title: TMS2N-R2-Treated

description: in vivo SHAPE probing

data_processing:
Reads were analyzed using ShapeMapper2 (v2.2) using default parameters.
Assembly: NA
Supplementary files format and content: SHAPE reactivity

treatment_protocol: HeLa cells were plated (1 x 106) on a 10 cm plate, a day prior to being transfected with 1 µg of either WT or A1824C 18S-H or 18S-tMS2 constructs using PolyJet DNA Transfection Reagent (SignaGen, SL100688) according to the manufacturer’s instructions. On day of treatment, cells were washed twice with 10 mL of PBS, trypsinized, and spun down at 500 x g for 5 minutes. The cells were resuspended in PBS buffered with 200 mM HEPES and were divided into treated or untreated conditions. 5-Nitroisatoic anhydride (5NIA) (Sigma, S889075) was added to a final concentration of 25 mM to the treated sample and untreated cells were incubated with an equal volume of DMSO at 37˚C for 10 minutes. Reactions were quenched by adding DTT to a final concentration of 125 mM.

value: Transfected with tMS2N, treated with 5NIA


title: LN ISO CD4_1

status: Public on Feb 26 2025

type: SRA

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

country: USA

institute: University of Pittsburgh

description: bulk RNAseq, each sample sequenced twice then combined bioinformatically, combination shown here

library_source: transcriptomic

data_processing:
Quality controlled FASTQ files were aligned to the Ensembl Mus musculus genome (GRCm38) using STAR aligner . We then used featureCounts to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file. Differential gene expression analysis between the different conditions was estimated using DESeq2 based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate, and differentially expressed genes were determined at the 5% threshold. Gene set enrichment analysis was used to assess the statistical enrichment of gene ontologies, and pathways, and visualized using Clusterprofiler. All statistical analyses were performed using R.
Assembly: Ensembl Mus musculus genome (GRCm38)

molecule: total RNA

organism: Mus musculus

source_name: non-draining lymph node

growth_protocol: Mice were injected with  250,000 MC38 and sacrificied at the indicated timepoints.

extract_protocol:
Tumors were prepared for single cell suspension with in Liberase (Sigma Aldrich) at 50 mg/mL for 15 minutes at 37°C in RPMI without fetal bovine serum (FBS) and mechanical disruption. Tumor samples were negatively selected to remove CD105+ epithelial cells using CD105 Biotin (eBioscience) and Pierce Streptavidin Beads (ThermoFisher).
Libraries were constructed for SMART-seq RNA following manufacturer's instructions

treatment_protocol: We treated mice injected with two MC38 tumors with isotype (Rat IgG2a, Leinco) or anti-PD1 (Leinco) at Day 7, 10, and 13

tag: tissue

value: non-draining lymph node

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment

value: Isotype


title: TMS2N-R2-Untreated

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description: in vivo SHAPE probing

organism: Homo sapiens

source_name: Flp-In T-REx HeLa

growth_protocol: Cells were grown in Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamin e and maintained in a 5% CO2 humidified incubator .

extract_protocol:
Cells were pelleted and lysed using the provided buffer from Quick-RNA Miniprep Kit (Zymo, R1054) and RNA was isolated per instructions including optional steps. To ensure proper digestion of all plasmid DNA, RNA was additionally treated with 100 U of TURBO DNase I (Thermo Fisher Scientific, AM2238) with appropriate buffering conditions and was subsequently precipitated.
Libraries were generated by using error-prone reverse transcription to generate cDNA.  Then libraries underwent gene specific  amplification to adding Illumina adaptors, and a second amplification to add Illumina barcodes.

tag: cell line

value: Flp-In T-REx HeLa

value: Cervical Cancer

value: WT

value: Transfected with tMS2N, treated with DMSO


title: Treg Skin_4

library_source: genomic

data_processing:
Raw ATAC sequencing data was quality controlled, trimmed, and aligned to the mouse reference genome (Mm10) using BWA-MEM. Peak calling was performed using MACS2 version 2.1.2 with the options -B, -q 0.01, – nomodel, -f BAM, -g mm. Peaks that overlapped blacklisted regions were removed. Read numbers, and feature distribution plots were obtained using the ataqv package in R. Count tables were generated using the Rsubread featureCounts on the filtered BAM alignments.
Assembly: Mm10

molecule: genomic DNA

source_name: Skin

growth_protocol: Mice were injected with 125,000 B16 or 250,000 MC38 and sacrificied at the indicated timepoints.

extract_protocol:
Tumors were prepared for single cell suspension with in Liberase (Sigma Aldrich) at 50 mg/mL for 15 minutes at 37°C in RPMI without fetal bovine serum (FBS) and mechanical disruption. Tumor samples were negatively selected to remove CD105+ epithelial cells using CD105 Biotin (eBioscience) and Pierce Streptavidin Beads (ThermoFisher).
Libraries were constructed for ATACseq following manufacturer's instructions

treatment_protocol: We treated mice injected with two MC38 tumors with isotype (Rat IgG2a, Leinco) or anti-PD1 (Leinco) at Day 7, 10, and 138

value: Skin

value: Treg


title: PC9_RNA_Seq_56d_osi_rep2

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale University

description: 56d Osimertinib-treated PC9 cells

data_processing:
Sequencing reads were aligned with STAR version 2.7.7a using a GRCh38 STAR index. Gene expression was quantified using featureCounts from Subread version 2.0.3.
Assembly: GRCh38
Supplementary files format and content: RNAseq_featureCounts_final.txt is a tab-delimited text file that contains the number of quantified reads from Subread.

molecule: polyA RNA

growth_protocol: PC9 cells were cultured in RPMI-1640 medium (Thermo Fisher, 11875119) with 1% penicillin-streptomycin (pen-strep, Thermo Fisher, 15140122) and 10% fetal bovine serum (FBS). Osimertinib-resistant cells were grown in 1uM osimertinib.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104O) and concentrations were measured via Nanodrop.
Library preparation was performed using approximately 1 ug of RNA. Library preparation and sequencing were performed by Novogene. Briefly, mRNA was purified from total RNA with poly-T oligo-attached magnetic beads. Fragmentation was performed and the first strand cDNA was synthesized with random hexamer primers followed by second strand cDNA synthesis. cDNA was then subject to end repair, A-tailing, adapter ligation, size selection, PCR amplification and purification. Qubit and RT-PCR were used to quantify resulting libraries, and bioanalyzer analysis was performed to determine size distribution. Libraries were pooled and loaded onto an S4 flowcell and sequenced with NovoSeq 6000.

value: lung adenocarcinoma

value: Wild-type PC9

value: Osimertinib

tag: time point


title: PC9_RNA_Seq_56d_osi_rep1

description: 56d Osimertinib-treated PC9 cells


title: TMS2N-R1-Treated

description: in vivo SHAPE probing


title: Clam CK267D-0004

type: genomic

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

description: CK Phase I

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Genotyping was performed at Neogen (Lincoln, Nebraska) on the Axiom 384HT arrays (Axiom HD Array [60K] Clam) following protocols outlined in the Axiom Assay 384HT Array Format Automated Workflow User Guide.

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

organism: Mercenaria mercenaria

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Adults M. mercenaria (12-14 months old) were collected from three farms in Cedar Key, Florida with one whole bag from each farm (1000-1200 clams). The clam seeds of each farm were originally sourced from different hatcheries. After purchase, the quahogs from each bag were cleaned at the farms using fresh water to remove sediment before being transported to the laboratory in a cooler (1 hr driving). After arriving at the laboratory, all quahogs were maintained in an indoor recirculating artificial seawater system equipped with a bead filter (Endurance 4000, Aquaculture Systems Technologies, Baton Rouge, LA) at 24 ± 0.55°C, 25 ppt salinity, and pH = 8.35. Quahogs were fed daily with a combination of microalgae, including Tetraselmis spp., Isochrysis spp., and Chaetoceros spp., at 50,000 cells/ml supplemented with commercial algal paste (Instant algae, Reed Mariculture, San Jose, CA, USA). System water quality was checked daily using a saltwater combination kit (AQ-4, Lamotte, Maryland, USA) for ammonia (< 0.01 mg/L), nitrite (< 0.01 mg/L), and nitrate levels (< 10 mg/L).

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

treatment_protocol: The heat shock challenge was applied by increasing water temperature at 1°C per day from 24°C to a final temperature of 35°C using a heat pump with a temperature controller (Model No. DC24S, Aqualogic, San Diego, CA, USA). When the total dead quahog numbers reached about 50% of the total initial clam number, the temperature decreased from 35°C to 27°C within 24 hr and gradually to 24°C within another 24 hr. For easy reading, the heat challenge was separated into three phases (Figure 1): Phase I (13 days) – temperature increased from 24°C to 35°C and stayed at 35°C; Phase II (9 days) – temperature decreased from 35°C to 24°C with more clams died, and Phase III – temperature was maintained at 24°C and no quahog mortality was found in two days. Two HOBO pendant temperature loggers (UA-001–64, Onset, MA, USA) were submerged in the tank to record the temperature changes. No feeding was conducted after the temperature reached 28°C, and water quality was monitored twice a day.

value: Adductor muscle


title: Clam CK268S-0319

description: CK Phase III

value: Hemocytes in ethanol


title: CD4 Skin_4


title: TMS2N-R1-Untreated

description: in vivo SHAPE probing


title: PC9_RNA_Seq_35d_osi_rep2

description: 35d Osimertinib-treated PC9 cells


title: PC9_RNA_Seq_35d_osi_rep1

description: 35d Osimertinib-treated PC9 cells


title: Treg LN_4


title: MS2N-R2-Treated

description: in vivo SHAPE probing

value: Transfected with 18S-H(MS2N), treated with 5NIA


title: HCC827_WT_IgG_rep2

description: ChIP Antibody: IgG

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC. Bowtie2 version 2.4.2 was used to align reads to the GRCh37 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30. Macs2 version 2.2.7.1 was used to call peaks with default peak-calling settings. Peaks were called against input chromatin. IDR was used to determine significant peaks between two biological replicates. Deeptools version 3.5.1 was used for ChIP-seq data visualization. Plots depicting ChIP-seq signal were generated by using Deeptools bamCoverage to normalize signal by CPM and duplicates were ignored. Peak intersections were performed using BEDTools v2.30.
Assembly: GRCh37
Supplementary files format and content: bigWig files are mean count per million signal files.
Supplementary files format and content: Files with postfix idr.txt are peak files that were generated from running idr to identify highly reproducible peaks.

growth_protocol: Cells were cultured in RPMI-1640 medium (Thermo Fisher, 11875119) with 1% penicillin-streptomycin (pen-strep, Thermo Fisher, 15140122) and 10% fetal bovine serum (FBS).

extract_protocol:
ChIP-seq was performed using the Active Motif ChIP-IT Express Kit (Active Motif 53008) according to the manufacturer’s instructions. Approximately 2 x 10^7 cells were used per biological replicate. Chromatin was sheared using a Covaris S220 using a peak power of 175W, duty factor of 10%, 200 cycles/burst, and 160 seconds per run. One uL of decrosslinked chromatin was analyzed via Agilent TapeStation to determine fragment size, and DNA concentration was measured using Qubit (Invitrogen Q32854). The following antibodies were used: IgG isotype control (CST 5415S) and c-MYC-tag (Cell Signaling Technologies 2276S). 20 ug of chromatin was pre-incubated with antibody overnight at 4ºC. Protein G beads were subsequently added to antibody-bound chromatin and incubated for 4 hours at 4ºC.
2.5 ng of immunoprecipitated chromatin was subject to library preparation using EpiCypher CUT&RUN Library Kit (EpiCypher 141001) according to the manufacturer’s instructions. Pooled libraries were sequenced by Novogene with NovaSeq 6000 with 20 million paired-end reads sequenced per library.

treatment_protocol: Osimertinib-resistant cells were grown in 1uM osimertinib.

value: Wild-Type

value: Untreated

tag: antibody

value: IgG


title: Clam CK264D-0064

description: CK Phase I


title: MS2N-R2-Untreated

description: in vivo SHAPE probing

value: Transfected with 18S-H(MS2N), treated with DMSO


title: Clam CK263S-0318

description: CK Phase III


title: Treg Skin_3


title: PC9_RNA_Seq_28d_osi_rep1

description: 28d Osimertinib-treated PC9 cells


title: MS2N-R1-Treated

description: in vivo SHAPE probing


title: CD4 Skin_3


title: PC9_RNA_Seq_0d_osi_rep2

description: Untreated PC9 cells

value: No treatment


title: CD4 LN_4

value: non-draining lymph node


title: Clam CK261S-0317

description: CK Phase III


title: MS2N-R1-Untreated

description: in vivo SHAPE probing

value: Flp-In T-REx HeLa

value: Cervical Cancer


title: Clam CK260S-0316

description: CK Phase III


title: PC9_RNA_Seq_0d_osi_rep1

description: Untreated PC9 cells


title: Treg LN_3


title: gcn2KO18SWTIPm2

description: Monosome footprints

data_processing:
3’ adapter (NNNNNNCACTCGGGCACCAAGGA) was trimmed off using skewer, and 4 random nucleotides included in the RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed. Trimmed reads were aligned to human ribosomal and non-coding RNA sequences using STAR10. Unmapped reads were then mapped to an hg19 transcriptome file.
Assembly: hg19
Supplementary files format and content: wig files from STAR alignments

extract_protocol:
Two days after transfection, cells were harvested in lysis buffer A (20 mM Tris-Cl [pH 7.5], 100 mM NH4Cl, 10 mM MgCl2, 0.1% Tween20 supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail [Roche, 11836170001]).
Footprints were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

treatment_protocol: 20 µg of 18S-tMS2 wild-type or A1824C expression constructs were transfected into ~7 x 106 cells in a 15-cm plate using PolyJet DNA transfection reagent (SignaGen, SL100688) according to the manufacturer’s instructions. 3 plates per condition were used for purification.

value: Transfected with 18S:WT


title: PC9_RNA_Seq_rep3

description: Untreated PC9 cells


title: Clam CK25D-0031

description: CK Phase I

source_name: Clam CK25D-0031


title: gcn2KO18SWTIPm1

description: Monosome footprints


title: Clam CK259D-0025

description: CK Phase I


title: Clam CK266P-0209

description: CK Phase II


title: Treg Skin_2

value: Skin


title: PC9_RNA_Seq_rep2

description: Untreated PC9 cells


title: gcn2KO18SA1824CIPm2

description: Monosome footprints

value: Transfected with 18S:A1824C


title: CD4 Skin_2


title: Clam CK258S-0315

description: CK Phase III


title: PC9_RNA_Seq_rep1

description: Untreated PC9 cells

value: lung adenocarcinoma


title: gcn2KO18SA1824CIPm1

description: Monosome footprints


title: Treg LN_2

value: Treg


title: PC9_RNA_Seq_28d_osi_rep2

description: 28d Osimertinib-treated PC9 cells

value: Wild-type PC9

value: Osimertinib


title: Clam CK256S-0314

description: CK Phase III

value: Hemocytes in ethanol


title: CD4 LN_2


title: WT18SA1824CIPm2

description: Monosome footprints

value: WT


title: Clam CK255D-0081

description: CK Phase I

value: Adductor muscle


title: PC9-OR_RNA_Seq_rep2

description: Osimertinib-resistant PC9 cells


title: PC9-OR_RNA_Seq_rep1

description: Osimertinib-resistant PC9 cells


title: WT18SWTIPm2

description: Monosome footprints


title: Clam CK254P-0222

description: CK Phase II


title: CD4 LN_3


title: WT18SA1824CIPm1

description: Monosome footprints


title: Clam CK252P-0252

description: CK Phase II


title: WT18SWTIPm1

description: Monosome footprints


title: Clam CK250P-0228

description: CK Phase II


title: Treg LN_1


title: HCC827_RNA_Seq_rep2

description: Untreated HCC827 cells

value: Wild-type HCC827


title: CD4 LN_1


title: HCC827_RNA_Seq_rep1

description: Untreated HCC827 cells


title: WT18SA1824CIPm3

description: Monosome footprints


title: HCC827-OR_RNA_Seq_rep2

description: Osimertinib-resistant HCC827 cells


title: WT18SWTIPm3

description: Monosome footprints


title: PC9-OR_RNA_Seq_rep3

description: Osimertinib-resistant PC9 cells


title: Clam CK24P-0210

description: CK Phase II

source_name: Clam CK24P-0210


title: Clam CK247P-0201

description: CK Phase II


title: Treg TIL Late_4

source_name: tumor

value: tumor


title: H1975_RNA_Seq_rep2

description: Untreated H1975 cells

value: Wild-type H1975


title: gcn2KO18SWTIPd2

description: 43S-80S footprints


title: Treg TIL Early_4


title: Clam CK245D-0088

description: CK Phase I


title: gcn2KO18SWTIPd1

description: 43S-80S footprints


title: Clam CK244P-0244

description: CK Phase II


title: H1975_RNA_Seq_rep1

description: Untreated H1975 cells

value: No treatment


title: Treg TIL NR_4


title: Treg Skin_1


title: CD4 Skin_1


title: H1975-OR_RNA_Seq_rep2

description: Osimertinib-resistant H1975 cells


title: gcn2KO18SA1824CIPd2

description: 43S-80S footprints


title: Clam CK240S-0313

description: CK Phase III


title: Clam CK23P-0231

description: CK Phase II

source_name: Clam CK23P-0231


title: H1975-OR_RNA_Seq_rep1

description: Osimertinib-resistant H1975 cells


title: gcn2KO18SA1824CIPd1

description: 43S-80S footprints


title: CD4 TIL Early_4


title: Clam CK238S-0312

description: CK Phase III


title: WT18SA1824CIPd2

description: 43S-80S footprints


title: CD4 TIL NR_4


title: Mac24_ETYA_LPS

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include estimates counts values for each Sample

source_name: macrophages

growth_protocol: Macrophages were generated from iPSPC using the STEMdiff™ Hematopoietic Kit (Stemcell Tech) and differentiation protocol

extract_protocol:
Qiagen AllPrep RNA/DNA Mini Kit
TruSeq RNA sample library preparation

treatment_protocol: iPSC-derived macrophages were assayed under basal conditions or following LPS (100 ng/mL for 72 hours) ± ETYA (50 mM for 72 hours) stimulation

tag: group


title: HCC827-OR_RNA_Seq_rep1

description: Osimertinib-resistant HCC827 cells


title: WT18SA1824CIPd1

description: 43S-80S footprints


title: Mac23_ETYA_LPS


title: Clam CK236D-0024

description: CK Phase I


title: CD4 TIL Iso_4

value: Isotype


title: Clam CK235P-0206

description: CK Phase II


title: Clam CK234D-0063

description: CK Phase I


title: Mac22_ETYA_LPS


title: WT18SWTIPd1

description: 43S-80S footprints

value: Flp-In T-REx HeLa


title: Mac21_ETYA_LPS


title: Treg LN Early_4

value: non-draining lymph node


title: DisomeA1824CshGCN2

description: Disome footprints

data_processing:
3’ adapter (NNNNNNCACTCGGGCACCAAGGA) was trimmed off using skewer, and 4 random nucleotides included in the RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed. Trimmed reads were aligned to human ribosomal and non-coding RNA sequences using STAR10. Unmapped reads were then mapped to an hg19 transcriptome file.
Assembly: hg19
Supplementary files format and content: Metagene analysis at translation start sites from all the datasets.

extract_protocol:
Cells were harvested in lysis buffer A (20 mM Tris-Cl [pH 7.5], 100 mM NH4Cl, 10 mM MgCl2, 0.1% Tween20 supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail [Roche, 11836170001]).
Footprints were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

treatment_protocol: HeLa cells expressing 18S:WT or 18S:A1824C were infected with lentivirus carrying non-tageting or GCN2 shRNA.

value: Cervical Cancer

value: Expressing shRNA targeting GCN2


title: Treg LN Late_4


title: Mac20_ETYA_LPS


title: Clam CK232S-0311

description: CK Phase III


title: Treg TIL Iso_4


title: Treg LN NR_4


title: DisomeA1824CNT

description: Disome footprints

value: Expressing scrambled shRNA


title: Mac19_ETYA_LPS


title: Clam CK231S-0310

description: CK Phase III


title: CD4 TIL Late_4


title: Treg LN Iso_4


title: WT18SWTIPd2

description: 43S-80S footprints

value: Transfected with 18S:WT


title: Clam CK225D-0054

description: CK Phase I


title: CD4 LN Late_4


title: DisomeWTNT

description: Disome footprints


title: DisomeWTshGCN2

description: Disome footprints


title: Mac17_ETYA

value: ETYA


title: Mac16_ETYA


title: Mac18_ETYA


title: CD4 LN Early_4


title: Clam CK224S-0308

description: CK Phase III


title: Clam CK229S-0309

description: CK Phase III


title: 80SA1824CNT

description: Monosome footprints


title: CD4 LN NR_4


title: Clam CK223P-0255

description: CK Phase II


title: 80SA1824CshGCN2

description: Monosome footprints


title: 80SWTshGCN2

description: Monosome footprints


title: CD4 LN Iso_4


title: Clam CK222P-0220

description: CK Phase II


title: 80SWTNT

description: Monosome footprints


title: Mac14_ETYA


title: Treg TIL Late_3

value: Treg


title: Clam CK220P-0207

description: CK Phase II


title: etohwtr2

description: DMS-MaP Seq

data_processing:
Reads  were processed using the ShapeMapper2 pipeline(v2.2) using the --dms command.
Assembly: hg19 rRNA
Supplementary files format and content: Concatenated raw mutation rates computed using ShapeMapper2(v2.2) are provided in .csv format.

extract_protocol:
Two days after transfection, unless specified cells were harvested in lysis buffer A (20 mM Tris-Cl [pH 7.5], 100 mM NH4Cl, 10 mM MgCl2, 0.1% Tween20 supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail [Roche, 11836170001]). For Figure 4D, cells were trypsinzed and resuspended in PBS. Then the cells were crosslinked with DSP (Thermo Fisher Scientific, PG82081) at 0.5 mM for 30 minutes at RT and quenched by adding Tris-Cl [pH 8] to 50 mM followed by incubation at RT for 15 minutes. After centrifugation at 350 rpm for 5 minutes, cells were lysed in lysis buffer B (50 mM HEPES [pH 7.5], 100 mM NH4Cl, 10 mM MgCl2, 0.1% Tween20 supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail [Roche, 11836170001]). 750 µg purified MS2 coat protein was added to lysate containing 1 mg of total RNA, and samples were nutated at 4 ˚C overnight. Add 445 unit of Nuclease P1 (NEB, M0660S) to the lysate and shake in a thermomixer at 37˚C for 30 min. Nuclease-treated lysates were layered on a sucrose cushion (20 mM Tris-Cl [pH 8], 150 mM KCl, 5 mM MgCl2, 1 mM DTT, 1 M sucrose). Ribosomes were pelleted by ultracentrifugation at a TLA100.3 rotor at 100,000 rpm for 1 hour at 4˚C. Resuspend ribosome pellets thoroughly binding buffer (100 mM HEPES [pH 7.5], 200 mM KCl, 5 mM MgCl2, 1 mM DTT, 10 mM BME, 0.02% Tween 20, supplemented with 1X cOmplete™ mini protease inhibitor cocktail). Add 111 µL of pre-equilibrated amylose resin slurry (NEB, E8021) into resuspended ribosomes, and nutate at 4˚C for 90- 120 minutes. Wash resin 10 times with wash buffer (100 mM HEPES [pH 7.5], 400 mM KCl, 5 mM MgCl2, 1 mM DTT, 10 mM BME, 0.02% Tween 20, 5% ethanol). Elute tMS2-tagged ribosomes in elution buffer (100 mM HEPES pH 7.5, 200 mM KCl, 5 mM MgCl2, 1 mM DTT, 10 mM BME, 0.02% Tween20, 10 mM maltose, supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail) with nutation at 4˚C for 30 minutes. Tenth of eluate was then extracted with hot acidic phenol/chloroform and precipitated for primer extension analysis. Footprints were extracted and size-selected on 15% TBE-urea gels between 40-80 nt. The rest of library construction procedures was as described previously3. Libraries were sequenced on a NextSeq 1000 machine.
Libraries were generated by using error-prone reverse transcription to generate cDNA.  Then libraries underwent gene specific  amplification to adding Illumina adaptors, and a second amplification to add Illumina barcodes.

value: Transfected with 18S:WT, treated with ethanol


title: Treg TIL Early_3


title: Clam CK21P-0212

description: CK Phase II

source_name: Clam CK21P-0212


title: Mac13_ETYA


title: Mac12_LPS

value: LPS


title: etohwtr1

description: DMS-MaP Seq

value: WT


title: Clam CK219S-0307

description: CK Phase III

value: Hemocytes in ethanol


title: Treg TIL NR_3


title: etohmutr2

description: DMS-MaP Seq

value: Transfected with 18S:A1824C, treated with ethanol


title: Mac11_LPS


title: Clam CK218S-0306

description: CK Phase III


title: Treg TIL Iso_3

value: tumor


title: Clam CK217S-0305

description: CK Phase III


title: etohmutr1

description: DMS-MaP Seq


title: Mac10_LPS


title: Mac15_ETYA


title: Clam CK216S-0304

description: CK Phase III


title: Mac8_LPS


title: dmswtr1

description: DMS-MaP Seq

value: Transfected with 18S:WT, treated with DMS


title: CD4 TIL NR_3


title: Mac7_LPS


title: Clam CK213D-0039

description: CK Phase I

value: Adductor muscle


title: dmsmutr2

description: DMS-MaP Seq

value: Transfected with 18S:A1824C, treated with DMS


title: CD4 TIL Iso_3

value: Isotype


title: Clam CK212D-0038

description: CK Phase I


title: Mac6_Ctrl

value: Ctrl


title: dmsmutr1

description: DMS-MaP Seq

value: Flp-In T-REx HeLa

value: Cervical Cancer


title: Clam CK211D-0037

description: CK Phase I


title: Treg LN Late_3

value: non-draining lymph node


title: Mac5_Ctrl


title: 5637 cells, siANKRD10-2, rep3

city: Wuhan

first: Jingtian

last: Yu

address: 169 Donghu

country: China

institute: Wuhan University

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA2_3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: 5637 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: Tumor cells


title: Treg LN Early_3


title: Clam CK210P-0218

description: CK Phase II


title: Mac9_LPS


title: dmswtr2

description: DMS-MaP Seq


title: Mac4_Ctrl


title: Treg LN NR_3


title: CD4 TIL Late_3


title: CD4 TIL Early_3


title: 5637 cells, siANKRD10-2, rep1

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA2_1


title: Mac3_Ctrl


title: Mac2_Ctrl


title: Clam CK208D-0046

description: CK Phase I


title: Treg LN Iso_3


title: CD4 LN Late_3


title: Mac1_Ctrl


title: 5637 cells, siANKRD10-1, rep3

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA1_3


title: Clam CK207D-0059

description: CK Phase I


title: 5637 cells, siANKRD10-1, rep2

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA1_2


title: Clam CK205D-0062

description: CK Phase I


title: CD4 LN Early_3


title: 5637 cells, siANKRD10-1, rep1

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA1_1


title: EndoC-βH1 sgZHX3-3 c (biol rep 3)

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Samples were analyzed using the nf-core rnaseq pipeline version 1.4.2 [https://nf-co.re/rnaseq/1.4.2] with nextflow version v19.10.0.
The intial fastq reads of all the samples were processed by Trimmgalore to trim/filter Illumina adapter sequences if any before processing further.
Reads aligned by STAR and gene expression values of each samples generated by featurecount programme.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
Stranded NEBNext® Ultra™ Directional RNA Library Prep Kit

value: Human pancreatic beta cells

value: ZHX3 KO


title: Clam CK204S-0302

description: CK Phase III


title: EndoC-βH1 sgZHX3-3 b (biol rep 2)


title: 5637 cells, siNC, rep3

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
NC3

value: siNC


title: EndoC-βH1 sgZHX3-3 a (Biol rep 1)


title: CD4 LN Iso_3


title: Clam CK203D-0027

description: CK Phase I


title: Clam CK209S-0303

description: CK Phase III


title: 5637 cells, siANKRD10-2, rep2

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
SIA2_2


title: 5637 cells, siNC, rep2

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
NC2


title: Clam CK202P-0217

description: CK Phase II


title: Treg TIL Late_2

value: Treg


title: EndoC-βH1 Empty c (biol rep 3)

value: WT


title: Treg TIL Early_2


title: 5637 cells, ANKRD10-2, rep3

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A2_3

value: ANKRD10-2 overexpression


title: Clam CK201D-0043

description: CK Phase I


title: EndoC-βH1 Empty b (Biol rep 2)


title: 5637 cells, siNC, rep1

description:
gene_count_matrix_siNC_siANKRD1-1_siANKRD10-2.txt
NC1


title: Treg TIL NR_2


title: 5637 cells, ANKRD10-2, rep2

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A2_2


title: Clam CK199D-0079

description: CK Phase I


title: CD4 LN NR_3


title: 5637 cells, ANKRD10-2, rep1

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A2_1


title: WX164_HepG2_Z9_b

data_processing:
Samples were analyzed using the nf-core rnaseq pipeline version 1.4.2 [https://nf-co.re/rnaseq/1.4.2] with nextflow version .
The intial fastq reads of all the samples were processed by Trimmgalore to trim/filter Illumina adapter sequences if any before processing further.
Reads aligned by STAR and gene expression values of each samples generated by featurecount prog.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human hepatoma line HepG2

growth_protocol: HepG2 cells were cultured in DMEM low glucose + 10% FBS + 1% glutamax + 1% NEAA and passaged weekly.

extract_protocol:
RNA was extracted using the NucleoSpin RNA Kit (MACHEREY-NAGEL), following the manufacturer's protocol.
250-300bp cDNA library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®

treatment_protocol: HepG2 cells were transfected with either an empty, Z2, Z5 or Z9 CRISPR vector using lipofectamine 2000. 48h after transfection, cells were selected with blasticidin.

value: transfected with sgZHX3-9 (Z9) CRISPR construct


title: Clam CK19D-0028

description: CK Phase I

source_name: Clam CK19D-0028


title: 5637 cells, ANKRD10-1, rep3

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A1_3

value: ANKRD10-1 overexpression


title: Clam CK198P-0250

description: CK Phase II


title: CD4 TIL Late_2

value: tumor


title: Treg TIL Iso_2


title: EndoC-βH1 Empty a (Biol rep 1)


title: CD4 TIL NR_2


title: Clam CK197D-0036

description: CK Phase I

value: Adductor muscle


title: 5637 cells, ANKRD10-1, rep2

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A1_2


title: CD4 TIL Iso_2


title: WX164_HepG2_Z5_c

value: transfected with sgZHX3-5 (Z5) CRISPR construct


title: Clam CK196P-0205

description: CK Phase II


title: Treg LN Late_2


title: 5637 cells, ANKRD10-1, rep1

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
A1_1


title: Clam CK194S-0301

description: CK Phase III

value: Hemocytes in ethanol


title: 5637 cells, Vector, rep3

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
VE_3

value: Vector only


title: WX164_HepG2_Z5_b


title: Clam CK193S-0300

description: CK Phase III


title: Treg LN NR_2


title: Treg LN Early_2


title: WX164_HepG2_Z9_c


title: 5637 cells, Vector, rep2

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
VE_2


title: 5637 cells, Vector, rep1

description:
gene_count_matrix_Vector_ANKRD1-1_ANKRD10-2.txt
VE_1


title: Clam CK190D-0080

description: CK Phase I


title: Treg LN Iso_2

value: Isotype


title: WX164_HepG2_Z2_b

value: transfected with sgZHX3-2 (Z2) CRISPR construct


title: WX164_HepG2_Z9_a


title: WX164_HepG2_Z2_a


title: CD4 LN Late_2

value: non-draining lymph node


title: CD4 LN Early_2


title: HOFs_siARR1_rep3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Raw reads were assessed for quality by FastQC and preprocessed  for adapter trimming and low quality (Q<30) filtering of the reads.
Filtered sequence reads were aligned to the reference Genome assembly version GRCh38.p12 with HISAT2 aligner.
To identify differentially expressed genes (DEGs) gene-level normalization and differential gene expression analysis were performed using Bioconductor R (version 4.1.2) package DESeq2 version 1.34. DEGs were assessed with a comparison of β-arrestin-1 knockdown lines over control lines, using a moderated t-test with a false discovery rate threshold of (FDR) < 0.05.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file with raw counts for each Sample

source_name: Human Ovary

growth_protocol: Human ovarian fibroblasts (HOFs) were obtained from ScienCell (Cat# 7330-SC) and cultured in Fibroblast Medium (Cat# 2301-SC) supplemented with 10% FBS, containing penicillin (10.000 U/ml)-streptomycin (10 mg/ml).

extract_protocol:
Total RNA was extracted from cells using PureZol (Cat# 7326880 BioRad), according to the manufacturer's instructions
Poly-A RNA-Seq library preparation and sequencing was performed by the BGI Genomics Co., Ltd.

value: Human Ovary

value: Primary cells

value: Human ovarian fibroblasts

value: ARR1 knockdown


title: Clam CK186S-0297

description: CK Phase III


title: HOFs_siARR1_rep2


title: WX164_HepG2_Empty_c

value: transfected with empty CRISPR construct


title: HOFs_siARR1_rep1


title: WX164_HepG2_Empty_b

value: WT


title: Clam CK184S-0295

description: CK Phase III


title: CD4 LN Iso_2


title: WX164_HepG2_Empty_a


title: Treg TIL Late_1

value: Treg


title: Clam CK183D-0009

description: CK Phase I


title: WX164_HepG2_Z5_a


title: Clam CK182P-0221

description: CK Phase II


title: WX164_HepG2_Z2_c


title: HOFs_rep2


title: HOFs_rep1


title: 524_OxLDL_72h

city: Kiel

first: Kristina

last: Schlicht

address: Düsternbrooker Weg 17

country: Germany

institute: UKSH Kiel

data_processing:
Raw FastQ files were aligned, quality controlled and transformed into read counts using the Nextflow nfcore/RNAseq pipeline
Read counts were analyzed in R v3.6.2 via edgeR and DeSEQ2 packages.
Differential expression analysis (DEA) was done in edgeR using the Quasi-Likelihood F-test function with multi-level contrasting.
Contrasts in the main analysis were modeled for the effect of OxLDL, Cytokines and normal conditions at 24h and 72h.
Assembly: GRCh37
Supplementary files format and content: raw_counts_oxLDL.txt: tab-deliminated file includes raw read counts of all samples, samples in columns

source_name: Gingiva

growth_protocol: Gingival collars biopsies from three healthy patients (n=18) were taken to grow-out gingival connective tissue cells, using the tissue explant method. The obtained cells were immunomagnetically sorted using anti STRO-1 antibody (BioLegend, San Diego, CA, USA) and anti-IgM MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany) to isolate gingival mesenchymal stem cells (G-MSCs). G-MSCs were characterized for their colony-forming-units (CFUs) ability, multilineage propensity and CD14, CD34, CD45, CD73, CD90 and CD105 stemness markers as previously explained (El-Sayed et al., 2015).

extract_protocol:
RNeasy Kit (Qiagen)
TruSeq Stranded mRNA Library Prep Workflow

treatment_protocol: G-MSCs were incubated at 37°C with 5% CO2 till 80% confluence was reached. Media were exchanged three times per week. The experimental groups were as follows: 1- Control-group: G-MSCs cultured in basic medium, comprising Eagle’s minimum essential medium (alpha modification, Sigma-Aldrich GmbH, Hamburg, Germany) with 15% fetal calf serum (FCS, HyClone, Logan, UT, USA), 400 mmol/mL L-glutamine, augmented with 1% amphotericin and antibiotics (100 µg/mL streptomycin and 100 U/mL penicillin, all from Biochrom, Berlin, Germany).  2- Cytokine-group: Basic medium supplemented with 10 ng/mL TNF-α, 100 ng/mL IFN-γ  and 1 ng/mL IL-1β (Pepro Tech Inc., Rocky Hill, NJ, USA) to mimic a classical inflammatory cocktail (Zhang et al., 2017). 3- oxLDL-group: Basic medium supplemented with 50 µg/ml oxLDL to simulate a metabolic inflammation (Zhang et al., 2022)

value: Gingiva

value: Gingival Mesenchymal Stem/Progenitor Cells

tag: individual

tag: culture medium

value: OxLDL


title: Treg TIL Early_1

value: tumor


title: Treg TIL NR_1


title: Clam CK189D-0073

description: CK Phase I

value: Adductor muscle


title: Clam CK187S-0298

description: CK Phase III

value: Hemocytes in ethanol


title: Clam CK180S-0294

description: CK Phase III


title: 523_Cytokine_72h

value: Cytokine


title: Treg TIL Iso_1

value: Isotype


title: S_Ctrl

city: Vienna

first: Gerwin

last: Heller

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Fastq files were quality trimmed by TrimGalore followed by standard STAR alignment to GRCh38. Counts were exported from SeqMonk software.
Assembly: GRCh38
Supplementary files format and content: Count table

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using Rneasy kit (Qiagen).
IlluminaTruSeqRNA Sample Prep Kit

value: Peripheral blood

tag: disease state

value: Control


title: 522_Control_72h


title: 37_AP_PB

tag: diagnosis

value: CML


title: Clam CK181D-0061

description: CK Phase I


title: CD4 TIL Late_1


title: Clam CK17S-0260

description: CK Phase III

source_name: Clam CK17S-0260


title: CD4 TIL NR_1


title: HOFs_rep3

value: Human Ovary

value: Primary cells


title: 36_AP_BM

source_name: Bone marrow

value: Bone marrow


title: Clam CK178D-0030

description: CK Phase I


title: CD4 TIL Iso_1


title: 35_CPAP_BM


title: Clam CK177D-0032

description: CK Phase I


title: Clam CK174P-0243

description: CK Phase II


title: 34_CP_PB


title: Treg LN Late_1

value: non-draining lymph node


title: 33_CP_BM


title: 519_Control_24h


title: 518_OxLDL_72h


title: Treg LN Early_1


title: Clam CK173D-0008

description: CK Phase I


title: 517_Cytokine_72h


title: 32_CP_PB


title: 516_Control_72h


title: 521_OxLDL_24h


title: Treg LN NR_1


title: Clam CK172S-0293

description: CK Phase III


title: Clam CK171P-0242

description: CK Phase II


title: 515_OxLDL_24h


title: 30_BC_PB


title: CD4 LN Late_1


title: 514_Cytokine_24h


title: 520_Cytokine_24h


title: Clam CK170D-0020

description: CK Phase I


title: 29_CP_PB


title: CD4 LN Early_1


title: 513_Control_24h


title: Clam CK16D-0058

description: CK Phase I

source_name: Clam CK16D-0058


title: CD4 LN NR_1

source_name: non-draining lymph node


title: 28_BC_PB


title: 506_OxLDL_72h


title: 27_AP_BM


title: Clam CK168D-0053

description: CK Phase I


title: Clam CK169S-0292

description: CK Phase III


title: CD4 LN Iso_1


title: 505_Cytokine_72h


title: Normal_BM


title: MC38_CD4 TIL Day 20_2


title: 31_CP_BM


title: 504_Control_72h


title: Clam CK165P-0237

description: CK Phase II


title: 503_OxLDL_24h


title: Clam CK164D-0072

description: CK Phase I


title: 25_CP_PB


title: MC38_CD4 TIL Day 20_1


title: 26_AP_BM


title: Treg LN Iso_1


title: MC38_CD4 TIL Day 16_2


title: K1_Ctrl


title: Clam CK161D-0077

description: CK Phase I


title: MC38_CD4 TIL Day 16_1


title: 502_Cytokine_24h


title: 24_AP_BM


title: 501_Control_24h


title: MC38_CD4 TIL Day 12_2


title: Wild-type M. tuberculosis, log phase, replicate 4

city: Guildford

first: Graham

last: Stewart

address: Stag Hill, University Campus, Guildford GU2 7XH

country: United Kingdom

institute: University of Surrey

description: Library name: WT4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were then mapped to the Mycobacterium tuberculosis_H37Rv reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. 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. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within gene regions were counted.
Assembly: Mycobacterium tuberculosis H37Rv (NC_000962.3)
Supplementary files format and content: csv file containing raw counts for all samples.

organism: Mycobacterium tuberculosis

extract_protocol:
Cultures were crash cooled with  frozen PBS and centrifuged at 4°C for 10 minutes at 4100 g. Cell pellets were resuspended in 1.2 ml Trizol and RNA extracted as manufacturer’s instructions with the final RNA pellet being dissolved in 40 µl water. The RNA was DNase (Qiagen) treated for 10 minutes at 30°C followed by a second on-column DNase treatment using the Zymo RNA Clean and Concentrate columns and finally eluted in water
Illumina TruSeq Paired-End kit as manufactures protocol

value: bacterium

value: log phase 7H9

value: wild-type


title: MC38_CD4 TIL Day 12_1


title: Clam CK15P-0202

description: CK Phase II

source_name: Clam CK15P-0202


title: Clam CK160P-0219

description: CK Phase II


title: Wild-type M. tuberculosis, log phase, replicate 3

description: Library name: WT3


title: G2_Ctrl


title: 23_BC_PB


title: Wild-type M. tuberculosis, log phase, replicate 2

description: Library name: WT2


title: MC38_CD4 TIL Day 8_2


title: G1_Ctrl


title: Clam CK162S-0078

description: CK Phase I


title: Clam CK157D-0019

description: CK Phase I


title: 22_AP_BM


title: Wild-type M. tuberculosis, log phase, replicate 1

description: Library name: WT1


title: MC38_CD4 TIL Day 8_1


title: Clam CK155S-0291

description: CK Phase III


title: Clam CK154D-0014

description: CK Phase I


title: MC38_CD4 LN Day 20_2


title: DarTG-knockout M. tuberculosis, stationary phase, replicate 4

description: Library name: S8

value: stationary phase 7H9

value: {delta}darT-darG


title: DarTG-knockout M. tuberculosis, stationary phase, replicate 3

description: Library name: S7


title: MC38_CD4 LN Day 20_1


title: MC38_CD4 LN Day 16_2


title: C1_Ctrl


title: DarTG-knockout M. tuberculosis, stationary phase, replicate 2

description: Library name: S6


title: MC38_CD4 LN Day 16_1


title: B1_Ctrl


title: Clam CK153D-0023

description: CK Phase I


title: DarTG-knockout M. tuberculosis, stationary phase, replicate 1

description: Library name: S5


title: Clam CK152S-0290

description: CK Phase III


title: Clam CK158P-0216

description: CK Phase II


title: Clam CK151S-0289

description: CK Phase III


title: Wild-type M. tuberculosis, stationary phase, replicate 4

description: Library name: S4


title: MC38_CD4 LN Day 12_2


title: Wild-type M. tuberculosis, stationary phase, replicate 3

description: Library name: S3


title: Clam CK149P-0241

description: CK Phase II


title: 20_CP_BM


title: MC38_CD4 LN Day 12_1


title: 18_CP_BM


title: 19_CP_PB


title: MC38_CD4 LN Day 8_2


title: MC38_CD4 LN Day 8_1


title: Wild-type M. tuberculosis, stationary phase, replicate 1

description: Library name: S1


title: B2_Ctrl


title: Clam CK148S-0288

description: CK Phase III


title: DarTG-knockout M. tuberculosis, log phase, replicate 4

description: Library name: DAR8


title: 17_CP_BM


title: Clam CK145S-0287

description: CK Phase III


title: Clam CK146D-0076

description: CK Phase I


title: B16_CD4 TIL Day 20_2

value: tumor


title: B16_CD4 TIL Day 20_1


title: Clam CK144P-0204

description: CK Phase II

value: Adductor muscle


title: DarTG-knockout M. tuberculosis, log phase, replicate 3

description: Library name: DAR7


title: B16_CD4 TIL Day 16_2


title: 21_CP_PB


title: DarTG-knockout M. tuberculosis, log phase, replicate 2

description: Library name: DAR6


title: Clam CK143S-0286

description: CK Phase III

value: Hemocytes in ethanol


title: Clam CK142D-0285

description: CK Phase I


title: B16_CD4 TIL Day 16_1


title: 14_CP_BM


title: DarTG-knockout M. tuberculosis, log phase, replicate 1

description: Library name: DAR5


title: 13_CP_BM


title: B16_CD4 TIL Day 12_1


title: Wild-type M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 4

description: Library name: WTPEN4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were then mapped to the Mycobacterium tuberculosis_H37Rv reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. 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. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within gene regions were counted.
Assembly: Mycobacterium tuberculosis H37Rv (NC_000962.3)
Supplementary files format and content: csv file containing raw counts for all samples

value: 0.6 µM TPEN


title: Wild-type M. tuberculosis, stationary phase, replicate 2

description: Library name: S2


title: Clam CK141D-0071

description: CK Phase I


title: Clam CK140S-0284

description: CK Phase III


title: B16_CD4 TIL Day 8_2


title: 12_CP_BM


title: 16_CP_BM


title: Wild-type M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 2

description: Library name: WTPEN2


title: 10_CP_BM


title: Clam CK139P-0239

description: CK Phase II


title: Clam CK13D-0084

description: CK Phase I

source_name: Clam CK13D-0084


title: B16_CD4 TIL Day 8_1


title: Wild-type M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 3

description: Library name: WTPEN3


title: 15_CP_BM


title: B16_CD4 LN Day 20_2


title: 9_CP_BM


title: Wild-type M. tuberculosis, Sautons media, replicate 4

description: Library name: WT4

value: control


title: Clam CK137S-0283

description: CK Phase III


title: Wild-type M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 1

description: Library name: WTPEN1


title: B16_CD4 LN Day 20_1


title: B16_CD4 LN Day 16_2


title: Clam CK136D-0035

description: CK Phase I


title: 7_AP_BM


title: 8_CP_BM


title: B16_CD4 LN Day 16_1


title: Clam CK135S-0282

description: CK Phase III


title: 6_BC_BM


title: Clam CK134S-0281

description: CK Phase III


title: B16_CD4 LN Day 12_2


title: Wild-type M. tuberculosis, Sautons media, replicate 1

description: Library name: WT1


title: 11_CP_BM


title: 5_BC_BM


title: DarTG-knockout M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 4

description: Library name: DTPEN4


title: Clam CK131D-0022

description: CK Phase I


title: B16_CD4 LN Day 12_1


title: B16_CD4 LN Day 8_2


title: Clam CK130P-0248

description: CK Phase II


title: DarTG-knockout M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 3

description: Library name: DTPEN3


title: 3_BC_BM


title: B16_CD4 LN Day 8_1


title: Clam CK12S-0259

description: CK Phase III

source_name: Clam CK12S-0259


title: DarTG-knockout M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 2

description: Library name: DTPEN2


title: 2_BC_BM


title: Clam CK129D-0016

description: CK Phase I


title: Wild-type M. tuberculosis, Sautons media, replicate 3

description: Library name: WT3


title: MC38_Treg TIL Day 20_2

value: Treg


title: DarTG-knockout M. tuberculosis, Sautons media + 0.6 µM TPEN, replicate 1

description: Library name: DTPEN1


title: Wild-type M. tuberculosis, Sautons media, replicate 2

description: Library name: WT2


title: MC38_Treg TIL Day 20_1


title: Clam CK128D-0012

description: CK Phase I


title: DarTG-knockout M. tuberculosis, Sautons media, replicate 4

description: Library name: D4


title: DarTG-knockout M. tuberculosis, Sautons media, replicate 3

description: Library name: D3


title: Clam CK127P-0251

description: CK Phase II


title: 1_CP_PB

value: Peripheral blood


title: MC38_Treg TIL Day 16_2


title: DarTG-knockout M. tuberculosis, Sautons media, replicate 2

description: Library name: D2


title: Bulk MARS seq- 6h200_5

city: Rishon Lezion

first: Padma Malini

last: Ravi

address: Hamacabim

institute: ARO

description: Library name: Sample10

data_processing:
100bp single reads were sequenced on a Novaseq 6000 sequencing system. The output was ~16 million reads per sample
Poly-A/T stretches and Illumina adapters were trimmed from the reads using Cutadapt. The resulting reads shorter than 30bp were discarded. The remaining reads were mapped onto 3′ UTR regions (1000 bases) of the Gallus genome (galGal5.0, UCSD) according to Refseq annotations, using STAR with EndToEnd option and out Filter Mismatch Nover Lmax was set to 0.05. Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Read counts per gene were quantified using HTSeq-count. UMI counts were corrected for saturation by considering the expected number of unique elements when sampling without replacement
Differentially expressed genes were identified using DESeq2 with the betaPrior, cooksCutoff and independent Filtering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was run using snakemake
Assembly: galGal5_0
Supplementary files format and content: DEoutput Naive_mir_200.xlsx which contains the raw and normalised counts for each sample

organism: Gallus gallus

source_name: PO/AH

growth_protocol: Cobb strain broiler (Gallus gallus) chicks were obtained on the first day of life and raised under climate-controlled rooms at 30°c temperature with free access to food and water.

extract_protocol:
RNA was isolated using Trireagent
15ng of purified RNA was used for library preparation with the bulk MARS-seq method, involving barcoding of samples by reverse transcription using an oligo dT primer, pooling of samples, and subsequent molecular reactions for linear amplification and preparation for Illumina sequencing

treatment_protocol: On day 3 posthatch has-mir-200a-3p mimic was injected into the PO/AH and sacrifieced after 6h and the naïve chicks were maintained under the controlled conditions.

value: PO/AH

value: whole tissue lysate


title: 4_CP_BM

value: CML


title: Bulk MARS seq- 6h200_4

description: Library name: Sample9


title: MC38_Treg TIL Day 16_1

data_processing:
Raw ATAC sequencing data was quality controlled, trimmed, and aligned to the mouse reference genome (Mm10) using BWA-MEM. Peak calling was performed using MACS2 version 2.1.2 with the options -B, -q 0.01, – nomodel, -f BAM, -g mm. Peaks that overlapped blacklisted regions were removed. Read numbers, and feature distribution plots were obtained using the ataqv package in R. Count tables were generated using the Rsubread featureCounts on the filtered BAM alignments.
Assembly: Mm10

source_name: tumor


title: Bulk MARS seq- 6h200_3

description: Library name: Sample8


title: DarTG-knockout M. tuberculosis, Sautons media, replicate 1

description: Library name: D1


title: Clam CK126P-0215

description: CK Phase II


title: MC38_Treg TIL Day 12_2


title: nonfailure_patient_4

type: RNA

city: Chicago

first: David

last: Zemmour

state: Illinois

address: 924 E 57th St

department: Pathology

institute: University of Chicago

hyb_protocol: Samples were processed following NanoString's standard protocol (Manual Slide Preparation, MAN-10159-01, November 2022), sections were hybridized with the 1K Human Universal Cell Characterization Panel, comprising 974 spatially barcoded probes targeting 950 genes of interest, 10 control genes and a 20-gene custom panel (CCR4, CCR6, CD57, CD73, EBI3, EGR1, FOSB, GPR15, GPR25, HOPX, ID2, IKZF2, KLRG1, LEF1, NR4A1, RORC, SLC2A3, TGFBI, TXNIP, ZFP36L2).

scan_protocol: Samples were processed following NanoString's standard protocol (CosMx SMI Instrument User Manual, MAN-10161-01, November 2022).

data_processing:
Cells were filtered out if they had more than 5% negative control probe counts, or fewer than 10 transcript counts. Additionally, cell area outliers were identified and removed using the interquartile range (IQR) method, with cells having an area more than 1.5 times the IQR below the first quartile or above the third quartile being excluded. The IQR method was also applied to filter out FoVs where the mean count per cell was 1.5 times the IQR below the first quartile. After applying these quality control measures, 96.53% of cells across samples and FoVs were retained.
Please refer to the ReadMe_SMI_Data_File.txt for a detailed description of the values in the data files.

label: 1K Human Universal Cell Characterization Panel with 20 custom genes

source_name: Left colon, non-failure

extract_protocol: Samples were processed following NanoString's standard protocol (Manual Slide Preparation, MAN-10159-01, November 2022).

treatment_protocol: Colectomy specimens collected during IPAA surgery in IBD patients prior to pouch formation.

tag: experiment date

tag: age (years)

tag: Sex

value: M

value: ulcerative colitis

value: left colon

value: severely active

tag: pouch outcome

value: non failure


title: Bulk MARS seq- 6h200_2

description: Library name: Sample7

tag: tissue


title: Bulk MARS seq- 6h200_1

description: Library name: Sample6


title: Clam CK125S-0280

description: CK Phase III

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal


title: Clam CK122D-0087

description: CK Phase I


title: nonfailure_patient_3

label_protocol: Samples were processed following NanoString's standard protocol (Manual Slide Preparation, MAN-10159-01, November 2022), sections were hybridized with the 1K Human Universal Cell Characterization Panel, comprising 974 spatially barcoded probes targeting 950 genes of interest, 10 control genes and a 20-gene custom panel (CCR4, CCR6, CD57, CD73, EBI3, EGR1, FOSB, GPR15, GPR25, HOPX, ID2, IKZF2, KLRG1, LEF1, NR4A1, RORC, SLC2A3, TGFBI, TXNIP, ZFP36L2).

value: F


title: MC38_Treg TIL Day 12_1

extract_protocol:
Tumors were prepared for single cell suspension with in Liberase (Sigma Aldrich) at 50 mg/mL for 15 minutes at 37°C in RPMI without fetal bovine serum (FBS) and mechanical disruption. Tumor samples were negatively selected to remove CD105+ epithelial cells using CD105 Biotin (eBioscience) and Pierce Streptavidin Beads (ThermoFisher).
Libraries were constructed for ATACseq following manufacturer's instructions

tag: tumor cell_line


title: Clam CK121D-0050

description: CK Phase I


title: MC38_Treg TIL Day 8_2

tag: cell type


title: Clam CK120S-0279

description: CK Phase III


title: Bulk MARS seq- Naïve5

description: Library name: Sample5

value: Naïve


title: MC38_Treg TIL Day 8_1

value: tumor

tag: genotype


title: Bulk MARS seq- Naïve4

description: Library name: Sample4

tag: treatment


title: nonfailure_patient_1


title: MC38_Treg LN Day 20_2

value: non-draining lymph node


title: failure_patient_4

source_name: Left colon, failure

value: failure


title: Bulk MARS seq- Naïve3

description: Library name: Sample3


title: Clam CK115S-0278

description: CK Phase III

value: Hemocytes in ethanol


title: MC38_Treg LN Day 20_1


title: Bulk MARS seq- Naïve2

description: Library name: Sample2


title: MC38_Treg LN Day 16_2


title: failure_patient_3


title: Clam CK113D-0011

description: CK Phase I

value: Adductor muscle


title: failure_patient_2


title: Clam CK112P-0236

description: CK Phase II


title: MC38_Treg LN Day 16_1

value: Treg


title: RRBS_spermF0EHC_rep4

description:
Library name: Sample9
EHC-152_S10

data_processing:
Trimming of Illumina adapters, as well as quality trimming, were performed with Trim Galore
Reads were mapped to the chick genome (galGal5.0) using Bismark v. 0-22-3, bowtie mode. Next, methylation calls were extracted with Bismark, methylation extractor mode.
Differential methylation on a single CpGs site (DMS) was extracted and analyzed by edgeR, with the recommended cutoff of at least 8 reads in every sample before being considered in the analysis and FDR < 0.05. DMRs were extracted and  analyzed by metilene v. 0.2-8.
Assembly: galGal5_0
Supplementary files format and content: methyl_DMR_metilene.xlsx
Supplementary files format and content: methyl_edgeR.xlsx it contains the raw methylated reads and unmethylated reads and methylation percentages

source_name: Sperm

growth_protocol: We have collected sperm from the Embryonic heat conditioned (eggs were incubated at 39.5°C and 65% relative humidity for 12 h/day on embryonic days 7 to 16) and control chicken (eggs were incubated at 37.8°C and 56% relative humidity throughout the 21 days of the incubation period) after attaining sexual maturity individually and was kept immediately in -80°C.

extract_protocol:
DNA was isolated from the sperm sample using Genomic Mini AX Swab & Semen Spin (A&A Biotechnology, Gdansk, Poland)
Libraries were prepared using Zymo-Seq RRBS Library Kit (Zymo).

treatment_protocol: Hatched chicks were weighed, their sex was identified according to wing feathering, and they were tagged and randomly divided into 8 chicks per pen in climate-controlled rooms at 32°C under a 22/2 h cycle of artiﬁcial illumination with ad libitum access to food and water. On day 7 posthatch, the temperature was changed to 30°C and chicks were further divided into 5 chicks per pen and grown until attaining sexual maturity

value: Sperm

value: EHC conditioned


title: MC38_Treg LN Day 12_2


title: failure_patient_1


title: nonfailure_patient_2


title: MC38_Treg LN Day 12_1


title: Clam CK111D-0042

description: CK Phase I

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).


title: SRR1 mutant, young fruiting gill, rep3

city: Szeged

first: Zhihao

last: Hou

address: Temesvári krt. 62

country: Hungary

institute: HUN-REN Biological Research Centre Szeged

data_processing:
Trimmed by bbduk.sh (version 38.92, qtrim=r trimq=10 minlength=20)
Trimmed reads were mapped to the reference genome using STAR (version 2.6.1, --alignIntronMin 20 --alignIntronMax 3000)
Featurecount (version 2.0.1) was used for quantification based on CDS features in the GFF file
Assembly: Coprinopsis cinerea
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Coprinopsis cinerea

source_name: Gill

extract_protocol:
Quick-RNA Miniprep Kit (Zymo Research, USA),
RNA libraries for RNA-seq were prepared using  mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Gill


title: Clam CK110S-0277

description: CK Phase III


title: RRBS_spermF0EHC_rep2

description:
Library name: Sample7
EHC-145_S8


title: Clam CK10D-0075

description: CK Phase I

source_name: Clam CK10D-0075


title: Clam CK116P-0200

description: CK Phase II


title: SRR1 mutant, young fruiting gill, rep2


title: RRBS_spermF0EHC_rep1

description:
Library name: Sample6
EHC-142_S6


title: MC38_Treg LN Day 8_1


title: Clam CK106D-0029

description: CK Phase I


title: B16_Treg TIL Day 20_2


title: Wild type, young fruiting gill, rep3


title: RRBS_spermF0C_rep5

description:
Library name: Sample5
Cntrl-224_S5

value: Non Conditioned


title: Clam CK105S-0276

description: CK Phase III


title: Bulk MARS seq- Naïve1

description: Library name: Sample1

value: PO/AH

value: whole tissue lysate


title: Wild type, young fruiting gill, rep2


title: B16_Treg TIL Day 20_1


title: RRBS_spermF0C_rep4

description:
Library name: Sample4
Cntrl-222_S4


title: RRBS_spermF0C_rep3

description:
Library name: Sample3
Cntrl-205_S3


title: B16_Treg TIL Day 16_2


title: Wild type, young fruiting gill, rep1


title: Clam CK103P-0235

description: CK Phase II


title: RRBS_spermF0C_rep2

description:
Library name: Sample2
Cntrl-202_S2


title: B16_Treg TIL Day 16_1


title: MC38_Treg LN Day 8_2


title: RRBS_spermF0EHC_rep3

description:
Library name: Sample8
EHC-151_S9


title: father

city: Houston

first: James

middle: R.

last: Lupski

state: TX

address: One Baylor Plaza

institute: Baylor College of medicine

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0)

data_processing:
Agilent Feature Extraction Software (version 12.0) was used for background subtraction and normalization.
normalized log10 ratio (Cy5/Cy3) representing patient/reference

source_name: Whole Blood Extracted Genomic DNA

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: gender

value: male

source_name: Blood


title: B16_Treg TIL Day 12_2


title: HH24-25, miR-455-3p mimic 3

city: Norwich

first: Ian

last: Clark

state: Norfolk

address: Earlham Road

institute: University of East Anglia

data_processing:
FASTQC followed by TrimGalore to trim adapter sequences and low quality reads
Transcripts obtained from Ensembl and Kallisto to map reads to all transcripts
Sleuth used to identify differential expression
Assembly: GRCg6a
Supplementary files format and content: Excel files of normalised counts for each sample

source_name: Limb bud

extract_protocol:
Total RNA was purified using Qiagen Rneasy Micro
Libraries constructed and sequenced by Novogene

value: Limb bud

value: wild-type

value: miR-455-3p mimic


title: RRBS_spermF0C_rep1

description:
Library name: Sample1
Cntrl-201_S1


title: Clam CK102S-0275

description: CK Phase III


title: mother

value: female


title: B16_Treg TIL Day 12_1

value: tumor


title: SRR1 mutant, young fruiting gill, rep1


title: proband


title: HH24-25, miR-455-3p mimic 1


title: B16_Treg TIL Day 8_2


title: B16_Treg TIL Day 8_1


title: Clam CK104D-0021

description: CK Phase I


title: HH24-25, control 4

value: control mimic


title: B16_Treg LN Day 20_2

value: non-draining lymph node


title: HH24-25, control 3


title: B16_Treg LN Day 20_1


title: B16_Treg LN Day 16_2


title: B16_Treg LN Day 16_1


title: HH24-25, control 2


title: B16_Treg LN Day 12_2


title: HH24-25, control 1


title: B16_Treg LN Day 12_1


title: B16_Treg LN Day 8_2


title: HH24-25, miR-455-3p mimic 2


title: B16_Treg LN Day 8_1


title: Prox1cKO, healthy retina

city: Daejeon

first: Jin Woo

last: Kim

state: Daejeon

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: library1

data_processing:
The processed data files were generated using the Cell Ranger pipeline (version 7.0). The cellranger count command was used to process the data with default parameters, without any custom modifications. The mouse reference genome mm10 (version 2020-A) was used for alignment and gene quantification.
Assembly: genome build number: GRCm38
Supplementary files format and content: features.tsv lists all the genes or features measured in the experiment. Each row contains the gene ID and gene name. It corresponds to the rows of the count matrix. barcodes.tsv contains a list of unique cell barcodes, one per line. Each barcode represents an individual cell captured in the experiment. It corresponds to the columns of the count matrix. matrix.mtx stores the raw count matrix in a sparse format, containing the number of UMIs detected for each gene in each cell. The rows map to genes (from features.tsv), and the columns map to cells (from barcodes.tsv). It efficiently stores the expression data by recording only non-zero values.

source_name: retina

extract_protocol:
Freshly prepared samples were resuspended in the resuspension buffer (PBS containing 0.04% BSA and 0.5U/ml RNase inhibitor). Dissociated cells were then filtered through a 50-ml cell filter.
Cells (~10,000) were loaded into a 10x Genomics Chromium Next GEM Single Cell system (10x Genomics). Single cell cDNA libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Kit according to the manufacturer’s instructions.

value: retina

value: cKO


title: Prox1WT, MNU injured retina, dpi4

description: Library name: library4

value: WT

value: MNU injection


title: Prox1cKO, MNU injured retina, dpi4

description: Library name: library2


title: Prox1WT, healthy retina

description: Library name: library3


title: GFP_JUG2_+DOX_rep1

first: Francois

last: Cossais

address: Otto-Hahn-Platz 8

department: Institute of Anatomy

institute: Kiel University

description: gene expression data from GFP JUG2 cell, Dox treated

hyb_protocol: cRNA were hybridized on mouse Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (fluidics protocol FS450_007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Transcriptomic Analysis Console Version 4.0.1.36 (TAC 4.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Rattus norvegicus

source_name: GFP EGC cell line, +dox

label_protocol: cRNA was performed using the GeneChip WT Plus Reagent Kit on 100ng total RNA  (Thermo-fisher Scientific)

growth_protocol: JUG2 cells were grown in DMEM+10% FCS for 24h

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: cells were treated with 1µg/ml doxycycline for 48h and compared to untreated cells (controls)

tag: cell

value: rat EGC cell line


title: GFP_JUG2_control_rep1

description: gene expression data from GFP JUG2 cell, control

source_name: GFP EGC cell line, control


title: SOX10_JUG2_+DOX_rep4

description: gene expression data from SOX10 JUG2 cell, Dox treated

source_name: SOX10 EGC cell line, +dox


title: MYOPIA 5

status: Public on Feb 25 2025

city: beijing

first: heyan

last: li

state: beijing

address: 1 Beijing Legation Quarter Road, Dongcheng District

institute: Beijing Tongren Hospital

description: MYOPIA, replicate biosample 5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Cavpor3.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Cavia porcellus

source_name: Scleral tissue of the eye

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

value: Scleral tissue of the eye

value: MYOPIA


title: SOX10_JUG2_control_rep3

description: gene expression data from SOX10 JUG2 cell, control

source_name: SOX10 EGC cell line, control


title: MYOPIA 2

description: MYOPIA, replicate biosample 2


title: MYOPIA 3

description: MYOPIA, replicate biosample 3


title: SOX10_JUG2_control_rep4


title: SOX10_JUG2_+DOX_rep2


title: SOX10_JUG2_control_rep2


title: control 4

description: control group, replicate biosample 4

value: control


title: control 5

description: control group, replicate biosample 5


title: control 3

description: control group, replicate biosample 3


title: control 1

description: control group, replicate biosample 1


title: SOX10_JUG2_+DOX_rep3


title: SOX10_JUG2_control_rep1


title: MYOPIA 4

description: MYOPIA, replicate biosample 4


title: CN144 Biorep 2

city: Quezon City

first: Ma. Anita

middle: Mascareñas

last: Bautista

state: Metro Manila

address: Ma. Regidor St., National Science Complex

department: National Institute of Molecular Biology and Biotechnology

country: Philippines

institute: University of the Philippines Diliman

description:
Library name: Sample 11
Column name in featurecounts_indiv_mm.txt: CN144_biorep2

data_processing:
reads were trimmed and filtered using fastp v0.23.4 (trimming of adapters, poly-G, and poly-X tails; Phred Score threshold = Q30).
Reads were mapped to the reference genome using STAR's two-pass mapping protocol.
Quantification of gene expression was done using featureCounts (Subread Package v2.0.6)
Differential Gene Expression analysis was performed using DESeq2 v1.44.0 in R Studio (v2024.04.2+764). Genes with padj<0.1 & |log2FoldChange|>1 were considered differentially expressed.
Assembly: NCBI GCF_030269925.1
Supplementary files format and content: featurecounts_indiv_mm.txt

organism: Bombyx mori

source_name: whole B.mori larva, 3rd day of 5th instar

growth_protocol: Silkworm samples for both parental and hybrid strains were reared in DOST-CAR, La Trinidad, Benguet (Coordinates: 16.45846597579819, 120.58826862840532). A relative humidity of 80 to 85% and a temperature of 26 to 28°C were maintained from 1st to 3rd instar, and a relative humidity of 75 to 80% and a temperature of 22 to 24°C from 4th to 5th instar. During rearing, feeding with mulberry leaves was also done three (3) times per day: in the morning, afternoon, and evening

extract_protocol:
RNA samples were extracted using a modified TRIzol RNA extraction, with an additional wash step with 1X PBS prior to homogenization to eliminate plant and waste material in the gut.
Libraries for RNAseq were prepared using the TruSeq Stranded Total RNA kit from Illumina following manufacturer's protocol.

tag: strain


title: MYOPIA 1

description: MYOPIA, replicate biosample 1


title: CN144 Biorep 3

description:
Library name: Sample 12
Column name in featurecounts_indiv_mm.txt: CN144_biorep3

value: whole B.mori larva, 3rd day of 5th instar


title: NC144 Biorep 1

description:
Library name: Sample 7
Column name in featurecounts_indiv_mm.txt: NC144_biorep1


title: B221 Biorep 1

description:
Library name: Sample 4
Column name in featurecounts_indiv_mm.txt: B221_biorep1


title: NC144 Biorep 3

description:
Library name: Sample 9
Column name in featurecounts_indiv_mm.txt: NC144_biorep3


title: NC144 Biorep 2

description:
Library name: Sample 8
Column name in featurecounts_indiv_mm.txt: NC144_biorep2


title: Lat21 Biorep 2

description:
Library name: Sample 2
Column name in featurecounts_indiv_mm.txt: Lat21_biorep2


title: B221 Biorep 3

description:
Library name: Sample 6
Column name in featurecounts_indiv_mm.txt: B221_biorep3


title: BA2-methy

city: yangzhou

first: Liu

middle: zi

last: yu

address: shuangqiao

institute: Yangzhou University

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
The raw data was processed to obtain high quality clean reads using FastQC to removing adapters, high contents of unknown bases reads and low quality reads.
Bismark software (version 0.16.3) was used to perform alignments of bisulfite-treated reads to a reference genome ((https://www.rosaceae.org/rosaceae_downloads/Pyrus_x_bretschneideri/Pbretschneideri-genome.v1.1/assembly/pbr.v1.1.chr.fa.gz) )
Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts   (mC+umC) and the non-conversion rate (r). Differentially methylated regions (DMRs) were identified using the DSS software.
Genome_build: Pyrus x bretschneideri ‘DangshanSuli’  Genome(assembly Pbr_v1.1)
Supplementary_files_format_and_content: Excel files include mean methylation level, differentially methylated regions and C context (.xls)

organism: Pyrus pyrifolia

source_name: Cuiguan

growth_protocol: Seven-year-old  ‘Cuiguan’ pears growing in an orchard in Yizheng, Jiangsu, China.

extract_protocol:
Genomic DNA was extracted by the ethyl ammonium bromide (CTAB) method using skin tissues collected from fruits with control and fruit bagging treatment 115 DAFB with three biological replicates.
Bisulfite seq library was generated with Accel-NGS® Methyl-Seq DNA Library Kit and the library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Half of the pear fruitlets were covered with Kobayashi paper bags. Single-layer white bags (F-PK2) were used 20 days after full bloom (DAFB) and double-layer yellow-white bags were used 40 DAFB. The other fruits without fruit bagging were set as control. Fruit samples were collected at  115 DAFB.

tag: cultivar

value: Cuiguan

value: pear fruit harvested 115 DAFB with fruit bagging treatment

tag: organ

value: fruit skin


title: Lat21 Biorep 3

description:
Library name: Sample 3
Column name in featurecounts_indiv_mm.txt: Lat21_biorep3


title: Lat21 Biorep 1

description:
Library name: Sample 1
Column name in featurecounts_indiv_mm.txt: Lat21_biorep1


title: BA1-methy


title: CG3-methy

value: pear fruit harvested 115 DAFB without treatment


title: B221 Biorep 2

description:
Library name: Sample 5
Column name in featurecounts_indiv_mm.txt: B221_biorep2


title: BA3-methy


title: CN144 Biorep 1

description:
Library name: Sample 10
Column name in featurecounts_indiv_mm.txt: CN144_biorep1


title: SOX10_JUG2_+DOX_rep1


title: control 2

description: control group, replicate biosample 2

value: male


title: CG2-methy


title: Calcitriol Pool 3

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

description: Gene expression data from Calcitriol treatment 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom D Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with TAC Affymetrix

source_name: CaSki cells + Calcitriol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA extraction was performed using the standard protocol described by Chomczynski and Sacchi employing Trizol reagent [11] . The obtained RNA was quantified spectrophotometrically, and the integrity of the RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), ensuring that the RNA samples exhibited an integrity value equal to or greater than 9.0 to undergo processing for microarray analysis.

treatment_protocol: CaSki cells were seeded (150,000 cells) onto 4-well cell culture slides in growth medium. After 24 hours, the medium was aspirated and replaced with either 0.1% ethanol as vehicle or 1x10 -8 M calcitriol in treatment medium. Cells were then incubated for 24 hours, washed twice with warm saline solution, and fixed with absolute ethanol at -20°C for 8 minutes. Following fixation, cells were permeabilized and blocked in fixation/permeabilization solution for 1 hour at room temperature (BD Biosciences, Franklin Lakes, NJ, USA). Slides were incubated overnight at 4°C with primary antibodies against VDR (mouse monoclonal anti-VDR antibody, 1:100, sc-13133X, Santa Cruz Biotechnology, Dallas, TX, USA) and RXR (rabbit polyclonal anti RXR α,β,γ antibody, 1:100, sc-774X, Santa Cruz Biotechnology). Negative controls were incubated with perm/wash solution (BD Biosciences) without primary antibodies. After primary antibody incubation and 3 washes, slides were incubated for 1 hour at room temperature with goat anti-mouse IgG secondary  antibody conjugated with Cy3 (1:1000, A10521, Life Technologies, Carlsbad, CA, USA) or goat anti-rabbit IgG secondary antibody conjugated with Alexa Fluor 488 (1:500, 111- 547-003, Jackson ImmunoResearch, West Grove, PA, USA). Slides were mounted with mounting medium and analyzed using an epifluorescence microscope (Olympus BX51, Japan).

tag: cell line

value: CaSki

value: Cervical Cancer

value: Calcitriol


title: Calcitriol Pool 2

description: Gene expression data from Calcitriol treatment 2


title: Control Pool3

description: Gene expression data from Control 3

source_name: CaSki cells + vehicle

value: vehicle


title: Control Pool2

description: Gene expression data from Control 2


title: CG1-methy


title: Control Pool1

description: Gene expression data from Control 1


title: 22 weeks BBN treated bladder mucosa

city: Bergen

first: Luiza

last: Ghila

address: Haukelandsbakken 15

department: Department of Clinical Science

country: Norway

institute: University of Bergen

description:
Library name: Sample 3
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation was performed using Cell Ranger V8.0.1.
Assembly: GRCm39-2024-A and GRCh38
Supplementary files format and content: Filtered feature matrix files

source_name: Bladder mucosa

extract_protocol:
Separated mucosa was minced into small pieces and then digested at 37oC in a buffer containing 1 mg/mL Collagenase IV and 100 ug/mL DNase I in PBS for 3o minutes. After the incubation period, the digestion solution was triturated using a 5 mL pipette for 1 minute before centrifuging for 10 minutes at 350xg at 4oC. The supernatant was then removed, and the pellet was resuspended in 700 uL of accutase (STEMCELL Technologies, 07922). The suspension was incubated in a nutator mixer for 10 minutes at 37oC, which was then centrifuged for 10 minutes at 350xg at 4oC. Next, the pellet was resuspended using 0.5 mL of RBC lysis buffer containing NH4Cl, NaHCO3 and EDTA in Millipore water and incubated for 1 minute before adding 4.5 mL of PBS to stop the RBC lysis. The suspension was then passed through 70 um cell strainer into a different 50 mL tube and centrifuged for 10 minutes at 350xg at 4oC. The supernatant was then removed and 300 uL of cell staining buffer (PBS with 2% FBS) was added to the cells. The cells were sorted using fluorescence-activated cell sorting and propidium iodide (PI) (1:300) staining was used to sort the live cell.
Following the manufacturer’s protocol, Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics) was used to perform single-cell RNA sequencing. In short, a single-cell suspension was prepared ensuring >90% cell viability using 1% BSA-PBS. The concentration of cells was adjusted to 700-1000 cells/uL and capture of ~10,000 cells per sample was targeted. To encapsulate single cells with barcoded Gel Beads, cells were loaded into Chromium Chip B and the Chromium Controller was used to generate Gel Beads-in-Emulsion (GEMs). Further, to generate barcoded cDNA, reverse transcription was implemented within GEMs and the cleanup was performed after using silane magnetic beads. PCR was performed to amplify the barcoded cDNA, and the product purification was done using SPRIselect magnetic beads. Then, fragmenting the cDNA, end repairing, A-tailing and ligating sequencing adapters were performed to construct the sequencing libraries. The libraries were purified using SPRIselect beads after another round of PCR amplification and quantification was performed using Tapestation 4150 (Agilent G2992AA). The 10x Genomics gene expression libraries were pooled together and sequenced on an Illumina NovaSeq 6000 system using an S1-100 flowcell. Each library contained ~10,000 cells and 53,000 reads per cell were targeted. Paired-End sequencing with a configuration of read 1 = 28bp, read 2 = 90bp, dual-index = 10bp was performed and 1% of phiX control library was added to the flowcell to serve as a sequencing control.

value: Bladder mucosa

value: BBN (carcinogen)


title: Calcitriol Pool 1

description: Gene expression data from Calcitriol treatment 1


title: Non-treated bladder muscosa 1

description:
Library name: Sample 1
10X Genomics

value: No treatment


title: Old,blood neutrophils,scRNAseq

city: Shanghai

first: guiheng

last: zhang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

description:
Library name: sample2
BD Rhapsody

data_processing:
Cell Ranger software was used to process Chromium single cell data to align reads, generate feature-barcode matrices, make gene counting and aggregation.
Assembly: mm10
Supplementary files format and content: Compressed tab-separated values files and matrix files.

source_name: blood

extract_protocol:
The whole blood containing EDTA was suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were stained with mouse CD45, CD11b and Ly6G antibody, and underwent flow sorting to obtain live CD45+ CD11b+ and Ly6G+ cells. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
BD Rhapsody system was used to capture the transcriptomic information of the old and young mouse blood sorted Ly6G+ single cells.Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

value: blood

tag: age

value: 24 month

value: sorted CD11b and Ly6G double positive cells


title: Mouse2 lung, Klebsiella pneumoniae wzi deletion mutant infected, 10 hour

city: Shenzhen

first: Sha

last: Wei

address: Dongmen North Road No. 1017, Shenzhen, China

institute: Shenzhen People’s Hospital

description:
Library name: R22040320-WH-RNA-118-3-822-077wzi-10-2
Column name in raw counts TPM.csv: wzi-10-2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic(v0.39)
Trimmed sequence reads were mapped to mm10 using hisat2(v2.1.0)
Read count extraction and normalization were performed using featureCounts(v2.0.3)
Assembly: mm10
Supplementary files format and content: csv file includes TPM for each Sample

source_name: lung

growth_protocol: C57BL/6 mice were bred and maintained under specific pathogen-free (SPF) conditions, and 5-7 weeks old mice were used in the experiments.

extract_protocol:
Total RNAs from lung samples were extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER Mrna-seq Library Prep kit following manufacture protocols.

treatment_protocol: Mice were infected intranasally with  WT or wzi deletion K. pneumoniae for 5 and 10 hours.

value: lung

value: WT

tag: time

value: 10 hour


title: Mouse2 lung, Klebsiella pneumoniae wzi deletion mutant infected, 5 hour

description:
Library name: R22040319-WH-RNA-118-2-822-077wzi-5-2
Column name in raw counts TPM.csv: wzi-5-2

value: 5 hour


title: Mouse1 lung, Klebsiella pneumoniae wzi deletion mutant infected, 5 hour

description:
Library name: R22040319-WH-RNA-118-2-822-077wzi-5-1
Column name in raw counts TPM.csv: wzi-5-1


title: Young,blood neutrophils,scRNAseq

description:
Library name: sample1
BD Rhapsody

value: 2 month


title: Mouse1 lung, Klebsiella pneumoniae WT infected, 5 hour

description:
Library name: R22040318-WH-RNA-118-1-822-077WT-5-1
Column name in raw counts TPM.csv: WT-5-1

value: Klebsiella pneumoniae WT infected


title: Mouse3 lung, PBS treated control, 5 hour

description:
Library name: R22040318-WH-RNA-118-1-822-077PBS-3
Column name in raw counts TPM.csv: PBS-3

value: PBS treatment


title: Mouse2 lung, Klebsiella pneumoniae WT infected, 10 hour

description:
Library name: R22040320-WH-RNA-118-3-822-077WT-10-2
Column name in raw counts TPM.csv: WT-10-2


title: Mouse3 lung, Klebsiella pneumoniae WT infected, 10 hour

description:
Library name: R22040320-WH-RNA-118-3-822-077WT-10-3
Column name in raw counts TPM.csv: WT-10-3


title: VEH, H3K27Ac

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany St

institute: Rutgers Cancer Institute of New Jersey

description: Library name: LONG_TERM_VEH_H3K27Ac

data_processing:
ChIP-seq reads were aligned to the mm39 genome using bwa version 0.7.17. Only uniquely mapping reads with at most two mismatches were retained. In addition, duplicate reads (“PCR duplicates”) were removed using BAMtools (v2.5.2) and Samtools (v1.17).
Peaks were called uing MACS2 v2.7.1 with the significance cut-off q-value <=0.01
Differential peak analysis was performed using edgeR (v 4.20)
bigWig files were generated using deepTools (v 3.5.1).
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Leukemic spleen

growth_protocol: Acly conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice.

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. Pellets of 25 million cells were formaldehyde-crosslinked and frozen.
ChIP-seq libraries were obtained using Active Motif-validated antibodies and anti-H3K27ac (ThermoFisher Scientific, MA5-2351), and subsequently prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were allowed to become overtly leukemic and then treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection, and leukemic spleens were collected 72h later or terminally.

value: Leukemic spleen

value: Leukemic splenocytes

value: Acly-WT


title: Mouse1 lung, Klebsiella pneumoniae wzi deletion mutant infected, 10 hour

description:
Library name: R22040320-WH-RNA-118-3-822-077wzi-10-1
Column name in raw counts TPM.csv: wzi-10-1


title: Mouse1 lung, PBS treated control, 5 hour

description:
Library name: R22040318-WH-RNA-118-1-822-077PBS-1
Column name in raw counts TPM.csv: PBS-1


title: Non-treated bladder muscosa 2

description:
Library name: Sample 2
10X Genomics

value: male


title: Mouse2 lung, PBS treated control, 5 hour

description:
Library name: R22040318-WH-RNA-118-1-822-077PBS-2
Column name in raw counts TPM.csv: PBS-2


title: Mouse1 lung, Klebsiella pneumoniae WT infected, 10 hour

description:
Library name: R22040320-WH-RNA-118-3-822-077WT-10-1
Column name in raw counts TPM.csv: WT-10-1


title: TMX, H3K27Ac

description: Library name: LONG_TERM_TMX_H3K27Ac

value: Acly-deleted


title: Cpt1aFlox_SpcKO_MHV68_replicate_4

city: Columbus

first: Jhonny

last: Rodriguez Lopez

state: Ohio

address: Holly Ave 1383 203A

department: Internal medicine

institute: The Ohio State University

description:
Library name: Sample 8
10x genomics

data_processing:
Raw sequencing reads were processed using the Cell Ranger pipeline (v7.1.0, 10x Genomics) for quality assessment and alignment to the mouse reference genome.
The reference datasets used were refdata-gex-mm10-2020-A and Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10 provided by 10x Genomics.
A unique molecular identifier (UMI) count matrix was generated as the output of Cell Ranger, which was then used to create a Seurat object for downstream analysis.
Quality control metrics included filtering cells based on gene expression counts and mitochondrial RNA content.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed data files include raw counts and normalized counts, which contain information on cell, respectively.

source_name: Mouse Lung

extract_protocol:
From FFPE lung tissue, two 50-µm scrolls were obtained and dissociated into a single-cell suspension according to demonstrated Protocol CG000632, Rev B by 10x Genomics. The cell suspension was counted to determine the single cell reaction input between 5x10^5 and 2x10^6 cells.
From isolated cells, fixed RNA profiling and library preparation (Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples, User Guide CG000527, Rev E. 10x Genomics) were conducted with the Chromium X platform.

treatment_protocol: Lung tissues were obtained from mice with specific genotypes (Cpt1a-flox or SpcKO) and infected with MHV68. No additional treatments were applied before tissue processing.

value: Mouse Lung

value: Lung cell types


title: Cpt1aFlox_SpcKO_MHV68_replicate_3

description:
Library name: Sample 7
10x genomics


title: Cpt1aFlox_SpcKO_MHV68_replicate_2

description:
Library name: Sample 6
10x genomics


title: Mouse3 lung, Klebsiella pneumoniae wzi deletion mutant infected, 10 hour

description:
Library name: R22040320-WH-RNA-118-3-822-077wzi-10-3
Column name in raw counts TPM.csv: wzi-10-3


title: Cpt1aFlox_SpcKO_MHV68_replicate_1

description:
Library name: Sample 5
10x genomics


title: Cpt1a_Flox_MHV68_replicate_3

description:
Library name: Sample 3
10x genomics


title: Cpt1aFlox_SpcKO_MHV68_replicate_5

description:
Library name: Sample 9
10x genomics


title: Cpt1a_Flox_MHV68_replicate_2

description:
Library name: Sample 2
10x genomics


title: Mouse3 lung, Klebsiella pneumoniae wzi deletion mutant infected, 5 hour

description:
Library name: R22040319-WH-RNA-118-2-822-077wzi-5-3
Column name in raw counts TPM.csv: wzi-5-3


title: Cpt1a_Flox_MHV68_replicate_1

description:
Library name: Sample1
10x genomics


title: Vesicular Stomatitis Virus Challenge in PBS-Treated Group 2

first: yangdian

last: lai

address: South Chongqing Road 281

institute: Shanghai Jiaotong University School of Medicine

description: Library name: PV2

data_processing:
Raw reads of fastq form at were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed usi ng R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: NCBI:GRCm39
Supplementary files format and content: FASTQ Files

source_name: ascites tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end read swere generated.

value: ascites tumor

value: macrophages

value: VSV challenge

tag: batch


title: Vesicular Stomatitis Virus Challenge in BCG-Treated Group 2

description: Library name: BGV2


title: Vesicular Stomatitis Virus Challenge in BCG-Treated Group 1

description: Library name: BGV1


title: Vesicular Stomatitis Virus Challenge in PBS-Treated Group 1

description: Library name: PV1


title: BCG-lysate Control Group 2

description: Library name: BGM2

value: mock


title: Phosphate-Buffered Saline Control Group 2

description: Library name: PM2

value: WT


title: BCG-lysate Control Group 1

description: Library name: BGM1


title: 921_Veh

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: Library name: 921

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned and quantitated with Illumina DRAGEN version 3.9.3-8 Bio-IT platform
Assembly: Ensembl GRCm38.101
Supplementary files format and content: Gene counts with CPM and TPM in tab-delimitted text format

source_name: Cortex

extract_protocol:
Frozen cortical tissue was weighed and homogenized in RNAase-free beaded tubes (REDE, Next Advance) in chloroform with TRIzol™. Samples were centrifuged for 15 minutes at 12’000xg at 4°C and the aqueous upper supernatant transferred for RNA isolation with the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.
Takara Clontech SMARTer Ultra Low RNA

treatment_protocol: Mice were gavaged daily with a single 30mg/kg dose of lemborexant or 0.5% methylcellulose vehicle at ZT13, starting at 7.5M of age until euthanizing at 9.5M of age.

value: Cortex

value: Veh


title: 907_Lem

description: Library name: 907

value: Lem


title: 933_Veh

description: Library name: 933


title: Phosphate-Buffered Saline Control Group 1

description: Library name: PM1