title: LCM_seq_p112wtSC [P6362_1113]

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

institute: Stockholm University

data_processing:
Reads were mapped to the mouse reference genome mm39 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version106 (GRCm39.106) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Genes with counts expression greater than 0 in at least 5 out of 54 samples were retained.
Assembly: mm39
Supplementary files format and content: A counts table for all bulk samples named 'counts_SOD1.csv'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms_SOD1.csv'.

extract_protocol:
Cells isolated by Laser Capture microdissection were placed in lysis buffer containing 0.2%Triton X-100 with 2U/ul recombinant RNAse inhibitor (Clontech)
Bulk libraries were prepared using the Smart-Seq2 protocol.  One ng of cDNA was used as input for the tagmentation which was carried out with in-house Tn5 (Piccelli S. 2014, Nat. Protoc. 9, 171-181). For ligation of sequencing indices we used Nextera XT Sequencing Index Kit (Illumina) and 10 cycles of enrichment PCR.

value: wt

tag: age


title: MSC_5

status: Public on Jul 07 2025

type: SRA

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

country: USA

institute: Mayo Clinic

description:
Treatment
MSC_P33P941GV.FCHHCGKBBXY_L7_R1_IGATCTATC-ATGAGGCT

library_source: transcriptomic

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: susScr11
Supplementary_files_format_and_content: The average RPKMs of each group (C or MSC) were calculated and MSC/C was considered as fold change.  The genes that were >1.5 or <0.75 were considered as differentially expressed genes and the genes that were <1.5 or > 0. 75 were excluded. A simple t-test was performed to determine the P value and P<0.05 was considered as significant different compared to KI-V and the genes that were >0.05 were excluded.

molecule: total RNA

organism: Sus scrofa

source_name: Vein

extract_protocol: Extraction protocol 0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: Chronic Kidney disease created to pigs as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein and adipose derived MSCs in ringer lactate were layred on the adventia of the AVF outflow vein (MSC) immidatly after AVF creation or  untreated vessels (C) . 28 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.

tag: tissue

value: AVF outflow veins

tag: disease state

value: chronic kidney disease model

tag: treatment

value: MSC Treatment


title: A20

city: Lexington

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

description: Library name: A20

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to mouse genome mm10 using STAR (v2.6.1d, mismatch=2).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

organism: Mus musculus

source_name: Aorta

extract_protocol:
RNA was extracted using Rneasy fibrous tissue mini kits (Qiagen, #74704). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA library prep kits for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Aortic samples were harvested from male Fbn1 C1041G/+ mice administered control ASO or AGT-ASO, and from wild type littermates.

value: Aorta

tag: genotype

tag: region

value: Ascending

value: AGT-ASO


title: Dhx16_fl3

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

country: China

institute: Southwest Hospital, Army Medical University

data_processing:
The raw sequencing data was preprocessed using SMRT Link software, and the full-length transcript sequences were obtained using the Iso-Seq analysis pipeline.
The single-molecule sequencing polymerase reads were split to obtain subreads. The subreads from the same polymerase read were self-corrected to form Circular Consensus Sequences (CCS).
By detecting concatemers (chimeric sequences) and 5' and 3' end primers (sequencing primers), the CCS sequences were classified to identify Full-Length Non-Concatemer (FLNC) sequences for subsequent analysis.
The FLNC sequences, both pre- and post-correction, are aligned to the reference genome using GMAP software.
Assembly: GRCm39
Supplementary files format and content: Summary of Differential Alternative Splicing Genes

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using TRIzol reagent (Takara).
The full length transcripts were prepared using a custom protocol based on Smart-seq2. VN-anchored oligo-dT primers and TSO were used for reverse transcription (RT) of total RNA. The resulting full-length double-stranded cDNA was pre-amplified using ISPCR primers and purified with AMPure XP beads to remove primer dimers.The full-length cDNA was end-repaired, and SMRTbell adapters were ligated.Unligated fragments were digested with exonuclease, and the library was purified again using magnetic beads to obtain the sequencing library.After the library construction was completed, the quality of the library was checked. Sequencing was performed only after the quality was confirmed to meet the requirements.

value: Bone marrow

tag: cell line

value: primary cell

tag: cell type

value: Hematopoietic stem cells (HSC)

value: WT


title: LCM_seq_p112wtSC [P6362_1121]

country: Sweden

molecule: polyA RNA


title: LCM_seq_p112wtSC [P6362_1108]


title: C12

description: Library name: C12

value: Control-ASO


title: MSC_2

description:
Treatment
MSC_P33P028GV.FCHHCGKBBXY_L7_R1_ICGGAACTG-CACTACGA


title: C13

description: Library name: C13


title: Dhx16_fl2


title: A19

description: Library name: A19


title: LCM_seq_p112mSODSC [P11355_1278]

value: mSOD


title: LCM_seq_p112wtSC [P10814_1368]


title: LCM_seq_p112wtSC [P10814_1362]


title: D_07

description: Library name: D_07

value: Descending


title: A18

description: Library name: A18


title: A15

description: Library name: A15


title: LCM_seq_p112wtCN12 [P10814_1378]


title: A14

description: Library name: A14


title: D_03

description: Library name: D_03


title: C8

description: Library name: C8


title: LCM_seq_p112mSODCN12 [P11355_1279]


title: D_08

description: Library name: D_08


title: CLIP_SRBSDV-infected_IP

city: Hangzhou

first: Ming

last: Zeng

address: 866 Yuhangtang Road

institute: Zhejiang university

description: Library name: CLIP_SRBSDV-infected_IP

data_processing:
For CLIP-seq, The clean reads were mapped to the reference genome of O. sativa L. japonica at the NCBI (https://www.ncbi.nlm.nih.gov/) using the STAR software (version 2.5.3a) with default parameters. The R package exomePeak software was then used to find peak callings and the peaks were presented using the Integrative Genomics Viewer (IGV) software (https://www.igv.org/).
For RNA-seq,  Adaptor and low-quality reads were removed by using Trimmomatic software (version 0.38). The clean reads were mapped to reference genome of O. sativa L. japonica (https://www.ncbi.nlm.nih.gov/) using Tophat (version 1.4.6). Gene expression levels were calculated as fragments per kilobase per million reads (FPKM) and DEseq2 was used to analyzed differentially expressed genes.
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Oryza sativa

source_name: 30-day rice plants

extract_protocol:
For RNA-seq, Total RNA samples were collected from WT, P6-OE, uninfected and SRBSDV-infected rice plants by using TRIzol Reagent. For CLIP-seq, RNA samples were IP from uninfected and SRBSDV-infected rice and extracted using TRI-Reagent®.
For RNA-seq, The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. For CLIP-seq, RNA sequencing library was constructed using the KC-Digital Stranded mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: leaves and shoots

value: Wildtype

value: virus-innoculation


title: LCM_seq_p112mSODSC [P10814_1377]


title: D_06

description: Library name: D_06


title: D_05

description: Library name: D_05


title: LCM_seq_p112mSODSC [P6362_1107]


title: D_02

description: Library name: D_02


title: D_04

description: Library name: D_04


title: LCM_seq_p112wtCN12 [P10814_1364]

value: wt


title: D_01

description: Library name: D_01


title: LCM_seq_p112mSODCN12 [P10814_1371]


title: LCM_seq_p112wtCN12 [P10814_1367]


title: Meninges pooled from 4 mice, homecage control, replicate 2

city: Cambridge

first: Stacey

middle: L

last: Kigar

address: Herchel Smith Building, Robinson Way

department: Departments of Medicine and Psychiatry

country: United Kingdom

institute: University of Cambridge

description:
Library name: HC pool 2
In combined processed files, this library is Group 2 in the 'group' column

library_source: transcriptomic single cell

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed using the Cell Ranger v2 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files
Supplementary files format and content: RData file containing the processed single cell object with assays 'counts' and 'logcounts'- code for data processing available at https://github.com/maryellenlynall/2019_bcell_stress/ (processing from raw files starts at bcellstress020.Rmd) and https://github.com/staceykigar/meningeal_neut/

source_name: Meninges

extract_protocol:
Meninges samples were collected by first cutting around the lateral sutures of the skull; the dorsal skull and ventral skull were transferred to a fresh petri dish filled with cold HBSS + 0.1% BSA and kept on ice while pial and arachnoid meningeal membranes were gently picked off the entire outer surface of the brain into a second ‘working dish’ with Dumont #5 forceps. Extra care was taken to avoid inclusion of choroid plexus from the 4th ventricle. Once finished with the brain, skull pieces were transferred as necessary into the working dish to remove attached meninges; we avoided leaving skull pieces in the ’working dish’ to minimize contamination with cells from skull bone marrow. Upon completion of the meningeal dissection, samples were transferred to a fresh tube and cells were pelleted by centrifugation, then resuspended in 2mL of BSA-free HBSS supplemented with 2.5 mg/mL Collagenase D  and 12.5 μL of 0.5 mg/mL DNAseI for cell dissociation. The samples were incubated at 37C for 30 min, diluted with cold HBSS + 0.1% BSA, and mashed through a 70 μm cell strainer into single cell suspension. The cells were then stained with viability dyes (DAPI and DRAQ5). Live, nucleated, single cells (DAPI- DRAQ5+) were sorted on a BD FACS Aria Fusion into HBSS + 10% FBS before droplet encapsulation using the 10x Genomics Chromium platform.
Library construction was performed according to the manufacturer's protocol (single cell 3' Chromium v2 protocol, 10x Genomics). 3 pooled samples of 4 mice each (two HC pools and one CSD pool) were generated and run in their own lane of the same 10x Chromium chip.

treatment_protocol: C57BL/6J mice were exposed to chronic social defeat stress for 14 days; the urine scent marking and open field tests were used to identify stress-susceptible mice.

value: Meninges

value: 10-12 weeks

tag: Sex

value: male

value: home cage (unstressed)

tag: 10x chip_lane


title: Meninges pooled from 4 mice, CSD, replicate 1

description:
Library name: CSD pool 3
In combined processed files, this library is Group 3 in the 'group' column

value: chronic social defeat


title: LCM_seq_p112mSODCN10 [P10814_1375]


title: CLIP_Uninfected_IP

description: Library name: CLIP_Uninfected_IP

value: none-virus-innoculation


title: A_07

description: Library name: A_07

value: Aorta

value: Ascending


title: Meninges pooled from 4 mice, homecage control, replicate 1

description:
Library name: HC pool 1
In combined processed files, this library is Group 1 in the 'group' column


title: HC11R1_Par_EtOH_3rd

city: Minneapolis

first: Kaylee

last: Schwertfeger

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

data_processing:
CHRUP pipeline (https://dl.acm.org/doi/10.1145/3332186.3333156) used to process raw sequence data
trimmomatic version 0.33 was used to clean reads for adapter contamination and low-quality sequence
HISAT2 version 2.1.0 was used to align samples
featureCounts v1.6.2 was used to count mapped reads to genes
Assembly: Mus musculus GRCm38.98
Supplementary files format and content: count table with raw count data for all genes and samples

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) from cell lines treated with B/B or solvent control for 2 hours
Stranded RNAseq libraries were prepared using the TruSeq RNA library kit

treatment_protocol: Cells were starved overnight in serum free medium and treated with 30 nM B/B Homodimerizer or an equivalent amount of solvent (100% ethanol) for 2 hours prior to harvest and RNA isolation

value: Mammary epithelial cell

value: 2 hours solvent


title: CLIP_Uninfected_input

description: Library name: CLIP_Uninfected_input


title: LCM_seq_p112wtCN10 [P10814_1379]


title: CLIP_SRBSDV-infected_input

description: Library name: CLIP_SRBSDV-infected_input


title: HC11R1_Par_EtOH_2nd


title: HC11R1_Par_EtOH_1st


title: A_06

description: Library name: A_06


title: HC11R1_Par_BB_3rd

value: 2 hours B/B


title: HC11R1_Par_BB_1st


title: LCM_seq_p112mSODCN12 [P10814_1374]

value: mSOD


title: A_04

description: Library name: A_04


title: LCM_seq_p112mSODCN10 [P10814_1372]


title: A_08

description: Library name: A_08


title: HC11R1_Par_BB_2nd


title: HC11R1_19Q_EtOH_1st


title: LCM_seq_p112wtCN10 [P10814_1369]


title: A_05

description: Library name: A_05

value: WT


title: LCM_seq_p112mSODCN3.4 [P10814_1380]


title: HC11R1_19Q_BB_2nd


title: A_02

description: Library name: A_02


title: LCM_seq_p112mSODCN3.4 [P10814_1373]


title: LCM_seq_p112wtCN3.4 [P10814_1376]


title: HC11R1_19Q_BB_1st


title: LCM_seq_p112wtCN10 [P10814_1363]


title: HC11R1_19Q_EtOH_3rd


title: HC11R1_19Q_EtOH_2nd


title: LCM_seq_p112mSODCN10 [P10814_1361]


title: HC11R1_12Q_EtOH_2nd


title: A_03

description: Library name: A_03


title: HC11R1_12Q_BB_2nd


title: LCM_seq_p112mSODCN3.4 [P10814_1370]


title: HC11R1_12Q_EtOH_1st


title: dnOGAh, Zeitgeber Time 12, Replicate 5

city: Birmingham

first: Martin

last: Young

state: Alabama

address: 703 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: 80

data_processing:
Basecalls were performed using Illumina's bclconvert version 4.0.3
Raw sequence FASTQ files were trimmed using Trim Galore (version 0.6.7) with parameters --paired --trim-n --nextseq 20
Trimmed sequence FASTQ files were then aligned to the genome using STAR (version 2.7.10b) with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the STAR alignment files using HTSeq-count (version 2.0.2) with parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm39 Release M26
Supplementary files format and content: Tab-delimited Excel file containing raw transcript abundances for each gene in each sample

source_name: Heart

extract_protocol:
Trizol
RNA libraries for RNA-Seq were prepared using NEB's polyA + Ultra II Directional RNA kit following manufacturer's protocols.

treatment_protocol: At 10 weeks old, all mice were injected with 100 μg doxycycline (DOX) (MilliporeSigma, Burlington, MA, USA) in 0.9 % NaCl solution and immediately switched to 1 g / kg DOX-supplemented NIH31 diet (Envigo, Madison, WI, USA)

value: Heart

value: Mixed

value: dnOGAh

value: Zeitgeber Time 12


title: HC11R1_12Q_EtOH_3rd


title: GSC_Stag1Stag2dKO_HEK293T_Input_2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

library_source: genomic

data_processing:
Single-end reads were processed using Trim-Galore v0.4.1/cutadapt v1.9.1 to remove adaptor sequence.
The truncated reads were then aligned to (GRCm38p3) using Bowtie2 v2.3.4.1 with the “-very-sensitive” option.
The reads aligned to chromosome 1 to 19, X, Y were transformed to BAM format by SAMtools v1.7. BED files were obtained from the BAM files using the bamtobed command of BEDTools v2.29.2.
Assembly: mm10
Supplementary files format and content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” option of deepTools v3.5.0.The blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary files format and content: narrowPeak files describe peaks files detected by macs2

molecule: genomic DNA

source_name: Acrosin-EGFP; beta-Actin-EGFP (AAG)

extract_protocol:
The ChIP-seq library preparation was performed as previously described (Nagano et al.,2022). We used harvested mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2PGCLCs and d4c7PGCLCs samples, and FACS-sorted AAG-positive cells for GSCs samples. Briefly, the harvested cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific)/PBS for 10 min at RT and quenched with 125 mM glycine. Crosslinked cells were lysed consecutively using LB1 (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% Triton-100, protease inhibitors (Roche, 11873580001)), LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease inhibitors), and LB3 (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors) and then sonicated by picoruptor to achieve a mean DNA fragment size of around 200-400 bp. Sonicated chromatin was incubated with  Dynabeads M-280 Sheep anti Mouse IgG beads (Thermo Fisher Scientific) or Dynabeads ProteinA beads (Thermo Fisher Scientific) for 35 min at 4°C for preclear. Precleared chromatin was then incubated with antibody that was preincubated with the appropriate Dynabeads in 0.5% BSA (Gibco) in PBS as follows: chromatin equivalent of 5 x 105 cells with anti-H3K4me1 (rabbit monoclonal, CST, D1A9, 5 μl),  anti-H3K9me2 (mouse monoclonal, MBL, MABI0317, 5 μl), anti-H3K27me3 (mouse monoclonal, MBL, MABI0323, 5 μl); 1 x 106 cells with anti-H3K4me3 (mouse monoclonal, MBL, MABI0304, 5 μl), anti-H3K9me3 (mouse monoclonal, MBL, MABI0318, 5 μl), anti-H3K36me2 (rabbit monoclonal, CST, C75H12, 5 μl), anti-H2AK119ub1 (rabbit monoclonal, D27C4, 10 μl), anti-H3K36me3 (rabbit polyclonal, Active Motif, 61101, 2 μl); 1.5 x 106 cells with anti-H3K27ac (mouse monoclonal, MBL, MABI0309, 5 μl); 2 x 106 cells with anti-CTCF (rabbit monoclonal, CST, D31H2, 5 μl), anti-Laminb1 (rabbit polyclonal, Proteintech, 12987-1-AP, 10 μl); 3 x 106 cells with anti-Setdb1 (rabbit ployclonal, Proteintech, 11231-1-AP, 10 μl); 4 x 106 cells with anti-Ring1b (rabbit monoclonal, CST, D22F2, 10 μl); and 4.5 x 106 cells with anti-Rad21 (rabbit monoclonal, ab992, 5 μl). After incubation for 6 h at 4°C, the beads were washed 4 times in wash buffer 1 (20 mM Tris-HCl pH8.0, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 0.1% SDS), 2 times in wash buffer 2 (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.1% SDS), and 2 times in wash buffer 3 (10 mM Tris-HCl  pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% Na-Deoxycolate, 1% NP-40). Then, the washed beads were eluted in 10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 1% SDS, and crosslinks were reversed overnight at 65°C. Input samples were treated in a similar manner. The following day, IP and Input samples were incubated with RNaseA (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific). IP or Input DNA was purified using QIA quick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA) following the manufacturer’s guidelines. An adaptor kit (Fastgene, FG-NGSAD24) was used for the sample indexes. The average size and concentration of libraries were analyzed using LabChIP GX (PerkinElmer) and KAPA library Quantification kit (KAPA), respectively.

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC


title: HC11R1_12Q_BB_3rd


title: dnOGAh, Zeitgeber Time 8, Replicate 4

description: Library name: 83

value: Zeitgeber Time 8


title: HC11R1_19Q_BB_3rd


title: dnOGAh, Zeitgeber Time 16, Replicate 5

description: Library name: 70

value: Zeitgeber Time 16


title: GSC_Stag1Stag3dKO_HEK293T_Input_2


title: LCM_seq_p112wtCN3.4 [P10814_1366]

value: wt


title: LCM_seq_p112wtCN3.4 [P10814_1365]


title: GSC_Stag1Stag2dKO_HEK293T_Input_1


title: GSC_Stag1Stag3dKO_HEK293T_Input_1


title: LCM_seq_p56mSODSC [P6362_1102]


title: A_01

description: Library name: A_01


title: LCM_seq_p56wtSC [P6362_1124]


title: GSC_Stag2Stag3dKO_HEK293T_Input_1


title: GSC_Stag3KO_HEK293T_Input_1

value: Stag3 KO


title: Control, Zeitgeber Time 24, Replicate 5

description: Library name: 67

value: Control

value: Zeitgeber Time 24


title: dnOGAh, Zeitgeber Time 20, Replicate 4

description: Library name: 66

value: Zeitgeber Time 20


title: GSC_Stag2Stag3dKO_HEK293T_Input_2


title: HC11R1_12Q_BB_1st

value: Mammary epithelial cell


title: LCM_seq_p56mSODSC [P6362_1115]


title: LCM_seq_p56mSODSC [P6362_1120]


title: GSC_Stag1Stag3dKO_HEK293T_Rad21_1

description: GSC_Stag1Stag3dKO_Rad21_spkike_normalized.bw


title: GSC_Stag1Stag3dKO_HEK293T_Rad21_2


title: LCM_seq_p56mSODSC [P6362_1129]


title: GSC_WT_HEK293T_Input_2


title: dnOGAh, Zeitgeber Time 8, Replicate 3

description: Library name: 64


title: GSC_WT_HEK293T_Input_1


title: dnOGAh, Zeitgeber Time 4, Replicate 5

description: Library name: 61

value: Zeitgeber Time 4


title: GSC_Stag1Stag2dKO_HEK293T_Rad21_2

description: GSC_Stag1Stag2dKO_Rad21_spkike_normalized.bw


title: GSC_Stag1Stag2dKO_HEK293T_Rad21_1


title: GSC_Stag3KO_HEK293T_Input_2


title: dnOGAh, Zeitgeber Time 20, Replicate 5

description: Library name: 79


title: LCM_seq_p56wtSC [P6362_1119]


title: Control, Zeitgeber Time 12, Replicate 5

description: Library name: 63


title: LCM_seq_p56wtSC [P6362_1122]


title: dnOGAh, Zeitgeber Time 12, Replicate 4

description: Library name: 62


title: LCM_seq_p56mSODSC [P6362_1105]

value: mSOD


title: Control (MC3T3-E1)

city: Jinju-si

first: Se Hyo

last: Jeong

state: Gyeongsangnam-do

address: 501, Jinju-daero

country: South Korea

institute: Gyeongsang national unversity

description: Library name: C

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: mouse calvaria

growth_protocol: The preosteoblast MC3T3-e1 cells were obtained from the American Type Culture Collection (ATCC) and were cultured in MEM-α containing 10% FBS and supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin (P/S). The cells were incubated at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Maxwell® RSC miRNA from Kits (Promega™ Corporation) were used to isolate total RNA. The Agilent 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: MC3T3-e1 cells were cultivated in a 37°C incubator for 24 hours. They were seeded in 60 mm plates at a density of 1 × 10⁶ cells per well, treated with 100 µg/mL Ilex paraguariensis extracts

value: mouse calvaria

value: preosteoblasts

value: Subclone 4

value: X


title: GSC_Stag3KO_HEK293T_Rad21_2


title: Control, Zeitgeber Time 16, Replicate 5

description: Library name: 58

value: Heart

value: Mixed


title: MT (Ilex paraguariensis extracts treated to MC3T3-E1)

description: Library name: MT

value: Ilex paraguariensis


title: E2-I14E-C-PanCK-023

city: Calgary

first: Esteban

middle: Enrique

last: Elias

state: Alberta

address: 3300 Hospital Dr

country: Canada

institute: University of Calgary

description:
Library name: E2-I14E-C-PanCK-023
GeoMx Nanostring

data_processing:
FASTQ files were processed using the NanoString GeoMx NGS Pipeline (v1.1), which includes demultiplexing, UMI deduplication, and alignment to the mouse genome (mm10), generating raw count matrices for each area of illumination (AOI).
Further preprocessing and quality control were performed by the Applied Spatial Omics Centre (ASOC) at the University of Calgary using R (v4.3.1), following the GeoMx Workflows vignette (https://www.bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html). The analysis used the following R packages: NanoStringNCTools (v1.8.0), GeoMxWorkflows (v1.6.0), GeomxTools (v3.4.0), and others for data wrangling and visualization (e.g., dplyr, ggplot2, plotly).
Quality control included assessment of sequencing depth, tissue area coverage, and background signal. Limit of quantification (LOQ) was calculated using negative control probes; low-performing probes and AOIs with low signal were removed. Multiple probes mapping to the same gene were aggregated at the gene level. Genes with low detection rates across AOIs were filtered out. Raw counts were normalized using the Upper Quartile method. Two AOIs were excluded as outliers based on PCA and expression distribution analyses.
Assembly: Mouse mm10
Supplementary files format and content: .dcc

source_name: kidney

extract_protocol:
FFPE kidney sections were deparaffinized, rehydrated, and subjected to antigen retrieval in Tris-EDTA buffer (pH 9.0) followed by proteinase K digestion. Mouse Whole Transcriptome Atlas probes were hybridized to the tissue at 37°C for 16–24 hours. After washing, UV-cleavable oligonucleotide tags were released from selected regions of interest (ROIs) and collected into a 96-well plate for library preparation.
FFPE kidney sections were processed using the NanoString GeoMx DSP with the Mouse Whole Transcriptome Atlas. After deparaffinization, antigen retrieval, and proteinase K digestion, probes were hybridized overnight. Slides were stained with SYTO 13, PanCK-AF532, CD10-AF647, and IBA1-AF594 to guide ROI selection in cortex and medulla. UV-cleaved oligonucleotide tags from selected AOIs were collected into a 96-well plate and amplified using Illumina i5/i7 dual indexing primers. Libraries were purified with AMPure XP beads, quantified by Qubit, quality-checked with Bioanalyzer, and sequenced on an Illumina NextSeq 2000. Data were processed with the GeoMx NGS Pipeline (v1.1).

treatment_protocol: C57BL/6 male mice were pretreated with the SYK inhibitor Entospletinib or vehicle control 24 hours before undergoing unilateral renal ischemia-reperfusion injury (IRI). Kidneys were collected at days 1, 7, and 14 post-injury. Contralateral (uninjured) kidneys were used as internal controls.

value: kidney


title: GSC_Stag2Stag3dKO_HEK293T_Rad21_1

description: GSC_Stag2Stag3dKO_Rad21_spkike_normalized.bw

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC


title: dnOGAh, Zeitgeber Time 24, Replicate 4

description: Library name: 59

value: dnOGAh


title: Control, Zeitgeber Time 16, Replicate 4

description: Library name: 56

value: Control

value: Zeitgeber Time 16


title: E2-I14E-C-IBA1-023

description:
Library name: E2-I14E-C-IBA1-023
GeoMx Nanostring


title: LCM_seq_p56wtSC [P11355_1267]

value: wt


title: GSC_Stag3KO_HEK293T_Rad21_1

value: Stag3 KO


title: GSC_Stag2Stag3dKO_HEK293T_Rad21_2


title: GSC_WT_HEK293T_Rad21_2

value: WT


title: LCM_seq_p56wtSC [P11355_1254]


title: LCM_seq_p56mSODCN12 [P11355_1270]

value: mSOD


title: Control, Zeitgeber Time 12, Replicate 4

description: Library name: 55

value: Zeitgeber Time 12


title: E2-I14E-M-PanCK-021

description:
Library name: E2-I14E-M-PanCK-021
GeoMx Nanostring


title: GSC_Stag3KO_Rad21_2


title: E2-I14E-C-PanCK-022

description:
Library name: E2-I14E-C-PanCK-022
GeoMx Nanostring


title: GSC_WT_HEK293T_Rad21_1


title: GSC_Stag3KO_K27me3_2


title: Control, Zeitgeber Time 4, Replicate 5

description: Library name: 54

value: Zeitgeber Time 4


title: E2-I14E-C-IBA1-022

description:
Library name: E2-I14E-C-IBA1-022
GeoMx Nanostring


title: LCM_seq_p56wtCN12 [P11355_1269]


title: GSC_Stag3KO_K27ac_2


title: Control, Zeitgeber Time 24, Replicate 4

description: Library name: 53

value: Zeitgeber Time 24


title: E2-I14E-M-PanCK-020

description:
Library name: E2-I14E-M-PanCK-020
GeoMx Nanostring


title: GSC_Stag3KO_Input_2


title: LCM_seq_p56wtCN12 [P11355_1265]


title: E2-I14E-M-IBA1-021

description:
Library name: E2-I14E-M-IBA1-021
GeoMx Nanostring


title: GSC_Stag3KO_CTCF_2


title: dnOGAh, Zeitgeber Time 12, Replicate 2

description: Library name: 47


title: LCM_seq_p56mSODCN12 [P11355_1262]


title: Control, Zeitgeber Time 8, Replicate 5

description: Library name: 51

value: Zeitgeber Time 8


title: E2-I14V-C-PanCK-019

description:
Library name: E2-I14V-C-PanCK-019
GeoMx Nanostring


title: LCM_seq_p56wtCN10 [P11355_1274]


title: LCM_seq_p56mSODCN12 [P11355_1260]


title: dnOGAh, Zeitgeber Time 24, Replicate 3

description: Library name: 49

value: Heart


title: E2-I14E-M-IBA1-020

description:
Library name: E2-I14E-M-IBA1-020
GeoMx Nanostring


title: LCM_seq_p56wtCN12 [P11355_1256]


title: GSC_Stag2Stag3dKO_Input_2


title: E2-I14V-M-PanCK-018

description:
Library name: E2-I14V-M-PanCK-018
GeoMx Nanostring


title: GSC_Stag2Stag3dKO_K9me3_2


title: Control, Zeitgeber Time 4, Replicate 4

description: Library name: 46

value: Mixed


title: E2-I14V-C-IBA1-019

description:
Library name: E2-I14V-C-IBA1-019
GeoMx Nanostring


title: GSC_Stag2Stag3dKO_CTCF_2


title: LCM_seq_p56mSODCN10 [P11355_1263]


title: Control, Zeitgeber Time 8,Replicate 4

description: Library name: 43


title: LCM_seq_p56mSODCN10 [P11355_1271]


title: dnOGAh, Zeitgeber Time 12, Replicate 3

description: Library name: 52


title: LCM_seq_p56mSODCN10 [P11355_1261]


title: Control, Zeitgeber Time 20, Replicate 3

description: Library name: 42

value: Zeitgeber Time 20


title: E2-I14V-M-IBA1-018

description:
Library name: E2-I14V-M-IBA1-018
GeoMx Nanostring

value: kidney


title: E2-I14V-M-PanCK-017

description:
Library name: E2-I14V-M-PanCK-017
GeoMx Nanostring


title: GSC_Stag1Stag2dKO_K9me3_2

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: GSC_Stag1Stag3dKO_CTCF_2

value: GSC


title: LCM_seq_p56wtCN10 [P11355_1266]


title: dnOGAh, Zeitgeber Time 4, Replicate 4

description: Library name: 45

value: dnOGAh


title: E2-I14V-M-IBA1-017

description:
Library name: E2-I14V-M-IBA1-017
GeoMx Nanostring


title: LCM_seq_p56wtCN10 [P11355_1259]


title: GSC_Stag1Stag3dKO_Input_2


title: GSC_Stag1Stag2dKO_CTCF_2


title: LCM_seq_p56mSODCN3.4 [P11355_1272]


title: E2-I14V-C-PanCK-016

description:
Library name: E2-I14V-C-PanCK-016
GeoMx Nanostring


title: LCM_seq_p56wtCN3.4 [P11355_1268]


title: GSC_Stag1Stag2dKO_Input_2


title: LCM_seq_p56wtCN3.4 [P11355_1264]


title: E2-I7E-C-IBA1-015

description:
Library name: E2-I7E-C-IBA1-015
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 8, Replicate 2

description: Library name: 39


title: Control, Zeitgeber Time 4, Replicate 3

description: Library name: 44

value: Control


title: LCM_seq_p56mSODCN3.4 [P11355_1258]


title: E2-I7E-C-PanCK-015

description:
Library name: E2-I7E-C-PanCK-015
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 4, Replicate 2

description: Library name: 36


title: Control, Zeitgeber Time 8, Replicate 3

description: Library name: 40


title: E17_GC_M_RNA_1

data_processing:
Raw 3’ RNA-seq data were directly used with Salmon v1.4.0 (Patro et al., 2017) with default parameters and --noLengthCorrection to quantify the expression of GENCODE vM25 features on GRCm38.p6. Gene-level expression estimates were aggregated from transcript-level abundance using tximport v1.16.1 (Soneson et al., 2015).
Alternatively, all reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCm38.p6 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted from cells using a RNeasy Micro kit (QIAGEN, 74004) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification as previously described  (Nakamura et al, 2015). Sequencing libraries were generated from amplified cDNA as described previously   (Nakamura et al, 2015).

value: testis

value: Germ cells


title: ESC_Stag3OEStag1Stag2dKO_GFP_2

source_name: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

value: ESC


title: E2-I7E-C-PanCK-014

description:
Library name: E2-I7E-C-PanCK-014
GeoMx Nanostring


title: E17_GC_M_RNA_2


title: E2-I7E-C-IBA1-014

description:
Library name: E2-I7E-C-IBA1-014
GeoMx Nanostring


title: mem B cell, M6_pre_boost_memory, 10x VDJ (BCR)

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
Library name: RHH920_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger multi v.8.0.1 (10X Genomics), using the Cell Ranger GEX reference Mmul_8.0.1, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets were excluded.
Single-cell BCR libraries were processed with Cell Ranger VDJ v.8.0.1 without a VDJ reference genome using the parameters –denovo –chain=auto.
Antibody sequences were subsequently annotated with igblastn v.1.22.0 using a custom Rhesus macaque germline database. Contigs containing fewer than 50 reads and more than one heavy or light chain were removed.
Assembly: Mmul_8.0.1
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files: fmt19
Library strategy: BCR-Seq

organism: Macaca mulatta

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

extract_protocol:
PBMCs from immunized Rhesus macaques were thawed. Gross memory (CD27+) B cells were sorted by FACS.
Sorted macaque B cells were loaded onto the Chromium X controller for bead formation using the Chromium Next GEM Single Cell v3.1 kit. Cell-barcoded cDNA libraries were generated according to the manufacturer’s instruction. VDJ libraries were prepared using the Chromium Single Cell VDJ enrichment mix, using custom primers. Libraries with unique Illumina adapters were pooled and sequenced.

value: Memory B cells

value: ~7 years

value: Male

value: Animals immunized with the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine (2023–24 formulation)


title: Control, Zeitgeber Time 12, Replicate 3

description: Library name: 38

value: Zeitgeber Time 12


title: dnOGAh, Zeitgeber Time 16, Replicate 4

description: Library name: 33

value: Zeitgeber Time 16


title: Control, Zeitgeber Time 8, Replicate 2

description: Library name: 34

value: Heart

value: Zeitgeber Time 8


title: LCM_seq_p56wtCN3.4 [P11355_1255]

value: wt


title: E16_GC_M_RNA_2


title: E2-I14V-C-IBA1-016

description:
Library name: E2-I14V-C-IBA1-016
GeoMx Nanostring

value: kidney


title: E2-I7V-C-PanCK-012

description:
Library name: E2-I7V-C-PanCK-012
GeoMx Nanostring


title: E2-I7E-M-IBA1-013

description:
Library name: E2-I7E-M-IBA1-013
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 4, Replicate 3

description: Library name: 37

value: Mixed

value: Zeitgeber Time 4


title: GSC_Stag3KO2_RNA_2

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC

value: Stag3 KO


title: E2-I7E-M-PanCK-013

description:
Library name: E2-I7E-M-PanCK-013
GeoMx Nanostring


title: E16_GC_M_RNA_1

value: testis

value: Germ cells


title: Control, Zeitgeber Time 16, Replicate 2

description: Library name: 31

value: Control


title: LCM_seq_p56mSODCN3.4 [P11355_1257]

value: mSOD


title: mem B cell, M5_pre_boost_memory, 10x VDJ (BCR)

description:
Library name: RDHI0N_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: Memory B cells

value: ~7 years

value: Male


title: dnOGAh, Zeitgeber Time 16, Replicate 3

description: Library name: 32

value: Heart

value: dnOGAh

value: Zeitgeber Time 16


title: mem B cell, M4_pre_boost_memory, 10x VDJ (BCR)

description:
Library name: RHDHBH_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Animals immunized with the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine (2023–24 formulation)


title: dnOGAh, Zeitgeber Time 4, Replicate 1

description: Library name: 29

value: Mixed


title: GSC_Stag3KO2_RNA_1


title: dnOGAh, Zeitgeber Time 24, Replicate 2

description: Library name: 28

value: Zeitgeber Time 24


title: mem B cell, M3_pre_boost_memory, 10x VDJ (BCR)

description:
Library name: RHDGZ8_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: dnOGAh, Zeitgeber Time 20, Replicate 3

description: Library name: 26

value: Zeitgeber Time 20


title: E2-I7V-C-PanCK-011

description:
Library name: E2-I7V-C-PanCK-011
GeoMx Nanostring

value: kidney


title: GSC_WT_RNA_1

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC

value: WT


title: mem B cell, M1_pre_boost_memory, 10x VDJ (BCR)

description:
Library name: RHDGX6_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: E2-I7V-C-IBA1-012

description:
Library name: E2-I7V-C-IBA1-012
GeoMx Nanostring


title: mem B cell, M2_pre_boost_memory, 10x VDJ (BCR)

description:
Library name: RHDGK7_BCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: dnOGAh, Zeitgeber Time 8, Replicate 1

description: Library name: 27

value: Zeitgeber Time 8


title: E2-I7V-M-PanCK-010

description:
Library name: E2-I7V-M-PanCK-010
GeoMx Nanostring


title: Control, Zeitgeber Time 4, Replicate 2

description: Library name: 25

value: Control

value: Zeitgeber Time 4


title: mem B cell, pre_boost_memory, replicate 2, 10x VDJ (BCR)

description:
Library name: LD_RM_t_2_PBMC_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: Memory B cells


title: GSC_WT_RNA_2


title: mem B cell, pre_boost_memory, replicate 2, HTO

description:
Library name: LD_RM_t_2_PBMC_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

data_processing:
Hashtag-oligos unique molecular identifier quantification were performed with Cell Ranger multi v.8.0.1 (10X Genomics), using the Cell Ranger GEX reference Mmul_8.0.1, and analyzed in R with Seurat v.5.1.0. Cells were demultiplexed with MULTISeqDemux, and those classified as doublets were excluded.
Single-cell BCR libraries were processed with Cell Ranger VDJ v.8.0.1 without a VDJ reference genome using the parameters –denovo –chain=auto.
Antibody sequences were subsequently annotated with igblastn v.1.22.0 using a custom Rhesus macaque germline database. Contigs containing fewer than 50 reads and more than one heavy or light chain were removed.
Assembly: Mmul_8.0.1
Supplementary files format and content: CellRanger output files:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files: fmt19
Library strategy: CITE-Seq

value: ~7 years

value: Male


title: E2-I7V-M-IBA1-010

description:
Library name: E2-I7V-M-IBA1-010
GeoMx Nanostring


title: mem B cell, pre_boost_memory, replicate 1, 10x VDJ (BCR)

description:
Library name: LD_RM_t1_PBMC_VDJ
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: d4c7PGCLC_WT_Stag2_3

value: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: E2-I1E-C-PanCK-009

description:
Library name: E2-I1E-C-PanCK-009
GeoMx Nanostring


title: Control, Zeitgeber Time 16, Replicate 1

description: Library name: 23

value: Heart

value: Zeitgeber Time 16


title: d4c7PGCLC_WT_Stag1_2


title: dnOGAh, Zeitgeber Time 12, Replicate 1

description: Library name: 24

value: Mixed

value: dnOGAh

value: Zeitgeber Time 12


title: d4c7PGCLC_WT_Stag2_2


title: E2-I7V-C-IBA1-011

description:
Library name: E2-I7V-C-IBA1-011
GeoMx Nanostring

value: kidney


title: E2-I1E-C-IBA1-009

description:
Library name: E2-I1E-C-IBA1-009
GeoMx Nanostring


title: GSC_Stag3KO1_RNA_1

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: Stag3 KO


title: E2-I1E-M-PanCK-008

description:
Library name: E2-I1E-M-PanCK-008
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 20, Replicate 2

description: Library name: 21

value: Zeitgeber Time 20


title: d4c7PGCLC_WT_Stag1_1

value: WT


title: GSC_Stag3KO1_RNA_2

value: GSC


title: d4c7PGCLC_WT_Stag2_1


title: mem B cell, pre_boost_memory, replicate 1, HTO

description:
Library name: LD_RM_t1_PBMC_HTO
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains hashtag

value: Animals immunized with the Pfizer-BioNTech SARS-CoV-2 mRNA vaccine (2023–24 formulation)


title: E2-I1E-C-PanCK-007

description:
Library name: E2-I1E-C-PanCK-007
GeoMx Nanostring


title: Control, Zeitgeber Time 4, Replicate 1

description: Library name: 18

value: Control

value: Zeitgeber Time 4


title: Control, Zeitgeber Time 24, Replicate 2

description: Library name: 19

value: Zeitgeber Time 24


title: E2-I1E-M-IBA1-008

description:
Library name: E2-I1E-M-IBA1-008
GeoMx Nanostring


title: d2PGCLC_WT_Stag2_3


title: MTB20_44_V1_PT_Rep1_TCRB.tsv

city: La Jolla

first: Bjoern

last: Peters

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Library name: MTB20_44_V1_PT_Rep1_TCRB.tsv

data_processing:
Raw reads were aligned and quantified using the Cell Ranger Multi pipeline (version 5.0.0) against the GRCh38 (2020-A) human reference genome and the VDJ was aligned with refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0. GEX and HTO data were aggregated as feature/barcode matrices and imported into the R environment using Seurat where additional QCs and downstream analysis were conducted. Before creating the Seurat object, in the GEX matrix, TCR genes belonging to each category of TCR alpha, beta, gamma and delta were averaged across the cells to prevent the formation of individual TCR gene expression clusters in downstream analysis.
Supplementary files format and content: tab-delimited text file includes template counts for each sample
Library strategy: TCR-seq

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Cells were harvested on day 14. CD4 T cells were purified from the ex vivo samples using the EasySep™ Human CD4 Positive Selection Kit II (STEM cellTM Technologies), according to the manufacturer’s instructions. DNA extraction (DNeasy Blood and Tissue kit; Qiagen) was performed according to the manufacturer’s instructions for both the purified CD4 T cells and the cultured cells.
TCR sequencing of the V-β chain was performed by Adaptive Biotechnologies and their ImmunoSeq platform. Ex vivo samples were sequenced at a higher depth   than cultured samples for greater sensitivity to detect rare clonotypes and to assess a broader range of the repertoire.

value: PBMC

tag: library type

value: TCR


title: MTB20_44_V1_PT_Rep2_TCRB.tsv

description: Library name: MTB20_44_V1_PT_Rep2_TCRB.tsv


title: d2PGCLC_WT_Stag2_2

value: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: dnOGAh, Zeitgeber Time 20, Replicate 1

description: Library name: 16

value: Heart


title: Control, Zeitgeber Time 20, Replicate 2

description: Library name: 17

value: Mixed


title: E2-I1E-C-IBA1-007

description:
Library name: E2-I1E-C-IBA1-007
GeoMx Nanostring


title: MTB20_44_V1_MTB_Rep2_TCRB.tsv

description: Library name: MTB20_44_V1_MTB_Rep2_TCRB.tsv


title: d2PGCLC_WT_Stag2_1


title: dnOGAh, Zeitgeber Time 16, Replicate 1

description: Library name: 15

value: dnOGAh

value: Zeitgeber Time 16


title: MTB20_44_V1_MTB_Rep1_TCRB.tsv

description: Library name: MTB20_44_V1_MTB_Rep1_TCRB.tsv


title: E2-CTRL-C-IBA1-006

description:
Library name: E2-CTRL-C-IBA1-006
GeoMx Nanostring

value: kidney

value: CTRL


title: E2-CTRL-C-PanCK-005

description:
Library name: E2-CTRL-C-PanCK-005
GeoMx Nanostring


title: d2PGCLC_WT_Stag1_2


title: Control, Zeitgeber Time 12, Replicate 2

description: Library name: 13

value: Zeitgeber Time 12


title: GSC_WT_Stag3_3

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: d2PGCLC_WT_Stag1_1

value: WT


title: E2-CTRL-C-IBA1-005

description:
Library name: E2-CTRL-C-IBA1-005
GeoMx Nanostring


title: GSC_WT_Stag3_2

value: GSC


title: Control, Zeitgeber Time 12, Replicate 1

description: Library name: 11


title: E2-CTRL-M-IBA1-004

description:
Library name: E2-CTRL-M-IBA1-004
GeoMx Nanostring


title: GSC_WT_Stag3_1


title: E2-CTRL-M-PanCK-004

description:
Library name: E2-CTRL-M-PanCK-004
GeoMx Nanostring


title: Control, Zeitgeber Time 24, Replicate 1

description: Library name: 10


title: E2-I1V-C-PanCK-003

description:
Library name: E2-I1V-C-PanCK-003
GeoMx Nanostring


title: MTB20_37_V1_MTB_Rep1_TCRB.tsv

description: Library name: MTB20_37_V1_MTB_Rep1_TCRB.tsv


title: E2-CTRL-C-PanCK-006

description:
Library name: E2-CTRL-C-PanCK-006
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 8, Replicate 5

description: Library name: 9

value: Zeitgeber Time 8


title: GSC_WT_Stag2_3


title: MTB20_37_V1_Exvivo_TCRB.tsv

description: Library name: MTB20_37_V1_Exvivo_TCRB.tsv


title: GSC_WT_Stag2_2


title: MTB20_44_V1_Exvivo_TCRB.tsv

description: Library name: MTB20_44_V1_Exvivo_TCRB.tsv


title: Control, Zeitgeber Time 8, Replicate 1

description: Library name: 14

value: Control


title: MTB20_43_V1_PT_Rep2_TCRB.tsv

description: Library name: MTB20_43_V1_PT_Rep2_TCRB.tsv


title: E2-I1V-C-PanCK-002

description:
Library name: E2-I1V-C-PanCK-002
GeoMx Nanostring


title: Control, Zeitgeber Time 20, Replicate 5

description: Library name: 8

value: Zeitgeber Time 20


title: MTB20_37_V1_PT_Rep2_TCRB.tsv

description: Library name: MTB20_37_V1_PT_Rep2_TCRB.tsv


title: E2-I1V-C-IBA1-003

description:
Library name: E2-I1V-C-IBA1-003
GeoMx Nanostring


title: MTB20_37_V1_PT_Rep1_TCRB.tsv

description: Library name: MTB20_37_V1_PT_Rep1_TCRB.tsv


title: E2-I1V-C-IBA1-002

description:
Library name: E2-I1V-C-IBA1-002
GeoMx Nanostring


title: MTB20_43_V1_PT_Rep1_TCRB.tsv

description: Library name: MTB20_43_V1_PT_Rep1_TCRB.tsv


title: E2-I1V-M-PanCK-001

description:
Library name: E2-I1V-M-PanCK-001
GeoMx Nanostring


title: dnOGAh, Zeitgeber Time 24, Replicate 5

description: Library name: 7

value: Zeitgeber Time 24


title: GSC_WT_Stag1_2


title: Control, Zeitgeber Time 20, Replicate 4

description: Library name: 5


title: Control, Zeitgeber Time 16, Replicate 3

description: Library name: 4


title: MTB20_43_V1_MTB_Rep2_TCRB.tsv

description: Library name: MTB20_43_V1_MTB_Rep2_TCRB.tsv

value: PBMC


title: GSC_WT_Stag1_1


title: E2-I1V-M-IBA1-001

description:
Library name: E2-I1V-M-IBA1-001
GeoMx Nanostring


title: MTB20_43_V1_MTB_Rep1_TCRB.tsv

description: Library name: MTB20_43_V1_MTB_Rep1_TCRB.tsv

value: TCR


title: GSC_Stag3KO_Stag3_2

value: Stag3 KO


title: MTB20_43_V1_Exvivo_TCRB.tsv

description: Library name: MTB20_43_V1_Exvivo_TCRB.tsv


title: Control, Zeitgeber Time 24, Replicate 3

description: Library name: 3

value: Heart


title: E1-I14E-C-PanCK-023a

description:
Library name: E1-I14E-C-PanCK-023a
GeoMx Nanostring


title: E1-I14E-C-PanCK-023

description:
Library name: E1-I14E-C-PanCK-023
GeoMx Nanostring


title: GSC_WT_Stag2_1


title: Control, Zeitgeber Time 20, Replicate 1

description: Library name: 1

value: Mixed


title: dnOGAh, Zeitgeber Time 16, Replicate 2

description: Library name: 2

value: dnOGAh


title: GSC_Stag3KO_Rad21_1


title: MTB20_38_V1_PT_Rep1_TCRB.tsv

description: Library name: MTB20_38_V1_PT_Rep1_TCRB.tsv


title: GSC_Stag3KO_K27me3_1


title: MTB20_38_V1_MTB_Rep2_TCRB.tsv

description: Library name: MTB20_38_V1_MTB_Rep2_TCRB.tsv


title: GSC_Stag3KO_K27ac_1


title: MTB20_38_V1_MTB_Rep1_TCRB.tsv

description: Library name: MTB20_38_V1_MTB_Rep1_TCRB.tsv


title: 20567X24 dKO Tfh Rep 2

city: Salt Lake City

first: J. Scott

last: Hale

state: Utah

address: 15 N Medical Drive

department: Pathology

institute: University of Utah

description: Library name: 20567X24

data_processing:
Alignment to the mm10 reference genome was performed using Bismark v0.19.0. Deduplication was performed with deduplicate_bismark.
Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context and considered sufficient when this value was less than 3%.
Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0.
This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow.
Differentially methylated regions (DMR) were detected using Bsmooth, Bsmooth.tstat and dmrFinder in the bsseq R package
Assembly: mm10
Supplementary files format and content: Tab-delimited bismark coverage files
Library strategy: EM-seq

source_name: Spleen

extract_protocol:
Quick-DNA Micro-prep (Zymo Research)
NEBNext Enzymatic Methyl-seq Kit

treatment_protocol: Tamoxifen (2mg/mouse x4 days), LCMV-cl13 (2*10^6 PFU/mL)

value: Spleen

value: SMARTA-Tg

value: Tfh

value: Dnmt3a f/f; Tet2 KO (Cre+)


title: E1-I14E-C-IBA1-022

description:
Library name: E1-I14E-C-IBA1-022
GeoMx Nanostring

value: kidney


title: E1-I14E-C-PanCK-022

description:
Library name: E1-I14E-C-PanCK-022
GeoMx Nanostring


title: 20567X23 Tet2 Tfh Rep 3

description: Library name: 20567X23

value: Tet2 KO (Cre+)


title: GSC_Stag3KO_Input_1

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC


title: 20567X22 Dnmt3a Tfh Rep 3

description: Library name: 20567X22

value: Dnmt3a f/f (Cre+)


title: MTB20_38_V1_Exvivo_TCRB.tsv

description: Library name: MTB20_38_V1_Exvivo_TCRB.tsv


title: E1-I14E-M-PanCK-021

description:
Library name: E1-I14E-M-PanCK-021
GeoMx Nanostring


title: GSC_Stag3KO_CTCF_1


title: E1-I14E-M-IBA1-021

description:
Library name: E1-I14E-M-IBA1-021
GeoMx Nanostring


title: MTB20_54_V3_PT_TCRB.tsv

description: Library name: MTB20_54_V3_PT_TCRB.tsv


title: GSC_Stag3KO_Stag3_1


title: MTB20_37_V1_MTB_Rep2_TCRB.tsv

description: Library name: MTB20_37_V1_MTB_Rep2_TCRB.tsv


title: GSC_Stag2Stag3dKO_Stag1_2


title: MTB20_38_V1_PT_Rep2_TCRB.tsv

description: Library name: MTB20_38_V1_PT_Rep2_TCRB.tsv


title: MTB20_54_V3_MTB_TCRB.tsv

description: Library name: MTB20_54_V3_MTB_TCRB.tsv


title: E1-I14E-C-IBA1-023

description:
Library name: E1-I14E-C-IBA1-023
GeoMx Nanostring


title: 20567X19 Tet2 Tfh Rep 2

description: Library name: 20567X19


title: MTB20_54_V1_PT_TCRB.tsv

description: Library name: MTB20_54_V1_PT_TCRB.tsv


title: GSC_Stag2Stag3dKO_Stag1_1


title: GSC_Stag2Stag3dKO_Rad21_2


title: E1-I14E-M-IBA1-020

description:
Library name: E1-I14E-M-IBA1-020
GeoMx Nanostring


title: 20567X18 Dnmt3a Tfh Rep 2

description: Library name: 20567X18


title: E1-I7E-M-PanCK-019

description:
Library name: E1-I7E-M-PanCK-019
GeoMx Nanostring


title: MTB20_54_V1_MTB_TCRB.tsv

description: Library name: MTB20_54_V1_MTB_TCRB.tsv


title: 20567X17 WT Tfh Rep 2

description: Library name: 20567X17

value: WT (Cre+)


title: GSC_Stag2Stag3dKO_Rad21_1


title: dnOGAh, Zeitgeber Time 24, Replicate 1

description: Library name: 12

value: Zeitgeber Time 24


title: MTB20_36_V3_PT_TCRB.tsv

description: Library name: MTB20_36_V3_PT_TCRB.tsv

value: PBMC


title: GSC_Stag2Stag3dKO_K9me3_1


title: E1-I7E-M-IBA1-019

description:
Library name: E1-I7E-M-IBA1-019
GeoMx Nanostring


title: MTB20_36_V3_MTB_TCRB.tsv

description: Library name: MTB20_36_V3_MTB_TCRB.tsv

value: TCR


title: E1-I7E-C-PanCK-018

description:
Library name: E1-I7E-C-PanCK-018
GeoMx Nanostring


title: 20567X15 Tet2 Tfh Rep 1

description: Library name: 20567X15


title: 20567X21 WT Tfh Rep 3

description: Library name: 20567X21


title: GSC_Stag2Stag3dKO_Input_1


title: MTB20_36_V1_PT_TCRB.tsv

description: Library name: MTB20_36_V1_PT_TCRB.tsv


title: 20567X14 Dnmt3a Tfh Rep 1

description: Library name: 20567X14


title: E1-I7E-C-IBA1-018

description:
Library name: E1-I7E-C-IBA1-018
GeoMx Nanostring


title: E1-I14E-M-PanCK-020

description:
Library name: E1-I14E-M-PanCK-020
GeoMx Nanostring


title: 20567X20 dKO Tfh Rep 1

description: Library name: 20567X20


title: GSC_Stag2Stag3dKO_CTCF_1


title: 20567X13 WT Tfh Rep 1

description: Library name: 20567X13


title: E1-I7E-C-PanCK-017

description:
Library name: E1-I7E-C-PanCK-017
GeoMx Nanostring


title: 20567X12 dKO Th1 Rep 2

description: Library name: 20567X12


title: MTB20_36_V1_MTB_TCRB.tsv

description: Library name: MTB20_36_V1_MTB_TCRB.tsv


title: GSC_Stag1Stag3dKO_Stag2_2


title: E1-I7E-C-IBA1-017

description:
Library name: E1-I7E-C-IBA1-017
GeoMx Nanostring


title: MTB20_19_V3_PT_TCRB.tsv

description: Library name: MTB20_19_V3_PT_TCRB.tsv


title: GSC_Stag1Stag3dKO_Stag2_1


title: GSC_Stag1Stag3dKO_Rad21_2


title: MTB20_19_V3_MTB_TCRB.tsv

description: Library name: MTB20_19_V3_MTB_TCRB.tsv


title: 20567X11 Tet2 Th1 Rep 3

description: Library name: 20567X11


title: MTB20_19_V1_PT_TCRB.tsv

description: Library name: MTB20_19_V1_PT_TCRB.tsv


title: 20567X9 WT Th1 Rep 3

description: Library name: 20567X9


title: GSC_Stag1Stag3dKO_Rad21_1


title: E1-I14V-M-PanCK-015

description:
Library name: E1-I14V-M-PanCK-015
GeoMx Nanostring


title: GSC_Stag1Stag3dKO_Input_1


title: E1-I14V-M-IBA1-015

description:
Library name: E1-I14V-M-IBA1-015
GeoMx Nanostring


title: 20567X8 dKO Th1 Rep 1

description: Library name: 20567X8


title: GSC_Stag1Stag3dKO_CTCF_1


title: E1-I14V-C-IBA1-016

description:
Library name: E1-I14V-C-IBA1-016
GeoMx Nanostring


title: MTB20_19_V1_MTB_TCRB.tsv

description: Library name: MTB20_19_V1_MTB_TCRB.tsv


title: MTB20_7_V3_PT_TCRB.tsv

description: Library name: MTB20_7_V3_PT_TCRB.tsv


title: 20567X7 Tet2 Th1 Rep 2

description: Library name: 20567X7


title: 20567X6 Dnmt3a Th1 Rep 2

description: Library name: 20567X6


title: MTB20_7_V3_MTB_TCRB.tsv

description: Library name: MTB20_7_V3_MTB_TCRB.tsv


title: MTB20_44_V3_PT_TCRB.tsv

description: Library name: MTB20_44_V3_PT_TCRB.tsv


title: GSC_Stag1Stag2dKO_Stag3_2


title: GSC_Stag1Stag2dKO_Stag3_1


title: E1-I14V-C-PanCK-016

description:
Library name: E1-I14V-C-PanCK-016
GeoMx Nanostring


title: E1-I14V-M-IBA1-014

description:
Library name: E1-I14V-M-IBA1-014
GeoMx Nanostring


title: E1-I14V-C-PanCK-013

description:
Library name: E1-I14V-C-PanCK-013
GeoMx Nanostring


title: 20567X5 WT Th1 Rep 2

description: Library name: 20567X5


title: 20567X10 Dnmt3a Th1 Rep 3

description: Library name: 20567X10


title: MTB20_44_V3_MTB_TCRB.tsv

description: Library name: MTB20_44_V3_MTB_TCRB.tsv


title: GSC_Stag1Stag2dKO_Rad21_2


title: E1-I14V-C-IBA1-013

description:
Library name: E1-I14V-C-IBA1-013
GeoMx Nanostring


title: MTB20_37_V3_PT_TCRB.tsv

description: Library name: MTB20_37_V3_PT_TCRB.tsv


title: 20567X3 Tet2 Th1 Rep 1

description: Library name: 20567X3


title: GSC_Stag1Stag2dKO_Rad21_1


title: MTB20_37_V3_MTB_TCRB.tsv

description: Library name: MTB20_37_V3_MTB_TCRB.tsv


title: E1-I14V-M-PanCK-014

description:
Library name: E1-I14V-M-PanCK-014
GeoMx Nanostring


title: 20567X1 WT Th1 Rep 1

description: Library name: 20567X1


title: 20928X16 dKO Tfh Rep 3

description: Library name: 20928X16

data_processing:
The mouse GRCm39 genome and gene feature files were downloaded from Ensembl release 108 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3. Differentially expressed genes were identified using DESeq2 version 1.36.0 with a 5% FDR.
Assembly: mm39
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited matrix

growth_protocol: None.

extract_protocol:
Direct-zol RNA micro-prep Kit (Zymo Research)
NEBNext Ultra II Direction RNA Library Prep with poly(A) mRNA isolation

treatment_protocol: Tamoxifen (2mg/mouse for 4 days); adoptive-transfer; LCMV-cl13 infection (2*10^6 PFU/mL)


title: GSC_Stag1Stag2dKO_K9me3_1


title: E1-I7V-C-PanCK-012

description:
Library name: E1-I7V-C-PanCK-012
GeoMx Nanostring


title: MTB20_51_V1_PT_TCRB.tsv

description: Library name: MTB20_51_V1_PT_TCRB.tsv


title: MTB20_51_V1_MTB_TCRB.tsv

description: Library name: MTB20_51_V1_MTB_TCRB.tsv


title: 20567X2 Dnmt3a Th1 Rep 1

description: Library name: 20567X2


title: E1-I7V-C-PanCK-011

description:
Library name: E1-I7V-C-PanCK-011
GeoMx Nanostring


title: E1-I7V-C-IBA1-012

description:
Library name: E1-I7V-C-IBA1-012
GeoMx Nanostring


title: GSC_Stag1Stag2dKO_CTCF_1


title: E1-I7V-C-IBA1-011

description:
Library name: E1-I7V-C-IBA1-011
GeoMx Nanostring


title: 20928X15 dKO Tfh Rep 2

description: Library name: 20928X15


title: MTB20_18_V3_PT_TCRB.tsv

description: Library name: MTB20_18_V3_PT_TCRB.tsv


title: E1-I7V-M-PanCK-010

description:
Library name: E1-I7V-M-PanCK-010
GeoMx Nanostring


title: 20928X14 Tet2 Tfh Rep 3

description: Library name: 20928X14


title: EpiLC_WT_Stag2_2

value: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

value: EpiLC

value: WT


title: MTB20_18_V3_MTB_TCRB.tsv

description: Library name: MTB20_18_V3_MTB_TCRB.tsv


title: MTB20_18_V1_PT_TCRB.tsv

description: Library name: MTB20_18_V1_PT_TCRB.tsv


title: 20928X13 Tet2 Tfh Rep 2

description: Library name: 20928X13


title: E1-I7V-M-IBA1-010

description:
Library name: E1-I7V-M-IBA1-010
GeoMx Nanostring


title: EpiLC_WT_Stag1_2


title: EpiLC_WT_Stag2_1


title: GSC_Stag1Stag2dKO_Input_1


title: MTB20_18_V1_MTB_TCRB.tsv

description: Library name: MTB20_18_V1_MTB_TCRB.tsv


title: 20928X12 Dnmt3a Tfh Rep 3

description: Library name: 20928X12


title: E1-I1E-C-PanCK-009

description:
Library name: E1-I1E-C-PanCK-009
GeoMx Nanostring


title: 20928X11 Dnmt3a Tfh Rep 2

description: Library name: 20928X11


title: MTB20_28_V1_PT_TCRB.tsv

description: Library name: MTB20_28_V1_PT_TCRB.tsv


title: EpiLC_WT_Stag1_1


title: 20928X10 WT Tfh Rep 3

description: Library name: 20928X10


title: ESC_WT_Stag2_2

value: ESC


title: 20928X9 WT Tfh Rep 2

description: Library name: 20928X9

value: Spleen


title: MTB20_28_V1_MTB_TCRB.tsv

description: Library name: MTB20_28_V1_MTB_TCRB.tsv


title: E1-I1E-M-PanCK-008

description:
Library name: E1-I1E-M-PanCK-008
GeoMx Nanostring


title: MTB20_21_V1_PT_TCRB.tsv

description: Library name: MTB20_21_V1_PT_TCRB.tsv


title: E1-I1E-M-IBA1-008

description:
Library name: E1-I1E-M-IBA1-008
GeoMx Nanostring


title: ESC_WT_Stag1_2


title: MTB20_21_V1_MTB_TCRB.tsv

description: Library name: MTB20_21_V1_MTB_TCRB.tsv


title: 20928X8 dKO Th1 Rep 3

description: Library name: 20928X8

value: SMARTA-Tg


title: E1-I1E-C-PanCK-007a

description:
Library name: E1-I1E-C-PanCK-007a
GeoMx Nanostring


title: ESC_WT_Stag1_1


title: E1-I1E-C-PanCK-007

description:
Library name: E1-I1E-C-PanCK-007
GeoMx Nanostring


title: 20928X7 dKO Th1 Rep 2

description: Library name: 20928X7


title: 20928X6 Tet2 Th1 Rep 3

description: Library name: 20928X6


title: MTB20_16_V1_MTB_TCRB.tsv

description: Library name: MTB20_16_V1_MTB_TCRB.tsv


title: E1-I1E-C-IBA1-007

description:
Library name: E1-I1E-C-IBA1-007
GeoMx Nanostring


title: E1-I1E-C-IBA1-009

description:
Library name: E1-I1E-C-IBA1-009
GeoMx Nanostring


title: ESC_Stag3OEStag1Stag2dKO_Stag3_2

description: ESC_Stag3OEStag1Stag2dKO_Stag3_pool.bw (available on GSM7799818)

data_processing:
Single-end reads were processed using Trim-Galore v0.4.1/cutadapt v1.9.1 to remove adaptor sequence.
The truncated reads were then aligned to (GRCm3ESC_Stag3OEStag1Stag2dKO_Stag3_pool.bw8p3) using Bowtie2 v2.3.4.1 with the “-very-sensitive” option.
The reads aligned to chromosome 1 to 19, X, Y were transformed to BAM format by SAMtools v1.7. BED files were obtained from the BAM files using the bamtobed command of BEDTools v2.29.2.
Assembly: mm10
Supplementary files format and content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” option of deepTools v3.5.0.The blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary files format and content: narrowPeak files describe peaks files detected by macs2


title: ESC_Stag3OEStag1Stag2dKO_Stag3_1


title: ESC_Stag3OEStag1Stag2dKO_Rad21_2


title: MTB20_10_V1_PT_TCRB.tsv

description: Library name: MTB20_10_V1_PT_TCRB.tsv


title: ESC_WT_Stag2_1


title: 20928X4 Dnmt3a Th1 Rep 3

description: Library name: 20928X4


title: 20928X5 Tet2 Th1 Rep 2

description: Library name: 20928X5


title: E1-I1V-C-PanCK-006

description:
Library name: E1-I1V-C-PanCK-006
GeoMx Nanostring


title: ESC_Stag3OEStag1Stag2dKO_Rad21_1


title: MTB20_10_V1_MTB_TCRB.tsv

description: Library name: MTB20_10_V1_MTB_TCRB.tsv


title: 20928X3 Dnmt3a Th1 Rep 2

description: Library name: 20928X3


title: MTB20_47_V1_PT_TCRB.tsv

description: Library name: MTB20_47_V1_PT_TCRB.tsv


title: E1-I1V-C-IBA1-006

description:
Library name: E1-I1V-C-IBA1-006
GeoMx Nanostring


title: 20928X2 WT Th1 Rep 3

description: Library name: 20928X2


title: ESC_Stag3OEStag1Stag2dKO_GFP_1


title: E1-I1V-M-IBA1-005

description:
Library name: E1-I1V-M-IBA1-005
GeoMx Nanostring


title: MTB20_47_V1_MTB_TCRB.tsv

description: Library name: MTB20_47_V1_MTB_TCRB.tsv


title: E1-I1V-C-PanCK-004

description:
Library name: E1-I1V-C-PanCK-004
GeoMx Nanostring


title: MTB20_40_V1_PT_TCRB.tsv

description: Library name: MTB20_40_V1_PT_TCRB.tsv


title: GSC_Stag3KO_ATAC_2

data_processing:
ATAC-seq data processing including public data was performed as previously described (Nagano et al., 2022). First, adaptor sequences were trimmed from the reads using trim galore!.
These reads were aligned using Bowtie2 v2.3.4.1 to GRCm38p3 with the “--very-sensitive -X 2000” option.
The properly mapped reads with the flag (99, 147, 83 or 163) were extracted by awk, and mitochondrial reads were excluded.
Duplicated reads were removed using MarkDuplicates command of Picard Tools v2.18.23.
These de-duplicated reads were then filtered for high quality (MAPQ≧30).
The reads whose insert size was less than 100 bp were extracted as nucleosome free region (NFR) reads.
Bed files for downstream analysis were generated by the bamtobed command of BEDTools v2.29.2 with the “-bedpe” option.
Peak calling was performed using MACS v2.1.1 with the “--nomodel --shift -100 --extsize 200 --keep-dup all” option after shifting NFR reads with the offset by +4bp in the + strand and by -5bp in the - strand.
Assembly: mm10
Supplementary files format and content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” option of deepTools v3.5.0. The blacklist regions (https://www.encodeproject.org/files/ENCFF999QPV/)  were excluded.
Supplementary files format and content: narrowPeak files describe peaks files detected by macs2

extract_protocol:
ATAC-seq experiment was performed as described previously (Nagano et al., 2022). We used FACs-sorted viable cells for FACS-sorted AAG-positive cells for GSCs. 50,000 cells were permeabilized in cold lysis buffer 1 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin (Promega)) for 3 min followed by addition of 1 ml of cold lysis buffer 2 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20). Nuclei were centrifuged and resuspended with a 50 ul of transposase reaction mixture (25 ul of 2xTD buffer (Illumina, 20034197), 2.5 ul of Transposase (Illumina, 20034197), 16.5 ul of PBS, 0.5 ul of Digitonin, 0.5 ul of Tween-20, 5 ul of DDW). After incubation at 37°C for 30 min, the tagged DNA was purified using the Minelute PCR purification kit (QIAGEN).
The purified DNA was amplified 8 cycles by a PCR reaction (NEB, M0541S) followed by size selection using AMPure XP beads (Corning) to remove primer dimers.

value: Stag3 KO


title: 20928X1 WT Th1 Rep 2

description: Library name: 20928X1


title: MTB20_16_V1_PT_TCRB.tsv

description: Library name: MTB20_16_V1_PT_TCRB.tsv


title: GSC_Stag3KO_ATAC_1


title: 20541X32 dKO Tfh Rep 1

description: Library name: 20541X32

value: Tfh

value: Dnmt3a f/f; Tet2 KO (Cre+)


title: MTB20_40_V1_MTB_TCRB.tsv

description: Library name: MTB20_40_V1_MTB_TCRB.tsv


title: E1-I1V-C-IBA1-004

description:
Library name: E1-I1V-C-IBA1-004
GeoMx Nanostring

value: kidney


title: 20541X31 Tet2 Tfh Rep 1

description: Library name: 20541X31

value: Tet2 KO (Cre+)


title: MTB20_32_V1_PT_TCRB.tsv

description: Library name: MTB20_32_V1_PT_TCRB.tsv


title: E1-CTRL-C-PanCK-003

description:
Library name: E1-CTRL-C-PanCK-003
GeoMx Nanostring

value: CTRL


title: 20541X30 Dnmt3a Tfh Rep 1

description: Library name: 20541X30

value: Dnmt3a f/f (Cre+)


title: MTB20_32_V1_MTB_TCRB.tsv

description: Library name: MTB20_32_V1_MTB_TCRB.tsv


title: E1-CTRL-C-IBA1-003

description:
Library name: E1-CTRL-C-IBA1-003
GeoMx Nanostring


title: MIX_IT_24

city: , Nueva Industrial Vallejo, Gustavo A. Madero

first: Israel

last: Lara-Vega

state: Ciudad de México, CDMX

address: v. Wilfrido Massieu 399

country: Mexico

institute: IPN

description: Library name: A24MIX_IT

data_processing:
First, the raw FASTQ files were assessed for quality using FastQC [44] (version 0.12.1 released). Low-quality reads and adapter sequences were removed using Trimmomatic [45] (version 0.39). Cleaned reads were then aligned to the Ensembl release reference mouse genome (version GRCm39) using the STAR aligner [46] (version 2.7.11b). The resulting BAM files were sorted and indexed, and gene expression levels were quantified using STAR (version 2.7.11b).
Assembly: GRCm39
Supplementary files format and content: csv file contains counts of samples

source_name: tumor

extract_protocol:
Total RNA was extracted from tumor samples using the PureLink RNA Mini Kit® (Thermo Fisher Scientific, USA), following the manufacturer’s protocol. The extracted RNA from tumor samples was subsequently used for cDNA library preparation.
cDNA libraries from tumors of mice were prepared using the Collibri™ 3′ mRNA Library Prep Kit for Illumina™ (Thermo Fisher Scientific, USA), following the recommended guide-lines for RNA purification, amplification, and library construction for bulk RNA-Seq analysis.

value: tumor

value: cancer - melanoma

value: 60mg/kg (PTX) + 3mg/kg (NCTD)

tag: batch

value: intratumoral treatment


title: MTB20_2_V1_PT_TCRB.tsv

description: Library name: MTB20_2_V1_PT_TCRB.tsv

value: PBMC

value: TCR


title: MIX_IT_22

description: Library name: A22MIX_IT


title: E1-I1V-M-PanCK-005

description:
Library name: E1-I1V-M-PanCK-005
GeoMx Nanostring


title: E1-CTRL-C-PanCK-002

description:
Library name: E1-CTRL-C-PanCK-002
GeoMx Nanostring


title: MTB20_2_V1_MTB_TCRB.tsv

description: Library name: MTB20_2_V1_MTB_TCRB.tsv


title: MIX_IT_21

description: Library name: A21MIX_IT


title: E1-CTRL-C-IBA1-002

description:
Library name: E1-CTRL-C-IBA1-002
GeoMx Nanostring


title: 20541X29 WT Tfh Rep 1

description: Library name: 20541X29

value: WT (Cre+)


title: NCTD_IT_20

description: Library name: A20NCTD_IT


title: E1-CTRL-M-PanCK-001

description:
Library name: E1-CTRL-M-PanCK-001
GeoMx Nanostring


title: NCTD_IT_19

description: Library name: A19NCTD_IT


title: 20541X26 Dnmt3a Th1 Rep 1

description: Library name: 20541X26


title: 20541X27 Tet2 Th1 Rep 1

description: Library name: 20541X27


title: NCTD_IT_18

description: Library name: A18NCTD_IT


title: E1-CTRL-M-IBA1-001

description:
Library name: E1-CTRL-M-IBA1-001
GeoMx Nanostring


title: 20541X25 WT Th1 Rep 1

description: Library name: 20541X25


title: MIX_IT_23

description: Library name: A23MIX_IT


title: MTB20_25_V3_PT_TCRB.tsv

description: Library name: MTB20_25_V3_PT_TCRB.tsv


title: ATAC-seq of CD8 Tex sgIcos cells, replicate 3

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Tex_sgIcos 3

data_processing:
Read pairs were aligned to the mm10 assembly with bowtie2 v.2.4.1 3. Multi-mapping, mitochondrial genome and duplicated reads were removed using sambamba v.0.5.6 4  and genome coverage calculation for visualization purposes on the UCSC genome browser was performed using deepTools v.3.5.5 5 excluding blacklisted regions 6.  Peaks were called for each sample with macs3 v.3.0.2 7 using parameters --nomodel --nolambda --keepdup all -q 10-7. Differential peak analysis was preformed using DiffBind v.3.12.0 8  where reads in consensus peaks were quantified within 100bp of peak summits, RLE normalization was performed on reads in peaks, and differentially accessible chromatin regions were called using the DESeq2 method with a Benjamini-Hochberg adjusted p value < 0.05 and abs(log2FoldChange) > 0.5. Significant peaks shared or specific between conditions were identified using BEDTools v.2.31.0 9 and analyzed for transcription factor motif enrichment using Homer v.4.10 10  against a background consisting of static peaks in the corresponding condition. For plotting, fold enrichment was calculated as the ratio of percentages of target and background peaks containing a given motif.
1. Li, R., Grimm, S. A. & Wade, P. A. Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression. STAR Protoc. 2, 100764 (2021). 2. Corces, M. R. et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 48, 1193–1203 (2016). 3. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). 4. Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J. & Prins, P. Sambamba: fast processing of NGS alignment formats. Bioinformatics 31, 2032–2034 (2015). 5. Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44, W160–W165 (2016). 6. Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep-uk 9, 9354 (2019). 7. Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008). 8. Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–393 (2012). 9. Quinlan, A. R. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Curr. Protoc. Bioinform. 47, 11.12.1-34 (2014). 10. Heinz, S. et al. Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol. Cell 38, 576–589 (2010).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
70,000 Tpex or Tex cells per replicate were sorted into 1.5 ml tubes precoated with MACS buffer and processed for ATAC-seq as described in 1 with modifications as follows: centrifugation was performed at 800 x g for 8 min at 4ºC in a swing-bucket rotor; the transposition mix omitted RNAse inhibitor and a volume of 50 μl was used per sample; transposed DNA was purified using a Monarch DNA cleanup kit (NEB) and eluted in 22 μl.
The optimal number of PCR cycles was determined on 2 μl of eluate and libraries were amplified and barcoded according to 2. NEBNext Ultra II Q5 mastermix (NEB) was preheated at 98ºC for 30 sec to restore its nick translation activity, then reactions were assembled on ice and amplified for 9 cycles. Libraries were cleaned up with SPRIselect beads (Beckman-Coulter) at 0.6X (right) and 1.5X (left) ratios for two-sided size selection and sequenced on the NextSeq 2000 system (Illumina) in 60bp paired-end mode at a target depth of 40M read pairs per replicate.

value: sgIcos

tag: population

value: Tex


title: NCTD_IT_17

description: Library name: A17NCTD_IT


title: Microglia, MAVS KO, infected, rep3

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

country: Germany

institute: Twincore, Centre for Experimental and Clinical Infection Research

description: Library name: Sample 12

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b). Gene abundance was also determined by STAR. Differential expression analysis was performed using DESeq2 package in R environment (version 1.26.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

source_name: Brain

extract_protocol:
The RNA from microglia was isolated using NucleoSpin® RNA Kit following manufactures instruction. RNA quality and concentrations were accessed using Bioanalyzer RNA kit and samples with RIN value >8.0 were selected for further processing.
RNA libraries for RNA-seq were prepared using NEBNext Low input RNA library Prep Kit for Illumina (NEB, E6420) following manufacturer's protocols.

value: Brain

value: Microglia

value: MAVS Knockout

value: Infected


title: ATAC-seq of CD8 Tex sgIcos cells, replicate 2

description: Library name: Tex_sgIcos 2


title: MTB20_25_V3_MTB_TCRB.tsv

description: Library name: MTB20_25_V3_MTB_TCRB.tsv


title: Microglia, MAVS KO, infected, rep2

description: Library name: Sample 11


title: ATAC-seq of CD8 Tex sgIcos cells, replicate 1

description: Library name: Tex_sgIcos 1


title: PTX_IT_15

description: Library name: A15PTX_IT


title: MTB20_25_V1_PT_TCRB.tsv

description: Library name: MTB20_25_V1_PT_TCRB.tsv


title: MTB20_25_V1_MTB_TCRB.tsv

description: Library name: MTB20_25_V1_MTB_TCRB.tsv


title: 20541X28 dKO Th1 Rep 1

description: Library name: 20541X28

value: Spleen

value: SMARTA-Tg

value: Dnmt3a f/f; Tet2 KO (Cre+)


title: PTX_IT_16

description: Library name: A16PTX_IT


title: Microglia, MAVS KO, infected, rep1

description: Library name: Sample 10


title: ATAC-seq of CD8 Tex sgCtrl cells, replicate 1

description: Library name: Tex_sgCtrl 1

value: sgCtrl


title: ATAC-seq of CD8 Tex sgCtrl cells, replicate 2

description: Library name: Tex_sgCtrl 2


title: MTB20_3_V3_PT_TCRB.tsv

description: Library name: MTB20_3_V3_PT_TCRB.tsv


title: MTB20_59_V1_PT_TCRB.tsv

description: Library name: MTB20_59_V1_PT_TCRB.tsv


title: CTRL_IT_12

description: Library name: A12CTRL_IT

value: tumor

value: DMSO


title: MTB20_59_V1_MTB_TCRB.tsv

description: Library name: MTB20_59_V1_MTB_TCRB.tsv


title: Microglia, MAVS KO, uninfected, rep3

description: Library name: Sample 9

value: Uninfected


title: Microglia, MAVS KO, uninfected, rep2

description: Library name: Sample 8


title: ATAC-seq of CD8 Tpex sgIcos cells, replicate 3

description: Library name: Tpex_sgIcos 3

value: Tpex


title: MTB20_3_V3_MTB_TCRB.tsv

description: Library name: MTB20_3_V3_MTB_TCRB.tsv

value: PBMC


title: MTB20_3_V1_PT_TCRB.tsv

description: Library name: MTB20_3_V1_PT_TCRB.tsv

value: TCR


title: Microglia, MAVS KO, uninfected, rep1

description: Library name: Sample 7


title: CTRL_IT_10

description: Library name: A10CTRL_IT

value: cancer - melanoma

value: intratumoral treatment


title: MTB20_3_V1_MTB_TCRB.tsv

description: Library name: MTB20_3_V1_MTB_TCRB.tsv


title: ATAC-seq of CD8 Tpex sgIcos cells, replicate 1

description: Library name: Tpex_sgIcos 1

value: sgIcos


title: Microglia, WT, infected, rep2

description: Library name: Sample 5

value: Brain

value: Wild Type


title: Microglia, WT, infected, rep3

description: Library name: Sample 6

value: Microglia


title: CTRL_IT_9

description: Library name: A9CTRL_IT


title: ATAC-seq of CD8 Tpex sgCtrl cells, replicate 2

description: Library name: Tpex_sgCtrl 2


title: PTX_IT_13

description: Library name: A13PTX_IT


title: MTB20_48_V1_PT_TCRB.tsv

description: Library name: MTB20_48_V1_PT_TCRB.tsv


title: MIX_IP_8

description: Library name: A8MIX_IP

value: 60mg/kg (PTX) + 3mg/kg (NCTD)

value: intraperitoneal treatment


title: Microglia, WT, infected, rep1

description: Library name: Sample 4

value: Infected


title: MTB20_48_V1_MTB_TCRB.tsv

description: Library name: MTB20_48_V1_MTB_TCRB.tsv


title: Microglia, WT, uninfected, rep3

description: Library name: Sample 3


title: Old_rep 4

city: Tokyo

first: Yasuaki

last: Mohri

address: 4-6-1 Shirokanedai, Minato-ku

institute: The Institute of Medical Science, The University of Tokyo

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software (version 6.1.1).
scRNA-seq libraries were aligned to the reference genome (mm10) using Cellranger count.
The output files from multiple samples were aggregated using the Cellranger aggr.
Quality control of all data sets was performed using the Scanpy (v1.8.2) and visualized with Loupe Cell Browser (v.6.0.0).
Assembly: mm10
Supplementary files format and content: nishimura_scRNAseq_Yamanashi_20220407_JS_20240119.h5ad

source_name: Skin

extract_protocol:
Epithelial cell suspensions were isolated from the dorsal skin of C57BL/6N mice. Subcutaneous fat was removed with a scalpel, and then the whole skin was placed dermis down in 0.25% trypsin-EDTA for 45min at 37℃ to separate the epidermis from the dermis. Single epidermal cell suspensions were obtained by gently scraping the epidermis and then filtering the cells through a cell strainer (40 µM). Dead cells were removed using the MACS Dead Cell Removal Kit.
Single-cell cDNA libraries were prepared using the Chromium Next GEM Single cell 3' Reagent Kit v3.1 (10x Genomics) according to the manufacturer's instructions.

value: Skin

value: epidermis

tag: strain

value: male


title: ATAC-seq of CD8 Tpex sgCtrl cells, replicate 1

description: Library name: Tpex_sgCtrl 1

value: sgCtrl


title: MIX_IP_7

description: Library name: A7MIX_IP

value: tumor


title: Microglia, WT, uninfected, rep2

description: Library name: Sample 2

value: Uninfected


title: ATAC-seq of CD8 Tpex sgIcos cells, replicate 2

description: Library name: Tpex_sgIcos 2

value: Tpex


title: Old_rep 3

description: 10x Genomics


title: NCTD_IP_5

description: Library name: A5NCTD_IP


title: Microglia, WT, uninfected, rep1

description: Library name: Sample 1


title: MTB20_30_V1_MTB_TCRB.tsv

description: Library name: MTB20_30_V1_MTB_TCRB.tsv

value: PBMC

value: TCR


title: MTB20_23_V1_PT_TCRB.tsv

description: Library name: MTB20_23_V1_PT_TCRB.tsv


title: CTRL_IT_11

description: Library name: A11CTRL_IT

value: cancer - melanoma

value: DMSO

value: intratumoral treatment


title: PTX_IP_4

description: Library name: A4PTX_IP


title: Old_rep 2

description: 10x Genomics


title: Old_rep 1

description: 10x Genomics


title: PTX_IP_3

description: Library name: A3PTX_IP


title: MTB20_53_V1_PT_TCRB.tsv

description: Library name: MTB20_53_V1_PT_TCRB.tsv


title: Young_rep 4

description: 10x Genomics


title: MTB20_23_V1_MTB_TCRB.tsv

description: Library name: MTB20_23_V1_MTB_TCRB.tsv


title: CTRL_IP_2

description: Library name: A2CTRL_IP

value: SALINE SOLUTION


title: MTB20_53_V1_MTB_TCRB.tsv

description: Library name: MTB20_53_V1_MTB_TCRB.tsv


title: MTB20_30_V1_PT_TCRB.tsv

description: Library name: MTB20_30_V1_PT_TCRB.tsv


title: Young_rep 3

description: 10x Genomics


title: CTRL_IP_1

description: Library name: A1CTRL_IP


title: Young_rep 2

description: 10x Genomics


title: MTB20_42_V1_PT_TCRB.tsv

description: Library name: MTB20_42_V1_PT_TCRB.tsv


title: P6_WT_M_Jejunum_L41800-1

city: Durham

first: Staci

last: Bilbo

state: North Carolina

address: 207 Research Dr, GSRB2

department: Psychology and Neuroscience

institute: Duke University

description: Library name: Sample 15

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the mouse genome (mm10)  using STAR 2.5.3.a
Reads were counted using featureCounts in the Subread package (v1.6.3)
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Intestine

extract_protocol:
The small intestine was dissected and a 2 cm segment of the region of interested was collected and opended. The flat tissue sheet was in HBSS with EDTA for ~15 mins and the epithelial cells were released by using mechanical force. Epithelial cells were washed 2 times in HBSS then snap frozen in liquid nitrogen. Total RNA was extracted using trizol.
RNA-sequencing libraries were made from ≥500ng of purified mouse intestinal cells using the Kapa Stranded mRNA-seq kit

value: Intestine

tag: tissue region

value: Jejunum

value: Male


title: P6_WT_M_Ileum_L42150-2

description: Library name: Sample 14

value: Ileum


title: P6_WT_M_Ileum_L41800-1

description: Library name: Sample 13


title: NCTD_IP_6

description: Library name: A6NCTD_IP

value: intraperitoneal treatment


title: P6_WT_F_Jejunum_L42150-1

description: Library name: Sample 12

value: Female


title: MTB20_42_V1_MTB_TCRB.tsv

description: Library name: MTB20_42_V1_MTB_TCRB.tsv


title: Young_rep 1

description: 10x Genomics

value: Skin

value: epidermis

value: male


title: Lymph node, combination treated, 2

city: Miramar

first: Varghese

last: George

state: FL

address: 2929 N Commerce Pkwy

institute: HCW Biologics

description: Library name: Lymph node, combination treated, 2

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The human GO list was used to cluster the set of genes based on their biological process and determine their statistical significance.A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Assembly: ENSEMBL STAR aligner v.2.5.2b
Supplementary files format and content: tab separated values files and matrix file

source_name: Lymph node

extract_protocol:
Total RNA was extracted using the Trizol method. Samples were quantified using Qubit 3.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Lymph node

value: WT

value: HCW9218+ anti PD1


title: P6_WT_F_Jejunum_L41800-3

description: Library name: Sample 11


title: MTB20_34_V1_PT_TCRB.tsv

description: Library name: MTB20_34_V1_PT_TCRB.tsv

value: PBMC

value: TCR


title: P6_WT_M_Jejunum_L42150-2

description: Library name: Sample 16


title: MTB20_34_V1_MTB_TCRB.tsv

description: Library name: MTB20_34_V1_MTB_TCRB.tsv


title: P6_WT_F_Ileum_L42150-1

description: Library name: Sample 10


title: P4352_8

city: Montreal

first: Marc

middle: J

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

institute: Université de Montréal

description: Library name: P4352_8

data_processing:
RNA-seq
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 40 (based on Ensembl 106)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 40
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: puromycine resistant HaCat cell population

value: immortalized human keratinocytes

value: cell population stably expressing Flag-ZnF 4x UBP

value: LPA 60 min


title: P4352_7

description: Library name: P4352_7

value: LPA 30 min


title: Lymph node, combination treated, 3

description: Library name: Lymph node, combination treated, 3


title: P6_WT_F_Ileum_L41800-3

description: Library name: Sample 9

value: Intestine


title: Lymph node, monotherapy treated, 3

description: Library name: Lymph node, monotherapy treated, 3


title: MTB20_14_V1_PT_TCRB.tsv

description: Library name: MTB20_14_V1_PT_TCRB.tsv


title: P4352_4

description: Library name: P4352_4

value: cell population stably transfected with the pMRX plasmid


title: Lymph node, monotherapy treated, 1

description: Library name: Lymph node, monotherapy treated, 1


title: Lymph node, monotherapy treated, 2

description: Library name: Lymph node, monotherapy treated, 2


title: P36_WT_M_Jejunum_AA3018

description: Library name: Sample 7

value: Jejunum

value: Male


title: MTB20_14_V1_MTB_TCRB.tsv

description: Library name: MTB20_14_V1_MTB_TCRB.tsv


title: MTB20_12_V1_PT_TCRB.tsv

description: Library name: MTB20_12_V1_PT_TCRB.tsv


title: P4352_1

description: Library name: P4352_1

value: Skin

value: LPA 0 min


title: testis_BdE_6

city: Changchun

first: Tong

last: Chen

state: Jilin

address: No. 5333, Xi'an Road, Lvyuan District

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: dEXO+Busulfan


title: P36_WT_M_Ileum_AA3023

description: Library name: Sample 6

value: Ileum


title: P36_WT_M_Ileum_AA3018

description: Library name: Sample 5


title: P4329_9

description: Library name: P4329_9


title: MTB20_5_V1_PT_TCRB.tsv

description: Library name: MTB20_5_V1_PT_TCRB.tsv


title: Lymph node, combination treated, 1

description: Library name: Lymph node, combination treated, 1

value: Lymph node

value: WT

value: HCW9218+ anti PD1


title: P36_WT_F_Jejunum_AA3022

description: Library name: Sample 4

value: Female


title: testis_BdE_5


title: MTB20_5_V1_MTB_TCRB.tsv

description: Library name: MTB20_5_V1_MTB_TCRB.tsv

value: PBMC

value: TCR


title: P36_WT_F_Jejunum_AA3021

description: Library name: Sample 3


title: P4329_8

description: Library name: P4329_8

value: puromycine resistant HaCat cell population

value: immortalized human keratinocytes

value: cell population stably expressing Flag-ZnF 4x UBP


title: testis_BE_8

value: EXO+Busulfan


title: MTB20_24_V3_PT_TCRB.tsv

description: Library name: MTB20_24_V3_PT_TCRB.tsv


title: P36_WT_F_Ileum_AA3022

description: Library name: Sample 2

value: Intestine


title: testis_BE_7


title: P4352_5

description: Library name: P4352_5


title: P36_WT_M_Jejunum_AA3023

description: Library name: Sample 8

value: Jejunum

value: Male


title: P4329_6

description: Library name: P4329_6

value: Skin

value: LPA 0 min


title: MTB20_24_V3_MTB_TCRB.tsv

description: Library name: MTB20_24_V3_MTB_TCRB.tsv


title: MTB20_12_V1_MTB_TCRB.tsv

description: Library name: MTB20_12_V1_MTB_TCRB.tsv


title: P4352_3

description: Library name: P4352_3

value: cell population stably transfected with the pMRX plasmid

value: LPA 30 min


title: MTB20_24_V1_PT_TCRB.tsv

description: Library name: MTB20_24_V1_PT_TCRB.tsv


title: testis_BE_6

value: testis


title: testis_BP_7

value: PBS+Busulfan


title: P36_WT_F_Ileum_AA3021

description: Library name: Sample 1

value: Ileum


title: P4329_3

description: Library name: P4329_3


title: testis_BdE_7

value: dEXO+Busulfan


title: all mix sample 8

description:
Library name: E12K8
Parse Bioscience

data_processing:
The resulting FASTQ files were analyzed using the Parse Biosciences data analysis pipeline (v1.1) (https://www.parsebiosciences.com) which demultiplexes reads and assigns cells and samples. Reads were aligned to the mouse genome (mm10).
Assembly: Mouse mm10
Supplementary files format and content: .csv, .mtx

extract_protocol:
Euthanized mice were perfused with chilled 1× PBS via the left ventricle. After removing the renal capsule and fat, kidneys were minced into approximately 1 mm3 cubes and digested using Multi-Tissue Dissociation kit (Miltenyi, 130-110-201). Up to 250 mg of tissue was digested with 50 μl of enzyme D, 25 μl of enzyme R, and 6.75 μl of enzyme A in 1 ml of RPMI and incubated for 30 min at 37 °C. Digestion was deactivated by 10% fetal bovine serum (FBS). The suspension was passed through a 70 μm cell strainer. After centrifugation at 400 ×g for 5 min, cell pellet was incubated with 1 ml of RBC lysis buffer on ice for 3 min and washed again. Cells were resuspended in PBS and passed through a 40 μm cell strainer. Cells were resuspended in staining buffer (1× PBS, 1% BSA, 2 mM EDTA) for further analysis.
Kidneys were collected from C57BL/6 mice subjected to ischemia-reperfusion injury (IRI) or left untreated as controls (n=3 per condition). Single-cell suspensions were prepared from pooled kidneys (3 mice per condition), and live leukocytes were enriched by fluorescence-activated cell sorting (FACS) using SYTOX™ Blue exclusion and forward/side scatter gating. Cell viability was confirmed by Trypan Blue exclusion (>80%). Live cells were fixed using the Evercode™ Cell Fixation Kit (V2) (Parse Biosciences) and stored at –80 °C. Fixed cells were thawed and processed with the Evercode™ WT (V2) kit for single-cell library preparation according to manufacturer protocols. Libraries were sequenced at ~50,000 reads per cell on a NovaSeq 6000 platform (Illumina) with 5% PhiX spike-in, performed by Novogene.

treatment_protocol: ischemia reperfusion injury +/- entospletinib

value: kidney


title: all mix sample 7

description:
Library name: E12K7
Parse Bioscience


title: testis_BP_6


title: MTB20_17_V3_PT_TCRB.tsv

description: Library name: MTB20_17_V3_PT_TCRB.tsv

value: PBMC

value: TCR


title: P4329_1

description: Library name: P4329_1

value: puromycine resistant HaCat cell population

value: immortalized human keratinocytes


title: MTB20_24_V1_MTB_TCRB.tsv

description: Library name: MTB20_24_V1_MTB_TCRB.tsv


title: Differentiated, KDi, biol rep 3

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

institute: NIAID

description:
Library name: Sample 8
D3_KDi_3_S8

data_processing:
Eight ATAC samples were pooled and subjected to 2 x 100 bp paired-end read sequencing on the Illumina NextSeq 2000 P2 platform
All the samples had Q30 bases above 93% and yields between 103 and 141 million pass filter reads.
Reads were trimmed for adapters using Cutadapt v1.18 and aligned to the human reference genome using Bowtie 2 v2.3.4.1 with flag -k 10
Peaks were called using Genrich v0.6 (https://github.com/jsh58/Genrich) with the following flags: -j -y -r -v -d 150 -m 5 -e chrM, chrY. Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
Assembly: hg19
Supplementary files format and content: BigWig files of ATAC-seq peaks.

growth_protocol: CIN612-9E cervical keratinocytes were grown in Rheinwald-Green F-medium (3:1 Ham’s F-12/high-glucose Dulbecco’s modified Eagle’s medium [DMEM], 5% fetal bovine serum [FBS], 0.4 µg/ml hydrocortisone, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 2mM glutamine, 6 µg/ml insulin, 100 U/ml penicillin, and 100 µg/ml streptomycin) on a layer of lethally irradiated J2/3T3 mouse fibroblast cells. J2/3T3 fibroblasts were grown in DMEM, 10% newborn calf serum, 2 mM glutamine,100 U/ml penicillin, and 100 µg/ml streptomycin. For ATAC-seq, cells were seeded onto 10 cm plates at 6x10e5 and 1.5x10e6 cells per plate for the growing and differentiated conditions, respectively. Cells were cryopreserved in 5% DMSO/F-media two- (growing cells) and seven-days (differentiated cells) post-seeding. For cellular differentiation, confluent cells were cultured in complete KGM™ Keratinocyte Growth Medium (Lonza, CC-4131), excluding GA-1000, for 24 hours and then cultured in KBM™ Keratinocyte Basal Medium (Lonza, CC-3101) supplemented with 1.5 mM CaCl2 for 72 hours.

extract_protocol:
Omni-ATAC protocol, https://doi.org/10.1038/nmeth.4396
Omni-ATAC protocol, https://doi.org/10.1038/nmeth.4397

treatment_protocol: Differentiated cells were stimulated with 0.5 µM keratinocyte differentiation inducer (KDi, CK2 inhibitor IV, Santa Cruz, CAS 863598-09-8, Sc-311368, lot E3012) or DMSO vehicle control for 48 hours prior to harvesting total RNA.

value: HPV31-positive cervical keratinocytes

value: WT

value: 0.5 µM keratinocyte differentiation inducer (KDi), differentiated cells

tag: time

value: 48 hour KDi; 72 hour Ca2+


title: all mix sample 6

description:
Library name: E12K6
Parse Bioscience