title: PS33G

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

description: Library name: PS33G-7669

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (hg38 from UCSC). Human reference was used for gene annotation and counting gencode.v42. Uniquely mapped reads were quantified using featureCounts using protein coding genes.
Assembly: Human hg38
Supplementary files format and content: tab-delimited text files raw counts

source_name: lung cancer

growth_protocol: Cells were maintaned in RPMI media supplemented with 10% heat-inactivated FBS and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extractected using the TRIzol Reagent from Invitrogen following the manufacturer's instructions. Total RNA was purified using the NucleoSpin RNA Clean-up Kit (Macherey-Nagel).
NEBNext Ultra II Directional RNA Library Prep kit was used for polyA RNA-seq library preparation

treatment_protocol: Cells were treated with 1 μM CS47 (in-house synthesized), 1 μM AURA (Cayman Chemicals), or 0.5 %DMSO (VEH) for 24h in RPMI media supplemented with 5% dyalized FBS and antibiotics in a humidified atmosphere with 5% CO2 at 37C

value: lung cancer

value: WT

value: AURA


title: BT-549_CTRL_1_cells expressing the negative control sgRNA_1

status: Public on Jun 30 2026

type: SRA

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

library_source: transcriptomic

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were converted into TPM and all templated forms for each miRNA were summed together
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: TPM_counts.xlsx: excel file that includes normalized reads (transcript per million reads, TPM, normalized  to the size of each library) for all miRNAs in all samples

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA, including microRNAs, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: Cells were treated infected with lentivirus expressing the sgRNAs and then treated with 1 ug/mL doxycycline, to activate the dCas9-KRAB transgene, for 7 passages

tag: cell line

tag: cell type

value: BREAST CANCER

tag: genotype

tag: treatment

value: untreated


title: MRR, 2007134

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description:
Library name: 2007134
MRR

data_processing:
Read quality was checked with fastqc
Trimmed adapter seq and low phredscore 3’ ends; if a read became shorter than 50 bp it and it’s pair was removed; read pairs where one at least on of the reads consisted of only 3 type of nucleotides were removed
STAR aligner (2.7.10a) was used to align reads to the reference and to count reads mapped to genes; reads mapped to introns were not considered valid
Assembly: Mouse genome mm39 with ensEMBL annotation v110 was supplemented with Addgene_pAAV-EF1a-DIO-mCherry (Plasmid #50459); Cre (NCBI/Nucleotide:NC_005856.1); and sYFP (NCBI/Nucleotide:GQ221700.1).
Supplementary files format and content: A tab separated count matrix on a gene level consisting of genes as rows and samples as columns

molecule: polyA RNA

organism: Mus musculus

source_name: MRR

growth_protocol: We used vGluT2-iRES-Cre adult (at least 6 weeks-old) mice that had access to food and water ad libitum and were housed in a vivarium (3-5 mice/cage) until used in experiments. Mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) then were placed into separate cages. After 2-5 weeks of incubation time mice were sacrificed during the light phase and 200-250 μm thick horizontal slices were made from the pontine region of the brainstem of vGLuT2-Cre mice.

extract_protocol:
Mice were decapitated under deep anesthesia and slices were prepared in ice-cold cutting solution (85 mM NaCl, 75 mM sucrose, 2.5 mM KCl, 25 mM glucose, 1.25 mM NaH2PO4, 4 mM MgCl2, 0.5 mM CaCl2, and 24 mM NaHCO3) using a VT1200S vibratome (Leica). Slices were incubated at 35 °C for ~30 min and then kept at room temperature until use. During recordings the slices are kept at 35 °C in continuously perfused with artificial cerebrospinal fluid (126 mM NaCl, 2.5 mM KCl, 26 mM NaHCO3, 2 mM CaCl2, 2 mM MgCl2, 1.25 mM NaH2PO4, and 10 mM glucose, saturated with carbogen,) Fluorescently labeled MRR neurons were visualized in an upright microscope (Eclipse FN-1; Nikon) with epifluorescent illumination (Lambda FLED @ 530 nm; Sutter Instrument) combined with a CMOS camera (DaVinci 1k, RedShirtImaging). The neurons were patched with thin-wall borosilicate pipettes (pipette resistance: 3.69±0.09 MΩ, BF150-117-10, Sutter Instrument) filled with small amount (~1 µl) of intracellular solution containing 133.5 mM K-gluconate, 1.8 mM NaCl, 1.7 mM MgCl2, 0.05 mM EGTA, 10 mM HEPES, 2 mM Mg-ATP, 0.4 mM Na2-GTP, 10 mM phosphocreatine, and 8 mM biocytin (pH 7.25;  290-300 mOsm). Pipette capacitance and the bridge balance were carefully compensated in all current clamp recordings. For the RNA harvesting, the recordings were made using a HEKA EPC800 amplifier (HEKA Elektronik) digitized with a Digidata1440A A/D converter (Molecular Devices). The data acquisition was controlled by the pClamp10 software package. After patching the identified neurons, we measured the basic electrophysiological parameters of the cells including the resting membrane potential, the spontaneous synaptic activity, and the firing pattern. The length of the recording session was limited to 5 min from the break-in. The cytosol together with the nucleus was extracted from the neuron by the application of small negative pressure to the pipette. The tip of the quickly removed pipette was gently pushed into a microtube containing ice cold reaction buffer (lysis buffer with RNase inhibitor, Takara SMART-Seq HT PLUS Kit). The sample containing tubes was spun briefly and snap-frozen on dry ice. To suppress RNase contamination, the workplace including parts of the experimental setup was cleaned each day before the start of the sample collection with RNase AWAY (Thermo Fisher).
Sample collection: After electrophysiological recordings, the cells’ cytosol was aspirated via the same recording glass pipette that used for recording, and using a positive pressure, expelled into microtubes containing 1 µl of 1x lysis buffer with RNase inhibitor (SMART-Seq HT PLUS Kit, Takara). The samples were immediately frozen on dry ice and stored at -80°C until further processing. cDNA and library preparation for next-generation sequencing: Single-cell mRNA processing was performed using the SMART-Seq HT PLUS Kit (Takara) and according to manufacturer’s protocol. In brief, samples were reverse transcribed to cDNA, amplified, and purified with AMPure XP beads (Beckman Coulter). The quantity and the quality of the purified cDNA was assessed using Fragment Analyzer (Advanced Analytical). Subsequently, the cDNA was fragmented and adapters including indices for cell identification were added to the fragments. The quality and quantity were again assessed using Fragment Analyzer. For library preparation, the single cell samples with unique index adapters were pooled in equal amounts. The sequencing was performed on a NovaSeq 6000 (Illumina) instrument using 150 bp paired end configuration and a full SP-flowcell. Processing of sequencing data: After sequencing, raw reads were de-multiplexed with Illumina’s bcl2fastq2 (v2.20).

treatment_protocol: All vGluT2-Cre mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) to label MRR vGluT2 neurons.

value: MRR


title: PS32G

country: USA

description: Library name: PS32G-7669

tag: tissue


title: MRR, 199794

description:
Library name: 199794
MRR


title: PS30G

description: Library name: PS30G-7669

value: EGFR-MUT


title: PS29G

description: Library name: PS29G-7669


title: SUM159PT_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2

value: ZSWIM8 knock down


title: MRR, 199793

description:
Library name: 199793
MRR


title: PS28G

description: Library name: PS28G-7669

value: VEH


title: PS27G

description: Library name: PS27G-7669


title: MRR, 199689

description:
Library name: 199689
MRR


title: PS26G

description: Library name: PS26G-7669


title: SUM159PT_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: PS24G

description: Library name: PS24G-7669


title: MRR, 199586

description:
Library name: 199586
MRR


title: SUM159PT_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3


title: PS23G

description: Library name: PS23G-7669


title: SUM159PT_CTRL_2_cells expressing the negative control sgRNA_2


title: PS22G

description: Library name: PS22G-7669


title: MRR, 199584

description:
Library name: 199584
MRR


title: PS21G

description: Library name: PS21G-7669


title: Final-185-Aug-Benign-08-16-2024-EPI-005

city: Kansas City

first: Harsh

last: Pathak

state: KS

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660019855-D-G07

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Library strategy: Spatial Transcriptomics

source_name: Benign

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

value: Epi

value: Benign

tag: transformed status


title: H27556_H3K4me3

city: Toronto

first: Shraddha

last: Pai

state: ON

address: 160 College Street, Room 602

country: Canada

institute: University of Toronto

description: Library name: 4_08YC_017CSCRI_27556-132M_H3K4me3_hs_i92

library_source: genomic

data_processing:
Sequence Analysis: The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm(Li and Durbin 2009) (“bwa aln/samse” with default settings). Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) were  removed. Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags were extended in silico (using Active Motif software) at their 3´- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined. Peak calling: Processing statistics are in Supplementary Table 10. Peaks were called using either MACS 2.1.019 or SICER20 algorithms. MACS default cutoff was pvalue 1e-7 for narrow peaks and 1e-1 for broad peaks. SICER default cutoff was FDR 1e-10 with gap parameter of 600 bp. Peak filtering was performed by removing false ChIP-Seq peaks as defined within the ENCODE blacklist. Proximal H3K27ac peaks within 2 kbp upstream or downstream of transcription start sites that did not overlap with H3K4me3 peaks or distal H3K27ac peaks residing outside the +-2k bp window were annotated as enhancer-like elements. H3K4me3 peaks overlapping transcription start site +- 200 bp windows were annotated as canonical promoter-like elements22. The elements were annotated for each sample and then combined for downstream analyses. Superenhancers were called by the ActiveMotif pipeline. The identification of Super Enhancers uses a proprietary algorithm that gives a very similar result as the ROSE software. In a first step, MACS or SICER peaks generated by the standard ChIP-Seq analysis are merged (or “stitched together”) if their inner distance is equal or less than 12,500 bp. In the second step, the stitched peak regions with the strongest signals (top 5%) are identified as Super Enhancers. Super Enhancer intervals are ranked by their signal strength (= tag numbers in stitched peak regions). For each sample, the top-ranked Super Enhancer is thus at the top of the list.
Assembly: hg38
Supplementary files format and content: BED file containing histone peak calls. BED files containing "_SE" in the filename are super-enhancer calls

molecule: genomic DNA

source_name: Cerebellum

extract_protocol:
A standard laboratory protocol for DNA extraction was used by ActiveMotif
ActiveMotif used a standard library extraction protocol.

treatment_protocol: Fresh frozen cerebellum (130-180 mg) was sent to Active Motif for ChIP-seq using the following antibodies: H3K4me3 (Active Motif, cat#39159), H3K27Ac (Active Motif, cat #39133) and RNA Pol II (Active Motif, cat # 91151).

value: Cerebellum

tag: sample

tag: post conception_weeks

tag: antibody

tag: Sex

value: male


title: SUM159PT_CTRL_1_cells expressing the negative control sgRNA_1


title: Final-149-Aug-OSCC-08-16-2024-Immune-001

description: Library name: DSP-1001660019855-D-G10

source_name: OSCC

value: Immune

value: OSCC


title: PS20G

description: Library name: PS20G-7669


title: MRR, 199482

description:
Library name: 199482
MRR


title: PS19G

description: Library name: PS19G-7669


title: Liver, Wc1982 treatment, biological replicate 6

city: Beijing

first: Ruoshi

last: Wang

address: 155 Changbai Road

department: National Institute for Communicable Disease Control and Prevention

country: China

institute: Chinese Center for Disease Control and Prevention

description:
Library name: Wc1982_6_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 6.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

data_processing:
Raw sequencing reads were filtered to remove adapter-contaminated reads, low-quality reads, and reads containing excessive ambiguous bases; clean paired-end reads were retained for downstream analysis.
Clean reads were aligned to the Mesocricetus auratus reference genome Mesocricetus_auratus.MesAur1.0.genome.fa using HISAT2.
Mapped reads were assembled and transcript abundances were quantified using StringTie.
Gene-level expression was summarized as raw read counts and fragments per kilobase of transcript per million mapped reads (FPKM).
Differential expression was analyzed using DESeq2. P values were adjusted using the Benjamini-Hochberg method; genes with |log2 fold change| ≥ 1 and false discovery rate < 0.05 were considered differentially expressed.
Assembly: Mesocricetus_auratus.MesAur1.0.genome.fa (MesAur1.0)
Supplementary files format and content: Gzip-compressed, tab-delimited matrix containing raw gene-level counts for 24,464 features across 18 liver RNA-seq libraries. Rows include feature_id, gene_name, and nr_symbol; sample column headers match the GEO library names.
Supplementary files format and content: Gzip-compressed, tab-delimited matrix containing FPKM-normalized gene expression values for 24,464 features across 18 liver RNA-seq libraries. Rows include feature_id, gene_name, and nr_symbol; sample column headers match the GEO library names.

organism: Mesocricetus auratus

source_name: liver

growth_protocol: Specific-pathogen-free male Golden Syrian (LVG) hamsters with an initial mean body weight of 125 ± 15 g were housed at 23 ± 2 °C and 40%–50% humidity under a 12 h light/12 h dark cycle, two animals per cage, with food and water available ad libitum. After a one-week acclimatization period, animals were randomly assigned to the NC, HFD, or Wc1982 group.

extract_protocol:
Total RNA was extracted from frozen liver tissue using TRIzol reagent (Life Technologies, USA). RNA concentration and purity were measured using a NanoDrop 2000 spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer.
Poly(A)+ mRNA was isolated from qualified total RNA using oligo(dT)-attached magnetic beads and randomly fragmented. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Double-stranded cDNA was purified with AMPure XP beads, end-repaired, A-tailed, ligated to sequencing adapters, and size-selected for 300–400 bp fragments. Libraries were amplified by PCR and sequenced on an Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads.

treatment_protocol: The NC group was fed normal diet D12102, whereas the HFD and Wc1982 groups were fed high-fat diet D12108C. The Wc1982 group received 1 mL/day of a Wc1982 suspension containing 5 × 10^8 CFU by oral gavage for six weeks. The NC and HFD groups received an identical volume of PBS. After a 12-h fast, hamsters were anesthetized and liver tissues were collected and frozen for RNA extraction.

value: liver

value: LVG strain

value: High-fat diet (D12108C) and oral Weissella confusa Wc1982 (5 × 10^8 CFU/day) for 6 weeks


title: MRR, 199480

description:
Library name: 199480
MRR


title: Liver, Wc1982 treatment, biological replicate 5

description:
Library name: Wc1982_5_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 5.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: PS17G

description: Library name: PS17G-7669

value: lung cancer

value: KRAS-MUT


title: PS18G

description: Library name: PS18G-7669

value: AURA


title: PS16G

description: Library name: PS16G-7669


title: MRR, 199376

description:
Library name: 199376
MRR


title: PS15G

description: Library name: PS15G-7669


title: Liver, Wc1982 treatment, biological replicate 4

description:
Library name: Wc1982_4_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 4.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: PS31G

description: Library name: PS31G-7669

value: WT


title: PS14G

description: Library name: PS14G-7669


title: PS13G

description: Library name: PS13G-7669


title: MRR, 199273

description:
Library name: 199273
MRR

value: MRR


title: Liver, Wc1982 treatment, biological replicate 3

description:
Library name: Wc1982_3_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 3.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: PS12G

description: Library name: PS12G-7669


title: PS11G

description: Library name: PS11G-7669


title: MRR, 198958

description:
Library name: 198958
MRR


title: Liver, Wc1982 treatment, biological replicate 2

description:
Library name: Wc1982_2_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 2.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: PS10G

description: Library name: PS10G-7669


title: MRR, 198957

description:
Library name: 198957
MRR


title: Liver, Wc1982 treatment, biological replicate 1

description:
Library name: Wc1982_1_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the Wc1982 intervention group; biological replicate 1.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: SUM159PT_CTRL_3_cells expressing the negative control sgRNA_3

value: BREAST CANCER

value: untreated


title: PS8G

description: Library name: PS8G-7669


title: MRR, 199688

description:
Library name: 199688
MRR


title: PS25G

description: Library name: PS25G-7669

value: EGFR-MUT

value: VEH


title: PS9G

description: Library name: PS9G-7669


title: MRR, 198855

description:
Library name: 198855
MRR


title: Slide-063-PreMalignant-07-10-2023-EPI-004

description: Library name: DSP-1001660015531-A-B12

source_name: OED

value: Epi

value: OED

value: Yes


title: PS7G

description: Library name: PS7G-7669


title: Liver, high-fat diet, biological replicate 6

description:
Library name: HFD_6_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 6.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: High-fat diet (D12108C) and oral PBS (1 mL/day) for 6 weeks


title: Slide-063-PreMalignant-07-10-2023-EPI-002

description: Library name: DSP-1001660015531-A-B10


title: PS6G

description: Library name: PS6G-7669


title: MRR, 198754

description:
Library name: 198754
MRR


title: RNA-seq sequencing data 1 of mice liver tissues with DEHP exposuree

city: wuhan

first: neng

middle: bin

last: xie

address: 115 donghu road

institute: wuhan university

description: Library name: Simple 4

data_processing:
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with a ratio of ‘N’ exceeding 10%) and low-quality sequences (with a quality score below 5), the remaining clean reads were assembled using Trinity software for de novo transcriptome assembly.
Assembly: GRCm38.p6
Supplementary files format and content: excel file of raw gene counts for all samples

source_name: liver tissues

extract_protocol:
Total RNA was isolated from mouse liver tissues using TRIzol (Beyotime); mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Briefly, total RNA was isolated from mouse liver tissues using TRIzol (Beyotime). RNA concentration and integrity were assessed using a Nanodrop photometer and an Agilent 5400 bioanalyzer. Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina in accordance with the manufacturer’s recommendations. First, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and subsequently fragmented in NEBNext First Strand Synthesis Reaction Buffer with divalent cations. The first cDNA strand was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The synthesis of the second cDNA strand was performed with DNA polymerase I, where all dTTPs in the reaction buffer were replaced by dUTPs. The remaining overhangs were converted into blunt ends through exonuclease and polymerase activities. Following the adenylation of the 3' end of the DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated. Next, 3 μl of USER Enzyme (NEB, USA) was incubated with the size-selected, adaptor-ligated cDNA at 37 °C for 15 min, followed by a 5-min incubation at 95 °C. PCR amplification was then performed using Phusion High-Fidelity DNA polymerase, universal PCR primers, and index primers. The PCR products were purified using KAPA Pure Beads. Library quality was assessed with the Agilent 5400 system (Agilent, USA). Paired-end sequencing of the samples was performed on the Illumina platform (Illumina, USA)

value: liver tissues


title: PS5G

description: Library name: PS5G-7669


title: Liver, high-fat diet, biological replicate 5

description:
Library name: HFD_5_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 5.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: liver


title: PS4G

description: Library name: PS4G-7669


title: MRR, 198650

description:
Library name: 198650
MRR


title: PS3G

description: Library name: PS3G-7669


title: PS2G

description: Library name: PS2G-7669


title: RNA-seq sequencing data 3 of mice liver tissue without DEHP exposuree

description: Library name: Simple 3


title: MRR, 198345

description:
Library name: 198345
MRR


title: Liver, high-fat diet, biological replicate 4

description:
Library name: HFD_4_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 4.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: LVG strain


title: PS1G

description: Library name: PS1G-7669


title: Liver, high-fat diet, biological replicate 3

description:
Library name: HFD_3_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 3.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: MGO_hRECs_miRNA-seq_rep3

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

data_processing:
iSMART suite was used for read filtering (Cutadapt), mapping (sRNAbench) and data normalization (NOISeq). Differentially expressed miRNAs were measured by NOISeq (Probability>0.90). The miRNA Pathway Dictionary Database (miRPathDB; release 2.0; https://mpd.bioinf.uni-sb.de/) was used for analyzing the number of significant miRNAs per pathway/cellular components for the different target sets (experimental evidence: strong)
The samples labeled "control_hRECs_rep1" and "MGO_hRECs_rep1" were removed from further analyses after quality check.
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing normalized counts for all analyzed samples ("control_hRECs_rep1" and "MGO_hRECs_rep1" are not included)

source_name: retina

growth_protocol: Human Retinal Endothelial Cells were cultured in Endothelial cell medium supplemented with fetal Bovine Serum (FBS), Endothelial Cell Growth Supplement (ECGS) and penicillin/streptomycin (P/S) solution.

extract_protocol:
Total RNA samples were extracted by cell pellets using TRIzol Reagent (Life Technologies) according to the manufacturer’s instructions. NanoDrop spectrophotometer was used for RNA quantification for samples to be processed by smallRNA-Seq
Illumina TruSeq small RNA library Preparation Kit

treatment_protocol: Before treatments, cells were serum starved for 16h. Cells were treated with 500 μM MGO for 72h (non-toxic and chronic exposure) before transcriptome and miRNome analysis.

value: retina

value: hREC

value: Retinal Endothelial

value: methylglyoxal (500 μM)


title: MDA-MB-436_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2

value: ZSWIM8 knock down


title: Slide-094-PreMalignant-07-10-2023-Immune-001

description: Library name: DSP-1001660015531-A-B02

value: Immune


title: MGO_hRECs_miRNA-seq_rep2

value: WT


title: Liver, high-fat diet, biological replicate 2

description:
Library name: HFD_2_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 2.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: MGO_hRECs_miRNA-seq_rep1


title: MDA-MB-436_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1

value: BREAST CANCER


title: control_hRECs_miRNA-seq_rep3

value: untreated


title: Liver, high-fat diet, biological replicate 1

description:
Library name: HFD_1_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the high-fat diet group; biological replicate 1.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: control_hRECs_miRNA-seq_rep1


title: Liver, normal control, biological replicate 6

description:
Library name: NC_6_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 6.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: Normal diet (D12102) and oral PBS (1 mL/day) for 6 weeks


title: MRR, 198140

description:
Library name: 198140
MRR

value: MRR


title: Liver, normal control, biological replicate 5

description:
Library name: NC_5_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 5.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: WT2

first: Zhiqiang

last: Peng

address: 38 Life Science Park Road

institute: State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics

description:
Library name: sample5
Column name in raw_counts_All_Samples.txt:WT2

data_processing:
CLC genomics workbench v11.0.1
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: xlsx file includes FPKM values for each Sample

source_name: intestine

extract_protocol:
RNA was harvested using  Oligo(dT) beads. RNA was diluted at 2 nM for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacturer’s protocols.

value: intestine


title: WT1

description:
Library name: sample4
Column name in raw_counts_All_Samples.txt:WT1


title: WT3

description:
Library name: sample6
Column name in raw_counts_All_Samples.txt:WT3


title: HET3

description:
Library name: sample3
Column name in raw_counts_All_Samples.txt:HET3

value: HET


title: MRR, 198039

description:
Library name: 198039
MRR


title: Liver, normal control, biological replicate 4

description:
Library name: NC_4_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 4.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: HET2

description:
Library name: sample2
Column name in raw_counts_All_Samples.txt:HET2


title: MRR, 198037

description:
Library name: 198037
MRR


title: HET1

description:
Library name: sample1
Column name in raw_counts_All_Samples.txt:HET1


title: ID_615

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

description:
Library name: Sample 72
Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs

source_name: Diversity Outbred

extract_protocol:
Frozen cells were lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 20-35 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 71-500 ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 NovaSeq Reagent Kit (200 or 300 Cycles) (Illumina).  An average of 69 million paired reads was generated per sample. Ribosomal reads represented 0.1-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: Diversity Outbred

value: Neural Progenitor Cells


title: MRR, 198036

description:
Library name: 198036
MRR


title: ID_602

description:
Library name: Sample 70
Ribodepleted bulk RNA_seq


title: Liver, normal control, biological replicate 2

description:
Library name: NC_2_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 2.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: liver


title: MRR, 197935

description:
Library name: 197935
MRR


title: MRR, 197934

description:
Library name: 197934
MRR


title: ID_542

description:
Library name: Sample 69
Ribodepleted bulk RNA_seq


title: ID_540

description:
Library name: Sample 68
Ribodepleted bulk RNA_seq


title: ID_537

description:
Library name: Sample 66
Ribodepleted bulk RNA_seq


title: 3_4_19_TWB3_C_TTCCGC_R1

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: 12685_5751_144725_HW3JMBGXJ_NSF023_D08_3_4_19_TWB3_C_TTCCGC_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

organism: Vitis hybrid cultivar

source_name: Bud

growth_protocol: Standard commercial vineyard management, Tuckers Walk, Garretson SD.

extract_protocol:
Total RNA was extracted from grapevine bud tissue using a modified CTAB protocol or standard commercial RNA isolation kit optimized for woody plant tissues. RNA quality and quantity were assessed using an Agilent Bioanalyzer or NanoDrop spectrophotometer to ensure high-quality material prior to library preparation.
Sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's standard protocols. Poly-A selected mRNA was fragmented, converted to cDNA, ligated with TruSeq adapters, and PCR amplified to generate single-end sequencing libraries.

treatment_protocol: Controled chilling (4ºC) in dark.  Field natural chilling temperatures.

value: Bud

value: Controlled Chilling

value: total RNA

value: single


title: MRR, 197833

description:
Library name: 197833
MRR


title: 3_4_19_TWB2_C_GGTGAG_R1

description:
Library name: 12685_5751_144724_HW3JMBGXJ_NSF023_C08_3_4_19_TWB2_C_GGTGAG_R1
Total RNA single illumina


title: ID_525

description:
Library name: Sample 64
Ribodepleted bulk RNA_seq


title: MRR, 197519

description:
Library name: 197519
MRR


title: ID_523

description:
Library name: Sample 63
Ribodepleted bulk RNA_seq


title: 3_4_19_TWB1_C_ATAAGA_R1

description:
Library name: 12685_5751_144723_HW3JMBGXJ_NSF023_B08_3_4_19_TWB1_C_ATAAGA_R1
Total RNA single illumina


title: ID_520

description:
Library name: Sample 62
Ribodepleted bulk RNA_seq


title: 2_12_19_TWB3_C_AGTACT_R1

description:
Library name: 12685_5751_144722_HW3JMBGXJ_NSF023_A08_2_12_19_TWB3_C_AGTACT_R1
Total RNA single illumina


title: ID_516

description:
Library name: Sample 61
Ribodepleted bulk RNA_seq


title: ID_511

description:
Library name: Sample 60
Ribodepleted bulk RNA_seq


title: 2_12_19_TWB2_C_ATATCC_R1

description:
Library name: 12685_5751_144721_HW3JMBGXJ_NSF023_H07_2_12_19_TWB2_C_ATATCC_R1
Total RNA single illumina


title: ID_507

description:
Library name: Sample 59
Ribodepleted bulk RNA_seq


title: ID_506

description:
Library name: Sample 58
Ribodepleted bulk RNA_seq


title: Multiome, tumor DC1, control bio rep2, ATAC

city: Boston

first: Xixi

last: Zhang

state: Massachusetts

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: ATAC tumor DC1 Ctrl2

library_source: genomic single cell

data_processing:
Sample demultiplexing, barcode processing, UMI counting, read alignment, filtering and cell calling on both RNA and Assay for Transposase-Accessible Chromatin (ATAC) data were performed using the 10X CellRanger Arc v2.0.2 pipeline with FASTQ sequencing files as input. Reads were aligned to the GRCm38 (mm10) mouse genome reference (CellRanger reference: refdata-cellranger-arc-mm10-2020-A-2.0.0).
Assembly: Mouse(mm10)
Supplementary files format and content: RDS objects

source_name: tumor-infiltrating dendritic cells

extract_protocol:
CD11c+MHCII+XCR1+cells were harvested and sorted from MC38 tumors, and were resuspended in PBS containing 0.1% BSA.
Libraries were constructed using chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle according to the manufacturer's protocol.

value: tumor-infiltrating dendritic cells

tag: library type

value: ATAC


title: 2_12_19_TWB1_C_ACAACG_R1

description:
Library name: 12685_5751_144720_HW3JMBGXJ_NSF023_G07_2_12_19_TWB1_C_ACAACG_R1
Total RNA single illumina


title: Multiome, tumor DC1, control bio rep1, ATAC

description: Library name: ATAC tumor DC1 Ctrl1


title: ID_444

description:
Library name: Sample 55
Ribodepleted bulk RNA_seq


title: 1_13_19_TWB3_C_AATGAA_R1

description:
Library name: 12685_5751_144719_HW3JMBGXJ_NSF023_F07_1_13_19_TWB3_C_AATGAA_R1
Total RNA single illumina


title: Multiome, tumor DC1, KO bio rep2, GEX

description: Library name: GEX tumor DC1 KO2

library_source: transcriptomic single cell

value: mRNA


title: ID_436

description:
Library name: Sample 53
Ribodepleted bulk RNA_seq


title: ID_435

description:
Library name: Sample 52
Ribodepleted bulk RNA_seq


title: Multiome, tumor DC1, KO bio rep1, GEX

description: Library name: GEX tumor DC1 KO1


title: ID_434

description:
Library name: Sample 51
Ribodepleted bulk RNA_seq


title: Multiome, tumor DC1, control bio rep2, GEX

description: Library name: GEX tumor DC1 Ctrl2


title: ID_430

description:
Library name: Sample 49
Ribodepleted bulk RNA_seq


title: 12_28_18_TWB3_C_CACTAA_R1

description:
Library name: 12685_5751_144716_HW3JMBGXJ_NSF023_C07_12_28_18_TWB3_C_CACTAA_R1
Total RNA single illumina


title: Multiome, tumor DC1, control bio rep1, GEX

description: Library name: GEX tumor DC1 Ctrl1


title: 1021-pop4, LPCs

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

institute: Università di Roma Tor Vergata

data_processing:
Paired reads were aligned to the human reference genome (GRCh38/hg38) using the splice-aware aligner STAR v 2.5.0c
Per-gene read counts were generated using the STAR quantMode geneCounts option.
Raw per-gene read counts were then processed using the Bioconductor package DESeq2 package v. 1.30 in order to perform the differential expression analysis.
Assembly: hg38
Supplementary files format and content: excel with normalised counts

source_name: primary Acute myeloid leukemia cells

extract_protocol:
Trizol extraction
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian protocol.

value: primary Acute myeloid leukemia cells

tag: sorted cells

value: LPCs

tag: pair id


title: ID_418

description:
Library name: Sample 47
Ribodepleted bulk RNA_seq


title: 12_28_18_TWB2_C_TCGAGG_R1

description:
Library name: 12685_5751_144715_HW3JMBGXJ_NSF023_B07_12_28_18_TWB2_C_TCGAGG_R1
Total RNA single illumina


title: 1_13_19_TWB1_C_GGTATA_R1

description:
Library name: 12685_5751_144717_HW3JMBGXJ_NSF023_D07_1_13_19_TWB1_C_GGTATA_R1
Total RNA single illumina


title: ID_432

description:
Library name: Sample 50
Ribodepleted bulk RNA_seq


title: ID_415

description:
Library name: Sample 46
Ribodepleted bulk RNA_seq


title: Tumor-infiltrating dendritic cells from Carm1fl/flZbtb46Cre mice, GEX

description: Library name: GEX Carm1Zbtb46 KO tumor DC

data_processing:
We conducted all the pre-processing steps for scRNA-seq , including running Fastqc for quality control, aligning to UCSC mm10 mouse genome (Cell Ranger v7.1.0, 10X Genomics), to obtain gene count matrices and hashtag for each cell. Downstream analysis was performed using the R software package Seurat (v4.3.0, http://satijalab.org/seurat/). Low-quality cells with insufficient gene detection or a mitochondrial percentage exceeding thresholds determined for each sample were filtered out to ensure data quality. We performed demultiplexing by using the HTODemux function with a default parameter in the Seurat package to capture only the unique hashtag for each cell. The raw gene expression matrix was normalized, and highly variable genes were identified.
Assembly: Mouse mm10
Supplementary files format and content: RDS objects

extract_protocol:
CD11c+MHCII+cells were stained with desired antibodies and hashtags, and sorted from MC38 tumors and resuspended in PBS containing 0.1% BSA.
Libraries were constructed using 10X single-cell from chromium Next GEM Single Cell 3' GEM Kit v3.1 according to the manufacturer's protocol.

value: GEX


title: B16.F10 cells, Negative control siRNA biol rep 3

city: Cluj-Napoca

first: Bogdan

last: Dume

address: Mihail Kogălniceanu, no. 1

country: Romania

institute: Babes-Bolyai University

description: Library name: Sample 6

data_processing:
Raw data quality was assessed using FastQC v0.11.7.
Adapter sequences and low-quality bases were removed using Trimmomatic v0.38.
Trimmed reads were aligned to Mus musculus reference genome (mm10, NCBI_108 annotation) using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1.
Aligned reads were assembled into transcripts with StringTie v2.1.3b and transcript abundance was determined, quantified as read counts, and normalized to FPKM and TPM values.
Assembly: mm10, NCBI_108 annotation
Supplementary files format and content: csv files include raw counts for each sample

growth_protocol: B16.F10 murine melanoma cells were cultured as monolayer in DMEM (37°C, 80% humidity, 5% CO2, and 1% O2) supplemented with 10% (v/v) FBS, 1mM sodium pyruvate, 4 mM L-glutamine, and antibiotics (100 μg/ml streptomycin and 100 IU/ml penicillin).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Reference guide #1000000040498 v00, Illumina).

treatment_protocol: B16.F10 cells were seeded at the density of 2.5×104 cells/cm2 and revers-transfected with lipoplexes containing siRNA at a final concentration of 25 nM and incubated for 24 h. After, doxorubicin hydrochloride was added to the culture media at a final concentration of 0.25 μM and cells were further incubated for another 24 h in 1% hypoxia.

value: Melanoma cell

value: WT

value: Negative control siRNA


title: ID_409

description:
Library name: Sample 45
Ribodepleted bulk RNA_seq


title: 12_28_18_TWB1_C_GTGCCA_R1

description:
Library name: 12685_5751_144714_HW3JMBGXJ_NSF023_A07_12_28_18_TWB1_C_GTGCCA_R1
Total RNA single illumina


title: Final-156-1-Aug-OSCC-08-14-2024-Immune-002

description: Library name: DSP-1001660019855-D-B09

value: Immune

value: OSCC


title: ID_406

description:
Library name: Sample 44
Ribodepleted bulk RNA_seq

value: Diversity Outbred

value: Neural Progenitor Cells


title: Tumor-infiltrating dendritic cells from Carm1fl/flXcr1Cre mice, GEX

description: Library name: GEX Carm1XCR1 KO tumor DC


title: 11_20_18_TWB3_C_AATAGC_R1

description:
Library name: 12685_5751_144713_HW3JMBGXJ_NSF023_H06_11_20_18_TWB3_C_AATAGC_R1
Total RNA single illumina

value: Bud


title: ID_402

description:
Library name: Sample 43
Ribodepleted bulk RNA_seq


title: ID_324

description:
Library name: Sample 42
Ribodepleted bulk RNA_seq


title: Tumor-infiltrating dendritic cells from control mice, GEX

description: Library name: GEX Ctrl tumor DC


title: ID_322

description:
Library name: Sample 41
Ribodepleted bulk RNA_seq


title: 11_20_18_TWB2_C_GCATGG_R1

description:
Library name: 12685_5751_144712_HW3JMBGXJ_NSF023_G06_11_20_18_TWB2_C_GCATGG_R1
Total RNA single illumina

value: Controlled Chilling


title: ID_321

description:
Library name: Sample 40
Ribodepleted bulk RNA_seq


title: Tumor-infiltrating dendritic cells from Carm1fl/flZbtb46Cre mice, HTO

description: Library name: 10x CSP Carm1Zbtb46 KO tumor DC

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeqB anti-mouse Hashtag1,TotalSeqB anti-mouse Hashtag2,TotalSeqB anti-mouse Hashtag3,TotalSeqB anti-mouse Hashtag4,TotalSeqB anti-mouse Hashtag5


title: MRR, 198344

description:
Library name: 198344
MRR

value: MRR


title: ID_320

description:
Library name: Sample 39
Ribodepleted bulk RNA_seq


title: ID_319

description:
Library name: Sample 38
Ribodepleted bulk RNA_seq


title: MRR, 198243

description:
Library name: 198243
MRR


title: B16.F10 cells, Negative control siRNA biol rep 1

description: Library name: Sample 4


title: 11_20_18_TWB1_C_CTCCAT_R1

description:
Library name: 12685_5751_144711_HW3JMBGXJ_NSF023_F06_11_20_18_TWB1_C_CTCCAT_R1
Total RNA single illumina

value: total RNA

value: single


title: MRR, 198141

description:
Library name: 198141
MRR


title: control_hRECs_miRNA-seq_rep2

value: retina

value: hREC

value: Retinal Endothelial

value: untreated


title: Tumor-infiltrating dendritic cells from Carm1fl/flXcr1Cre mice, HTO

description: Library name: 10x CSP Carm1XCR1 KO tumor DC

value: tumor-infiltrating dendritic cells


title: 3_4_19_TWB3_F_TAGGCT_R1

description:
Library name: 12685_5751_144710_HW3JMBGXJ_NSF023_E06_3_4_19_TWB3_F_TAGGCT_R1
Total RNA single illumina

value: Field Chilling


title: ID_315

description:
Library name: Sample 37
Ribodepleted bulk RNA_seq


title: ID_313

description:
Library name: Sample 36
Ribodepleted bulk RNA_seq


title: Tumor-infiltrating dendritic cells from control mice, HTO

description: Library name: 10x CSP Ctrl tumor DC


title: ID_311

description:
Library name: Sample 35
Ribodepleted bulk RNA_seq


title: ID_309

description:
Library name: Sample 34
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1, cut&run using IgG, bio rep2

description: Library name: IgG KO2

data_processing:
Raw sequenced reads pairs were filtered by Trim Galore (version 0.6.10)  with cutadapt (version 4.5)  using the following parameters: “--trim-n”. The filtered reads were mapped back to genome (mm10) using Bowtie 2 (version 2.5.2)  with following parameters: “--trim-to 3:40 --no-mixed --no-unal”. Mapped read paris (fragments) with MAPQ > 30 were kept and converted to BAM format files using SAMtools (version 1.18). BAM files were converted to BEDPE using `bamToBed` command in BEDTools (version 2.31.0). Duplicates were removed according to the start and end positions. Replicated were merged and down sampling to 26 million for each condition. Fragments were trimmed to 174 bp centered with the middle points of each fragment and transformed into bigwig format for visualization using `genomeCoverageBed` command in BEDTools and `bedGraphToBigWig` command in UCSCTools. Peak calling was performed using MACS (version 3.0.2) with following parameters: “-f BEDPE --nomodel --shift 37 --extsize 73 --keep-dup all” for each condition against IgG control.
Assembly: Mouse mm10
Supplementary files format and content: bed file and narrowpeak file
Library strategy: CUT&Run

source_name: dendritic cells

extract_protocol:
500000 FACS-sorted cells were collected in PBS containing 2%FBS. Samples were prepared using EpiCypher CUTANA ChIC/CUT&RUN Kit according to the manufacturer’s instructions.
Libraries were constructed using EpiCypher CUT and RUN library prep kit according to the manufacturer’s instructions.

value: dendritic cells


title: 3_4_19_TWB2_F_ACAGAT_R1

description:
Library name: 12685_5751_144709_HW3JMBGXJ_NSF023_D06_3_4_19_TWB2_F_ACAGAT_R1
Total RNA single illumina


title: Liver, normal control, biological replicate 3

description:
Library name: NC_3_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 3.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz

value: liver

value: LVG strain

value: Normal diet (D12102) and oral PBS (1 mL/day) for 6 weeks


title: ID_307

description:
Library name: Sample 33
Ribodepleted bulk RNA_seq

value: Diversity Outbred

value: Neural Progenitor Cells


title: ID_606

description:
Library name: Sample 71
Ribodepleted bulk RNA_seq


title: 3_4_19_TWB1_F_AAGACA_R1

description:
Library name: 12685_5751_144708_HW3JMBGXJ_NSF023_C06_3_4_19_TWB1_F_AAGACA_R1
Total RNA single illumina

value: Bud


title: ID_305

description:
Library name: Sample 32
Ribodepleted bulk RNA_seq


title: Liver, normal control, biological replicate 1

description:
Library name: NC_1_Liver_RNAseq
Frozen liver tissue from a male LVG Golden Syrian hamster in the normal control group; biological replicate 1.
Wc1982_liver_RNAseq_raw_counts.txt.gz
Wc1982_liver_RNAseq_FPKM.txt.gz


title: Carm1-KO cDC1, cut&run using IgG, bio rep1

description: Library name: IgG KO1


title: ID_304

description:
Library name: Sample 31
Ribodepleted bulk RNA_seq


title: ID_303

description:
Library name: Sample 30
Ribodepleted bulk RNA_seq


title: ID_538

description:
Library name: Sample 67
Ribodepleted bulk RNA_seq


title: 2_12_19_TWB3_F_TGACAC_R1

description:
Library name: 12685_5751_144707_HW3JMBGXJ_NSF023_B06_2_12_19_TWB3_F_TGACAC_R1
Total RNA single illumina


title: control cDC1, cut&run using IgG, bio rep2

description: Library name: IgG Ctrl2


title: ID_302

description:
Library name: Sample 29
Ribodepleted bulk RNA_seq


title: ID_301

description:
Library name: Sample 28
Ribodepleted bulk RNA_seq


title: 2_12_19_TWB2_F_CTCTCG_R1

description:
Library name: 12685_5751_144706_HW3JMBGXJ_NSF023_A06_2_12_19_TWB2_F_CTCTCG_R1
Total RNA single illumina


title: ID_531

description:
Library name: Sample 65
Ribodepleted bulk RNA_seq


title: control cDC1, cut&run using IgG, bio rep1

description: Library name: IgG Ctrl1


title: 2_12_19_TWB1_F_GATTGT_R1

description:
Library name: 12685_5751_144705_HW3JMBGXJ_NSF023_H05_2_12_19_TWB1_F_GATTGT_R1
Total RNA single illumina


title: ID_222

description:
Library name: Sample 26
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1, cut&run using anti-H3R17me2a, bio rep2

description: Library name: H3R17me2a KO2


title: ID_219

description:
Library name: Sample 25
Ribodepleted bulk RNA_seq


title: 1_13_19_TWB3_F_CAACAG_R1

description:
Library name: 12685_5751_144704_HW3JMBGXJ_NSF023_G05_1_13_19_TWB3_F_CAACAG_R1
Total RNA single illumina


title: ID_223

description:
Library name: Sample 27
Ribodepleted bulk RNA_seq


title: ID_216

description:
Library name: Sample 24
Ribodepleted bulk RNA_seq


title: Multiome, tumor DC1, KO bio rep2, ATAC

description: Library name: ATAC tumor DC1 KO2

value: ATAC


title: 1_13_19_TWB2_F_ACCGTG_R1

description:
Library name: 12685_5751_144703_HW3JMBGXJ_NSF023_F05_1_13_19_TWB2_F_ACCGTG_R1
Total RNA single illumina


title: Carm1-KO cDC1, cut&run using anti-H3R17me2a, bio rep1

description: Library name: H3R17me2a KO1


title: ID_211

description:
Library name: Sample 21
Ribodepleted bulk RNA_seq


title: 1_13_19_TWB1_F_TGGCGA_R1

description:
Library name: 12685_5751_144702_HW3JMBGXJ_NSF023_E05_1_13_19_TWB1_F_TGGCGA_R1
Total RNA single illumina


title: ID_215

description:
Library name: Sample 23
Ribodepleted bulk RNA_seq


title: ID_214

description:
Library name: Sample 22
Ribodepleted bulk RNA_seq


title: control cDC1, cut&run using anti-H3R17me2a, bio rep2

description: Library name: H3R17me2a Ctrl2


title: ID_207

description:
Library name: Sample 20
Ribodepleted bulk RNA_seq


title: control cDC1, cut&run using anti-H3R17me2a, bio rep1

description: Library name: H3R17me2a Ctrl1


title: ID_205

description:
Library name: Sample 19
Ribodepleted bulk RNA_seq


title: Multiome, tumor DC1, KO bio rep1, ATAC

description: Library name: ATAC tumor DC1 KO1


title: 12_27_18_TWB3_F_CGCAAC_R1

description:
Library name: 12685_5751_144701_HW3JMBGXJ_NSF023_D05_12_27_18_TWB3_F_CGCAAC_R1
Total RNA single illumina


title: DC1 express Carm1-HA, cut&run using IgG, bio rep2

description: Library name: Carm1 IgG-2


title: ID_204

description:
Library name: Sample 18
Ribodepleted bulk RNA_seq


title: ID_203

description:
Library name: Sample 17
Ribodepleted bulk RNA_seq


title: 12_27_18_TWB2_F_GTTACC_R1

description:
Library name: 12685_5751_144700_HW3JMBGXJ_NSF023_C05_12_27_18_TWB2_F_GTTACC_R1
Total RNA single illumina


title: DC1 express Carm1-HA, cut&run using IgG, bio rep1

description: Library name: Carm1 IgG-1


title: ID_505

description:
Library name: Sample 57
Ribodepleted bulk RNA_seq


title: ID_202

description:
Library name: Sample 16
Ribodepleted bulk RNA_seq


title: ID_114

description:
Library name: Sample 15
Ribodepleted bulk RNA_seq


title: 12_27_18_TWB1_F_TTGGTA_R1

description:
Library name: 12685_5751_144699_HW3JMBGXJ_NSF023_B05_12_27_18_TWB1_F_TTGGTA_R1
Total RNA single illumina


title: DC1 express Carm1-HA, cut&run using anti-HA, bio rep2

description: Library name: Carm1 HA-2


title: ID_108

description:
Library name: Sample 13
Ribodepleted bulk RNA_seq


title: 11_20_18_TWB3_F_AGATAG_R1

description:
Library name: 12685_5751_144698_HW3JMBGXJ_NSF023_A05_11_20_18_TWB3_F_AGATAG_R1
Total RNA single illumina


title: ID_111

description:
Library name: Sample 14
Ribodepleted bulk RNA_seq


title: DC1 express Carm1-HA, cut&run using anti-HA, bio rep1

description: Library name: Carm1 HA-1


title: ID_445

description:
Library name: Sample 56
Ribodepleted bulk RNA_seq


title: ID_102

description:
Library name: Sample 11
Ribodepleted bulk RNA_seq


title: 11_20_18_TWB2_F_CGAAGG_R1

description:
Library name: 12685_5751_144697_HW3JMBGXJ_NSF023_H04_11_20_18_TWB2_F_CGAAGG_R1
Total RNA single illumina


title: NPC_WSB_AC635

description:
Library name: Sample 10
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1 bio rep4

description: Library name: KO4

data_processing:
Raw sequenced reads pairs were filtered by Trim Galore (version 0.6.10)  with cutadapt (version 4.5) using the following parameters: “--trim-n”. The filtered reads were mapped back to genome (mm10) using Bowtie 2 (version 2.5.2)
Assembly: Mouse mm10
Supplementary files format and content: bed file and narrow peak file

extract_protocol:
50000 FACS-sorted cells were collected in PBS containing 2%FBS. Nuclei were extracted with 50ul of lysis buffer containing 10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin.The DNA tagmentation was performed using illumina Tagment DNA Enzyme and Buffer kit according to the manufacturer’s instructions.
Libraries were constructed using Illumina Nextera DNA Sample Preparation Kit following the manufacturer’s protocol.


title: 11_20_18_TWB1_F_ACCTAC_R1

description:
Library name: 12685_5751_144696_HW3JMBGXJ_NSF023_G04_11_20_18_TWB1_F_ACCTAC_R1
Total RNA single illumina


title: NPC_PWK_PWK

description:
Library name: Sample 9
Ribodepleted bulk RNA_seq


title: NPC_PWK_AC698

description:
Library name: Sample 8
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1 bio rep3

description: Library name: KO3


title: NPC_NZO_AC671

description:
Library name: Sample 7
Ribodepleted bulk RNA_seq


title: NPC_NZO_AC653

description:
Library name: Sample 6
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1 bio rep2

description: Library name: KO2


title: 3_4_19_TWM2_C_GCGAAT_R1

description:
Library name: 12685_5751_144694_HW3JMBGXJ_NSF023_E04_3_4_19_TWM2_C_GCGAAT_R1
Total RNA single illumina

value: Controlled Chilling


title: Carm1-KO cDC1 bio rep1

description: Library name: KO1


title: NPC_CAST_WM080

description:
Library name: Sample 4
Ribodepleted bulk RNA_seq


title: NPC_NOD_AC595

description:
Library name: Sample 5
Ribodepleted bulk RNA_seq


title: control cDC1 bio rep4

description: Library name: Ctrl4


title: NPC_CAST_WM078

description:
Library name: Sample 3
Ribodepleted bulk RNA_seq


title: NPC_B6_44

description:
Library name: Sample 1
Ribodepleted bulk RNA_seq


title: 2_12_19_TWM3_C_CAAGCA_R1

description:
Library name: 12685_5751_144692_HW3JMBGXJ_NSF023_C04_2_12_19_TWM3_C_CAAGCA_R1
Total RNA single illumina

value: total RNA


title: control cDC1 bio rep3

description: Library name: Ctrl3


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep3s

description: Library name: EZM2302-3s

data_processing:
Paired-end sequence reads were aligned to mouse mm10 using STAR.  Quality metrics were assessed using Samtools.Transcript counts from aligned reads were quantified using Salmon3, then summarized to the gene level using the R package Tximport4.Sequencing depth was normalized between samples using the median of ratios method in R package DESeq2.
Assembly: Mouse mm10
Supplementary files format and content: Raw count matrix
Supplementary files format and content: Normalized counts for each indicated samples

source_name: vaccination site

extract_protocol:
RNA was extracted by Trizol following manufacturer's protocol; 500ng of total RNA was used for construction of sequencing libraries.
RNA library preparation and sequencing were conducted at Azenta Life Sciences (South Plainfield, NJ, USA).

value: vaccination site


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep2s

description: Library name: EZM2302-2s


title: control cDC1 bio rep2

description: Library name: Ctrl2


title: control cDC1 bio rep1

description: Library name: Ctrl1


title: MSR scaffold from mice vaccinated with control vaccine, bio rep5s

description: Library name: Ctrl-5s


title: MSR scaffold from mice vaccinated with control vaccine, bio rep6s

description: Library name: Ctrl-6s


title: 1_12_19_TWM3_C_CCGCAA_R1

description:
Library name: 12685_5751_144689_HW3JMBGXJ_NSF023_H03_1_12_19_TWM3_C_CCGCAA_R1
Total RNA single illumina

value: single


title: Osteoclast treated with 100ng/ml lipopolysaccharide (LPS)-3

city: Saint Louis

first: Gabriel

last: Mbalaviele

state: Missouri

address: 425 S. Euclid Ave., Steven & Susan Lipstein BJCIH, Floor: 11, Room 11203

institute: WashU School of Medicine

description: Library name: OC_LPS_3

data_processing:
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform, and paired-end reads were generated
Raw FASTQ reads were processed with fastp to remove adapters, poly-N sequences, and low-quality reads. Clean paired-end reads were aligned to the reference genome (downloaded from NCBI/UCSC/Ensembl) using STAR.
FeatureCounts was used to quantify gene-level expression, and RPKM values were calculated.
Differential expression analysis (three biological replicates per group) was performed using DESeq2, with p-values adjusted by the Benjamini-Hochberg method. Genes with adjusted p < 0.05 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: tab delimited text file containing fpkm for all samples

source_name: Osteoclasts derived from BMDMs in presence of 100ng/ml RANKL

growth_protocol: The femurs and tibiae were harvested from WT mice and used to expand BMDMs in vitro. Bone marrow cells were flushed from the bones as previously described by Wang et al., 2024. Cells were cultured in 10 cm Petri dishes in the presence of CMG (a source of macrophage colony-stimulating factor, M-CSF) for 4–5 days. Expanded BMDMs were trypsinized and seeded into appropriate well plates at a density of 3 × 10⁴ cells per well in 24-well plates and 0.4 × 10⁶ cells per well in 6-well plates. OC differentiation was induced by the addition of receptor activator of nuclear factor kappa-B ligand (RANKL, 50–100 ng/mL) for 5–6 days.

extract_protocol:
RNA was isolated using the PureLink RNA Mini Kit, and on-column DNase I treatment (Ambion) was performed to eliminate any DNA contamination. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
One microgram (1 μg) of RNA per sample was used as input material for RNA library preparation. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s instructions. Library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: BMDMs were cultured for 5–6 days in 2% CMG, with or without RANKL, to induce mature osteoclasts. On day 5, both cell types were treated with or without LPS (100 ng/mL) for 3 hours.

value: D5, RANKL treated-LPS treatement

value: WT


title: MSR scaffold from mice vaccinated with control vaccine, bio rep3s

description: Library name: Ctrl-3s


title: MSR scaffold from mice vaccinated with control vaccine, bio rep4s

description: Library name: Ctrl-4s


title: 1_12_19_TWM2_C_CACACT_R1

description:
Library name: 12685_5751_144688_HW3JMBGXJ_NSF023_G03_1_12_19_TWM2_C_CACACT_R1
Total RNA single illumina


title: MSR scaffold from mice vaccinated with control vaccine, bio rep2s

description: Library name: Ctrl-2s


title: Osteoclast treated with 100ng/ml lipopolysaccharide (LPS)-2

description: Library name: OC_LPS_2

value: Osteoclasts derived from BMDMs in presence of 100ng/ml RANKL


title: MSR scaffold from mice vaccinated with control vaccine, bio rep1s

description: Library name: Ctrl-1s


title: 1_12_19_TWM1_C_GGAGGT_R1

description:
Library name: 12685_5751_144687_HW3JMBGXJ_NSF023_F03_1_12_19_TWM1_C_GGAGGT_R1
Total RNA single illumina


title: Osteoclast treated with 100ng/ml lipopolysaccharide (LPS)-1

description: Library name: OC_LPS_1


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep3

description: Library name: EZM2302-3


title: 12_28_18_TWM3_C_GAGTCC_R1

description:
Library name: 12685_5751_144686_HW3JMBGXJ_NSF023_E03_12_28_18_TWM3_C_GAGTCC_R1
Total RNA single illumina


title: Osteoclast untretaed control-3

description: Library name: OC_NT_3

value: D5, RANKL treated-control


title: MSR scaffold from mice vaccinated with EZM2302 vaccine, bio rep1

description: Library name: EZM2302-1


title: 12_28_18_TWM2_C_TATGTC_R1

description:
Library name: 12685_5751_144685_HW3JMBGXJ_NSF023_D03_12_28_18_TWM2_C_TATGTC_R1
Total RNA single illumina


title: MSR scaffold from mice vaccinated with control vaccine, bio rep5

description: Library name: Ctrl-5


title: Osteoclast untretaed control-2

description: Library name: OC_NT_2


title: MRR, 2004122

description:
Library name: 2004122
MRR

data_processing:
Read quality was checked with fastqc
Trimmed adapter seq and low phredscore 3’ ends; if a read became shorter than 50 bp it and it’s pair was removed; read pairs where one at least on of the reads consisted of only 3 type of nucleotides were removed
STAR aligner (2.7.10a) was used to align reads to the reference and to count reads mapped to genes; reads mapped to introns were not considered valid
Assembly: Mouse genome mm39 with ensEMBL annotation v110 was supplemented with Addgene_pAAV-EF1a-DIO-mCherry (Plasmid #50459); Cre (NCBI/Nucleotide:NC_005856.1); and sYFP (NCBI/Nucleotide:GQ221700.1).
Supplementary files format and content: A tab separated count matrix on a gene level consisting of genes as rows and samples as columns

extract_protocol:
Mice were decapitated under deep anesthesia and slices were prepared in ice-cold cutting solution (85 mM NaCl, 75 mM sucrose, 2.5 mM KCl, 25 mM glucose, 1.25 mM NaH2PO4, 4 mM MgCl2, 0.5 mM CaCl2, and 24 mM NaHCO3) using a VT1200S vibratome (Leica). Slices were incubated at 35 °C for ~30 min and then kept at room temperature until use. During recordings the slices are kept at 35 °C in continuously perfused with artificial cerebrospinal fluid (126 mM NaCl, 2.5 mM KCl, 26 mM NaHCO3, 2 mM CaCl2, 2 mM MgCl2, 1.25 mM NaH2PO4, and 10 mM glucose, saturated with carbogen,) Fluorescently labeled MRR neurons were visualized in an upright microscope (Eclipse FN-1; Nikon) with epifluorescent illumination (Lambda FLED @ 530 nm; Sutter Instrument) combined with a CMOS camera (DaVinci 1k, RedShirtImaging). The neurons were patched with thin-wall borosilicate pipettes (pipette resistance: 3.69±0.09 MΩ, BF150-117-10, Sutter Instrument) filled with small amount (~1 µl) of intracellular solution containing 133.5 mM K-gluconate, 1.8 mM NaCl, 1.7 mM MgCl2, 0.05 mM EGTA, 10 mM HEPES, 2 mM Mg-ATP, 0.4 mM Na2-GTP, 10 mM phosphocreatine, and 8 mM biocytin (pH 7.25;  290-300 mOsm). Pipette capacitance and the bridge balance were carefully compensated in all current clamp recordings. For the RNA harvesting, the recordings were made using a HEKA EPC800 amplifier (HEKA Elektronik) digitized with a Digidata1440A A/D converter (Molecular Devices). The data acquisition was controlled by the pClamp10 software package. After patching the identified neurons, we measured the basic electrophysiological parameters of the cells including the resting membrane potential, the spontaneous synaptic activity, and the firing pattern. The length of the recording session was limited to 5 min from the break-in. The cytosol together with the nucleus was extracted from the neuron by the application of small negative pressure to the pipette. The tip of the quickly removed pipette was gently pushed into a microtube containing ice cold reaction buffer (lysis buffer with RNase inhibitor, Takara SMART-Seq HT PLUS Kit). The sample containing tubes was spun briefly and snap-frozen on dry ice. To suppress RNase contamination, the workplace including parts of the experimental setup was cleaned each day before the start of the sample collection with RNase AWAY (Thermo Fisher).
Sample collection: After electrophysiological recordings, the cells’ cytosol was aspirated via the same recording glass pipette that used for recording, and using a positive pressure, expelled into microtubes containing 1 µl of 1x lysis buffer with RNase inhibitor (SMART-Seq HT PLUS Kit, Takara). The samples were immediately frozen on dry ice and stored at -80°C until further processing. cDNA and library preparation for next-generation sequencing: Single-cell mRNA processing was performed using the SMART-Seq HT PLUS Kit (Takara) and according to manufacturer’s protocol. In brief, samples were reverse transcribed to cDNA, amplified, and purified with AMPure XP beads (Beckman Coulter). The quantity and the quality of the purified cDNA was assessed using Fragment Analyzer (Advanced Analytical). Subsequently, the cDNA was fragmented and adapters including indices for cell identification were added to the fragments. The quality and quantity were again assessed using Fragment Analyzer. For library preparation, the single cell samples with unique index adapters were pooled in equal amounts. The sequencing was performed on a NovaSeq 6000 (Illumina) instrument using 150 bp paired end configuration and a full SP-flowcell. Processing of sequencing data: After sequencing, raw reads were de-multiplexed with Illumina’s bcl2fastq2 (v2.20).

value: MRR


title: 12_28_18_TWM1_C_ATACTG_R1

description:
Library name: 12685_5751_144684_HW3JMBGXJ_NSF023_C03_12_28_18_TWM1_C_ATACTG_R1
Total RNA single illumina


title: Osteoclast untretaed control-1

description: Library name: OC_NT_1


title: MSR scaffold from mice vaccinated with control vaccine, bio rep4

description: Library name: Ctrl-4


title: MSR scaffold from mice vaccinated with control vaccine, bio rep3

description: Library name: Ctrl-3


title: 11_20_18_TWM3_C_GTCAGG_R1

description:
Library name: 12685_5751_144683_HW3JMBGXJ_NSF023_B03_11_20_18_TWM3_C_GTCAGG_R1
Total RNA single illumina


title: MSR scaffold from mice vaccinated with control vaccine, bio rep2

description: Library name: Ctrl-2


title: MSR scaffold from mice vaccinated with control vaccine, bio rep1

description: Library name: Ctrl-1


title: 11_20_18_TWM2_C_TCTTAA_R1

description:
Library name: 12685_5751_144682_HW3JMBGXJ_NSF023_A03_11_20_18_TWM2_C_TCTTAA_R1
Total RNA single illumina


title: Carm1-KO cDC1 bio rep3

description: Library name: KO3

value: dendritic cells


title: Macrophage treated with 100ng/ml lipopolysaccharide (LPS)-2

description: Library name: MA_LPS_2

source_name: Bone marrow derived macrophages

value: D5, no RANKL, LPS treated

value: Bone marrow derived macrophages


title: ID_106

description:
Library name: Sample 12
Ribodepleted bulk RNA_seq


title: Carm1-KO cDC1 bio rep2

description: Library name: KO2


title: Carm1-KO cDC1 bio rep1

description: Library name: KO1


title: control cDC1 bio rep3

description: Library name: Ctrl3


title: 3_4_19_TWM3_F_GGCTGC_R1

description:
Library name: 12685_5751_144680_HW3JMBGXJ_NSF023_G02_3_4_19_TWM3_F_GGCTGC_R1
Total RNA single illumina

value: Field Chilling


title: control cDC1 bio rep2

description: Library name: Ctrl2


title: control cDC1 bio rep1

description: Library name: Ctrl1


title: Macrophage untretaed control-3

description: Library name: MA_NT_3

value: D5, no RANKL-control


title: 3_4_19_TWM2_F_AATCCG_R1

description:
Library name: 12685_5751_144679_HW3JMBGXJ_NSF023_F02_3_4_19_TWM2_F_AATCCG_R1
Total RNA single illumina


title: 3_4_19_TWM3_C_TGGATT_R1

description:
Library name: 12685_5751_144695_HW3JMBGXJ_NSF023_F04_3_4_19_TWM3_C_TGGATT_R1
Total RNA single illumina


title: EMT-6 tumor, anti-avb8, replicate 3, scRNAseq

city: San Francisco

first: Dean

last: Sheppard

state: CA

address: 555 Mission Bay Boulevard South

institute: University of California, San Francisco

description: 10X Genomics

data_processing:
Gene-barcode matrices were built with CellRanger v2.1.1.
Matrices were quality controlled and processed with Seurat v4 according to Satija Lab protocol (Hao, et al., 2021).
DoubleFinder v2 was used to remove doublets, then each sample was labeled for metadata and merged into one object.
The all-samples object was processed with mutual nearest neighbors (MNN) dimensional reduction with the SeuratWrappers package.
Cell populations were subsetted and reprocessed according to the previous MNN analysis.
Assembly: mm10
Supplementary files format and content: Seurat object (rds)

source_name: EMT-6 tumor

growth_protocol: 4 week old female BALB/c mice were inoculated with 1e5 EMT-6 cancer cells in the fourth mammary pad. Once tumors measured 5 mm in diameter (about 10 days), treatment was administered.

extract_protocol:
Tumors were isolated from the mouse mammary pad and placed in a Petri dish with C10 media (RPMI 1640, HEPES 1%, Penicillin/Streptomycin 1X, fetal calf serum 10%, sodium pyruvate 1 mM, non-essential amino acids 1X, and beta-mercaptoethanol 0.45%) and minced with sterile razor blades. The tissue slurry was digested with Collagenase XI 2 mg/mL, Hyaluronidase 0.5 mg/mL, and DNase 0.1 mg/mL prepared in C10 medium. Cells were incubated in a shaker at 255 rpm for 30 minutes at 37 C°, then digestion was stopped with ice cold media.  The slurry was passed through a 100 µm mesh strainer into a clean 50 mL conical tube. Cells were pelleted by centrifugation for 5 minutes at 200 x g at 4 C°and mixed with RBC lysis buffer and passed through a 40 µm mesh strainer and washed with PBS. Live cells stained with Thy1.2 and CD45 were sorted into tumor and non-tumor cells groups and resuspended to enrich non-tumor cells.
Library was constructed according to manufacturer's protocol (Chromium single cell 3' v2 protocol, 10X genomics)

treatment_protocol: Mice were intraperitoneally injected with anti-PD1 (clone RMP1-14, 2 mg/kg) on days 0, 4, and 8, or injected with anti-avb8 (ADWA-11, 2 mg/kg) on days 0 and 7, or both therapies.

value: EMT-6 tumor

tag: time

value: Day 12

value: F

value: BALB/c WT


title: Macrophage untretaed control-2

description: Library name: MA_NT_2


title: EMT-6 tumor, anti-avb8, replicate 2, scRNAseq

description: 10X Genomics


title: EMT-6 tumor, anti-avb8, replicate 1, scRNAseq

description: 10X Genomics


title: Macrophage untretaed control-1

description: Library name: MA_NT_1


title: EMT-6 tumor, anti-PD1, replicate 3, scRNAseq

description: 10X Genomics


title: 2_12_19_TWM3_F_ATGAAC_R1

description:
Library name: 12685_5751_144677_HW3JMBGXJ_NSF023_D02_2_12_19_TWM3_F_ATGAAC_R1
Total RNA single illumina

value: Bud

value: total RNA


title: EMT-6 tumor, anti-PD1, replicate 2, scRNAseq

description: 10X Genomics


title: EMT-6 tumor, anti-PD1, replicate 1, scRNAseq

description: 10X Genomics


title: EMT-6 tumor, combined anti-PD1 & anti-avb8, replicate 3, scRNAseq

description: 10X Genomics

value: combined anti-PD1 & anti-avb10


title: SWT scRNA-seq

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description:
Library name: Sample1
10xGenomics

data_processing:
For bioinformatics analysis, results from Illumina sequencing were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in thesequenced samples (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0).
Assembly: mm10
Supplementary files format and content: Taq-separated value files and matrix files

source_name: MC38 tumor

extract_protocol:
MC38 tumors from SPP1fl/fl and SPP1fl/fl-Lyz2-icre mice were dissected and digested with a solution containing collagenase IV (0.2 mg/ml) and deoxyribonuclease I (10 mg/ml; Sigma- Aldrich). The single- cell suspension was obtained by passing through a 70- mm cell mesh and re-suspending in Hanks’ buffer. Samples were stained for 30 min using an antibody against CD45. 7-AAD was freshly added before cell sorting. CD45+7-AAD- single cells were sorted for library construction of scRNA-seq.
For chromium 10´ Genomics library and sequencing, single-cell suspension was added to the 10´ Chromium chip according to the instructions for the 10´ Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: MC38 tumor

value: CD45+ cells


title: EMT-6 tumor, combined anti-PD1 & anti-avb8, replicate 2, scRNAseq

description: 10X Genomics

value: combined anti-PD1 & anti-avb9


title: 2_12_19_TWM1_F_CGGTTA_R1

description:
Library name: 12685_5751_144675_HW3JMBGXJ_NSF023_B02_2_12_19_TWM1_F_CGGTTA_R1
Total RNA single illumina

value: single


title: EMT-6 tumor, combined anti-PD1 & anti-avb8, replicate 1, scRNAseq

description: 10X Genomics

value: combined anti-PD1 & anti-avb8


title: ex_vivo_expanded_cKITenriched_cells_mouse4_L2_HTO

city: Warsaw

first: Vladyslava

last: Liudkovska

address: Flisa 6

country: Poland

institute: IMol Polish Academy of Sciences

description:
Library name: mouse_4_HTO_L2
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only

data_processing:
For single cell profiling, FASTQ files were processed using Cell Ranger (v7.2.0), with gene expression counts quantified through the cellranger count function. The resulting h5 object was analyzed in R (v4.2.2) using Seurat (v4.4.0). Sample demultiplexing was performed with MULTIseqDemux from Seurat (https://satijalab.org/seurat/reference/multiseqdemux), and normalization was applied using the Centered Log Ratio (CLR) method.
Assembly: GRCm39
Supplementary files format and content: the .h5 file stores the gene expression count matrix and associated metadata for single-cell RNA-seq experiment
Library strategy: CITE-seq

source_name: bone marrow

growth_protocol: Bone marrow cells were enriched for the cKit-positive fraction using MACS separation (Miltenyi Biotec) and plated at 100,000 cells per well in a fibronectin-coated (100 ng/mL, Sigma-Aldrich) 96-well plate in hematopoietic stem cell (HSC) expansion medium. HSC expansion medium consisted of Ham’s F-12 Nutrient Mix (Gibco) supplemented with 1% Insulin-Transferrin-Selenium-Ethanolamine (ITS-X, Gibco), 1% penicillin/streptomycin/glutamine (Gibco), 1% HEPES (Gibco), 1 mg/mL polyvinyl alcohol (PVA, Sigma-Aldrich), 10 ng/mL animal-free recombinant stem cell factor (SCF, Peprotech), and 100 ng/mL thrombopoietin (TPO, Peprotech). All cells were cultured at 37°C in 5% CO₂ and routinely tested for mycoplasma contamination using PCR.

extract_protocol:
For CITE-seq, cell suspensions containing 2.5 × 10⁶ cells per sample were pooled and centrifuged at 300 × g at 4°C for 10 minutes. Each pool included a sample from each tested condition, with replicates separated across different pools to control for batch effects. Next, cells were resuspended in 100 µL PBS and filtered through 40 µm Flowmi™ cell strainers (Scienceware). Cell density and viability were assessed using an EVE™ Automatic Cell Counter (NanoEnTek Inc., USA). If necessary, the cell suspension was diluted to a final density of 2,000 – 10,000 cells/µL. Sample pools were processed in quadruplicates, with each replicate loaded onto a separate chip well (Chip G, 10x Genomics).
Cell encapsulation and library preparation were performed using the Chromium Controller (10x Genomics) and the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 with Feature Barcoding technology for Cell Surface Protein (10x Genomics), following the manufacturer's user guide (CG000206 Rev D). Library quality and quantity were assessed using a High-Sensitivity DNA Kit (Agilent Technologies, USA) on a 2100 Bioanalyzer (Agilent Technologies, USA). Samples were sequenced on a NovaSeq 6000 in paired-end mode (Read 1: 28 cycles, i7 index read: 8 cycles, i5 index read: 0 cycles, Read 2: 91 cycles). The sequencing depth was targeted at 4 × 10⁴ mRNA reads and 7 × 10³ Ab-oligo reads per cell.

treatment_protocol: For CRISPR/Cas9 editing of the Sf1 5′ UTR we designed a gRNA oligonucleotide  with the CRISPR-Cas9 gRNA Design Checker and UCSC Genome Browser (Integrated DNA Technologies). Functional CRISPR-Cas9 complexes were assembled with the Alt-R® CRISPR-Cas9 Guide RNA Kit (Integrated DNA Technologies and cells were nucleofected using the P3 Primary Cell 4D X Kit (Lonza) with the DS-130 program. Single cell RNA sequencing with CITE-seq tagging was performed after 21 days of ex vivo expansion.

value: bone marrow

value: primary

value: hematopoietic stem and progenitor cells

value: wild type C57Bl6

value: pooled samples (CTRL, Sf1 del(51–100), Sf1 del(251–300)); CITE-seq hashed

tag: mouse


title: EMT-6 tumor, isotype control, replicate 3, scRNAseq

description: 10X Genomics

value: EMT-6 tumor

value: isotype control


title: 1_12_19_TWM3_F_TCAGGA_R1

description:
Library name: 12685_5751_144674_HW3JMBGXJ_NSF023_A02_1_12_19_TWM3_F_TCAGGA_R1
Total RNA single illumina

value: Field Chilling


title: EMT-6 tumor, isotype control, replicate 2, scRNAseq

description: 10X Genomics

value: Day 12

value: F

value: BALB/c WT


title: ex_vivo_expanded_cKITenriched_cells_mouse4_L1_HTO

description:
Library name: mouse_4_HTO_L1
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only


title: EMT-6 tumor, isotype control, replicate 1, scRNAseq

description: 10X Genomics


title: 1_12_19_TWM2_F_TGTGCA_R1

description:
Library name: 12685_5751_144673_HW3JMBGXJ_NSF023_H01_1_12_19_TWM2_F_TGTGCA_R1
Total RNA single illumina

value: Bud

value: total RNA


title: 1_12_19_TWM1_F_CTAGTC_R1

description:
Library name: 12685_5751_144672_HW3JMBGXJ_NSF023_G01_1_12_19_TWM1_F_CTAGTC_R1
Total RNA single illumina


title: UPM_TZ_5

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Library name: UPM_TZ_5

data_processing:
QuantSeq 3′ mRNA-Seq reads were aligned to the Mus musculus reference genome (GRCm39) using STAR aligner.
The resulting alignment files were used for transcript assembly, quantification, and differential gene expression analysis. Raw read counts were normalized using the trimmed mean of M values (TMM) method followed by counts per million (CPM) transformation using the edgeR package within R and Bioconductor
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Brain

growth_protocol: The BV-2 murine microglial cell line was obtained from AcceGen Biotechnology (Fairfield, NJ, USA) and maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin–streptomycin at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from BV-2 cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality was assessed using the TapeStation 4000 system (Agilent Technologies, Amstelveen, Netherlands) and RNA concentration was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). Only RNA samples with an integrity number (RIN) greater than 8.0 were used for subsequent QuantSeq analysis.
cDNA libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen, GmbH, Vienna, Austria) according to the manufacturer’s instructions. Briefly, each total RNA hybridized with oligo-(dT) primer containing an Illumina-compatible sequence at the 5′ end, followed by reverse transcription. After RNA template degradation, second-strand synthesis was performed using a random primer containing an Illumina-compatible linker sequence. The resulting double-stranded cDNA libraries were purified using magnetic beads, amplified by polymerase chain reaction (PCR) to incorporate complete adapter sequences, and purified again to remove residual components. High-throughput sequencing was performed as single-end 75-bp sequencing using the NextSeq 550 platform (Illumina, San Diego, CA, USA).

treatment_protocol: Cells were pretreated with TZ for 1 h, followed by exposure to UPM (50 μg/mL) for 23 h.

value: Brain

value: microglial cell line

value: UPM and TZ 5 μg/mL


title: ex_vivo_expanded_cKITenriched_cells_mouse4_L1_GEX

description:
Library name: mouse_4_GEX_L1
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

data_processing:
For single cell profiling, FASTQ files were processed using Cell Ranger (v7.2.0), with gene expression counts quantified through the cellranger count function. The resulting h5 object was analyzed in R (v4.2.2) using Seurat (v4.4.0). Sample demultiplexing was performed with MULTIseqDemux from Seurat (https://satijalab.org/seurat/reference/multiseqdemux), and normalization was applied using the Centered Log Ratio (CLR) method.
Assembly: GRCm39
Supplementary files format and content: the .h5 file stores the gene expression count matrix and associated metadata for single-cell RNA-seq experiment


title: UPM_TZ_1_25

description: Library name: UPM_TZ_1_25

value: UPM and TZ 1.25 μg/mL


title: 12_27_18_TWM3_F_GTGTAG_R1

description:
Library name: 12685_5751_144671_HW3JMBGXJ_NSF023_F01_12_27_18_TWM3_F_GTGTAG_R1
Total RNA single illumina

value: single


title: Normal

description: Library name: Cont

value: Normal control


title: UPM

description: Library name: UPM

value: UPM 50 μg/mL


title: ex_vivo_expanded_cKITenriched_cells_mouse3_L2_HTO

description:
Library name: mouse_3_HTO_L2
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only

value: bone marrow

value: primary

value: hematopoietic stem and progenitor cells

value: wild type C57Bl6


title: 12_27_18_TWM2_F_ACATTA_R1

description:
Library name: 12685_5751_144670_HW3JMBGXJ_NSF023_E01_12_27_18_TWM2_F_ACATTA_R1
Total RNA single illumina

value: Field Chilling


title: ex_vivo_expanded_cKITenriched_cells_mouse3_L1_HTO

description:
Library name: mouse_3_HTO_L1
10x Genomics
CITE-seq hashing (HTO) – sample demultiplexing only

value: pooled samples (CTRL, Sf1 del(51–100), Sf1 del(251–300)); CITE-seq hashed


title: Genome-wide BRIE screen day 5 chronic stimulation hypoxic input

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

description:
Library name: D5lib_2_12_cont_hypoxic
Unsorted sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation under 1% oxygen and collected on day 5 before transcription-factor sorting to measure input sgRNA representation. Processed guide-count matrix column is D5lib_2_12_cont_hypoxic in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

data_processing:
Guide sequencing reads were processed with PoolQ using sample-barcode or condition tables and the corresponding guide sequence sets.
Supplementary files format and content: Tab-delimited guide-by-sample count matrices. Rows are sgRNAs with guide sequence, guide identifier, and target-gene fields where available; columns contain complete sgRNA counts for the submitted samples or conditions.
Library strategy: CRISPR Screen

source_name: spleen and lymph node

growth_protocol: Primary Cas9-expressing mouse CD8 T cells were isolated from spleen and lymph node and transduced with pooled sgRNA lentiviral libraries on RetroNectin-coated plates in complete T cell medium containing IL-7, IL-15, and LentiBOOST. Cells were maintained without TCR activation through day 5 post-transduction before Thy1.1 enrichment or screen-specific culture. For in vivo Tcf7 sort screens, transduced Cas9 x OT-I CD8 T cells were transferred into congenic recipient mice, and recipients were implanted bilaterally with B16-OVA tumors 1 day after T cell transfer.

extract_protocol:
Genomic DNA was isolated from sorted cell populations, input cell populations, tumor-infiltrating T cell samples, draining-lymph-node samples, or plasmid-library controls for guide-count sequencing. Standard cell pellets were processed using QIAamp DNA Mini Kit or QIAamp Mini spin-column workflows. Fixed or low-input sorted material was recovered using SPRI-based DNA cleanup where appropriate. Tumor-infiltrating T cell guide-count samples were prepared from tumor digests enriched over Lympholyte-M and/or with CD8 TIL MicroBeads before pelleting or freezing for genomic DNA isolation. The extracted genomic DNA or plasmid DNA was used as input for integrated sgRNA cassette amplification.
Integrated sgRNA cassettes were amplified from genomic DNA using indexed Illumina-compatible primers following Broad/GPP pooled-screen PCR workflows. Standard pXPR guide-count PCR used up to 10 ug genomic DNA per 100 uL reaction with Titanium Taq DNA polymerase, DMSO, a staggered P5 primer mix, and a unique indexed P7 primer. Primer sets were selected for the vector backbone, including pXPR_045-compatible and pXPR_206 or pRDA_206-derived vectors. For lower-input or nested tissue workflows, PCR cycle number was selected by qPCR using Q5 Hot Start high-fidelity polymerase, and available genomic DNA was split across multiple reactions to limit PCR jackpotting. No-template controls and test gels were used to check contamination and expected amplicon size. PCR products were pooled by sample and purified by AMPure XP cleanup, double-sided AMPure XP size selection at 0.6x/1.2x, or gel extraction depending on amplicon workflow and input complexity. Purified amplicons were quantified by Qubit and Bioanalyzer or TapeStation, pooled, and sequenced on Illumina MiSeq or NextSeq instruments using custom sequencing primers where required.

treatment_protocol: In vitro screen samples included unsorted input and plasmid-library controls and sorted Tcf7-, Prdm1-, Eomes-, or Tox-high and -low populations. Acute stimulation used overnight culture on plates coated with anti-CD3 clone 145-2C11 and anti-CD28 clone 37.51 at 5 ug/mL each, followed by culture off stimulation plates in cytokine-containing T cell medium. Chronic stimulation kept cells on anti-CD3/CD28-coated plates throughout the experiment, and hypoxia screens were cultured under 1% oxygen. Tcf7, Prdm1, Eomes, and Tox screens used intracellular transcription-factor staining to identify high- and low-expressing cells except where Tcf7-GFP reporter sorting was used; some Tcf7 sorts were divided into four bins to separate highest and lower-high populations from lowest and higher-low populations. In vivo Tcf7 sort screens recovered input cells, draining-lymph-node samples, tumor-infiltrating Tcf7-high and Tcf7-low fractions, and plasmid-library controls, typically 14 days after tumor implantation; male and female samples were processed separately where indicated.

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation under 1% oxygen; day 5 pre-sort input


title: 12_27_18_TWM1_F_TGCACG_R1

description:
Library name: 12685_5751_144669_HW3JMBGXJ_NSF023_D01_12_27_18_TWM1_F_TGCACG_R1
Total RNA single illumina

value: Bud

value: total RNA


title: Final-Slide-017-OED-01-24-2024-Epi-003

first: Harsh

last: Pathak

address: 3901 Rainbow Blvd

institute: KUMC

description: Library name: DSP-1001660020045-D-D05

data_processing:
FASTQ files downloaded from the NextSeq are converted into the DCC file format using the GeoMxNGSPipeline (version-2.3.3.10).
Assembly: GRCh38.p13
Supplementary files format and content: .dcc: probe count data
Supplementary files format and content: .xlsx: annotation file containing segment annotation info
Supplementary files format and content: .pkc: probe metadata linking probe barcodes with target genes IDs
Library strategy: Spatial Transcriptomics

source_name: OED

extract_protocol:
Formalin-fixed paraffin-embedded (FFPE) slides were prepared following the “RNA Slide Preparation Protocol” in MAN-10150 in the Manual Slide Preparation User Manual, available from NanoString. The RNA probe hybridization solution was prepared using the GeoMx® Cancer Transcriptome Atlas (CTA) RNA probe mix (NanoString), following the recommended dilution (10% probe mix + 10% DEPC water + 80% Buffer R).
Library prep was performed according to instructions provided in NanoString’s NGS Readout Library Prep User Manual (MAN-10117-05), followed by paired-end (27 x 27 cycles) sequencing on the Illumina NextSeq 550 sequencer using a high-output flow cell.

value: Epi

value: OED

value: No


title: Genome-wide BRIE screen day 7 acute stimulation Eomes-high bin

description:
Library name: D7_std_eomes_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Eomes, and sorted into the Eomes-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_std_eomes_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Eomes-high sort


title: ex_vivo_expanded_cKITenriched_cells_mouse3_L2_GEX

description:
Library name: mouse_3_GEX_L2
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling


title: Genome-wide BRIE screen day 7 acute stimulation Eomes-low bin

description:
Library name: D7_std_eomes_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Eomes, and sorted into the Eomes-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D7_std_eomes_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Eomes-low sort


title: ex_vivo_expanded_cKITenriched_cells_mouse4_L2_GEX

description:
Library name: mouse_4_GEX_L2
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling


title: UPM_TZ_2_5

description: Library name: UPM_TZ_2_5

value: Brain

value: microglial cell line

value: UPM and TZ 2.5 μg/mL


title: 11_20_18_TWM3_F_ACCAGT_R1

description:
Library name: 12685_5751_144668_HW3JMBGXJ_NSF023_C01_11_20_18_TWM3_F_ACCAGT_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

value: single


title: Genome-wide BRIE screen day 7 acute stimulation Prdm1-high bin

description:
Library name: Day7_std_prdm1_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Prdm1, and sorted into the Prdm1-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is Day7_std_prdm1_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Prdm1-high sort


title: ex_vivo_expanded_cKITenriched_cells_mouse3_L1_GEX

description:
Library name: mouse_3_GEX_L1
10x Genomics
scRNA-seq (GEX) – used for gene expression profiling

value: bone marrow

value: primary

value: hematopoietic stem and progenitor cells

value: wild type C57Bl6


title: Genome-wide BRIE screen day 7 acute stimulation Prdm1-low bin

description:
Library name: Day7_std_prdm1_low
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells in the standard acute anti-CD3/CD28 stimulation arm were collected on day 7, stained for Prdm1, and sorted into the Prdm1-low bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is Day7_std_prdm1_low in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: spleen and lymph node

value: CD8 T cells

value: BRIE genome-wide sgRNA library; acute anti-CD3/CD28 stimulation; day 7 Prdm1-low sort


title: 11_20_18_TWM2_F_GATCAC_R1

description:
Library name: 12685_5751_144667_HW3JMBGXJ_NSF023_B01_11_20_18_TWM2_F_GATCAC_R1
Total RNA single illumina

value: Bud

value: Field Chilling

value: total RNA


title: Genome-wide BRIE screen day 5 chronic stimulation Prdm1-high bin

description:
Library name: D5_cont_prdm1_high
sgRNA amplicon sequencing library from the BRIE whole-genome in vitro CRISPR screen. CD8 cells were maintained on anti-CD3/CD28-coated plates for chronic stimulation, collected on day 5, stained for Prdm1, and sorted into the Prdm1-high bin. The library was sequenced to quantify sgRNA abundance in that sorted fraction. Processed guide-count matrix column is D5_cont_prdm1_high in file in_vitro_genome_wide.txt.
in_vitro_genome_wide.txt

value: BRIE genome-wide sgRNA library; chronic anti-CD3/CD28 stimulation; day 5 Prdm1-high sort


title: NPC_B6_51

description:
Library name: Sample 2
Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs

extract_protocol:
Frozen cells were lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 20-35 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 71-500 ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 NovaSeq Reagent Kit (200 or 300 Cycles) (Illumina).  An average of 69 million paired reads was generated per sample. Ribosomal reads represented 0.1-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: Neural Progenitor Cells