371

description: Library name: sample_1371

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: PBMCs, MS_5_t1 (scRNA-seq)

description: 10X Genomics

value: baseline diagnosis

value: NHW


title: PAB-SC144 Pig 1

description:
Library name: Sample 9
10x Genomics

value: RV tissue

value: male


title: PAB-Vehicle Pig 4

description:
Library name: Sample 8
10x Genomics

value: RV free wall

value: 10 weeks


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1370

description: Library name: sample_1370

value: yeast

value: WT


title: FOXF1.Y89C_446

value: GST-tagged protein


title: PBMCs, MS_4_t2 (scRNA-seq)

description: 10X Genomics

value: 3 month follow-up

value: PBMC

value: 43 yo


title: PBMCs, MS_6_t2 (scRNA-seq)

description: 10X Genomics

value: Blood

value: female

value: 24 yo

value: placebo


title: PBMCs, MS_4_t1 (scRNA-seq)

description: 10X Genomics

value: atorvastatin


title: PAB-Vehicle Pig 3

description:
Library name: Sample 7
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1368

description: Library name: sample_1368

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: PAB-Vehicle Pig 2

description:
Library name: Sample 6
10x Genomics

value: RV tissue


title: FOXF1.Y89C_421


title: PBMCs, MS_3_t2 (scRNA-seq)

description: 10X Genomics

value: 6 month follow-up

value: male

value: 30 yo

value: NHW


title: FOXF1.Y89C_422


title: PAB-Vehicle Pig 1

description:
Library name: Sample 5
10x Genomics

value: RV free wall

value: 10 weeks


title: PBMCs, MS_3_t1 (scRNA-seq)

description: 10X Genomics

value: baseline diagnosis


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1367

description: Library name: sample_1367

value: yeast

value: WT


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1028

description: Library name: sample_1028


title: FOXF1.ref_446

value: GST-tagged protein


title: FOXF1.ref_450


title: PBMCs, MS_2_t2 (scRNA-seq)

description: 10X Genomics

value: Blood

value: PBMC

value: female

value: 19 yo

value: HW


title: PBMCs, MS_2_t1 (scRNA-seq)

description: 10X Genomics

value: atorvastatin


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1026

description: Library name: sample_1026

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min

value: 90 min


title: Control Pig 2

description:
Library name: Sample 2
10x Genomics

value: RV tissue

value: male


title: FOXF1.ref_422


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1369

description: Library name: sample_1369


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1027

description: Library name: sample_1027


title: PBMCs, MS_1_t2 (scRNA-seq)

description: 10X Genomics

value: 12 month follow-up

value: 40 yo

value: NHW

value: placebo


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1016

description: Library name: sample_1016

value: yeast


title: PBMCs, MS_1_t1 (scRNA-seq)

description: 10X Genomics

value: baseline diagnosis


title: Control Pig 1

description:
Library name: Sample 1
10x Genomics

value: RV free wall

value: 10 weeks


title: TCR_isotype_1

city: VILLEJUIF

first: AZIZA

last: CAIDI

address: 114 RUE EDUARD VAILLANT

country: France

institute: GUSTAVE ROUSSY

description:
Library name: Sample16
10x Genomics

library_source: other

data_processing:
Raw BCL-files were then demultiplexed and converted to Fastq format with bcl2fastq (version 2.20.0.422 from Illumina). We processed scRNAseq data with cellranger count (v7.2).
Assembly: Mus musculus GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

molecule: other

source_name: MC38 tumor

extract_protocol:
TIL isolation, tumours were harvested on day 21 or 22, cut into small pieces and digested with the Tumour Dissociation Kit (Miltenyi Biotec 130-096–730) for 40 min at 37 °C in accordance with the manufacturer’s protocol. Cell suspensions were obtained by crushing and passage through 100 μm-mesh cell strainers. Red blood cells were removed with 1x Red Blood Cell Lysis Solution  (Miltenyi Biotec 130-094-183). The cells were washed twice with 2% FCS in PBS and for the preparation was enriched in CD8 and CD4 cells with the MultiMACS system (Miltenyi Biotec). Cells were labeled with anti-CD8a or anti-CD4 (L3T4) antibody-conjugated microbeads (Miltenyi Biotec 130–117–044 or 130-117-043, respectively) and then purified with the POSSEL program on MultiMACS.
CD3+ TIL were loaded onto a Chromium Single-Cell Chip (10x Genomics), according to the manufacturer’s instructions, for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis with Chromium Next GEM Single-Cell 5' GEM, Library Kit v2 (10X Genomics) according to the manufacturer’s instructions.

value: MC38 tumor

value: Tumor-infiltrating T lymphocytes

value: Isotype

tag: batch


title: FOXF1.ref_461

value: GST-tagged protein


title: FOXF1.R139Q_461


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1015

description: Library name: sample_1015

value: WT


title: Control Pig 4

description:
Library name: Sample 4
10x Genomics


title: FOXF1.ref_421


title: genotype: CNAG_00000, librarydate: 2013-04-17, sample: 1014

description: Library name: sample_1014

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: PBMCs, LTNP_1_t1 (scRNA-seq)

description: 10X Genomics

value: Blood

value: PBMC

value: 39 yo


title: PBMCs, LTNP_1_t2 (scRNA-seq)

description: 10X Genomics

value: 6 month follow-up

value: male


title: Control Pig 3

description:
Library name: Sample 3
10x Genomics

value: RV tissue


title: genotype: CNAG_00000, librarydate: 2012-07-02, sample: 651

description: Library name: sample_651

value: 90 min


title: TCR_anti-PD1_anti-CTLA4_1

description:
Library name: Sample14
10x Genomics


title: FOXF1.P83S_421


title: FOXF1.P83S_422


title: TCR_anti-PD1_anti-CTLA4_2

description:
Library name: Sample13
10x Genomics


title: FOXF1.P83A_421


title: genotype: CNAG_00000, librarydate: 2012-02-13, sample: 1378

description: Library name: sample_1378

value: yeast


title: genotype: CNAG_00000, librarydate: 2012-07-02, sample: 649

description: Library name: sample_649


title: FOXF1.P83A_422


title: TCR_anti-CTLA4_1

description:
Library name: Sample10
10x Genomics


title: FOXF1.R139Q_450


title: genotype: CNAG_00000, librarydate: 2012-01-23, sample: 611

description: Library name: sample_611


title: FOXF1.K108E_422


title: TCR_anti-CTLA4_2

description:
Library name: Sample9
10x Genomics


title: TCR_anti-PD1_1

description:
Library name: Sample12
10x Genomics


title: GE_isotype_2

description:
Library name: Sample7
10x Genomics

data_processing:
Raw BCL-files were then demultiplexed and converted to Fastq format with bcl2fastq (version 2.20.0.422 from Illumina). We processed scRNAseq data with cellranger count (v7.2).
Assembly: Mus musculus GRCm38
Supplementary files format and content: Tab-separated values files and matrix files


title: genotype: CNAG_00000, librarydate: 2012-01-23, sample: 612

description: Library name: sample_612


title: FOXB2.W87G_415


title: TCR_anti-PD1_2

description:
Library name: Sample11
10x Genomics


title: FOXF1.G112S_422


title: genotype: CNAG_00000, librarydate: 2012-07-02, sample: 650

description: Library name: sample_650


title: FOXF1.K108E_421


title: TCR_isotype_2

description:
Library name: Sample15
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 559

description: Library name: sample_559


title: genotype: CNAG_00000, librarydate: 2012-01-23, sample: 602

description: Library name: sample_602


title: GE_isotype_1

description:
Library name: Sample8
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 558

description: Library name: sample_558


title: genotype: CNAG_00000, librarydate: 2012-01-23, sample: 601

description: Library name: sample_601


title: FOXF1.G112S_421


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 557

description: Library name: sample_557


title: GE_anti-PD1_anti-CTLA4_2

description:
Library name: Sample5
10x Genomics


title: optic nerve, obesogenic diet, sample #1

value: optic nerve

value: AIN-76A w/ 58% Fat Energy/Sucrose/Red

value: GFAP-Cre; Nf1-Flox/R681X


title: GE_anti-PD1_1

description:
Library name: Sample4
10x Genomics

value: MC38 tumor


title: FOXB2.ref_455


title: FOXB2.W87G_414


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 549

description: Library name: sample_549


title: FOXB2.ref_460


title: FOXB2.ref_449


title: GE_anti-PD1_2

description:
Library name: Sample3
10x Genomics

value: Tumor-infiltrating T lymphocytes


title: GE_anti-PD1_anti-CTLA4_1

description:
Library name: Sample6
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 550

description: Library name: sample_550


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 537

description: Library name: sample_537


title: GE_anti-CTLA4_1

description:
Library name: Sample2
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 541

description: Library name: sample_541


title: HDM-induced AR mice treated with ribavirin, replicate 3, scRNAseq

city: Shanghai

first: Jin

last: Hou

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Library name: H6

data_processing:
The raw sequencing data (FASTQ files) were processed using “Cell Ranger”. After quantifying unique molecular identifiers (UMI), a gene-barcode matrix was generated for each sample.
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Nasal mucosa

extract_protocol:
The nasal mucosa was separated and digested in the 2 mL buffer with collagenase I 5,000 U/mL, hyaluronidase 11,400 U/mL, and DNase I (10104159001, Roche) 20 µL for 1 h at 37℃. The cells were filtered through a 40 μm cell strainer and then centrifuged to obtain the precipitates. CD45+ immune cells were enriched using magnetic beads from the nasal mucosa of PBS control and OVA- or HDM-induced AR mice treated with either vehicle or ribavirin.
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5' end (that is, the 3' end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly,  beads that were then  subject to  second-strand cDNA synthesis,  adaptor ligation,   and   universal   amplification. Sequencing   libraries   were   prepared   using   randomly interrupted  whole-transcriptome  amplification  products  to  enrich  the  3' end  of the  transcripts linked  with  the  cell  barcode  and  UMI.  All  the  remaining  procedures  including  the  library construction were performed according to the standard manufacturer's protocol (CG000206 Rev D).  Sequencing  libraries  were  quantified  using  a  High  Sensitivity  DNA  Chip  (Agilent)  on  a Bioanalyzer 2100 and the Qubit High  Sensitivity DNA Assay  (Thermo Fisher  Scientific).

value: Nasal mucosa

value: CD45+ immune cells


title: GE_anti-CTLA4_2

description:
Library name: Sample1
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 535

description: Library name: sample_535

value: WT


title: HDM-induced AR mice treated with ribavirin, replicate 2, scRNAseq

description: Library name: H5


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 536

description: Library name: sample_536

value: medium:DMEM atmosphere:CO2 5% temperature:37C time:90 min


title: FOXB2.ref_453

value: GST-tagged protein


title: HDM-induced AR mice treated with ribavirin, replicate 1, scRNAseq

description: Library name: H4


title: FOXB2.ref_431


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 528

description: Library name: sample_528


title: FOXB2.ref_430


title: HDM-induced AR mice treated with vehicle, replicate 2, scRNAseq

description: Library name: H2


title: HDM-induced AR mice treated with vehicle, replicate 3, scRNAseq

description: Library name: H3


title: FOXB2.ref_416


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 509

description: Library name: sample_509


title: FOXB2.ref_417


title: OVA-induced AR mice treated with ribavirin, replicate 3, scRNAseq

description: Library name: O6


title: FOXB2.ref_414


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 527

description: Library name: sample_527


title: FOXB2.R56P_415


title: FOXB2.ref_415


title: FOXB2.R46C_460


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 507

description: Library name: sample_507


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 508

description: Library name: sample_508


title: genotype: CNAG_00000, librarydate: 2012-05-01, sample: 519

description: Library name: sample_519


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 497

description: Library name: sample_497


title: HDM-induced AR mice treated with vehicle, replicate 1, scRNAseq

description: Library name: H1


title: OVA-induced AR mice treated with ribavirin, replicate 1, scRNAseq

description: Library name: O4


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 496

description: Library name: sample_496


title: OVA-induced AR mice treated with vehicle, replicate 3, scRNAseq

description: Library name: O3


title: OVA-induced AR mice treated with vehicle, replicate 2, scRNAseq

description: Library name: O2


title: FOXB2.R3Q_415


title: FOXB2.R56P_414


title: FOXB2.R46C_449


title: genotype: CNAG_00000, librarydate: 2012-07-28, sample: 495

description: Library name: sample_495


title: PBS control treated with ribavirin, replicate 3, scRNAseq

description: Library name: P6


title: FOXB2.R3Q_414


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 222

description: Library name: sample_222


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 223

description: Library name: sample_223


title: OVA-induced AR mice treated with vehicle, replicate 1, scRNAseq

description: Library name: O1


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 224

description: Library name: sample_224


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 215

description: Library name: sample_215


title: PBS control treated with ribavirin, replicate 2, scRNAseq

description: Library name: P5


title: PBS control treated with vehicle, replicate 3, scRNAseq

description: Library name: P3


title: OVA-induced AR mice treated with ribavirin, replicate 2, scRNAseq

description: Library name: O5


title: FOXB2.P35Q_430


title: FOXB2.P35Q_431


title: FOXB2.R46C_455


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 214

description: Library name: sample_214


title: FOXB2.P35L_431


title: FOXB2.P35L_453


title: FOXB2.K73N_414


title: PBS control treated with vehicle, replicate 1, scRNAseq

description: Library name: P1


title: genotype: CNAG_00000, librarydate: 2012-03-19, sample: 213

description: Library name: sample_213


title: FOXB2.G82S_431


title: FOXB2.K73N_415


title: FOXB2.P35L_430


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 171

description: Library name: sample_171


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 170

description: Library name: sample_170


title: Epidermis_Day2_Control

first: Michigan

middle: CDB

last: Bioinformatics

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

institute: University of Michigan

description:
Library name: Sample_309109
10x Genomics

data_processing:
Cell Ranger version 9.0.1 used to demultiplex and identify cells
standard seurat lognormalize pipeline used for preprocessing
harmony used for integration of genotypes
Assembly: GRCm39
Assembly: GENCODE Mouse Release M30 gene annotation
Supplementary files format and content: .mtx and .tsv standard, filtered, Cell Ranger output
Supplementary files format and content: seurat RDS contains the Keratinocyte seurat analysis, clustering, and UMAP. Load in R with obj <- readRDS(file.RDS)

source_name: Epidermis

extract_protocol:
Epidermal whole mounts were isolated from back skin of P2 control and Gli2 epidermal knockout mice. Therefore, skin was cut into small pieces of 1cm2 and incubated dermis-side down in Collagenase (2mg/ml, Gibco)/DNase (1U/ml, Millipore) for 1h 15 min at 37°C. Residues of digested dermis were removed by gently pipetting PBS over the skin tissues. The epidermal whole mounts were then incubated in 0.25% Trypsin (Life Technologies GmbH)/0.05mM EDTA (Gibco) for 1h at 37°C, with gentle shearing every 15 min. Trypsin was neutralised with 500 µl of FAD media (F12, Gibco + DMEM, Sigma-Aldrich + FBS Superior Merck Millipore). Cell suspension was filtered through a 30 µm cell strainer (Avantor), which was subsequently washed with additional 500 µl media to recover remaining cells. Cells were centrifuged and re-suspended in 0.004% BSA/PBS. Samples with a viability of more than 75% were processed for sequencing.
Single Cell 3' v4 (polyA) OCM 10x genomics libraries produced by the Cologne Center for Genomics using standard protocols

value: Epidermis

value: 2 Day


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 163

description: Library name: sample_163


title: Epidermis_Day2_Gli2_EKO

description:
Library name: Sample_309108
10x Genomics


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 161

description: Library name: sample_161


title: PBS control treated with ribavirin, replicate 1, scRNAseq

description: Library name: P4


title: Back dermis KO 3

city: hangzhou

first: Fan

last: Xu

state: zhejiang

address: 88 Jiefang Road,Shangcheng District Hangzhou,China

institute: Zhejiang university

description:
Library name: Sample 6
Column name in gene_count_all_samples.csv: KO3_back_D

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Paired-end clean reads were aligned to the Mus Musculus(GRCm38/mm10) using hisat2 (v2.0.5).
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: back dermis

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tamoxifen treatment was performed by oral gavage of tamoxifen 4 times/week for 5 weeks (0.1 mg/g body weight) of a 20 mg/ml solution in corn oil.

value: back dermis

value: tamoxifen administration


title: GS0837

type: genomic

city: Rotterdam

first: Martine

last: Lamfers

address: Dr. Molewaterplein 40

department: Neurosurgery

country: Netherlands

institute: Erasmus MC

hyb_protocol: not provided

scan_protocol: not provided

data_processing: GenomeStudio software (Illumina) was used to analyze CNV GSA manifest files. Final reports and visualizations were created using the Nexus Discovery software package (BioDiscovery El Segundo).  The minimum number of probes per segment was set to 20, and the minimum LOH length to 500 kB.

label: cy3, cy5

molecule: genomic DNA

source_name: tissue

label_protocol: not provided

extract_protocol: Cell pellets were snap frozen and Genomic DNA was extracted from snap frozen cell pellets and from cryosections of liquid N2 stored snap frozen tumor material. All DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

tag: disease

value: Glioblastoma

tag: idh

value: IDH-mutant

tag: type

value: Primary


title: Back dermis KO 1

description:
Library name: Sample 4
Column name in gene_count_all_samples.csv: KO1_back_D


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 162

description: Library name: sample_162

value: yeast

value: 90 min


title: Back dermis Ctrl 3

description:
Library name: Sample 3
Column name in gene_count_all_samples.csv: WT3_back_D


title: PBS control treated with vehicle, replicate 2, scRNAseq

description: Library name: P2


title: FOXB2.G82S_430


title: Back dermis Ctrl 2

description:
Library name: Sample 2
Column name in gene_count_all_samples.csv: WT2_back_D


title: Back dermis KO 2

description:
Library name: Sample 5
Column name in gene_count_all_samples.csv: KO2_back_D


title: GS0827


title: genotype: CNAG_00000, librarydate: 2012-03-12, sample: 172

description: Library name: sample_172


title: GS0815

value: IDH-WT


title: Back dermis Ctrl 1

description:
Library name: Sample 1
Column name in gene_count_all_samples.csv: WT1_back_D


title: FOXB2.G5R_430


title: GS0814


title: MAOI, TIIs

city: Los Angeles

first: Lili

last: Yang

state: California

address: 610 Charles E. Young Dr. East

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: Sample_01
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting aggregation,and merged digital expression matrix generation were made by Cell Ranger software v.9.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/downloads).
Assembly: mm39
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: tumor

growth_protocol: B16-OVA melanoma cells (1 × 10^6 per animal) were subcutaneously injected into experimental mice to form solid tumors.

extract_protocol:
Day 10 B16-OVA tumors (10 tumors were combined for each group) were harvested from experimental mice and mechanically meshed in 70-μm cell strainers to generate single cell suspensions. Single cells were washed once with T cell culture RPMI medium, resuspended in 50% Percoll, and centrifuged at 800g at 25°C for 30 min with brake off. Cell pellets enriched with TIIs were collected and sorted using a FACSAria II flow cytometer to purify live immune cells (gated as DAPI−CD45.2+ cells). Sorted TIIs were immediately delivered to the Technology Center for Genomics & Bioinformatics (TCGB) facility at UCLA for library construction and sequencing.
Purified TIIs were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 TIIs from each experimental group were loaded on the Chromium platform (10x Genomics), and libraries were constructed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (catalog no. PN-120237, 10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq using a NovaSeq 6000 S2 Reagent Kit (100 cycles; catalog no. 20012862, Illumina).

treatment_protocol: C57BL/6J mice received intraperitoneal injection of MAOI [i.e., phenelzine (30 mg/kg per day)] to block MAO-A activity.

value: tumor

value: CD45+ tumor-infiltrating immune cells (TIIs)


title: FOXB2.G100S_417


title: FOXB2.G5R_431


title: FOXB2.G100S_416


title: GS0921

value: Recurrent


title: Her2-negative

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

data_processing:
Fastq files were processed using the nf-core/rnaseq pipeline (version 3.12.0, https://nf-co.re/rnaseq/3.12).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.9a) to the mouse transcriptome (GRCm38, gene annotation from Ensembl release 102).
Gene quantification was performed using Salmon (version 1.10.1).
Tables with transcript and gene counts were generated by the tximport R package.
Assembly: GRCm38
Supplementary files format and content: Txt file containg gene counts

source_name: lung

growth_protocol: Mice were housed in the institution's mouse facility until 12-14 weeks old before treatment.

extract_protocol:
mRNA was isolated from sorted Her2 cells with the RNeasy plus micro kit according to manufacturer's instructions.
Libraries were prepared with the SMART-Seq mRNA LP kit (Takara) following the manufacturer's instructions.

treatment_protocol: 500 EIU of Influenza A virus in 50ul PBS were administered intranasally to each mouse anesthesized with isoflurane. Lungs were harvested 9dpi. Single cell suspension was generated using Miltenyi lung dissociation kit (130-095-927) according to manufacturer's instructions. Single cell suspensions were pre-incubated (5 min) with anti-CD16/CD32 Fc block (BD Biosciences 553141) followed by staining for CD45 and Her2. Her2 cells were sorted at the Astrios EQ flow cytometer (Beckman Coulter). Her2 cells were gated on CD45neg/Her2pos.

value: lung

value: Her2+ metastatic breast cancer cells in lungs

value: FVB Tg(MMTVneu)

value: Influenza A virus infection for 9 days


title: GS0916


title: PBS treatment, rep 3

value: PBS as control for influenza A virus infection


title: FOXB2.G100R_417

value: GST-tagged protein


title: FOXB2.G100D_417


title: FOXB2.G5R_453


title: GS0902


title: FOXB2.G100R_416


title: PBS treatment, rep 2


title: FOXB2.G100D_416


title: PBS treatment, rep 1


title: FOXB2.G100C_417


title: Flu treatment, rep3


title: FOXB2.G100C_416


title: GS0851


title: GS0852


title: FOXB2.E52G_414


title: Flu treatment, rep2


title: FOXB2.E52G_415


title: FOXB2.D95E_415


title: Flu treatment, rep1


title: GS0812


title: GS0845


title: GS0848


title: GsdmdFL/FL -IR

city: Guangzhou

first: Aoran

last: Dong

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.  Seurat package (version: 4.0.3 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.  PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. log2FC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: liver

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

value: liver

value: WT

value: IR


title: GS0843

value: Glioblastoma


title: GS0853

value: Primary


title: Flu_metastasis

data_processing:
Single cell RNA-seq (scRNAseq) fastq files were processed using Cell Ranger software (v7.0.1) (PMID: 28091601) (10X Genomics) to assign reads to genes based on Cell Ranger?s Chromium mouse transcriptome probe set (version 1.0.1). Demultiplexing to assign the cells to samples was performed based on the corresponding probe barcodes. The sample map file (sample_map_for_cellranger.csv) with this information has been supplied. The counts were analyzed using the Seurat R package. Genes found in fewer than 10 cells were excluded. Cells were excluded if they contained less than 201 genes, greater than 7500 unique molecular identifiers (UMIs), or greater than 2.5% of mitochondrial UMIs.
Assembly: mm10 GENCODE M23 gene annotations (refdata-gex-mm10-2020-A)
Supplementary files format and content: Text file containing UMIs by gene by cell (counts_matrix.txt) and text file containing metadata for each cell (cell_metadata.txt)

source_name: Lung

extract_protocol:
Whole lungs were harvested and digested using lung digestion mix (1.5 mg/mL collagenase A (Sigma Aldrich cat# COLLA-RO; St. Louis, MO), 0.4 mg/mL deoxyribonuclease I (Worthington cat# LS002139; Lakewood, NJ), 10 mM HEPES pH 7.2, 5% FBS) was injected into the lungs through cannulae and were incubated at 37°C for 30 min. Digested lungs were passed through a 50 mm cell strainer and red blood cells were lysed using hemolytic buffer (150 mM NH4Cl, 1 mM NaHCO3, 1.1 mM Na2EDTA).Live cells were enriched using the Miltenyi dead cell removal kit (130-090-101).
Cells were provided to the Genomics Shared Resource of the University of Colorado Cancer Center (RRID: SCR_021984) and subjected to library construction as follows. Cells exhibiting >80% viability are fixed in a 4% formaldehyde fixative solution and using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics). The whole transcriptome probe pairs (10X Genomics) are added to the fixed single cell suspensions to hybridize to their complementary target RNA in an overnight incubation at 42°C. After hybridization, the unbound probes are washed off. The fixed and probe-hybridized single cell suspensions are loaded onto Chromium X (10X Genomics) microfluidics instrument to generate partitioned nanoliter-scale droplets in oil emulsion. Each droplet contains a barcoded gel bead, a single cell, and enzyme Master Mix (10X Genomics) for probe pair ligation and gel bead primer barcode extension. The droplets in oil emulsion are place in a thermal cycler for 60 min at 25°C, 45 min at 60°C, and 20 min at 80°C. The single cell-barcoded, ligated probe product undergo library preparation to be compatible with Illumina next-generation sequencing.

treatment_protocol: 12-14 week old MMTV-erbB2/neu/HER2 (MMTV-Her2): MMTV-Her2 mice were infected with 500 EIU Puerto Rico A/PR/8/34 H1N1 influenza A (IAV) through intranasal administration or pbs control. For immune cell depletion, mice were injected intraperitoneally with 100 µg anti-CD4 or rat IgG as control 1 day before IAV infection and then every 6 days after. Mice were euthanized at 9 days and 15 days post infection

value: Lung

value: IAV or pbs

tag: time point

value: post IAV infection at 9 and 15 days


title: PFC, BCAS, Female, 4

city: Singapore

first: Vanessa

last: Wazny

address: 59 Nanyang Dr

country: Singapore

institute: Nanyang Technological University

description: 10X Genomics

data_processing:
Raw sequencing data were processed with cellranger (version 6.0.2) for sample demultiplexing, cell barcode detection and single-cell expression matrices generation.
Assembly: mm10
Supplementary files format and content: Cellranger output files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Prefrontal cortex

growth_protocol: Animals' care was in accordance with institutional guidelines, approved by the local Institutional Animal Care and Use Committee.

extract_protocol:
Mice were anesthetized with isoflurane and transcardially perfused with ice-cold, bubbled artificial cerebrospinal fluid (ACSF). The brain was dissected and mounted for sectioning. Coronal brain sections were generated with a Compresstome vibrating microtome. The vibratome chamber was filled with a sucrose-based cutting solution, and sections were cut to a thickness of 250 µm. Sections were subsequently transferred into ice-cold ACSF-Trehalose (ACSFT). Prefrontal cortex regions were excised from individual brain. Tissue were digested with Pronase (Sigma-Aldrich, 537088; 2 mg/ml) diluted in bubbled ACSFT at room temperature for 45 minutes. Subsequently, tissue was washed with 1% FBS in ACSFT three times. Mechanical dissociation of tissue into a single-cell suspension was achieved by pipetting the samples using pipette tips of decreasing bore sizes (p1000, p200, p100, p20). The resultant cell suspensions were filtered through a 0.2 µm cell strainer.
10X Chromium Next GEM Automated Single Cell 3ʹ (v3.1 Chemistry).

treatment_protocol: BCAS surgery was performed using on mice anesthetized with 2.0% isoflurane before a midline cervical incision was made. Both common carotid arteries were exposed by careful separation of tissue layers and the vagal nerves. 0.18 mm diameter microcoils (Sawane Spring Co., Ltd) were applied by rotating it around each common carotid artery. Body temperature was monitored and maintained at 36.5C-37.5°C with a heating blanket. After microcoil application, the incision was closed with a silk suture, and mice were left on the heating blanket after surgery. Sham mice underwent the same procedure without microcoil placement. Laser-Doppler flowmetry (OMEGAWAVE, INC) was used to confirm cerebral blood flow changes.

value: 80 days

value: Prefrontal cortex

value: Mixed

value: BCAS

value: Female


title: Gsdmd∆Hep-IR

value: gsdmd-ko


title: GsdmdFL/FL -Ctrl

value: Ctrl


title: Donor2, Ctrl & IL35, D4, multiplexing catpure

city: LYON cedex 08

first: Nathalie

last: Bendriss-Vermare

address: 28 rue Laennec

department: TERI

institute: CRCL

description: Control=CMO311; IL35=CMO312

data_processing:
Raw fastq files were processed with CellRanger 7.1.0 with default parameters and the human genome refdata-gex-GRCh38-2020-A.
For multiplexed data the algorithm "multi" was used, with the gene expression and multiplexing capture librairies.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger multi count output files: raw_feature_bc_matrix -> barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi multiplexing_analysis: assignment_confidence_table.csv

source_name: Human blood

growth_protocol: Primary Human NK cells NK cells were cultured in RPMI GlutaMAX complemented with 20% human AB Serum, 1% penicillin-streptomycin, 1x Non-Essential Amino Acids, 1x Sodium Pyruvate and supplemented with IL-2 at 100UI/mL, in presence or absence of IL-35 at 100ng/mL. Culture medium was renewed every 2 days.

extract_protocol:
For each collection day, NK treated with or without IL-35 were barcoded following Cell Multiplexing Oligos (CMOs) labeling protocol (CellPlex Kit) developed by 10X Genomics. NK were independently incubated with specific CMOs, washed 3 times in PBS + 1% BSA and pooled together. The number of live cells was loaded on a 10X G chip to obtain an expected cell recovery population of 11,000 cells per channel and run on the Chromium iX system (10X Genomics) according to manufacturer’s instructions.
Gene Expression and Cell Multiplexing single-cell RNA-seq libraries were generated with the Chromium Single Cell 3′ v.3.1 kit with feature barcoding technology (10X Genomics). Gene Expression and Cell Multiplexing libraries were sequenced on the NovaSeq 6000 platform (Illumina) to obtain around 50,000 reads and 5,000 reads per cell respectively.

treatment_protocol: Cells were either cultured in IL-2 alone or IL-2+IL-35, for 2 and 4 days

value: Human blood

value: NK cells

value: IL2 & IL2+IL35


title: GS0832

value: IDH-WT


title: GS0850


title: Donor2, Ctrl & IL35, D4, gene expression


title: GS0834


title: FOXA1.S188G_457

value: GST-tagged protein


title: FOXB2.D95E_414


title: PFC, BCAS, Female, 3

description: 10X Genomics


title: PFC, BCAS, Male, 2

description: 10X Genomics

value: Male


title: PFC, BCAS, Male, 1

description: 10X Genomics


title: GS0830

value: Glioblastoma

value: Primary


title: GS0838


title: FOXA1.S188G_447


title: FOXA1.S165R_446


title: FOXA1.S165R_441


title: FOXA1.ref_457


title: Donor2, Ctrl & IL35, D2, multiplexing catpure

description: Control=CMO309; IL35=CMO310


title: FOXA1.S165R_388


title: FOXA1.S165R_413


title: FOXA1.ref_447


title: GS0829


title: PFC, Sham, Female, 4

description: 10X Genomics

value: Sham


title: Donor2, Ctrl & IL35, D2, gene expression


title: PFC, Sham, Female, 3

description: 10X Genomics


title: GS0811


title: FOXA1.ref_446


title: PFC, Sham, Male, 2

description: 10X Genomics


title: FOXA1.ref_441


title: GS0828


title: Donor1, Wtrl & IL35, D4, multiplexing catpure

description: Control=CMO307; IL35=CMO308


title: GS0825


title: PFC, Sham, Male, 1

description: 10X Genomics


title: GS0824


title: Donor1, Ctrl & IL35, D2, multiplexing catpure

description: Control=CMO305; IL35=CMO306


title: B16-OVA aPD-1

description: 10x Genomics

data_processing:
The raw sequencing data were processed and mapped to the mouse reference genome (GRCm39/mm39) using the Cell Ranger software.
Assembly: GRCm39/mm39
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: B16-OVA Tumor

extract_protocol:
Day 10 B16-OVA tumors were harvested from experimental mice to prepare TII suspensions (10 tumors were combined for each group).
TII suspensions were then sorted using a FACSAria II flow cytometer to purify immune cells (gated as DAPI−CD45.2+ cells). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).
Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: B16-OVA Tumor

value: Tumor-infiltrating immune cells


title: B16-OVA FLX

description: 10x Genomics

value: fluoxetine


title: GS0823


title: GS0821


title: Donor1, Ctrl & IL35, D2, gene expression


title: B16-OVA NT

description: 10x Genomics

value: not treated


title: Arsenite_TXNL1SxxS_replicate2

first: Zachary

last: Mirman

address: 5 Lester Pl

institute: Brigham and Womens

data_processing:
Reads were aligned using qAlign to the GRCh8w primary assembly from gencodegenes.org
Data from two files for each sample were merged to obtain raw counts
Raw counts were filtered to remove genes with <10 counts in the three replicates of the control cells
DESeq2 was used to obtain log2 fold changes and adjusted p values
Assembly: GRCh38
Supplementary files format and content: processed data are provided in the form of a matrix of raw counts

growth_protocol: We cultured HEK293T (ATCC CRL-3216) cells at 37C and 5% CO2 in DMEM, high glucose, GlutaMAX™ Supplement, pyruvate (ThermoFisher Scientific) added with 10% fetal bovine serum (HyClone), 1% of 10,000 U/mL Penicillin-Streptomycin (ThermoFisher Scientific)

extract_protocol:
RNA was extracted using the Qiagen Rneasy mini kit.
Library was constructed by BGI Genomcis
DNBseq eukaryotic strand-specific transcriptome sequencing

value: cell line

value: TXNL1 KO

tag: treatment 2

value: Arsenite


title: Donor1, Ctrl & IL35, D4, gene expression

tag: tissue


title: FOXA1.ref_413

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores for each 8-mer.


title: GS0820


title: Arsenite_TXNL1SxxS_replicate3

tag: cell line


title: Arsenite_TXNL1SxxS_replicate1

tag: cell type


title: GS0819


title: KO3

city: 重庆

first: 蒋

last: 慧

address: 中国重庆

institute: 南华大学

data_processing:
Reads obtained from the sequencing machines were filtered by Cutadapt.Then sequence quality was verified using FastQC.
We aligned reads of all samples to the research species reference genome using HISAT2.The mapped reads of each sample were assembled using StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM values.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameters of false discovery rate (Q) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes.
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: Tab-delimited text files include raw reads for each sample
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was harvested using TRIzol reagent. 1 ug total RNA with RNA integrity number > 7.0  was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Lung

value: Alveolar macrophages


title: FOXA1.N3wingH1face_447

extract_protocol: GST fusion proteins were expressed by in vitro transcription and translation.


title: KO2


title: FOXA1.N3wing_457


title: FOXA1.ref_388


title: WT3


title: FOXA1.N3wingH1face_457


title: FOXA1.N3wing_447


title: GS0817


title: Arsenite_TXNL1DR-RD_replicate1


title: Arsenite_TXNL1DR-RD_replicate3


title: WT2


title: GS0818


title: GS0921c

source_name: cell culture

tag: culture

value: SCD-GSC

value: Recurrent


title: WT1


title: Arsenite_TXNL1DR-RD_replicate2


title: FOXA1.N256S_413


title: KO1


title: GS0916c

value: IDH-WT


title: FOXA1.N256S_446

value: GST-tagged protein


title: FOXA1.N256S_441


title: FOXA1.K237R_446


title: GS0809


title: Arsenite_vector_replicate2

value: vector


title: GS0837c

value: Glioblastoma

value: IDH-mutant


title: Arsenite_vector_replicate1


title: Arsenite_TXNL1WT_replicate3


title: GS0851c

value: Primary


title: Arsenite_TXNL1WT_replicate2


title: Arsenite_TXNL1WT_replicate1


title: GS0902c


title: GS0852c


title: Arsenite_vector_replicate3


title: H2O2_TXNL1SxxS_replicate3


title: FOXA1.N256S_388


title: H2O2_TXNL1SxxS_replicate2


title: HEK293T, biol rep1, 8h post-ActD treatment

first: Xinshu

middle: Grace

last: Xiao

state: CA

address: 610 Charles E. Young Drive South

department: Integrative Biology and Physiology

description: Library name: asRS-Pool__Asrs-8h-R1_S118_L002

data_processing:
Adapters were trimmed from reads using bbduk (tpe tbo ktrim=r k=23 mink=11 hdist=1) and then mapped using STAR-2.7.8a
Read counts were obtained at asRS variant positions using perbase0.10.0.
Assembly: hg38
Supplementary files format and content: tab-delimited file include counts at each prime-edited asRS variant position

source_name: human embryonic kidney

extract_protocol:
Total RNA was harvested from cells 0h (pre-treatment), 2h, 8h, and 24h after treatment with 10 ug/ml of ActD (3 replicates per timepoint).
RNA-seq

value: human embryonic kidney

value: 8h post-ActD


title: GS0845c


title: FOXA1.K237R_388

source_name: in vitro trancription and translation


title: HEK293T, biol rep3, 8h post-ActD treatment

description: Library name: asRS-Pool__Asrs-8h-R3_S120_L002


title: HEK293T, biol rep2, 8h post-ActD treatment

description: Library name: asRS-Pool__Asrs-8h-R2_S119_L002


title: HEK293T, biol rep3, 2h post-ActD treatment

description: Library name: asRS-Pool__Asrs-2h-R3_S117_L002

value: 2h post-ActD


title: H2O2_TXNL1DR-RD_replicate3


title: GS0843c


title: GS0832c


title: HEK293T, biol rep2, 2h post-ActD treatment

description: Library name: asRS-Pool__Asrs-2h-R2_S116_L002


title: H2O2_TXNL1SxxS_replicate1


title: H2O2_TXNL1DR-RD_replicate2


title: FOXA1.K237R_441


title: GS0834c


title: GS0823c


title: FOXA1.H1face_457


title: FOXA1.H1face_447


title: GS0819c


title: H2O2_TXNL1DR-RD_replicate1


title: GS0817c


title: FOXA1.K237R_413


title: scnasRNA-seq of BM, 24h post salmonella infection, Batch2

city: Beijing

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
Library name: BM_24h_Batch2
total RNA and nascent RNA

data_processing:
Data were processed to generate gene expression profiles using scnasRNA-seq pipeline (https://github.com/singleron-RD/CeleScope/blob/master/doc/assay/multi_dynaseq.md). Briefly, raw reads were processed with fastQC and fastp to remove low quality reads, such as those without poly T tails, cell barcode and UMI. Adapters and poly A tails were trimmed by Cutadapt before aligning paired reads to the mouse reference genome (GRCm38 with ensemble version 92 gene annotation) using STAR (version 2.5.3a). We then acquired gene counts and UMI counts by assigning uniquely mapped reads to genomic features with FeatureCounts (version 1.6.2). To quantify S4U labeled and unlabeled reads, we got T-to-C substitutions in each read. After excluding background T-to-C substitutions (presenting in control samples without metabolic labeling), we distinguished nascent RNA from old RNA based on whether reads contained T-to-C substitutions. Reads with the same cell barcode, UMI and gene were grouped together to count numbers of labeled and unlabeled UMIs for each gene per cell. Finally, we obtained two gene expression matrices (nascent RNA count and old RNA count matrix) for each sample. Total RNA count matrix is the sum of nascent RNA count matrx and old RNA count matrix.
Assembly: GRCm38
Supplementary files format and content: tsv file includes raw counts of new RNA for each Sample
Supplementary files format and content: tsv file includes raw counts of old RNA for each Sample

source_name: bone marrow

extract_protocol:
Single-cell suspension was loaded onto microwell chips for single cell partition, followed with bead loading and cell lysis. After 20 min incubation at room temperature (RT), mRNA in each well was captured on a magnetic bead coated with oligonucleotides, each containing a primer sequence, a cell barcode, a unique molecular identifier (UMI), and a poly-T tail.
We used DynaSCOPETM Single Cell Dynamic RNA Library Kit (Singleron Biotechnologies) to construct scnasRNA-seq libraries. After collecting all beads that captured mRNA, S4U integrated on nascent RNA was converted into cytidine analogs. mRNA was incubated with conversion reagent at 25°C for 60 min. Mutations were inserted at the indicated sites on reverse transcription. For reference control samples, mRNA was incubated in the same condition but without conversion reagent. The reverse transcription reaction was incubated at 42°C for 90 min. cDNA amplification was performed by PCR using 13 cycles. PCR amplification products were purified using AMPure XP beads. After cDNA fragmentation and adaptor ligation, products were purified and amplified by PCR. After size selection, libraries were sequenced.

treatment_protocol: 8 to10 week-old mice were deprived of food and water for 4 h. Then mice were gavaged with 20 mg streptomycin sulfate in 200 ml PBS. 24 h later, mice were again deprived of food and water for 4 h, and then were gavaged with 10^8 CFUs of Salmonella. Bone marrow and small intestinal cells were collected at the indicated time point. Nacent RNA was labeled with S4U (1% of body weight) through tail vein injection

value: bone marrow

value: WT

value: salmonella


title: HEK293T, biol rep2, 24h post-ActD treatment

description: Library name: asRS-Pool__Asrs-24h-R2_S122_L002

value: 24h post-ActD


title: GS0815c


title: H2O2_TXNL1WT_replicate3

value: cell line

value: TXNL1 KO


title: HEK293T, biol rep3, 24h post-ActD treatment

description: Library name: asRS-Pool__Asrs-24h-R3_S123_L002


title: H2O2_TXNL1WT_replicate1


title: H2O2_TXNL1WT_replicate2


title: HEK293T, biol rep1, 24h post-ActD treatment

description: Library name: asRS-Pool__Asrs-24h-R1_S121_L002


title: Periarticular tissue KO 3

description: Library name: Sample 6

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v6.1.2.
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix file

source_name: periarticular tissue

extract_protocol:
The periarticular tissue was minced and digested in RPMI 1640 medium (Gibco) supplemented with 1.5 mg/mL collagenase IV (Sigma), 0.5 mg/mL DNase I (Roche), and 2% FBS for 90 min at 37°C with gentle shaking.To obtain sufficient immune cells for analysis, four mice were pooled as one sample for the control group (12 control mice in total for n=3), and then CD45+ and CD45- cells were sorted and mixed at a ratio of 3:1 in both groups for scRNA-seq analysis.
The cells were loaded on a 10X Chromium Controller (10X Genomics) according to the manufacturer’s protocol to generate Gel-Bead in Emulsions (GEMs), which were used to generate barcoded, full-length cDNA through reverse transcription reactions. Barcoded scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kit. After final preparation and QC performed, the libraries were sequenced on a NovaSeq 6000 platform (Illumina), and 150 base pair (bp) paired-end reads were generated.

value: periarticular tissue

value: tamoxifen administration


title: scnasRNA-seq of BM, 12h post salmonella infection, Batch2

description:
Library name: BM_12h_Batch2
total RNA and nascent RNA


title: GS0921c3

value: SCD-UA-GSC

value: IDH-WT


title: scnasRNA-seq of BM, 72h post salmonella infection, Batch2

description:
Library name: BM_72h_Batch2
total RNA and nascent RNA


title: H2O2_vector_replicate3

value: vector


title: H2O2_vector_replicate2


title: GS0902c3

value: Glioblastoma


title: HEK293T, biol rep2, 0h ActD (pre-treatment)

description: Library name: asRS-Pool__Asrs-0h-R2_S113_L002


title: HEK293T, biol rep1, 2h post-ActD treatment

description: Library name: asRS-Pool__Asrs-2h-R1_S115_L002


title: GS0916c3


title: Periarticular tissue KO 2

description: Library name: Sample 5


title: HEK293T, biol rep1, 0h ActD (pre-treatment)

description: Library name: asRS-Pool__Asrs-0h-R1_S112_L002


title: H2O2_vector_replicate1


title: Periarticular tissue Ctrl 2

description: Library name: Sample 2


title: HEK293T, biol rep3, 0h ActD (pre-treatment)

description: Library name: asRS-Pool__Asrs-0h-R3_S114_L002


title: Periarticular tissue KO 1

description: Library name: Sample 4


title: Periarticular tissue Ctrl 3

description: Library name: Sample 3


title: GS0827c

value: IDH-mutant


title: scnasRNA-seq of BM, 0h post salmonella infection, Batch2

description:
Library name: BM_0h_Batch2
total RNA and nascent RNA


title: DMSO_TXNL1SxxS_replicate2

value: DMSO


title: DMSO_TXNL1SxxS_replicate3


title: Patient Sample, 004-023_d28

first: Alal

last: Eran

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: 004-023_d28

data_processing:
Sequence data were demultiplexed using bcl2fastq v2 and the resulting FASTQ files were trimmed using Trimommatic version 0.39 and aligned to the human genome (GRCh38.p14) using STAR version 2.7.10a.
GENCODE 40 gene abundance was calculated using RSEM version 1.3.3, and normalized using the trimmed mean of M values (TMM) approach in edgeR version 3.40.1.
Assembly: GRCh38.p14
Supplementary files format and content: Tab delimited text files include log TMM-normalized expression for each sample.
Supplementary files format and content: CD8_8_8_PBO_logTMM_expression.txt includes samples from GSE157280 labeled according to their GSM IDs.

source_name: Blood

extract_protocol:
CD4+ and CD8+ T cells were sorted from blood samples obtained from hematopoietic cell transplant patients in the placebo-control arm of the ABA2 clinical trial (NCT# NCT01743131). RNA was isolated from CD4+ and CD8+ sorted T cells for each patient using the RNeasy Micro kit (Qiagen) with on-column DNase digestion, and RNA quality was assessed using an Agilent Bioanalyzer..
Two nanograms of total RNA were used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using the Illumina NexteraXT DNA Library Preparation kit. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq3000, yielding on average 25 million 100bp single end reads per sample.

value: Blood

tag: patient id

value: CD8+ T cells

value: 28 days post hematopoietic cell transplant


title: GS0853c

value: Primary


title: GS0838c1


title: Periarticular tissue Ctrl 1

description: Library name: Sample 1


title: DMSO_TXNL1SxxS_replicate1


title: GS0850c


title: GS0828c


title: Patient Sample, 001-013_d21

description: Library name: 001-013_d21

value: 21 days post hematopoietic cell transplant


title: DMSO_TXNL1DR-RD_replicate3


title: Patient Sample, 004-117_d21_cd4

description: Library name: 004-117_d21_cd4

value: CD4+ T cells

value: 21_cd4 days post hematopoietic cell transplant


title: GS0921c2


title: GS0916c2


title: DMSO_TXNL1DR-RD_replicate1

value: cell line


title: Patient Sample, 004-114_d28_cd4

description: Library name: 004-114_d28_cd4

value: 28_cd4 days post hematopoietic cell transplant


title: DMSO_TXNL1WT_replicate3

value: TXNL1 KO


title: DMSO_TXNL1WT_replicate2


title: GS0902c2


title: Patient Sample, 004-114_d21_cd4

description: Library name: 004-114_d21_cd4


title: GS0814c


title: Patient Sample, 004-098_d28_cd4

description: Library name: 004-098_d28_cd4


title: DMSO_TXNL1WT_replicate1


title: Patient Sample, 004-113_d21_cd4

description: Library name: 004-113_d21_cd4


title: GS0812c


title: Patient Sample, 004-107_d28_cd4

description: Library name: 004-107_d28_cd4


title: DMSO_vector_replicate1


title: DMSO_vector_replicate3


title: Patient Sample, 004-102_d21_cd4

description: Library name: 004-102_d21_cd4


title: GS0811c


title: DMSO_TXNL1DR-RD_replicate2


title: DMSO_vector_replicate2


title: GS0830c


title: Patient Sample, 004-098_d21_cd4

description: Library name: 004-098_d21_cd4


title: GS0824c


title: Patient Sample, 004-096_d28_cd4

description: Library name: 004-096_d28_cd4


title: GS0825c


title: C4-2_siEZH2_1

city: Chicago

first: Chaehyun

last: Yum

state: IL

address: 303 E Superior St

institute: Northwestern University

data_processing:
The RNA-seq reads were mapped to the human genome GRCh38 and assigned to the reference genes using STAR 2.7.10b
Read counts for each gene were calculated by featureCounts v2.0.3.
Differential gene expression analysis was performed between the two groups of cells by R packages edgeR and limma
Assembly: hg38
Supplementary files format and content: featureCounts output file (raw counts of reads)

growth_protocol: C4-2 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from C4-2 cells using RNeasy Plus Kit (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI Stranded Total RNA Prep Kit following manufacturer's protocols.

value: epithelial cell


title: Patient Sample, 004-088_d28_cd4

description: Library name: 004-088_d28_cd4


title: C4-2_siEZH2_2


title: C4-2_siCTRL_1

value: siCTRL


title: GS0829c

value: IDH-WT


title: Patient Sample, 004-085_d28_cd4

description: Library name: 004-085_d28_cd4


title: Patient Sample, 004-096_d21_cd4

description: Library name: 004-096_d21_cd4


title: GS0921c4


title: C4-2_siCTRL_2


title: Patient Sample, 004-088_d21_cd4

description: Library name: 004-088_d21_cd4


title: C4-2_Control_replicate1

data_processing:
The RNA-seq reads were mapped to the human genome GRCh38 and assigned to the reference genes using HISAT2 version 2.2.1.
Read counts for each gene were calculated by featureCounts v2.0.3.
Differential gene expression analysis was performed between the two groups of cells by R packages edgeR and limma
Assembly: hg38
Supplementary files format and content: featureCounts output file (raw counts of reads)

treatment_protocol: C4-2 cells were treated with BHB (50 mM in RPMI) or RPMI medium (control) for three days.

value: control (RPMI medium)


title: GS0820c

data_processing: GenomeStudio software (Illumina) was used to analyze CNV GSA manifest files. Final reports and visualizations were created using the Nexus Discovery software package (BioDiscovery El Segundo).  The minimum number of probes per segment was set to 20, and the minimum LOH length to 500 kB.

value: Glioblastoma


title: ID3_Single_Positive Biol Rep 2

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA-seq reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Chromosomal coordinates of exons of gene Hobit were added to the annotation before quantification.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million) value of greater than 1 in at least two libraries. Genes with no valid gene symbols were also excluded from analysis.
Counts were converted to log2CPM, quantile normalized and precision weighted with the voom function of the limma package. log2CPM values of genes were then converted to log2FPKM (log2 fragments per kilobases per million) values. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. A FDR cut-off of 0.15 was applied for calling differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2-FPKM values for each library. The supplementary file, count_table.txt, includes raw read counts for genes in all the libraries.

source_name: AT3 tumor, subcutaneous

extract_protocol:
RNA was extracted from CD8+ T cells sorted from AT-3 tumors following the manufacturer’s protocol using the RNeasy Plus Mini Kit (QIAGEN).
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: AT3 tumor, subcutaneous

value: termed TPEX cells

value: Hobit-TomatoCre x ID3-GFP double reporter mice

tag: collection time

value: 8-12 weeks


title: C4-2_BHB_replicate1

tag: treatment

value: BHB(50 mM in RPMI)


title: Patient Sample, 004-081_d28_cd4

description: Library name: 004-081_d28_cd4

value: Blood


title: C4-2_Control_replicate2


title: ID3_Single_Positive Biol Rep 3


title: Patient Sample, 004-081_d21_cd4

description: Library name: 004-081_d21_cd4


title: Patient Sample, 004-082_d21_cd4

description: Library name: 004-082_d21_cd4


title: GS0848c

extract_protocol: Cell pellets were snap frozen and Genomic DNA was extracted from snap frozen cell pellets and from cryosections of liquid N2 stored snap frozen tumor material. All DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions.

value: Primary


title: GS0916c4


title: GS0902c4


title: Patient Sample, 004-083_d21_cd4

description: Library name: 004-083_d21_cd4

value: CD4+ T cells


title: Patient Sample, 004-074_d28_cd4

description: Library name: 004-074_d28_cd4


title: ID3_Single_Positive Biol Rep 1


title: GS0809c


title: Patient Sample, 004-073_d21_cd4

description: Library name: 004-073_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: GS0838c2


title: Hobit_Single_Positive Biol Rep 3

value: termed TRM-like cells


title: GS0818c


title: Hobit_Single_Positive Biol Rep 1


title: Hobit_Single_Positive Biol Rep 2


title: Patient Sample, 004-072_d28_cd4

description: Library name: 004-072_d28_cd4

value: 28_cd4 days post hematopoietic cell transplant


title: WT, FFS, biol repl 4

city: PITTSBURGH

first: Leigh

middle: M

last: Miller

state: PA

address: 4401 Penn Ave

institute: University of Pittsburgh

description:
Library name: WT_FFS4
Column in 2006932_FPKM.xlsx

data_processing:
Data processing was performed by MedGenome
Sequence reads were trimmed when necessary using fastq-mcf (v1.05) program and cutadapt (v2.5)
Contamination removal was performed using Bowtie2 (v2.5.1)
Raw read counts were estimated using HTSeq (v0.11.2)
Assembly: Trimmed sequences were mapped to GRCm38 reference sequence using STAR (2.7.3a)
Supplementary files format and content: Read count normalized via DESeq2 and reported as FPKM and TPM

extract_protocol:
Lungs were perfused priior to extraction and dissociated using collagenase media with Dnase for 1 hour followed by filtering in a 70uM filter to get a single cell suspension. Cells were rinsed with PBS and strained in a 40uM filter.  Dead cell removal was performed via negative selection using the EasySep Mouse Dead Cell Removal (Annexin V) kit. The flow through was centrifuged and resuspended in PBS (10% FBS, 1mM EDTA) and CD8+ T cells were isolated using the CD8+ T cell Isolation Kit as directed. RNA was extracted from isolated lung CD8+ T cells using TRI reagent (Zymo Research, Irvine, CA). Samples were digested on ice for 5 minutes with mechanical agitation of samples occurring 2-3 times. RNA was further extracted from samples using the Direct-zol Mini Prep kit as directed.
RNA was shipped to MedGenome for sequencing via Takara SMART-Seq mRNA kit (100 read length).

treatment_protocol: Mice were infected with 0.5-1 x 10^5 PFU of mouse-adapted influenza virus A/HKx31 H3N2 (X31) or PBS vehicle. After 54 days, the mice were rechallenged with 10^3 PFUs of a heterotypic strain of mouse-adapted influenza virus A/PR/8/34 H1N1 (PR8) or PBS vehicle. Six days after influenza virus rechallenge (day 60), the mice were challenged with 5 x 10^7 CFUs of USA300 MRSA suspended in PBS or vehicle and harvested a day later. All infections were given via oropharyngeal instillation and tissues were harvested 24 hours after MRSA challenge.

value: Lung

value: CD8 T cell

value: WT

value: FFS


title: Patient Sample, 004-074_d21_cd4

city: Boston

description: Library name: 004-074_d21_cd4


title: GS0821c

value: IDH-WT


title: INSR mutagenesis plasmid library

city: Edinburgh

first: Vahid

last: Aslanzadeh

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: The University of Edinburgh

data_processing:
PacBio sequencing data were aligned to INSR amplicon by minimp2 and variants were called by alignparse.
Barcode sequencing data were first trimmed by trimmomatic to get the only 30nts barcode sequences and then used Enrich2 to count frequency of each barcode in each bin.
Assembly: INSR reference gene was used for read alignment
Supplementary files format and content: CSV files contain processed CCS HiFi reads from PacBio data, listing mutations and barcode sequences
Supplementary files format and content: tsv files for barcode sequencings contain barcode counts in each bin

organism: Escherichia coli

source_name: Not applicable

growth_protocol: MEFs were cultured in DMEM  supplemented with 10% fetal bovine serum and Penicillin-Streptomycin (50 I.U./ml). Cells were passaged by trypsinization using 0.25% trypsin-EDTA and tested negative for Mycoplasma before use.

extract_protocol:
Used conventional phenol-chlorophorm methode to isolate gDNA
Plasmid library for PacBio sequencing was constructed using saturation mutagenesis, and library for sequencing barcodes from gDNA constructed using PCR primers tagged with p5 and p7 illumina sequencing primers
Amplicon sequencing by PacBio and illumina sequencing of PCR products from gDNA

value: Not applicable


title: Double_Positive Biol Rep 3

value: AT3 tumor, subcutaneous

value: termed tissue-resident TPEX cells


title: WT, FFS, biol repl 2

description:
Library name: WT_FFS2
Column in 2006932_FPKM.xlsx


title: Double_Negative Biol Rep 3

value: termed TEX cells

value: Hobit-TomatoCre x ID3-GFP double reporter mice


title: WT, FFS, biol repl 3

description:
Library name: WT_FFS3
Column in 2006932_FPKM.xlsx


title: Neurons_NaB_24h_1

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

description: Library name: 1-20-87

data_processing:
Sequenced reads were mapped to the Rnor6.0 version of rat genome using STAR (v. 2.7.9a) with default parameters.
For each dataset, raw read counts were obtained using FeatureCounts (v 2.0.1) with GTF file for Rnor 6.0, taken from ENSEMBL ftp. Used parameters: -T 8 -p -a Rattus_norvegicus.Rnor_6.0.101.gtf -s 0
Counts from both datasets were combined in single matrix,  normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).

organism: Rattus norvegicus

source_name: Primary neuron cultures

growth_protocol: Cell cultures were prepared as previously described (Borodinova et al., 2019). Briefly, Wistar rat pups were euthanized by decapitation with sharp scissors. The cortices were isolated in chilled DMEM medium supplemented with glutamine and glucose (Paneco), and gently cut into pieces with a sharp blade. Tissue fragments were treated with warm trypsin solution for 15 min at 37 °C to release the cells. To stop trypsin activity, the samples were centrifuged and washed with chilled DMEM solution. The pellet was then re-suspended in Neurobasal medium (Gibco) supplemented with 2% B-27 serum (Gibco) and alanyl-glutamine (Paneco) followed by series of mild trituration to isolate brain cells. The final concentration of isolated cells in the suspension was calculated manually in a Goryaev chamber. Approximately 0.25-0.3 million of isolated cells were plated into individual wells coated with poly-D-lysine hydrobromide (Sigma). Culture media was refreshed one hour later. Primary cortical neuron cultures were grown for two weeks in CO2 incubator (5% CO2, 37 °C), culture medium was partially refreshed every 2-3 days. HDAC inhibitors were applied on the 14th day in vitro (DIV) without washout.

extract_protocol:
total RNA was extracted using ExtractRNA reagent (Evrogen, Russia) following manufacturer’s protocol.
mRNA was purified from a total RNA mixture using oligo(dT)-coated magnetic beads, followed by mRNA fragmentation and cDNA synthesis. The synthesized cDNA was then subjected to end repair, 3’-adenylation and adapter ligation. Following amplification of cDNA fragments, the PCR products were purified using Ampure XP Beads (AGENCOURT) and dissolved in EB solution. Library was validated on the Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were then heat denaturated and circularized using splint oligo sequence to generate a final library of single-stranded circular DNA molecules. The library was amplified using phi29 DNA polymerase to create a DNA nanoball containing more than 300 copies of a single DNA molecule.

treatment_protocol: Two broad-spectrum histone deacetylase (HDAC) inhibitors with different chemical structures were used in the study. The HDAC inhibitor trichostatin A (TSA, 100 nM, Sigma) was applied for 19 hours as previously described (Borodinova et al., 2019). The HDAC inhibitor sodium butyrate (NaB, 5 μМ, Sigma-Aldrich) was applied for a longer time of 24 hours. Both inhibitors were applied without washout.

value: Primary neuron cultures

tag: condition

tag: strain

value: Wistar

tag: sample


title: C4-2_BHB_replicate2

value: epithelial cell

value: BHB(50 mM in RPMI)


title: Neurons_NaB_24h_2

description: Library name: 1-20-93


title: Double_Negative Biol Rep 2

tag: genotype

value: 8-12 weeks


title: Double_Positive Biol Rep 2


title: Patient Sample, 004-073_d28_cd4

description: Library name: 004-073_d28_cd4

value: Blood

value: CD4+ T cells

tag: time


title: Patient Sample, 004-071_d21_cd4

description: Library name: 004-071_d21_cd4

value: 21_cd4 days post hematopoietic cell transplant


title: Double_Positive Biol Rep 1


title: WT, FFS, biol repl 1

description:
Library name: WT_FFS1
Column in 2006932_FPKM.xlsx

value: Lung

value: CD8 T cell


title: Patient Sample, 004-072_d21_cd4

description: Library name: 004-072_d21_cd4


title: Patient Sample, 004-071_d28_cd4

description: Library name: 004-071_d28_cd4

value: 28_cd4 days post hematopoietic cell transplant


title: WT, FF, biol repl 4

description:
Library name: WT_FF4
Column in 2006932_FPKM.xlsx

value: WT

value: FF


title: Neurons_control_5

description: Library name: 1-20-92


title: Neurons_control_4

description: Library name: 1-20-86


title: Double_Negative Biol Rep 1

value: AT3 tumor, subcutaneous


title: Neurons_TSA_19h_3

description: Library name: 1-20-75


title: Patient Sample, 004-065_d28_cd4

description: Library name: 004-065_d28_cd4


title: WT, FF, biol repl 3

description:
Library name: WT_FF3
Column in 2006932_FPKM.xlsx


title: Tumor (AT3-OVA) and draining lymph node, hashtag antibody sequences

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

institute: University of Melbourne

description:
10x Genomics
AK_AT3o_CSP

data_processing:
Sequencing reads were aligned to the reference genome using cellranger (v 7.0.0)
We used the multi subcommand to align reads to the transcriptome and obtain gene counts (GEX), align reads to a custom hashtag reference and count hastag sequences (CSP), align reads to the alpha/beta TCR reference and assemble and count clonotypes (VDJ)
Assembly: Cellranger 10x genome mm10-2020-A (transcriptome), 10x TCR reference GRCm38-alts-ensembl-5.0.0 (VDJ)
Supplementary files format and content: Tar file of outputs from cellranger multi containing gene and antibody counts (sample_filtered_feature_bc_matrix), TCR sequences (VDJ), and hashtag reference

source_name: Tumor, LN

extract_protocol:
Tumors from untreated or anti-PDL1 and CTLA4-treated (day 12, 14, 16 after tumor inoculation) mice were harvested 18 days after tumor inoculation and finely minced using scalpel blades. Tumors were then digested enzymatically in RPMI with 1 mg/mL collagenase IV and 0.01 μg/mL DNase I for 45 minutes on a shaker at 37°C, vortexing samples midway. Digestion was stopped using cold PBS supplemented with 2% FCS. Tumor suspensions were gently mashed and filtered through a 70-μm nylon cell strainer. Lymphocytes were isolated by a 40:80 discontinuous percoll gradient centrifugation (500g, 20 minutes at 20 °C). Cells at the interface were collected and washed once prior to further use. To obtain single-cell suspensions, harvested swollen LNs (axillary and inguinal) were gently mashed and filtered through a 70-μm nylon cell strainer. CD4+ and CD19+ cell microbeads (Miltenyi Biotech) were used for negative selection and enrichment of CD8+ T cells, performed according to the manufacturer’s instructions. Single cell suspensions of CD8+ T cells from tumors and lymph nodes were stained and FACS sorted.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, tumoral and draining lymph node CD8+T cells with or without cehckpoint treatment were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM) after staining hashtag. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI), the 10x Barcode and template switch oligo. And DNA from cell surface protein feature barcode conjugated to the antibody are generated simultaneously in In the same partition. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+T cells

value: Tumor, LN

tag: age

value: 17-18 weeks


title: Patient Sample, 004-070_d21_cd4

description: Library name: 004-070_d21_cd4


title: Neurons_TSA_19h_2

description: Library name: 1-20-53

value: Primary neuron cultures


title: WT, FF, biol repl 1

description:
Library name: WT_FF1
Column in 2006932_FPKM.xlsx


title: WT, FF, biol repl 2

description:
Library name: WT_FF2
Column in 2006932_FPKM.xlsx


title: Tumor (AT3-OVA) and draining lymph node, RNA sequences

description:
10x Genomics
AK_AT3o_GEX


title: Patient Sample, 004-059_d21_cd4

description: Library name: 004-059_d21_cd4


title: Patient Sample, 004-057_d28_cd4

description: Library name: 004-057_d28_cd4


title: MuMT, FFS, biol repl 3

description:
Library name: MuMT_FFS3
Column in 2006932_FPKM.xlsx

value: uMT

value: FFS


title: Neurons_TSA_19h_1

description: Library name: 1-20-41

value: Wistar


title: sperm, TBT 100nM

city: Gainesville

first: Muhammad

middle: Sohail

last: Siddique

state: Florida

address: 1911 SW 40th Terrace Apt E

institute: Department of Animal Sciences

description: Library name: TBT 100nM, EMSeq,Bull A

library_source: genomic

data_processing:
EMSeq: The “nf-core/methylseq” (v1.6.1) automated bioinformatic pipeline for Methylation (Bisulfite) sequencing data was used to analyze all the samples. In particular, the “nf-core/methylseq” pipeline's "Bismark workflow" was used to align the reads on the medaka genome (assembly ASM223467v1). FASTQ files from different lanes were merged to generate a single FASTQ file per sample for each end of the paired-end reads.
EMSeq: The Bismark coverage files of each individual sample, which describe the methylation percentages and overall coverages of methylated and unmethylated cytosines at each CpG location, were collected for further downstream analyses using methylKit R package. The samples of all the generations (f0, f1 and f2) were processed in the same way.
Assembly: ARS-UCD1.3
Supplementary files format and content: Bismark coverage files (*.bismark.cov.gz) for each sample for EMSeq

organism: Bos taurus

source_name: sperm

extract_protocol:
Genomic DNA was isolated from TBT exposed and unexposed sperm using a modified protocol from Quiagen Blood and Tissue Kit (60954). After DNA isolation, an Enzymatic Methyl seq Conversion kit module (NEB#E7125S) was used to convert unmethylated cytosines in genomic DNA (gDNA) into uracils, generating methylation-converted DNA for PCR amplification and downstream epigenomic analyses.
For whole genome enzymatic methyl seq analysis (EMSeq), fragmentation of gDNA isolated from TBT exposed and unexposed sperm was performed on a M220 sonicator (Covaris). DNA fragments were end repaired/dA-tailed followed by adaptor ligation. A two-step enzymatic conversion protecting 5mC and 5hmC from deamination was performed prior to deamination of the cytosines residues. Fragments were PCR amplified to enrich libraries and incorporate barcodes. The final amplified cDNA constructs were purified by addition of Axyprep Mag PCR Clean-up beads (Axygen) selecting for an insert size of 550 bp.  Libraries were quantified with the Qubit HS DNA kit (Invitrogen) and the fragment size analyzed on a 5200 Fragment Analyzer (Agilent).  Libraries were diluted according to the standard protocol for sequencing on the NovaSeq 6000 (Illumina).

value: sperm

value: TBT 100nM


title: sperm, TBT 10nM

description: Library name: TBT 10nM, EMSeq, Bull A

value: TBT 10nM


title: Neurons_control_1

description: Library name: 1-20-40


title: Patient Sample, 004-056_d21_cd4

description: Library name: 004-056_d21_cd4

value: Blood

value: CD4+ T cells

value: 21_cd4 days post hematopoietic cell transplant


title: Neurons_control_2

description: Library name: 1-20-52


title: Patient Sample, 004-057_d21_cd4

description: Library name: 004-057_d21_cd4


title: sperm, vehicle control

description: Library name: Vehicle Control, EMSeq, BullA

value: vehicle control