title: Total RNA-sequencing of C636-NL cells uninfected

description: Library name: AeAlb_C636_Mock_lRNA


title: Small RNA-sequencing of C636-ATCC cells uninfected (rep2)

status: Public on Nov 23 2025

type: SRA

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

country: USA

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: AeAlb_C636-ATCC_2_sRNA

library_source: other

data_processing:
The Mosquioto Small RNA Genomics (MSRG)  pipeline published in PMIDs: 33419731 and 35796973. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt and Trimmomator. Total RNA reads were also further trimmed by length to 35 nt to be compatable for processing with the MSRG pipeline
Assembly: AaegL5
Supplementary files format and content: tab-delimited text file with Excel extension includes processed counts for each Sample for microRNA genes or protein-coding genes. csv files include RPM values for each Sample mapped to viruses

molecule: other

organism: Aedes albopictus

extract_protocol:
RNA was harvested using the NEB Monarch Total RNA extration kit.  0.5 to 1.0ug of total RNA was used for the construction of sequencing libraries.
Total RNA libraries for RNA-seq were prepared using Zymo RiboFree Zymo-Seq Library Prep Kit following manufacturer's protocols.  Small RNA libraries for microRNA-seq were prepared with the NEBNext Small RNA Library prep kit according to the manufacturer's protocols.

tag: cell line


title: Small RNA-sequencing of whole mosquito: AutoFL_MDC_Fem_1A

description: Library name: AutoFL_MDC_Fem_1A_sRNA

organism: Aedes aegypti

source_name: whole mosquito

tag: tissue

value: whole mosquito


title: Small RNA-sequencing of C636-ATCC cells uninfected (rep1)

description: Library name: AeAlb_C636-ATCC_sRNA


title: NTVKO PCGF1 KO SGC0946 3uM rep3

city: Melbourne

first: Daniel

last: Neville

state: Victoria

address: 99 Commercial Road Level 6, Alfred Centre

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

library_source: transcriptomic

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to mouse or human genome with STAR aligner
Differential expression analysis was performed using Degust (DEseq2)
Assembly: mm10 and hg38
Supplementary files format and content: .

molecule: total RNA

organism: Mus musculus

source_name: Blood

extract_protocol:
Bioline RNA extraction kit
3' Poolseq or 3' Lexogen library prep for Illumina

value: Blood

tag: cell type

value: Myeloid

tag: treatment


title: Small RNA-sequencing of C636-NL cells infected with PZR mosquitoes

description: Library name: AeAlb_C636-NL_PZR_sRNA


title: hKCs_C_24h_3

city: Kaifeng City, Henan Province

first: Hua

last: Yang

state: Henan Province

address: Jinming Campus of Henan University

country: China

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these

organism: Homo sapiens

source_name: keratinocytes

growth_protocol:
mDRGs were isolated from C57BL/6 mice and dissociated by collagenase I, as previously described . Cells were cultured in the presence of 10 µM cytosine β-d-arabinofuranoside and nerve growth factor (100 ng/ml) for 7 days in order to remove non-neuronal cells and enrich neurons in vitro before use for RNA-seq.
phKCs were seeded into 24 well plates and cultured in KBM-Gold medium with KBM  Gold SingleQuot KC supplement (Lonza, Basel, Switzerland). Cells were maintained in the  above medium for 3 days before use.

extract_protocol:
Remove the upper medium and wash it twice with cold PBS, frozen on ice, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol:
mDRGs were treated with UII(1UM) for 6h
phKCs were treated with UII(1UM) for 24h

value: keratinocytes

value: Vehicle


title: Small RNA-sequencing of whole mosquito: AutoFL_MDC_Fem_1C

description: Library name: AutoFL_MDC_Fem_1C_sRNA


title: Small RNA-sequencing of C636-NL cells uninfected (rep3)

description: Library name: AeAlb_C636-NL_Mock_3_sRNA


title: NTVKO PCGF1 KO DMSO rep3


title: NTVKO Control - VTP50469 8h 300nM rep2


title: Small RNA-sequencing of C636-NL cells uninfected

description: Library name: AeAlb_C636-NL_Mock_sRNA


title: Small RNA-sequencing of C636-NL cells infected with KIN mosquitoes (rep3)

description: Library name: AeAlb_C636-NL_KIN_3_sRNA


title: Small RNA-sequencing of C636-NL cells infected with KIN mosquitoes (rep4)

description: Library name: AeAlb_C636-NL_KIN_4_sRNA


title: hKCs_C_24h_1


title: NTVKO Control - VTP50469 48h 300nM rep2


title: Small RNA-sequencing of C636-NL cells infected with KIN mosquitoes

description: Library name: AeAlb_C636-NL_KIN_sRNA


title: hKCs_hUII_24h_2

value: UII activated


title: NTVKO Control - SGC0946 3uM rep2


title: Small RNA-sequencing of C636-NL cells infected with AWK mosquitoes (rep4)

description: Library name: AeAlb_C636-NL_AWK_4_sRNA


title: Small RNA-sequencing of C636-NL cells infected with BZL mosquitoes

description: Library name: AeAlb_C636-NL_BZL_sRNA


title: Small RNA-sequencing of C636-NL cells infected with BZL mosquitoes (rep4)

description: Library name: AeAlb_C636-NL_BZL_4_sRNA


title: NTVKO PCGF1 KO VTP50469 48h 300nM rep3


title: Small RNA-sequencing of C636-NL cells infected with PZR mosquitoes (rep4)

description: Library name: AeAlb_C636-NL_PZR_4_sRNA


title: hKCs_hUII_24h_3


title: Total RNA-sequencing of C636-ATCC cells infected with PZR mosquitoes

description: Library name: AeAlb_C636-ATCC_PZR_lRNA


title: Small RNA-sequencing of C636-NL cells infected with AWK mosquitoes (rep3)

description: Library name: AeAlb_C636-NL_AWK_3_sRNA


title: Small RNA-sequencing of C636-NL cells infected with AWK mosquitoes

description: Library name: AeAlb_C636-NL_AWK_sRNA


title: Total RNA-sequencing of C636-ATCC cells infected with KIN mosquitoes

description: Library name: AeAlb_C636-ATCC_KIN_lRNA


title: hKCs_hUII_24h_1


title: NTVKO PCGF1 KO VTP50469 48h 300nM rep2


title: NTVKO PCGF1 KO VTP50469 8h 300nM rep2


title: Total RNA-sequencing of C636-ATCC cells infected with BZL mosquitoes

description: Library name: AeAlb_C636-ATCC_BZL_lRNA


title: hKCs_C_24h_2


title: Total RNA-sequencing of C636-ATCC cells uninfected

description: Library name: AeAlb_C636-ATCC_Mock_lRNA


title: NTVKO Control - DMSO rep2


title: Total RNA-sequencing of C636-ATCC cells infected with AWK mosquitoes

description: Library name: AeAlb_C636-ATCC_AWK_lRNA


title: Total RNA-sequencing of Aag2 cells infected with PZR mosquitoes (rep4)

description: Library name: AeAeg_Aag2_PZR_4_lRNA


title: Total RNA-sequencing of Aag2 cells infected with BZL mosquitoes (rep4)

description: Library name: AeAeg_Aag2_BZL_4_lRNA


title: Total RNA-sequencing of Aag2 cells infected with AWK mosquitoes (rep4)

description: Library name: AeAeg_Aag2_AWK_4_lRNA


title: NTVKO PCGF1 KO DMSO rep2


title: CR_CCR_J1_d14

city: Amsterdam

first: Afroditi

last: Katsarou

address: De Boelelaan 1117

department: Department of Hematology

country: Netherlands

institute: Amsterdam UMC location Vrije Universiteit Amsterdam

description: Library name: CR_CCR_J1_d14.fastq

data_processing:
Paired-end reads were trimmed using Trimmomatic 0.39 before mapping to the human transcriptome (Gencode v42) using Salmon 1.9.0
Mapping results were imported in R 4.4.0 using the Tximeta 1.22.1 package and features were annotated using biomaRt 2.60.0.
Assembly: GRCh38.p13
Supplementary files format and content: .xlsx include counts matrix
Supplementary files format and content: .xlsx include tpm values

source_name: T cell

extract_protocol:
RNA isolation was performed with RNeasy Plus Mini kit (Qiagen)
Libraries were sequenced with the Illumina SBS technology at a sequencing depth of at least 75 million per sample (Macrogen)

value: T cell

tag: batch

value: Day 14


title: CR_CCR_J3_d0

description: Library name: CR_CCR_J3_d0.fastq

value: Day 0


title: Total RNA-sequencing of Aag2 cells infected with KIN mosquitoes (rep4)

description: Library name: AeAeg_Aag2_KIN_4_lRNA


title: Total RNA-sequencing of Aag2 cells uninfected (rep4)

description: Library name: AeAeg_Aag2_Mock_4_lRNA


title: CR_CCR_J1_d0

description: Library name: CR_CCR_J1_d0.fastq


title: NTVKO Control - VTP50469 48h 300nM rep1


title: CR_CCR_D2_d14

description: Library name: CR_CCR_D2_d14.fastq


title: CR_CCR_D2_d0

description: Library name: CR_CCR_D2_d0.fastq


title: HT-29 tumor_ALA100_20 Gy Fr X-ray_3

type: RNA

city: Kitakyushu

first: Junko

last: Takahashi

state: Fukuoka

address: 2-7 Hibikino, Wakamatsu-ku

department: Graduate School of Information, Production and Systems

country: Japan

institute: Waseda University

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, 10 daily administrations of 100 mg/kg 5-ALA followed by fractionated X-ray irradiation (2 Gy/day, total 20 Gy) (A100-20XT).

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent- G4112F Whole Human Genome Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20200924) to obtain background subtracted and spatially detrended processed signal intensities. The quantile normalization method was used in our microarray analysis.

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-20XT rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the RNeasy mini kit from HT-29 tumor preserved in RNAlater (Qiagen). Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAlater conservation at -80ºC

value: tumor

tag: Sex

value: female


title: HT-29 tumor_ALA control_1

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, single administration of 5-aminolevulinic acid (5-ALA) without irradiation (ALAT).

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, ALAT rep1


title: HT-29 tumor_ALA100_20 Gy Fr X-ray_1

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-20XT rep1


title: HT-29 tumor_ALA200_12 Gy X-ray_4

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, 200 mg/kg 5-ALA treatment followed by 12 Gy single-dose X-ray irradiation (A200-XT).

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A200-XT rep4


title: NTVKO PCGF1 KO SGC0946 3uM rep2


title: CR_CAVIR_J3_d14

description: Library name: CR_CAVIR_J3_d14.fastq


title: CR_CAVIR_J3_d0

description: Library name: CR_CAVIR_J3_d0.fastq


title: NTVKO Control - DMSO rep1


title: NTVKO Control - VTP50469 8h 300nM rep1


title: HT-29 tumor_ALA200_12 Gy X-ray_2

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A200-XT rep2


title: HT-29 tumor_ALA200_12 Gy X-ray_1

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A200-XT rep1


title: HT-29 tumor_ALA100_12 Gy X-ray_2

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, 100 mg/kg 5-ALA treatment followed by 12 Gy single-dose X-ray irradiation (A100-XT).

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-XT rep2


title: CR_CCR_J3_d14

description: Library name: CR_CCR_J3_d14.fastq


title: HT-29 tumor_ALA100_12 Gy X-ray_4

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-XT rep4


title: HT-29 tumor_ALA100_20 Gy Fr X-ray_2

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-20XT rep2


title: NTVKO PCGF1 KO SGC0946 3uM rep1


title: NTVKO PCGF1 KO VTP50469 8h 300nM rep1


title: CR_CAVIR_J1_d0

description: Library name: CR_CAVIR_J1_d0.fastq


title: NTVKO Control - SGC0946 3uM rep1


title: CR_CAVIR_J1_d14

description: Library name: CR_CAVIR_J1_d14.fastq


title: HT-29 tumor_ALA100_12 Gy X-ray_3

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-XT rep3


title: HT-29 tumor_ALA100_12 Gy X-ray_1

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A100-XT rep1


title: HT-29 tumor_12 Gy_X-ray_4

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, single-dose 12 Gy X-ray irradiation alone (XT).

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, XT rep4


title: HT-29 tumor_12 Gy_X-ray_3

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, XT rep3


title: CR_CAVIR_D2_d14

description: Library name: CR_CAVIR_D2_d14.fastq


title: Neutrophils TL1A ILC3s supernatant 3

city: New York

first: Silvia

last: Pires

address: 413E 69th st

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.  After trimming the adaptors with cutadapt (version1.18) (https://cutadapt.readthedocs.io/en/v1.18/), RNA reads were aligned and mapped to the GRCm38 mouse reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR). and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/).  The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Assembly: GRCm38 mouse reference genome
Supplementary files format and content: excel file includes normalized counts for each sample

source_name: bone marrow

extract_protocol:
RNA was extracted and purified using RNeasy Plus Mini Kit (Qiagen)
libraries were generated using SMART-Seq® v4 Ultra® Low Input RNA Kit

value: bone marrow

value: neutrophils

tag: genotype

value: WT

value: stimulated for 18h with either IL-23 and TL1A


title: NTVKO PCGF1 KO DMSO rep1

source_name: Blood


title: HT-29 tumor_12 Gy_X-ray_1

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, XT rep1


title: MSC-ATAC-SEQ force- 2

city: Chengdu

first: Li

last: Liao

state: Sichuan

address: No. 24, South Section 1, First Ring Road

institute: SiChuan University

description: Library name: force- 2

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the human genome reference sequence (hg38) using the BWA-MEM algorithm. To ensure data quality, duplicate reads were removed and reads with a MAPQ score below 30 were excluded. Additionally, genomic regions listed in the ENCODE blacklisted regions were omitted from the analysis.
Assembly: GRCh38
Supplementary files format and content: Force(-)-1.bw.gz, Force(-)-2.bw.gz, Force(+)-1.bw.gz, Force(+)-2.bw.gz, senescent-1.bw.gz, senescent-2.bw.gz, young_1.bw.gz, young_2.bw.gz

molecule: genomic DNA

source_name: BMSC

extract_protocol:
50,000 cells were used. Cells were washed twice with ice-cold 1× TW buffer (500 × g, 4 °C), resuspended in precooled lysis buffer, and incubated on ice for 5 min. After centrifugation at 500 × g for 5 min, the supernatant was removed, and the cell pellet was resuspended in a precooled Tn5 transposome/transposition reaction mix. The reaction mix was gently vortexed to ensure uniform distribution and incubated at 37 °C for 30 min to facilitate tag mentation. The reaction was terminated by adding a stop buffer, and the fragmented DNA was purified using VAHTS DNA Clean Beads, including two washes with 80% ethanol. The DNA was finally eluted in 26 μL of nuclease-free water.
Library amplification was performed under the following conditions: initial denaturation at 72°C for 3 min and 95°C for 3 min, followed by 14 PCR cycles (98°C for 10 s, 60°C for 5 s, 72°C for 1 min), with a final extension at 72°C for 1 min and a hold at 12°C. The amplified libraries were further purified with VAHTS DNA Clean Beads, washed twice with 80% ethanol, and eluted in 22 μL of nuclease-free water. Sequencing was conducted on an Illumina NovaSeq platform (150-bp paired-end reads), generating approximately 8 Gb of data per library. Read quality was evaluated using FastQC (v0.11.9), and sequencing services were provided by Berry Genomics Co., Ltd (China).

value: BMSC

value: softening


title: HT-29 tumor_control_4

description: Gene expression analysis performed on HT-29 xenograft tumor from Balb/c nu/nu mouse, no treatment (NT).

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, NT rep4


title: HT-29 tumor_control_3

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, NT rep3


title: Neutrophils TL1A ILC3s supernatant 2


title: HT-29 tumor_control_2

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, NT rep2


title: HT-29 tumor_control_1

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, NT rep1


title: MSC-ATAC-SEQ force- 1

description: Library name: force- 1


title: Neutrophils TL1A ILC3s supernatant 1


title: MSC-ATAC-SEQ young 2

description: Library name: young 2

value: non


title: mDRG_6h_C_3

source_name: mouse dorsal root ganglion neuronal cells


title: Neutrophils ILC3s supernatant 3

value: stimulated for 18h with ILC3s supernatants


title: mDRG_6h_C_2

value: mouse dorsal root ganglion neuronal cells


title: Neutrophils ILC3s supernatant 2


title: MSC-ATAC-SEQ young 1

description: Library name: young 1


title: CR_CAVIR_D2_d0

description: Library name: CR_CAVIR_D2_d0.fastq

source_name: T cell


title: Neutrophils ILC3s supernatant 1


title: HT-29 tumor_12 Gy_X-ray_2

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, XT rep2


title: MSC-ATAC-SEQ force+ 2

description: Library name: force+ 2

value: stretching


title: mDRG_6h_C_1

value: Vehicle


title: MSC-ATAC-SEQ force+ 1

description: Library name: force+ 1


title: Neutrophils control 3

value: unstimulated


title: MSC-ATAC-SEQ senescent-2

description: Library name: senescent-2


title: Piezo1-deficient CMT-93, ssRNA stimulated

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

hyb_protocol: Hybridization was done by using Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instruction.

scan_protocol: Scanning was performed by Agilent Microarray Scanner with 3 micro meter Scan Resolution and 20 bit TIFF dynamic range.

data_processing: Spot intensities were measured by using Agilent Feature Extraction 11.0.1.1. Array probes with Flag A in the samples were filtered out. Selected gProcessedSignal values were transformed by logarithm to base 2 and normalized by the quantile method

source_name: CMT-93 cell line

label_protocol: Labelling was performed by using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instruction.

growth_protocol: Cells were grown in DMEM supplemneted with 10 % FCS.

extract_protocol: Total RNA was extracted by using TRIzol reagent (Invitrogen).

treatment_protocol: Cells were stimulated with 25microG/mL ssRNA40 or 10 microM Yoda-1 for 24 hours.

value: Piezo 1-deficient

value: ssRNA stimulated


title: Neutrophils control 2


title: Wild-type CMT-93, Yoda-1 stimulated

value: wild type

value: Yoda-1 stimulated


title: MSC-ATAC-SEQ senescent-1

description: Library name: senescent-1


title: Piezo1-deficient CMT-93, Yoda-1 stimulated


title: mDRGUII_6h_1

value: UII activated


title: H1498

status: Public on Nov 22 2025

city: Memphis

first: Robert

middle: W

last: Williams

state: TN

address: 71 South Manassas

department: Genetics Genomics and Informatics

description: Library name: Sample 148

data_processing:
Raw fastq files were aligned to the reference mouse genome using STAR version 2.6.0c, using the UCSC genome assembly version GRCm38 (mm10). An average of 86.4±2.6% of reads were mapped per sample. Reads were counted using RSeQC version 2.6.4. Read counts were normalized to RPKM values using gene lengths from ENSEMBL82 v2015-10-02. All RNA-seq data were then scaled by adding 1 to the normalized counts and then taking the log2.
mm10
Assembly: RNA-seq and RNA integrity (RIN) checks were performed by an Agilent 2100 Bioanalyzer, and samples with RIN ≥ 6 were retained for RNA-seq, which was run on a NovoGene HiSeq 3000 with 150 bp end paired reads after polyA+ enrichment at the University of Tennessee Health Science Center transcriptomics platform. Samples were measured with an average of 24±2.7 million reads (mean±standard deviation).
Supplementary files format and content: Raw fastq files were aligned to the reference mouse genome using STAR version 2.6.0c, using the UCSC genome assembly version GRCm38 (mm10). An average of 86.4±2.6% of reads were mapped per sample. Reads were counted using RSeQC version 2.6.4. Read counts were normalized to RPKM values using gene lengths from ENSEMBL82 v2015-10-02. All RNA-seq data were then scaled by adding 1 to the normalized counts and then taking the log2.

source_name: Liver

extract_protocol:
Tissue collection started at approximately 9 am with the anesthetic Avertin used via intraperitoneal injection of 0.2 mL per 10 g of body weight. Animals were perfused with ice-cold phosphate-buffered saline. The liver was the first organ harvested. The gall bladder was removed, the liver weighed, and then immediately frozen in liquid nitrogen in 20 mL scintillator vials. Roughly 20 mg of pre-pulverized liver tissue was mixed with 1 mL of TRIzol reagent at 4°C for RNA extraction. The sample was then further homogenized in TRIzol with a metallic bead for 2x30s at 25 Hz. The homogenate was transferred to a new tube (without the bead) and 200 µL of chloroform was added and mixed. Samples were centrifuged at 12,000g for 15 minutes at 4°C. ~400 µL of the clear top phase was taken and added to a tube with 400 µL isopropanol, followed by vortexing and the same centrifugation. The RNA pellet was observed and the liquid was discarded. The RNA pellet was resuspended in ethanol by pipetting, then the samples were centrifuged again. The ethanol was removed and the sample was air dried and quantified by Nanodrop. Next, samples were cleaned up using the RNEasy MinElute kits (Qiagen) as per manufacturing instructions.
RNA-seq and RNA integrity (RIN) checks were performed by an Agilent 2100 Bioanalyzer, and samples with RIN ≥ 6 were retained for RNA-seq, which was run on a NovoGene HiSeq 3000 with 150 bp end paired reads after polyA+ enrichment at the University of Tennessee Health Science Center transcriptomics platform. Samples were measured with an average of 24±2.7 million reads (mean±standard deviation).

value: Liver

tag: caseid

tag: eartag

tag: age

tag: strain

value: F

value: HF


title: H1361

institute: University of Tennessee Health Science Center

description: Library name: Sample 150


title: H1363

description: Library name: Sample 149

value: CD


title: H1499

description: Library name: Sample 147


title: H1422

description: Library name: Sample 144


title: H0468

description: Library name: Sample 146


title: H2114

description: Library name: Sample 143


title: H2085

description: Library name: Sample 142


title: Wild-type CMT-93, mock treated

value: mock


title: mDRGUII_6h_3


title: H1187

description: Library name: Sample 139


title: H0248

description: Library name: Sample 141


title: H0247

description: Library name: Sample 140


title: mDRGUII_6h_2


title: Piezo1-deficient CMT-93, mock treated


title: H1355

description: Library name: Sample 137


title: H1190

description: Library name: Sample 138


title: Neutrophils control 1

value: bone marrow

value: neutrophils

value: WT


title: H1354

description: Library name: Sample 136


title: H1524

description: Library name: Sample 135


title: H1769

description: Library name: Sample 134


title: H1275

description: Library name: Sample 133


title: Wild-type CMT-93, ssRNA stimulated


title: H1273

description: Library name: Sample 131


title: H1702

description: Library name: Sample 128


title: H0883

description: Library name: Sample 129


title: H0881

description: Library name: Sample 130


title: H0756

description: Library name: Sample 126


title: H1093

description: Library name: Sample 127


title: H1425

description: Library name: Sample 145


title: H0555

description: Library name: Sample 124


title: H0736

description: Library name: Sample 125


title: Total RNA-sequencing of C636-NL cells infected with AWK mosquitoes

description: Library name: AeAlb_C636_AWK_lRNA


title: H0176

description: Library name: Sample 123


title: H1321

description: Library name: Sample 122


title: H0550

description: Library name: Sample 121


title: H0296

description: Library name: Sample 118


title: H1945

description: Library name: Sample 119


title: H0243

description: Library name: Sample 120


title: H0825

description: Library name: Sample 117


title: H0583

description: Library name: Sample 115


title: H1866

description: Library name: Sample 113


title: Total RNA-sequencing of C636-NL cells infected with BZL mosquitoes

description: Library name: AeAlb_C636_BZL_lRNA


title: H1555

description: Library name: Sample 116


title: H0183

description: Library name: Sample 112


title: H1742

description: Library name: Sample 132


title: H1398

description: Library name: Sample 114


title: H1545

description: Library name: Sample 110


title: H1466

description: Library name: Sample 109


title: H2071

description: Library name: Sample 108


title: H1906

description: Library name: Sample 105


title: H1447

description: Library name: Sample 107


title: H1451

description: Library name: Sample 106


title: H1855

description: Library name: Sample 103


title: H1512

description: Library name: Sample 102


title: H1728

description: Library name: Sample 101


title: H2142

description: Library name: Sample 100


title: H0591

description: Library name: Sample 97


title: H1087

description: Library name: Sample 99


title: H1328

description: Library name: Sample 98


title: H1290

description: Library name: Sample 94


title: H1080

description: Library name: Sample 93


title: H2128

description: Library name: Sample 91


title: H1793

description: Library name: Sample 85


title: H1713

description: Library name: Sample 88


title: H2124

description: Library name: Sample 92


title: H1766

description: Library name: Sample 87


title: H1790

description: Library name: Sample 86


title: H0458

description: Library name: Sample 83


title: H2098

description: Library name: Sample 84


title: H1787

description: Library name: Sample 81


title: H1560

description: Library name: Sample 89


title: H1715

description: Library name: Sample 80


title: H1784

description: Library name: Sample 82


title: H0188

description: Library name: Sample 104


title: H1416

description: Library name: Sample 78


title: H1414

description: Library name: Sample 77


title: H1071

description: Library name: Sample 96


title: H2091

description: Library name: Sample 75


title: H1436

description: Library name: Sample 73


title: H1847

description: Library name: Sample 74


title: H1558

description: Library name: Sample 90


title: H1722

description: Library name: Sample 70


title: H1068

description: Library name: Sample 95


title: H1770

description: Library name: Sample 68


title: H1843

description: Library name: Sample 67


title: H0184

description: Library name: Sample 111


title: H0235

description: Library name: Sample 65


title: H1841

description: Library name: Sample 66


title: H0171

description: Library name: Sample 64


title: H0833

description: Library name: Sample 62


title: H0818

description: Library name: Sample 79


title: H0848

description: Library name: Sample 63


title: H0210

description: Library name: Sample 61


title: H1872

description: Library name: Sample 76


title: H1835

description: Library name: Sample 56


title: H2054

description: Library name: Sample 58


title: H1377

description: Library name: Sample 55


title: H0209

description: Library name: Sample 60


title: H2046

description: Library name: Sample 57


title: H1762

description: Library name: Sample 54


title: H1940

description: Library name: Sample 53


title: H1826

description: Library name: Sample 52


title: H1825

description: Library name: Sample 51


title: H1922

description: Library name: Sample 69


title: H1315

description: Library name: Sample 71


title: HT-29 tumor_ALA200_12 Gy X-ray_3

source_name: HT-29 xenograft tumor in male Balb/c nu/nu mouse, A200-XT rep3

value: tumor

value: female


title: H1822

description: Library name: Sample 50


title: H1434

description: Library name: Sample 72


title: H1501

description: Library name: Sample 49


title: Enriched population, Transposition induced, 45 hr

city: Gwangju

first: YongHee

last: Han

address: 77 Yongbong-ro

department: School of Biological Sciences and Technology

country: South Korea

institute: Chonnam National University

data_processing:
To improve the efficiency of read alignment and ensure a sufficient number of reads for subsequent analysis, reads containing more than 10 consecutive ITR bases were filtered from the demultiplexed raw data (Cutadapt option: -a ITR=TGGATGATAA -O 10). The remaining ITR sequences at the 3’ end of the reads were then trimmed, leaving only the genomic DNA sequences (Cutadapt option: -u -6). Given the genome size (~5 Mbps) and the potential for very short reads to align at multiple genomic locations, reads containing genomic DNA sequences longer than 12 bp were filtered out from the ITR-removed reads (Cutadapt option: -m 12). The final processed reads were aligned to the genome of E. coli BL21(DE3) using Bowtie version 1.2.2 with default settings. Genomic annotations and Tn-seq signals were visualized for direct comparison using MetaScope and Circos version 0.69.8.
From the Bowtie alignment result file (BAM file), we counted the reads clustered in individual regions where transposition occurred and selected candidate genes for knockout. We used the Python script (localPNC.py) that is freely available at the public GitHub repository (https://github.com/SBML-Kimlab/DiffExo), with slight modifications for read counting. Initially, we defined transposon regions (Tn regions) as genomic areas where several reads overlapped or were adjacent to one another. Using the start and end positions of each Tn region from the Bowtie-aligned data, we counted and listed the number and location of the aligned reads.
Assembly: Escherichia coli BL21(DE3), Genbank accession number NC_012971.2
Supplementary files format and content: The information of aligned reads indicating genome-wide transposition sites, GFF format

organism: Escherichia coli

source_name: Escherichia coli

extract_protocol:
Genomic DNA was extracted from both control and enriched populations using a GeneAll Exgene™ Cell SV kit (GeneAll Biotechnology, Seoul, Korea).
The extracted gDNA was digested with the restriction enzyme MmeI. The digested DNA fragments, which include a short adjacent region of the Himar1 transposon insertion site, were ligated to an adapter with an NN tail. The adapter-ligated DNAs were used as a template for amplification, with the Tn-IR-P7 primer (which primes the transposon inverted repeat and includes an overhang for the P7 sequence) and the Adapter-P5 primer (which primes the adaptor and includes the P5 sequence). This produced the Tn-seq libraries for Illumina sequencing. The constructed libraries were validated using X-Mark LabChip with the DNA NGS 3K reagent kit (PerkinElmer, Waltham, MA, USA). The concentration of the libraries was measured using Qubit™ dsDNA Quantification Assay Kit (Thermo, Waltham, MA, USA).

value: Escherichia coli

value: IPTG (1 mM) and p-coumaric acid (100 mg/L) were added at the start of cultivation to induce the naringenin pathway. Arabinose (2% v/v) was also added at the start of cultivation to induce transposase activity. Tetracycline (10 mg/L) was applied 2 hours after the start of cultivation to enrich naringenin-overproducing strains.


title: H1505

description: Library name: Sample 48


title: Control population, 45 hr

value: IPTG (1 mM) and p-coumaric acid (100 mg/L) were added at the start of cultivation to induce the naringenin pathway. Arabinose (2% v/v) was also added at the start of cultivation to induce transposase activity.


title: H0699

description: Library name: Sample 59


title: H1687

description: Library name: Sample 47


title: Third methanol and 2mM ABA treated sample; reverse sequencing data

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
BY4741_3_Methanol_2mM_AA_2
rRNA-depleted total RNA

data_processing:
RNA sequencing was performed at NovoGene (Cambridge; 150bp PE). Raw fastq files were processed using the pyCRAC package (version 1.4.6; https://git.ecdf.ed.ac.uk/sgrannem/pycrac, https://pypi.org/search/?q=pyCRAC) using the CRAC_pipeline_PE pipeline (https://bitbucket.org/sgrann/kinetic_crac_pipeline/src/default/). Briefly, adapter trimming was performed using Flexbar (version 3.4.0) and reads were demultiplexed using pyBarcodeFilter.py. To remove PCR duplicates, reads were collapsed using the pyFastqDuplicateRemover.py script. Subsequently, fasta files with collapsed reads were aligned to the yeast genome (R64-1-1) using Novoalign (novoalign -d Saccharomyces_cerevisiae.R64-1-1.75.novoindex -f forward_reads.fasta reverse_reads.fasta -r Random; version 2.04; www.novocraft.com) and read counts were generated using pyReadCounters.py. Differential analysis of gene expression was performed using the DESeq2 R package.
Bedgraph files were generated by pyGTF2bedGraph.py using pyReadCounters.py GTF output files. The bedgraph files contain the raw nucleotide densities without any normalisation.
Genome_build: Saccharomyces_cerevisiae R64-1-1.75
Supplementary_files_format_and_content: bedGraph: Raw nucleotide densities.
Supplementary_files_format_and_content: DESeq2_analysis_results.xlsx: Excel; DESeq2 data analysis results.
Supplementary_files_format_and_content: Saccharomyces_cerevisiae.R64-1-1.75_1.2.gtf: Genome GTF annotation file.
Supplementary_files_format_and_content: Saccharomyces_cerevisiae.R64-1-1.75.fa: FASTA; genome sequence.

organism: Saccharomyces cerevisiae BY4741

source_name: whole cell lysate

growth_protocol: RNA-Seq was performed on RNA extracted from replicate samples generated from three different BY4741 colonies grown on different days. Cells were grown overnight in 5ml SD-TRP medium. Cells were diluted to OD600 = 0.1 and grown in 20ml SD-TRP, SD-TRP + 1% methanol, SD-TRP + 1% methanol + 0.5mM abscisic acid or SD-TRP + 1% methanol + 2mM abscisic acid medium. After 5 hours of growth, cells were harvested at OD ~0.5.

extract_protocol:
RNA was extracted by Guanidium Thiocyanate/acd Phenol extraction and ethanol precipitation. RNA integrity was verified using the total RNA Nano kit on the 2100 Bioanalyzer (Amersham).
Sequencing libraries from 3 biological replicates were created using a modified version of the RNAtag-Seq protocol. One microgram of RNA from each sample was fragmented in FastAP phosphatase buffer for six minutes at 92ºC in a final reaction volume of 20µl. Subsequently, fragmented RNA was dephosphorylated using FastAP phosphatase (10U) and DNase treated using Turbo DNase (8 Units; ThermoFisher), in the presence of 40 units of rRNasin RNase inhibitor (Promega) for 30 minutes at 37ºC in a 40μl reaction volume. Three prime RNA adaptors (RNAtag_3adap; P-(6nt barcode)-rUrArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrGrUrArG-SpC3) were ligated to the dephosphorylated 3’ ends for 1 hour 30 min at 22°C in a 40µl reaction volume with 1x T4 RNA ligase buffer, 9% DMSO, 10m ATP, 20% PEG8000 and 24 units rRNAsin (Promega). RNA was phenol-chloroform extracted and purified by ethanol precipitation. Ribosomal RNA was subsequently removed using the yeast RiboZero Gold (Illumina) kit according to the manufacturer’s procedures. Free adapters were removed using Terminator Exonuclease according to the manufacturer’s procedure. The cDNA synthesis reaction was performed with Superscript IV following manufacturer’s procedures at 55ºC for one hour in a final volume of 14µl. RNA was removed by adding 4µl of 1N NaOH. A second ligation reaction was performed 3Tr3 DNA adapter (P-AGATCGGAAGAGCACACGTCTG-SpC3) with CircLigase (Lucigen) according to the manufacturer’s procedures. Free adapter was subsequently again removed using the Terminator exonuclease. The cDNA library was amplified by PCR using the P5 forward and barcoded reverse primer (2P_rev_1 and 2P_rev_2; 5’-CAAGCAGAAGACGGCATACGAGATTCGTGTGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’, 5’-CAAGCAGAAGACGGCATACGAGATTCGCCAGAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’) for 24 cycles. PCR products were resolved on a 6% TBE gel (Invitrogen) and 180-400 bp fragments were gel excised. Final DNA Concentration was measured using the Qubit 4 (Invitrogen) and the High-Sensitivity DNA assay on the 2100 Bioanalyzer (Agilent).

value: Whole cells

value: Treated with 1% Methanol and 2.0 mM ABA


title: H1691

description: Library name: Sample 46


title: H1593

description: Library name: Sample 44


title: Third methanol and 0.5 mM ABA treated sample; forward sequencing data

description:
BY4741_3_Methanol_05mM_AA_1
rRNA-depleted total RNA

value: Treated with 1% Methanol and 0.5 mM ABA


title: Third methanol and 2mM ABA treated sample; forward sequencing data

description:
BY4741_3_Methanol_2mM_AA_1
rRNA-depleted total RNA


title: H0680

description: Library name: Sample 43


title: Third methanol and 0.5 mM ABA treated sample; reverse sequencing data

description:
BY4741_3_Methanol_05mM_AA_2
rRNA-depleted total RNA


title: H1473

description: Library name: Sample 42


title: Third methanol treated sample; forward sequencing data

description:
BY4741_3_Methanol_1
rRNA-depleted total RNA

value: Treated with 1% Methanol


title: Third methanol treated sample; reverse sequencing data

description:
BY4741_3_Methanol_2
rRNA-depleted total RNA


title: H1474

description: Library name: Sample 41

value: Liver


title: H1322

description: Library name: Sample 40

value: F


title: Third untreated sample; reverse sequencing data

description:
BY4741_3_2
rRNA-depleted total RNA

value: No treatment


title: H1488

description: Library name: Sample 45

value: HF


title: H0673

description: Library name: Sample 39

value: CD


title: Third untreated sample; forward sequencing data

description:
BY4741_3_1
rRNA-depleted total RNA


title: H1054

description: Library name: Sample 37


title: H1056

description: Library name: Sample 38


title: Second methanol and 0.5 mM ABA treated sample; reverse sequencing data

description:
BY4741_2_Methanol_05mM_AA_2
rRNA-depleted total RNA


title: Second methanol and 2mM ABA treated sample; reverse sequencing data

description:
BY4741_2_Methanol_2mM_AA_2
rRNA-depleted total RNA


title: Second methanol and 2mM ABA treated sample; forward sequencing data

description:
BY4741_2_Methanol_2mM_AA_1
rRNA-depleted total RNA


title: H1052

description: Library name: Sample 36


title: Second methanol and 0.5 mM ABA treated sample; forward sequencing data

description:
BY4741_2_Methanol_05mM_AA_1
rRNA-depleted total RNA


title: H2030

description: Library name: Sample 34


title: H0765

description: Library name: Sample 35


title: Second methanol treated sample; reverse sequencing data

description:
BY4741_2_Methanol_2
rRNA-depleted total RNA


title: H2034

description: Library name: Sample 33


title: Second methanol treated sample; forward sequencing data

description:
BY4741_2_Methanol_1
rRNA-depleted total RNA


title: H1137

description: Library name: Sample 31


title: H2494

description: Library name: Sample 32


title: Second untreated sample; reverse sequencing data

description:
BY4741_2_2
rRNA-depleted total RNA


title: Second untreated sample; forward sequencing data

description:
BY4741_2_1
rRNA-depleted total RNA


title: H2349

description: Library name: Sample 30


title: First methanol and 2mM ABA treated sample; reverse sequencing data

description:
BY4741_1_Methanol_2mM_AA_2
rRNA-depleted total RNA


title: First methanol and 0.5 mM ABA treated sample; reverse sequencing data

description:
BY4741_1_Methanol_05mM_AA_2
rRNA-depleted total RNA


title: First methanol and 0.5 mM ABA treated sample; forward sequencing data

description:
BY4741_1_Methanol_05mM_AA_1
rRNA-depleted total RNA


title: First methanol treated sample; reverse sequencing data

description:
BY4741_1_Methanol_2
rRNA-depleted total RNA


title: First methanol and 2mM ABA treated sample; forward sequencing data

description:
BY4741_1_Methanol_2mM_AA_1
rRNA-depleted total RNA


title: H1037

description: Library name: Sample 26


title: H1040

description: Library name: Sample 28


title: First methanol treated sample; forward sequencing data

description:
BY4741_1_Methanol_1
rRNA-depleted total RNA


title: H0669

description: Library name: Sample 27


title: H1044

description: Library name: Sample 25


title: H1792

description: Library name: Sample 24


title: First untreated sample; forward sequencing data

description:
BY4741_1_1
rRNA-depleted total RNA


title: H2577

description: Library name: Sample 22


title: First untreated sample; reverse sequencing data

description:
BY4741_1_2
rRNA-depleted total RNA


title: KO4 Th1

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

institute: tsinghua university

description: Library name: Sample 8

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence usi ing CLC genomic benchwork (paran meter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLCgenomic benchwork(parameters- mismath cost: 2 insertion cost: 3 de eletion cost: 3 length fr raction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork

Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 50 μM β-mercaptoethanol

extract_protocol:
Total RNA was extracted from B cells by using TRNzol reagent (Tiangen, China)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactrurer's protocols.

treatment_protocol: CD4+ T cells treated by plate bound CD3 and CD28 and supplement with IL2, IL12 and anti-IL4

value: Spleen

value: Primary

value: CD4 T cell

value: cKO

value: CD3,CD23,IL12,IL2,anti-IL4 for 3 days


title: H2259

description: Library name: Sample 23


title: H1009

description: Library name: Sample 21


title: KO2 Th1

description: Library name: Sample 6


title: H1006

description: Library name: Sample 20


title: KO1 Th1

description: Library name: Sample 5


title: H1302

description: Library name: Sample 19


title: H1223

description: Library name: Sample 18


title: H2290

description: Library name: Sample 17


title: WT2 Th1

description: Library name: Sample 2

value: WT


title: H0742

description: Library name: Sample 29


title: WT3 Th1

description: Library name: Sample 3


title: H2288

description: Library name: Sample 16


title: H1569

description: Library name: Sample 15


title: WT1 Th1

description: Library name: Sample 1


title: H1227

description: Library name: Sample 14


title: H1147

description: Library name: Sample 12


title: DMSO control 3

city: Houston

first: Liyang

last: Zhang

state: TX

address: 6670 Bertner Ave

department: Department of Medicine

institute: Houston Methodist Research Institute

description: Library name: Sample 3

data_processing:
After demultiplexing, sequence data was checked for overall quality and yield. Then, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the reference genomes using the STAR aligner v.2.5.2b. The STAR aligner is a splice aware 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 featureCounts from the Subread package v.1.5.2 Only unique reads 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 v1.1. The 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.
Supplementary files format and content: text file inculdes the raw counts for each sample

extract_protocol:
RNA was harvested using FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). At least 500 ng of total RNA was used to construct the sequencing libraries
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: Macrophage

value: DMSO


title: SKI-II 2

description: Library name: Sample 5

value: 4 μg/mL SKI-II


title: SKI-II 3

description: Library name: Sample 6


title: SKI-II 1

description: Library name: Sample 4


title: H1140

description: Library name: Sample 11

value: M


title: KO3 Th1

description: Library name: Sample 7


title: DMSO control 1

description: Library name: Sample 1


title: H1150

description: Library name: Sample 7


title: DMSO control 2

description: Library name: Sample 2


title: WT4 Th1

description: Library name: Sample 4


title: Control, biological replicate 2

city: San Francisco

first: Iowis

last: Zhu

state: CA

address: 1450 3rd Street, HD449

institute: University of California, San Francisco

description: Library name: Control2

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files were processed using CellRanger for alignment to the mm10 reference genome, identification of empty droplets, and determination of a count threshold. Cellranger generated filtered feature matrices were imported into a Seurat object. All downstream analyses were performed with Seurat v4.4.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz contains the barcode sequences, features.tsv.gz contains the gene names, and the matrix.mtx.gz contains the gene expression matrix table. All files are after filtering.

molecule: polyA RNA

source_name: tumor

growth_protocol: Mouse MPNST cell line JW23.3 were grown in Dulbecco’s Modified Eagle Medium (#11960069, Life Technologies) with 10% FBS and 1X Pen-Strep (#15140122, Life Technologies) in a cell culture incubator at 37oC and 5% CO2.

extract_protocol:
Mice were humanely euthanized using CO2. Tumors were excised and minced with sterile razor blades and then enzymatically dissociated with papain (#LS003, Worthington) at 37 degrees Celsius for 45 minutes. Samples were subsequently centrifuged for 5 minutes at 500g, resuspended in RBC lysis buffer (#00-4300-54, eBioscience), incubated for 10 minutes at room temperature, and then resuspended in 5% FBS in PBS. Cell suspensions were serially filtered through 70 mm and 40 mm filters before being resuspended again in 5% FBS in PBS for manual cell counting using a hemacytometer.
A total of 10,000 cells were loaded per single-cell RNA sequencing sample onto the 10x platform using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 on a 10X Chromium controller (10X Genomics) per the manufacturer recommended default protocol and settings.

treatment_protocol: Subcutaneous allografts were performed by implanting 5 million JW23.3 cells into the flanks of 5–6-week-old female C57/B6 wildtype mice (Charles River). For radiation treatments, 5 daily 2 Gy fractions were delivered using the XRAD 320 irradiation, and custom 3D printed lead shielding was used to prevent radiation delivery to regions outside the palpable, visualized subcutaneous tumor.

value: tumor

value: MPNST


title: H0646

description: Library name: Sample 5

value: Liver


title: NTVKO PCGF1 KO VTP50469 48h 300nM rep1

source_name: Blood

value: Blood

value: Myeloid


title: H1142

description: Library name: Sample 10

value: F

value: HF


title: H0642

description: Library name: Sample 6


title: H1818

description: Library name: Sample 9

value: CD


title: H1681

description: Library name: Sample 4


title: 2Gyx5, biological replicate 4

description: Library name: 2Gyx5-4


title: 2Gyx5, biological replicate 3

description: Library name: 2Gyx5-3


title: Control, biological replicate 3

description: Library name: Control3


title: H1590

description: Library name: Sample 3


title: H1144

description: Library name: Sample 13


title: Control, biological replicate 1

description: Library name: Control1


title: 2Gyx5, biological replicate 2

description: Library name: 2Gyx5-2


title: 2Gyx5, biological replicate 1

description: Library name: 2Gyx5-1


title: H0514

description: Library name: Sample 1


title: H1154

description: Library name: Sample 8


title: H1103

description: Library name: Sample 2


title: NCM460_LV_SHUHRF1

type: genomic

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

institute: Xijing Hospital of Fourth Military Medical University

hyb_protocol: Illumina Hybridization Oven (220V)

scan_protocol: AutoLoader 2.x, Dual-Scanner Configuration (110/220 V)

data_processing:
Array data (IDAT files) were analyzed with the ChAMP package in R to determine methylation levels.
The methylation status of each probe was represented as a β value, defined as the ratio of methylated probe intensity to total probe intensity (sum of methylated and unmethylated intensities plus a constant α, α = 100). CpG sites with |Δβ| ≥ 0.20 (test vs. control) and an adjusted P value ≤ 0.05 were considered differentially methylated. A CpG site was classified as hypermethylated if Δβ ≥ 0.20 or hypomethylated if Δβ ≤ −0.20.

label: Cy3 and Cy5

source_name: experimental group

label_protocol: Infinium Staining Rack (1)

extract_protocol: Genomic DNA was isolated from NCM460-shCtrl and NCM460-shUHRF1 cells using the QIAamp DNA Mini Kit (Qiagen). DNA purity and concentration were measured with a Nanodrop 2000 spectrophotometer (Thermo Scientific). Approximately 500 ng of DNA from each sample was subjected to sodium bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s protocol.

value: The human intestinal epithelial cell lines

value: cell lines

value: shUHRF1-transfected NCM460 cell line


title: CreER Stat3f/f S2, LPS treatment 6h

first: Xiaofeng

last: Zheng

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

description: Library name: F2_S03

data_processing:
FASTQ files of RNA samples are processed using STAR (Dobin et. al. 2012) and SAMtools (Li et. al. 2009) .
Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing read counts for all samples in a single file.

source_name: Bone marrow

growth_protocol: Bone marrow cells were isolated from CreER and CreER Stat3f/f mice and single-cell suspensions were prepared. Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% antibiotics and 10% M-CSF containing L929-conditioned medium to induce differentiation of macrophages in humidified atmosphere with 5% CO2 at 37C for 7 days. 1µm of 4-hydroxytamoxifen (Sigma-Aldrich, St. Louis, MO) was added to the cultures on day 2 and 4 to induce Stat3 deletion.

extract_protocol:
Total RNA was extracted from PBS and LPS stimulated BMDMs using RNeasy mini plus kit (Qiagen, Hilden, Germany). RNA purity and quality was measured by Nanodrop and 1µg of RNA per sample was sent to NOVOGENE (Beijing, China) for bulk-RNA sequencing.
RNA libraries were prepared using NEBNext Ultra II Non-Directional RNA Library Prep Kit with poly(A) selection by NOVOGENE (Beijing, China)

treatment_protocol: BMDMs were treated with PBS or LPS (100ng/ml) for 1 and 6 hours on day 7 of culture.

value: Bone marrow

value: Bone marrow-derived  macrophages

value: Stat3 knock out

value: LPS 6 hours


title: CreER Stat3f/f S3, LPS treatment 1h

description: Library name: F3_S02

value: LPS 1 hour


title: CreER Stat3f/f S3, LPS treatment 6h

description: Library name: F3_S03


title: CreER Stat3f/f S1, LPS treatment 6h

description: Library name: F1_S03


title: MPNST, sample 52

hyb_protocol: Bisulfite converted DNA was fragmented, amplified, and hybridized to human Infinium EPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Preprocessing, normalization, and downstream analysis were performed in R using the minfi Bioconductor package. Data were normalized via functional normalization and filtered based on the following criteria: (i) removal of probes targeting the X and Y chromosomes, (ii) removal of probes containing a common single nucleotide polymorphism (SNP) within the targeted CpG site or on an adjacent basepair, and (iii) removal of probes not mapping uniquely to the human reference genome. Unsupervised hierarchical clustering (Euclidean distance, complete linkage method) was performed using the top 2,000 most variable probes. β values were used for visualization of methylation levels (β=methylated/[methylated+unmethylated]) and M values were used for statistical analysis (M=log2[methylated/unmethylated]). ConsensusClusterPlus (v 1.62.0) analysis (hierarchical clustering, k range 2 to 10, 1000 repetitions) was used to assess optimal cluster size and stability.

label: biotin

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from archival FFPE blocks using the Qiagen FFPEasy kit


title: MPNST, sample 53


title: NCM460_LV_SHNC

source_name: control group

value: shCtrl-transfected NCM460 cell line


title: MPNST, sample 55

value: tumor

value: M


title: CreER Stat3f/f S3, no LPS treatment

description: Library name: F3_S01

value: PBS


title: MPNST, sample 51


title: MPNST, sample 50


title: CreER Stat3f/f S1, no LPS treatment

description: Library name: F1_S01


title: MPNST, sample 48


title: CreER S2, LPS treatment 6h

description: Library name: F2_R03

value: Wild-type


title: CreER Stat3f/f S2, LPS treatment 1h

description: Library name: F2_S02


title: CreER S1, LPS treatment 6h

description: Library name: F1_R03


title: CreER S3, LPS treatment 1h

description: Library name: F3_R02


title: Sample_9884-RS-1, C07, Abdominal biopsy

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
Library name: 9984.C07ab
MacDougald_Adipose_2025.2, 10x 3' v3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation from the raw FASTQ files were made using Cell Ranger software (v2.1.1 for MacDougald_Adipose_2025.2, v7.0.0 for MacDougald_Adipose_2025.1, v8.0.0 for MacDougald_Adipose_2025.3 & MacDougald_Adipose_2025.4, v8.0.1 for MacDougald_Adipose_2025.5, and v9.0.0 for MacDougald_Adipose_2025.6; https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes). Since these data were generated from single-nuceli, raw outputs were selected over filtered for upload.
Assembly: GRCh38
Assembly: Ensembl 110
Supplementary files format and content: raw_feature_bc_matrix.h5 - HDF5-formatted gene-barcode matrix output with the counts of unique molecular identifiers (UMIs) for each gene (feature) and barcode combination, including both cellular and background barcodes with at least one read

source_name: Abdominal biopsy

extract_protocol:
Nuclei were isolated from 150-250 mg of tissue, which was minced in 1 mL of nuclear extraction buffer (130-128-024, Miltenyi) and transferred into GentleMACS tubes. The h_tumor_01 protocol was run on the GentleMACS three times. Then, tubes were placed on ice for 10 minutes. The homogenate was then passed through a 70 mM filter and washed with 3 mL of nuclei extraction buffer. Samples were centrifuged at 500 x g for 10 minutes at 4°C. Supernatant was removed, and nuclear pellet was resuspended in 2 mL 1% BSA in PBS. Samples were then filtered using a 30 mM filter and rinsed with 2 mL 1% BSA in PBS Samples were centrifuged at 500 x g for 10 minutes at 4°C. Pellets were resuspended in 500 mL 1% BSA in PBS and filtered once more through a pre-wet 20 mM filter. Filters were washed with 500 mL 1% BSA in PBS. Samples were centrifuged at 500 x g for 10 minutes at 4°C, supernatant removed, and nuclear pellet resuspended in 50 mL 1% BSA in PBS. Nuclei were then counted at the University of Michigan Advanced Genomics Core using a Logos cell counter. Probes were hybridized, samples were pooled and processed according to manufacturer instructions for 10X Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples (PN 1000568). Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (ThermoFisher).
Libraries were generated according to the manufacturer's instructions (10x 3' v3 for MacDougald_Adipose_2025.1, MacDougald_Adipose_2025.2, and MacDougald_Adipose_2025.3 and 10x 3' v4 for MacDougald_Adipose_2025.4, MacDougald_Adipose_2025.5, MacDougald_Adipose_2025.6).

treatment_protocol: Frozen in -80oC human white adipose tissue biopsy samples

tag: donor

tag: disease state

value: control

value: Abdominal biopsy

value: Subcutaneous adipose tissue


title: Sample_9884-RS-2, C07, Upper neck biopsy

description:
Library name: 9984.C07up
MacDougald_Adipose_2025.2, 10x 3' v3

source_name: Upper neck biopsy

value: Upper neck biopsy


title: CreER Stat3f/f S1, LPS treatment 1h

description: Library name: F1_S02


title: MPNST, sample 49


title: CreER S3, LPS treatment 6h

description: Library name: F3_R03


title: Sample_6892-RS-3, B07, Abdominal biopsy

description:
Library name: 6892.B07ab
MacDougald_Adipose_2025.2, 10x 3' v3

value: diseased


title: CreER S3, no LPS treatment

description: Library name: F3_R01


title: Sample_6892-RS-4, B07, Upper neck biopsy

description:
Library name: 6892.B07up
MacDougald_Adipose_2025.2, 10x 3' v3


title: Sample_6892-RS-1, A07, Abdominal biopsy

description:
Library name: 6892.A07ab
MacDougald_Adipose_2025.2, 10x 3' v3

value: developing


title: CreER S2, LPS treatment 1h

description: Library name: F2_R02


title: CreER S1, LPS treatment 1h

description: Library name: F1_R02


title: CreER S1, no LPS treatment

description: Library name: F1_R01


title: Sample_6892-RS-2, A07, Upper neck biopsy

description:
Library name: 6892.A07up
MacDougald_Adipose_2025.2, 10x 3' v3


title: CreER S2, no LPS treatment

description: Library name: F2_R01


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 2

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

description: Library name: nipbl_24h_f_ko_2

data_processing:
Adaptors were removed using Trimmomatic v0.32
Reads were aligned to mm10 using Bowtie2 v2.3.4.1 with parameters [-q --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 1000]
Duplicates were removed using Picard MarkDuplicates v1.141
Reads mapped to regions from the ENCODE blacklist were removed
Assembly: mm10
Supplementary files format and content: CPM and E. coli normalized bigwig files for each Sample
Library strategy: CUT&Run

growth_protocol:
Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend)
Naïve samples were immediately subjected to CUT&RUN. Stimulated samples were incubated with 1uM CpG for 24 hours followed by CUT&RUN.

extract_protocol:
Cells were collected at respective timepoint and immobilized on concanavalin A-coated beads in Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail). 3ug of NIPBL antibody was incubated with immobilized cells at 4°C for 5 hours with rotation in Antibody Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin, 2mM EDTA). Cells were washed then incubated with pA-MNase fusion protein at 4°C for 1 hour with rotation in Digitonin Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin). Digestion was performed in Digitonin Wash Buffer at 0°C for 30 minutes by adding CaCl2 to 2mM. The digestion was stopped by adding one volume of 2X STOP Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 50ug/mL RNase A, 50ug/mL Linear Acrylamide, 2pg/mL Yeast Spike-In DNA). Chromatin was released from cells by shaking beads at 300rpm at 37°C for 10 minutes. The supernatant was incubated at 70°C for 10 min with SDS to 0.1% and 50ug of Proteinase K. DNA was then isolated with phenol:chloroform:isoamyl alcohol followed by precipitation with ammonium acetate.
Libraries were constructed with 2ng of CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: Spleen

value: Female

value: CD23+ B Cell

value: Xist cKO

value: CpG (24hr)

tag: antibody

value: NIPBL


title: Sample_6198-RS-2, B06, Upper neck biopsy

description:
Library name: 6198.B06up
MacDougald_Adipose_2025.1, 10x 3' v3


title: Sample_6158-RS-1, A06, Abdominal biopsy

description:
Library name: 6158.A06ab
MacDougald_Adipose_2025.1, 10x 3' v3


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 1

description: Library name: nipbl_24h_f_ko_1


title: Sample_6198-RS-1, A06, Abdominal biopsy

description:
Library name: 6198.A06up
MacDougald_Adipose_2025.1, 10x 3' v3


title: strain BPK275 promastigotes logarithmic post PAT-exposed Replicate 1

city: Antwerp

first: Pieter

last: Monsieurs

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine

description: Library name: BPK275_Pro_LOG_post_PAT_R1

data_processing:
Paired end sequencing data were aligned to the reference genome using BWA, as no alternative splicing is known in Leishmania species. Differential expression analyses were performed using DESeq2 with a design formula including the biological condition. Pairwise contrasts between conditions (e.g., Pro LOG vs. Pro PAT D2, Pro PAT D4 vs. Pro PAT D2) were obtained using the results() function. For selected comparisons, an alternative metadata configuration was used to restrict the analysis to high-quality replicates. For each contrast, log₂ fold change, p-values, and FDR-corrected p-values were extracted and merged into a single output table. Additional comparisons between strains were also performed using the same DESeq2 framework. Functional annotations and FPKM-normalized values were appended to all results before exporting to Excel. Summary statistics of up- and down-regulated genes at multiple fold-change thresholds were generated to support interpretation of differential expression patterns.
Assembly: Leishmania donovani BPK282 version 2
Supplementary files format and content: Raw read counts of all detected genes in the 26 samples.

organism: Leishmania donovani

source_name: parasitic cell

growth_protocol: The live Leishmania parasites were separated from dying cells under PAT exposure using a Percoll gradient as previously reported. In short, promastigotes were harvested, resuspended in 5 mL of M199, and passed through a 26G needle 4 times to disrupt cellular aggregates. The suspension was centrifuged at 1800 x g for 10 minutes, and the pellet was resuspended in 6 mL of 45% Percoll solution in PBS. Then, the discontinuous gradient was prepared based on 1.5 mL of 70% Percoll at the bottom, followed by a slow addition of the suspension of parasites diluted in 45% Percoll, and 2 mL of 25% Percoll at the top. The tubes with the gradient were carefully placed without mixing the layers and centrifuged at 2300 x g for 45 minutes at 4 °C. Live promastigotes from the fraction of 45% Percoll and the interface with the 70% Percoll fraction were recovered with a pipette and washed with 10 mL of cold PBS. After resuspension in 1 mL of cold PBS, parasites were counted, and aliquots were prepared for RNA extraction. The samples were stored at -80 °C for subsequent steps.

extract_protocol:
The total RNA was extracted using the Quick-RNA Microprep Kit (R1050, ZYMO RESEARCH) following the manufacturer’s instructions. The RNA's quantity and quality were evaluated using the Qubit RNA Quantification Assay Kit broad-range (Thermo Fisher) and RNA Screen tape system (Agilent).
The RNA-Gene Expression (poly-A selection) library preparation and sequencing service were performed by GenomeScan (Netherlands) on an Illumina NovaSeq6000 platform (2 x 150 bp paired-end reads) with a sequence depth of ~20 M PE reads/sample.

treatment_protocol: Promastigotes of L. donovani were harvested for BPK026 and BPK275 strains under different conditions: i) parasites at the logarithmic growth phase without drug pressure (No PAT D2) for both strains, ii) parasites exposed to normally lethal doses of PAT for 2 days (BPK026, 50µM) and for 2 - 4 days (BPK275, 200µM), and iii) parasites at the logarithmic growth phase after the recovery period in M199-sup following PAT exposure at normally lethal doses for both strains (Post PAT). Parasites exposed for 4 days under normally lethal doses of PAT were included only for BPK275 strain, as the number of live BPK026 parasites was insufficient for RNA extraction. The samples were prepared in triplicate or quadruplicate. A quantity of 1.5 x 10⁷ promastigotes were collected, purified with Percoll gradient, and washed with PBS, as mentioned above.

value: parasitic cell


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 3

description: Library name: nipbl_0h_f_ko_3

value: None (naïve)


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 1

description: Library name: nipbl_24h_f_wt_1

value: WT


title: Sample_12451-JM-2, C09, Upper neck biopsy

description:
Library name: 12451.C09up
MacDougald_Adipose_2025.6, 10x 3' v4


title: Sample_6158-RS-2, B06, Upper neck biopsy

description:
Library name: 6158.B06ab
MacDougald_Adipose_2025.1, 10x 3' v3


title: strain BPK275 promastigotes logarithmic post PAT-exposed Replicate 2

description: Library name: BPK275_Pro_LOG_post_PAT_R2


title: strain BPK275 promastigotes PAT-exposed  Day 4 Replicate 4

description: Library name: BPK275_Pro_PAT_D4_R4


title: CreER Stat3f/f S2, no LPS treatment

description: Library name: F2_S01

value: Bone marrow

value: Bone marrow-derived  macrophages

value: Stat3 knock out

value: PBS


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 2

description: Library name: nipbl_0h_f_ko_2


title: strain BPK275 promastigotes PAT-exposed  Day 4 Replicate 3

description: Library name: BPK275_Pro_PAT_D4_R3


title: strain BPK275 promastigotes logarithmic post PAT-exposed Replicate 3

description: Library name: BPK275_Pro_LOG_post_PAT_R3


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 2

description: Library name: nipbl_24h_f_wt_2


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 3

description: Library name: nipbl_24h_f_ko_3


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 1

description: Library name: nipbl_0h_f_wt_1


title: strain BPK275 promastigotes PAT-exposed  Day 4 Replicate 1

description: Library name: BPK275_Pro_PAT_D4_R1


title: Sample_12451-JM-1, C09, Abdominal biopsy

description:
Library name: 12451.C09ab
MacDougald_Adipose_2025.6, 10x 3' v4

value: control

value: Abdominal biopsy

value: Subcutaneous adipose tissue


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 1

description: Library name: nipbl_0h_f_ko_1


title: Unknown_BS540-005T0009

city: Guangzhou

first: fenghua

last: chen

address: 195 Dongfengxi Road, Yuexiu District

institute: Guangzhou Medical University

description: Library name: sample9

data_processing:
fastq data were mapped to human reference GRCh38 using STAR, and expression level of each gene was calculated by HTSeq-count. DESeq2 was used to calculate fold change and adjust pvalue between treatment and control
Assembly: GRCh38
Supplementary files format and content: expression matrix, row represents genes and column represents samples

source_name: lung

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand reaction system by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments with adapters were amplified by PCR, and the products were purified by Ampure XP Beads. The library was assessed quality and quantity using the Agilent 2100 bioanalyzer. Then, undergo DSN treatment. The DSN treated library was assessed quality to ensure the high quality of the sequencing data by two methods: checked the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantified the library using real-time quantitative PCR (qPCR). The qualified library was amplified on cBot to generate the cluster on the flowcell. And the amplified flowcell was sequenced single end on the Illumina Novaseq X plus platform (Tsingke-Beijing, China).

value: lung

value: human lung adenocarcinoma epithelial cell line

value: OE


title: Unknown_BS540-005T0007

description: Library name: sample7


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 2

description: Library name: nipbl_0h_f_wt_2

value: Spleen

value: Female

value: CD23+ B Cell


title: Sample_12450-JM-1, C02, Abdominal biopsy

description:
Library name: 12450.C02ab
MacDougald_Adipose_2025.6, 10x 3' v4

value: developing


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 3

description: Library name: nipbl_24h_f_wt_3

value: CpG (24hr)

value: NIPBL


title: Unknown_BS540-005T0005

description: Library name: sample5

value: KO


title: Sample_12448-JM-2, A04, Upper neck biopsy

description:
Library name: 12448.A04up
MacDougald_Adipose_2025.6, 10x 3' v4

value: Upper neck biopsy


title: Unknown_BS540-005T0003

description: Library name: sample3

value: WT


title: strain BPK275 promastigotes PAT-exposed  Day 2 Replicate 2

description: Library name: BPK275_Pro_PAT_D2_R2

value: parasitic cell


title: Sample_12450-JM-2, C02, Upper neck biopsy

description:
Library name: 12450.C02up
MacDougald_Adipose_2025.6, 10x 3' v4


title: Sample_12448-JM-1, A04, Abdominal biopsy

description:
Library name: 12448.A04ab
MacDougald_Adipose_2025.6, 10x 3' v4


title: strain BPK275 promastigotes PAT-exposed  Day 4 Replicate 2

description: Library name: BPK275_Pro_PAT_D4_R2


title: strain BPK275 promastigotes PAT-exposed  Day 2 Replicate 4

description: Library name: BPK275_Pro_PAT_D2_R4


title: strain BPK275 promastigotes PAT-exposed  Day 2 Replicate 1

description: Library name: BPK275_Pro_PAT_D2_R1


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 3

description: Library name: nipbl_0h_f_wt_3

value: None (naïve)


title: Sample_12449-JM-2, A08, Upper neck biopsy

description:
Library name: 12449.A08up
MacDougald_Adipose_2025.6, 10x 3' v4


title: Unknown_BS540-005T0008

description: Library name: sample8


title: Sample_12449-JM-1, A08, Abdominal biopsy

description:
Library name: 12449.A08ab
MacDougald_Adipose_2025.6, 10x 3' v4


title: Sample_12368-JM-2, C01, Upper neck biopsy

description:
Library name: 12368.C01ab
MacDougald_Adipose_2025.5, 10x 3' v4

value: control


title: RNA-Seq, Young 5

city: Palo Alto

first: Christoph

last: Thaiss

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

description: Library name: 50

data_processing:
Raw reads were mapped to the mouse reference transcriptome (GRCm38) using Kallisto version 0.46.0.
Subsequent analysis was carried out using the statistical computing environment R version 4.1.2 in RStudio version 1.4.17 and Bioconductor version 3.13 in a similar approach as recently published
Assembly: GRCm38
Supplementary files format and content: txt file with RNA-seq counts

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using the Trizol-Chloroform-Isopropanol method.
Libraries were prepared using the Illumina Stranded mRNA Prep kit (#20020595) according to manufacturer’s instructions and sequenced on a NextSeq 550 instrument using a 75-cycle kit
Quality and quantity control of RNA and libraries were performed using an Agilent 4200 TapeStation and Qubit 4, respectively

value: Hippocampus

value: Y


title: strain BPK275 promastigotes PAT-exposed  Day 2 Replicate 3

description: Library name: BPK275_Pro_PAT_D2_R3


title: Unknown_BS540-005T0006

description: Library name: sample6

value: lung


title: Unknown_BS540-005T0002

description: Library name: sample2

value: human lung adenocarcinoma epithelial cell line


title: Unknown_BS540-005T0004

description: Library name: sample4


title: Sample_12368-JM-1, C01, Abdominal biopsy

description:
Library name: 12368.C01up
MacDougald_Adipose_2025.5, 10x 3' v4

value: Abdominal biopsy

value: Subcutaneous adipose tissue


title: RNA-Seq, Cohouse Old 4

description: Library name: 47

value: CO


title: strain BPK275 promastigotes logarithmic Replicate 2

description: Library name: BPK275_Pro_LOG_R2


title: Unknown_BS540-005T0001

description: Library name: sample1


title: strain BPK275 promastigotes logarithmic Replicate 4

description: Library name: BPK275_Pro_LOG_R4


title: RNA-Seq, Young 2

description: Library name: 43


title: RNA-Seq, Old 5

description: Library name: 46

value: O


title: Sample_11024-RS-2, B02, Upper neck biopsy

description:
Library name: 11024.B02up
MacDougald_Adipose_2025.4, 10x 3' v4

value: diseased


title: strain BPK026 promastigotes logarithmic post PAT-exposed Replicate 3

description: Library name: BPK026_Pro_LOG_post_PAT_R3


title: strain BPK275 promastigotes logarithmic Replicate 3

description: Library name: BPK275_Pro_LOG_R3


title: RNA-Seq, Young 4

description: Library name: 48


title: Sample_11025-RS-2, B03, Upper neck biopsy

description:
Library name: 11025.B03up
MacDougald_Adipose_2025.4, 10x 3' v4


title: RNA-Seq, Young 3

description: Library name: 45


title: RNA-Seq, Cohouse Young 5

description: Library name: 42

value: CY


title: RNA-Seq, Old 3

description: Library name: 41


title: Sample_11025-RS-1, B03, Abdominal biopsy

description:
Library name: 11025.B03ab
MacDougald_Adipose_2025.4, 10x 3' v4


title: RNA-Seq, Old 4

description: Library name: 44


title: RNA-Seq, Cohouse Young 4

description: Library name: 40


title: Sample_10885-RS-2, A01, Upper neck biopsy

description:
Library name: 10885.A01up
MacDougald_Adipose_2025.4, 10x 3' v4

value: developing


title: Sample_11024-RS-1, B02, Abdominal biopsy

description:
Library name: 11024.B02ab
MacDougald_Adipose_2025.4, 10x 3' v4


title: strain BPK026 promastigotes PAT-exposed  Day 2 Replicate 4

description: Library name: BPK026_Pro_PAT_D2_R4


title: RNA-Seq, Young 1

description: Library name: 36


title: Sample_10885-RS-1, A01, Abdominal biopsy

description:
Library name: 10885.A01ab
MacDougald_Adipose_2025.4


title: RNA-Seq, Cohouse Old 3

description: Library name: 38


title: strain BPK026 promastigotes logarithmic post PAT-exposed Replicate 2

description: Library name: BPK026_Pro_LOG_post_PAT_R2


title: RNA-Seq, Cohouse Old 5

description: Library name: 49


title: Sample_10596-RS-2, C08, Upper neck biopsy

description:
Library name: 10596.C08up
MacDougald_Adipose_2025.3, 10x 3' v3


title: RNA-Seq, Old 1

description: Library name: 37


title: RNA-Seq, Old 2

description: Library name: 39


title: RNA-Seq, Cohouse Old 2

description: Library name: 35


title: strain BPK026 promastigotes PAT-exposed  Day 2 Replicate 3

description: Library name: BPK026_Pro_PAT_D2_R3


title: strain BPK275 promastigotes logarithmic Replicate 1

description: Library name: BPK275_Pro_LOG_R1


title: Sample_10596-RS-1, C08, Abdominal biopsy

description:
Library name: 10596.C08ab
MacDougald_Adipose_2025.3, 10x 3' v3


title: strain BPK026 promastigotes PAT-exposed  Day 2 Replicate 2

description: Library name: BPK026_Pro_PAT_D2_R2


title: RNA-Seq, Cohouse Old 1

description: Library name: 32


title: RNA-Seq, Cohouse Young 1

description: Library name: 31


title: RNA-Seq, Cohouse Young 2

description: Library name: 33


title: strain BPK026 promastigotes logarithmic post PAT-exposed Replicate 1

description: Library name: BPK026_Pro_LOG_post_PAT_R1


title: Sample_10566-RS-2, C03, Upper neck biopsy

description:
Library name: 10566.C03up
MacDougald_Adipose_2025.3, 10x 3' v3


title: Sample_10566-RS-1, C03, Abdominal biopsy

description:
Library name: 10566.C03ab
MacDougald_Adipose_2025.3, 10x 3'v3


title: Fecal Y 10

description: Library name: 125

data_processing:
QIIME2: reads were demultiplexed, quality-filtered, and denoised using deblur with `trim-length 200`
Assembly: Silva 138 database
Supplementary files format and content: feature-table with counts for each OUT
Supplementary files format and content: Taxonomy for OUT mapping
Library strategy: 16S rRNA-seq

source_name: Fecal

extract_protocol:
tool DNA was purified using DNeasy PowerSoil Pro Kit (Qiagen, Cat. No. 47014) according to manufacturer’s instructions.
DNA was amplified using the KAPA Hifi HotStart ReadyMix (Roche, KK2602) and the F27/R338 primer-pair targeting the V1V2 region of the 16S gene (F27: 5’- AGAGTTTGATCCTGGCTCAG-3’, R338: 5’- TGCTGCCTCCCGTAGGAGT-3’). After PCR amplification, the pooled library underwent bead- based size selection using AMPure XP beads (Beckman Coulter, A63881) and was sequenced using 500 bp paired-end sequencing (Illumina MiSeq).

value: Fecal

value: FMT


title: strain BPK026 promastigotes logarithmic Replicate 4

description: Library name: BPK026_Pro_LOG_R4


title: Fecal Y 9

description: Library name: 121

value: WT


title: Tfh PBMCs, lanes 1-2, TCR-derived cDNA

first: Ramin

last: Herati

state: New York

address: 430 E. 29th Street, 1st floor, room 135A-C

institute: NYU School of Medicine

description:
Library name: TCR-Tfh
10X Genomics

data_processing:
Cellranger software v8.0.1 (10X Genomics) was used to align FASTQ files to the human genome (GRCh38), evaluate gene and protein expression, and exclude empty droplets via the Barcode Rank Plot. Seurat v4.3.0 was used for single cell library processing and assay integration. HTO demultiplexing was conducted using CLR normalization (via NormalizeData()) and HTODemux(). Cells were filtered out and excluded based on high mitochondrial counts, and low and high UMI counts. Additional processing included normalizing and scaling. For doublet detection, scDblFinder() was used, with an estimated doublet rate of 0.4% per 1000 cells. HTODemux() negatives were removed. scRepertoire v1.11.0 and immunarch v0.9.1 was used for TCR and BCR sequence processing. Seurat allowed for integration, via SCTransform for normalization, SelectIntegrationFeatures() (utilizing 5000 features), and FindIntegrationAnchors() (utilizing the first 20 dimensions, rpca reduction, and 20 k.anchors).
Assembly: GRCh38 ensemble
Supplementary files format and content: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz, vdj_t_filtered_contig_annotations.csv

source_name: Peripheral blood mononuclear cells

extract_protocol:
For sample multiplexing, cells were stained with hashtag oligonucleotides (BioLegend). Acquisition and sorting were performed on a BD FACSymphony S6 Cell sorter. Sorting gates included CD3+ T cells, activated CD4+ and CD8+ T cells (defined as CD38+ HLA-DR+) and CXCR5+ PD-1+ Tfh cells. Sorted cells were processed for ECCITE-seq using the Chromium Next GEM Single Cell 5′ HT Kit v2 (10x Genomics). Cells were pooled, loaded onto Chromium GEM-X Chips, and run on a Chromium controller (10x Genomics).
Gene expression, TCR V(D)J, and surface protein expression libraries were made using the 5′ Feature Barcode Kit, the Chromium Single Cell V(D)J Amplification Kit, and the Chromium Next GEM Single Cell 5′ Library Kit (10x Genomics), following the manufacturer’s instructions. Libraries were pooled and sequenced using the NovaSeq 6000.

treatment_protocol: Cryopreserved PBMC were thawed and subjected to Fc receptor blockade using Human TruStain FcX (BioLegend) and NovaBlock (Thermo Fisher Scientific), both at at 1:100 dilution, for 10 min at room temperature. This was followed by surface antibody staining at room temperature for 30 min in the dark.

value: Peripheral blood mononuclear cells


title: strain BPK026 promastigotes PAT-exposed  Day 2 Replicate 1

description: Library name: BPK026_Pro_PAT_D2_R1

value: parasitic cell


title: Fecal Y 8

description: Library name: 119


title: Tfh PBMCs, lanes 1-2, mRNA-derived cDNA

description:
Library name: GEX-Tfh
10X Genomics


title: Fecal O 5

description: Library name: 120


title: strain BPK026 promastigotes logarithmic Replicate 3

description: Library name: BPK026_Pro_LOG_R3


title: strain BPK026 promastigotes logarithmic Replicate 2

description: Library name: BPK026_Pro_LOG_R2


title: RNA-Seq, Cohouse Young 3

description: Library name: 34


title: Tfh PBMCs, lanes 1-2, ADT-derived cDNA

description:
Library name: ADT-Tfh
10X Genomics

molecule: protein


title: Fecal Y 7

description: Library name: 118


title: strain BPK026 promastigotes logarithmic Replicate 1

description: Library name: BPK026_Pro_LOG_R1


title: Fecal O 3

description: Library name: 116


title: Fecal O 4

description: Library name: 117


title: Fecal Y 6

description: Library name: 115


title: CD3 PBMCs, lanes 1-2, TCR-derived cDNA

description:
Library name: TCR-CD3
10X Genomics


title: Fecal O 8

description: Library name: 126


title: Fecal Y 5

description: Library name: 112


title: Fecal Y 4

description: Library name: 111


title: Fecal O 7

description: Library name: 124


title: Fecal O 6

description: Library name: 122


title: CD3 PBMCs, lanes 1-2, ADT-derived cDNA

description:
Library name: ADT-CD3
10X Genomics


title: Fecal O 2

description: Library name: 104


title: S_939_24, Nbl1xCol4a5, WT, Batch 2

city: Bar Harbor

first: Courtney

last: Willey

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
Library name: S_939_24
Counts_S93924_GT24; TPM_S93924_GT24; FPKM_S93924_GT24

data_processing:
JAX RNA-seq Nextflow Pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR
Read count extraction and normalization were performed using featureCounts
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts, tpm, and fpkm for each sample.

source_name: Kidney

extract_protocol:
RNA was harvested using NucleoMag RNA Kit (Macherey-Nagel). Samples with RIN >8  was used for the construction of sequencing libraries.
RNA libraries for for RNA-seq were prepared using KAPA mRNA HyperPrep Kit (Roche) following manufacturer's protocols.

value: Kidney


title: S_938_24, Nbl1xCol4a5, WT, Batch 2

description:
Library name: S_938_24
Counts_S93824_GT24; TPM_S93824_GT24; FPKM_S93824_GT24


title: Fecal Y 3

description: Library name: 103


title: actCD4plusCD8 PBMCs, lanes 1-2, TCR-derived cDNA

description:
Library name: TCR-actCD4plusCD8
10X Genomics


title: Fecal Y 2

description: Library name: 101


title: S_936_24, Nbl1xCol4a5, WT, Batch 2

description:
Library name: S_936_24
Counts_S93624_GT24; TPM_S93624_GT24; FPKM_S93624_GT24


title: S_935_24, Nbl1xCol4a5, WT, Batch 2

description:
Library name: S_935_24
Counts_S93524_GT24; TPM_S93524_GT24; FPKM_S93524_GT24


title: Fecal Y 1

description: Library name: 100


title: Fecal O 1

description: Library name: 99


title: actCD4plusCD8 PBMCs, lanes 1-2, mRNA-derived cDNA

description:
Library name: GEX-actCD4plusCD8
10X Genomics


title: actCD4plusCD8 PBMCs, lanes 1-2, ADT-derived cDNA

description:
Library name: ADT-actCD4plusCD8
10X Genomics


title: Fecal O input

description: Library name: 98


title: T0, biological replicate 2

description: Library name: JH022_T0-2

data_processing:
Enrichment or depletion of sgRNA abundances were determined by down sampling trimmed sequencing reads to equivalent amounts across all samples, and then calculating the log2 ratio of sgRNA abundance in experimental conditions to sgRNA abundance in control conditions at T10 (rho), or between sequencing reads from T10 and T0 timepoints within experimental (tau) or control (gamma) conditions. Specifically, we computed normalized log2 ratios for radiation-treated sgRNA abundance at T10 compared to T0 in order to identify mediators of radiation responses and computed normalized log2 ratios for sgRNA abundance in the control group at T10 compared to T0 to identify regulators of cell fitness independent of treatment. Any sgRNA’s not represented with an average of at least 50 normalized sequencing reads across all replicates were excluded from analysis. Statistical significance was calculated using Wald test comparing replicates across conditions without a log2 fold change threshold. Hits were prioritized by normalizing log2 ratios to the total number of population doublings in the screen and the standard deviations of the non-targeting control sgRNAs. Genes were filtered at an adjusted p-value<0.05 for statistical significance.
Assembly: hg38
Supplementary files format and content: counts_JH022.txt contains the raw counts for each sgRNA prior to normalization. counts_JH022_DESeq2_normalized.txt contains the normalized counts for each sgRNA. rhoR2Gyx2_vs_Control.txt contains the ratios of normalized sgRNA abundances between the experimental and control groups. tauR2Gyx2_vs_T0.txt contains the ratios of normalized sgRNA abundances between the experimental and T0 groups. gammaRControl_vs_T0.txt contains the ratios of normalized sgRNA abundances between the control and T0 groups.
Library strategy: sgRNA library

growth_protocol: Human HEK 293T and JH-2-002 MPNST cells (gift from Christine Pratilas from Johns Hopkins University) were cultured in Dulbecco’s modified Eagle’s medium (#11960069, Life Technologies) with 10% FBS and 1X Pen-Strep (#15140122, Life Technologies) in a cell culture incubator at 37oC and 5% CO2.

extract_protocol:
gDNA from all cells was harvested and sgRNA barcodes were amplified and processed for sgRNA abundance library preparation using Q5 High-Fidelity DNA Polymerase (NEB) and sequenced on an Illumina NovaSeq 6000
We used a previously optimized and validated, compact, highly active sgRNA library containing the top 2 on-target sgRNAs for 23,483 genes cloned into the library expression vector pU6-sgRNA EF1alpha Puro-T2A-GFP derived from pJR85(#140095, Addgene) and modified to express a second sgRNA using the human U6 promoter as previously described. Knockdown efficiency of all guide sequences is publicly available at https://gwps.wi.mit.edu. 1137 non-targeting sgRNA pairs were also included as negative controls in the screen.

treatment_protocol: Cells transduced with the sgRNA library were then flow sorted to obtain a pure population prior, and a portion of the cell pellet were subsequently frozen down at a “T0” (Day 0) timepoint. The screen was then carried out in biologic triplicate, with cells receiving 2 daily doses of 2 Gy or no radiation. Cells were harvested at Day 10.

value: tumor

value: MPNST


title: Young 10

description: Library name: T39

value: Y


title: Fecal Y input

description: Library name: 97


title: Old 10

description: Library name: T40


title: S_6000_22, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_6000_22
Counts_2206_6000; TPM_2206_6000; FPKM_2206_6000


title: S_934_24, Nbl1xCol4a5, WT, Batch 2

description:
Library name: S_934_24
Counts_S93424_GT24; TPM_S93424_GT24; FPKM_S93424_GT24


title: Cohouse young 10

description: Library name: T38


title: T0, biological replicate 1

description: Library name: JH022_T0-1


title: S_5988_22, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_5988_22
Counts_2206_5988; TPM_2206_5988; FPKM_2206_5988


title: S_5328_22, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_5328_22
Counts_2206_5328; TPM_2206_5328_FPKM_2206_5328


title: Young 9

description: Library name: T36


title: CD3 PBMCs, lanes 1-2, mRNA-derived cDNA

description:
Library name: GEX-CD3
10X Genomics


title: Cohouse old 8

description: Library name: T33


title: S_5326_22, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_5326_22
Counts_2206_5326; TPM_2206_5326; FPKM_2206_5326


title: Control, biological replicate 2

description: Library name: JH022_Control-2


title: Old 8

description: Library name: T31


title: Cohouse old 9

description: Library name: T35


title: Control, biological replicate 1

description: Library name: JH022_Control-1


title: Cohouse young 8

description: Library name: T29


title: Control, biological replicate 3

description: Library name: JH022_Control-3


title: S_5327_22, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_5327_22
Counts_2206_5327; TPM_2206_5327; FPKM_2206_5327


title: S_941_24, Nbl1xCol4a5, HET, Batch 2

description:
Library name: S_941_24
Counts_S94124_GT24; TPM_S94124_GT24; FPKM_S94124_GT24

value: HET


title: Cohouse young 9

description: Library name: T32


title: Cohouse old 6

description: Library name: T26


title: Old 6

description: Library name: T25


title: S_932_24, Nbl1xCol4a5, HET, Batch 2

description:
Library name: S_932_24
Counts_S93224_GT24; TPM_S93224_GT24; FPKM_S93224_GT24


title: 2Gyx2, biological replicate 3

description: Library name: JH022_2Gyx2-3


title: Cohouse old 5

description: Library name: T23


title: S_931_24, Nbl1xCol4a5, HET Batch 2

description:
Library name: S_931_24
Counts_S93124_GT24; TPM_S93124_GT24; FPKM_S93124_GT24


title: Cohouse young 7

description: Library name: T28


title: Old 7

description: Library name: T30


title: S_24_23, Nbl1xCol4a5, WT, Batch 1

description:
Library name: S_24_23
Counts_2206_24; TPM_2206_24; FPKM_2206_24