title: 4238-008-60

description: Library name: 4238-008-60


title: PJH1130, Stag2-KO mouse urothelium, 1 week after TMX induction

status: Public on Feb 03 2026

type: SRA

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

country: Spain

institute: CNIO

description:
Library name: PJH1130_ko
gene_expression_htseqcount_1week.txt

library_source: transcriptomic

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's Real Time Analysis integrated primary analysis software (RTA v2). Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Analyses were performed using Nextpresso RNA-seq pipeline.
Raw files were aligned to mm10 reference genome using Bowtie and TopHat aligners.
Raw counts were generated using htseq
Differential expression analysis was performed using DEseq2.
Assembly: mm10
Supplementary files format and content: text file with gene expression raw counts

molecule: total RNA

organism: Mus musculus

source_name: peeled urothelium

extract_protocol:
Total RNA was extracted using a ReliaPrepTM System Kit (Promega), according to manufacturer’s instructions.
Total RNA samples (400ng; RQS average 9.0, range 8.7-9.3) were converted into cDNA sequencing libraries with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. {This library preparation kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq)}

treatment_protocol: Mice were fed a TMX-containing diet for a week at sacrificed one week or one month after treatment initiation.

tag: tissue

value: peeled urothelium

tag: genotype

tag: treatment

value: 1 week after TMX induction

tag: batch


title: 4795-044-60

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Library name: 4795-044-60

data_processing:
A Nextflow pipeline (https://github.com/compbiomed/RNA_Seq) was used to process the sequencing data to obtain the expression levels for each gene.
Both gene and transcript level counts were calculated using RSEM with Ensembl build 75 annotation.
Assembly: GRCh37
Supplementary files format and content: DECAMP2_mucus_plugging_filtered_counts.tsv: tab-separated values file containing 24599 x 48 matrix of counts for all Ensembl Gene IDs that passed filtering

organism: Homo sapiens

source_name: Nasal brushing

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA). RNA integrity was quantified by Agilent Bioanalyzer, and RNA purity was confirmed using a NanoDrop spectrophotometer.
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol.

value: Nasal brushing

tag: mp score

tag: copd status

value: No

tag: smoking status

value: Current Smoker (one puff in the last month)

tag: Sex

value: Female


title: H3K27ac_peChIP_mESC_Rep1_INPUT

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

country: United Kingdom

institute: MRC Human Genetics Unit, The University Of Edinburgh

description: INPUT library

library_source: genomic

data_processing:
We used FASTQC (version: 0.11.7) for quality control metrics. Filtering of poor-quality reads and trimming of adaptor sequences was performed using fastp (PMID: 30423086) using default settings
For single-end ChIP libraries: Filtered and trimmed reads were aligned to the mm10 assembly of mouse genome using bowtie and uniquely mapped reads were kept. Alignments were converted to BAM format and sorted using SAMtools and PCR duplicates removed using Picard. Bedtools was used to create BED files followed by conversion into HOMER tag directory format (makeTagDirectory) using default parameters. We called peaks using HOMERs findPeaks command with options -F 2 -localSize 50000 -size 150 -minDist 300 -fdr 0.01 –region. UCSC compatible bigwig files normalized to sequencing depth were generated using makeUCSCfile with parameters: -bigWig -style chipseq –fragLength 150.
Paired-end ChIP libraries: Filtered and trimmed reads were aligned to mm10 genome using bowtie2 with options (--no-discordant --no-mixed --no-unal -X 2000) followed by conversion to BAM format and removal of PCR duplicates as above. Read pairs were converted into ChIP fragments using bedtools bamtobed –bedpe and fractionated into sub-nucleosomes (<150 bp) and mono-nucleosomes (150-225 bp). Fragment coverage was computed at base-pair resolution with bedtools genomeCoverageBed and coverage normalized to sequencing depth and scaled to 107. Coverage data was converted to bigwig format using wigTobigWig (Kent utilities, UCSC).
Assembly: mm10
Supplementary files format and content: Read density in bigwig format

molecule: genomic DNA

source_name: mESC (46C)

growth_protocol: 46C cells were maintained in GMEM supplemented with 10% Serum and LIF.

extract_protocol:
Native MNase ChIP (detailed protocol: PMID: 27089178)
NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB catalogue # E7645)

treatment_protocol: For differentiation, three million 46C Cells were seeded 24 hours (h) prior to differentiation on 0.1% gelatine coated T75 Corning flasks in the maintenance medium. On Day-0, one flask of ESCs were harvested and rest of the cells were supplied with differentiation media ((1:1DMEM/F12: Neuro basal medium (GIBCO, #31330-032 and 21103-049 respectively) supplemented with 0.5x B27 (Invitrogen, #17504044), 0.5x N2 (Invitrogen, #17502048), L-Glutamine and 50mM 2--mercaptoethanol (GIBCO, #31350010)). Cells were then cultured for 7 days with daily media changes after day-2 NPC differentiation was monitored visually through expression of the Sox1-GFP reporter.

tag: cell line

value: mESC (46C)

tag: chip antibody


title: U_5_copulated

first: Lena

last: Arévalo

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

institute: INIA-CSIC

description: Library name: U_5

data_processing:
QC of raw sequencing reads and trimming were performed using FastQC and Trim Galore! 0.6.7 (Brabraham Bioinformatics) using a Phred score cutoff of 30 and minimum sequence length of 100 after trimming. In order to separate out reads derived from semen (C57/Bl6 strain) we obtained the lists of all 129S1/SvImJ SNPs compared to the mouse genome (GRCm38) from the Ensembl database (ftp://ftp.ensembl.org). Based on this SNP database we generated a pseudo-hybrid genome using the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). Briefly, 129S1/SvImJ SNPs relative to the mouse genome were then N-masked to allow mapping of both FRT and semen-derived reads. The trimmed read files were then mapped to this pseudo-hybrid genome using HISAT2 2.2.1. Alignment rate ranged from 89.28% to 96.85%. This was followed by splitting the mapped files into reads originating from FRT or semen. Splitting was performed using the program SNPsplit (Brabraham Bioinformatics). We retained the mapped reads assigned to the FRT and discarded the reads determined to be semen derived.
StringTie 2.2.1 was used for transcript quantification and annotation. Gene annotation was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org)(GRCm38.89).
Assembly: GRCm38
Supplementary files format and content: tab delimited table including raw read counts for each sample

molecule: polyA RNA

source_name: uterus

extract_protocol:
Plug-positive females were euthanized by cervical dislocation and tissue was dissected. Unpaired control females were euthanized and dissected in the morning, when determined to be in estrus. For each female the FRT was dissected, collecting tissue from both uterine horns (Us), both uterotubal junctions (UTJs) using precise microdissection and both oviducts (OVDs) (Fig. 1). For each female one of each U, UTJ and OVD was placed in RNAlater for RNA extraction. RNA was extracted from tissues stored in RNAlater using the RNeasy Plus Mini (uterine horn samples) or the RNeasy Plus Micro (for UTJ and OVD) kits (Qiagen) following the manufacturers recommendations. Samples were stored at -80º until sequencing.
Samples were sequenced on a Illumina NovaSeq X platform, producing ~30 M, 150bp, paired-end reads per sample. Sample quality control and library preparation was performed by the sequencing facility (Novogene Europe). RNA integrity ranged from 6.3 to 9.8.

treatment_protocol: Female 129SV/S2 mice were either paired 1-to-1 with intact (COP; n=4) or vasectomized (VAS; n=4) C57/Bl6 males or unpaired in estrus (CTR; n=5). Mice were maintained under standard laboratory conditions in environmentally controlled rooms (20–24ºC) on a 12L:12D photoperiod with nesting material and ad libitum food and water. All animal handling was conducted according to German law of animal protection and in agreement with the approval of the local institutional animal care committees (Landesamt für Natur, Umwelt und Verbraucherschutz, North Rhine-Westphalia, Germany, AZ81-02.04.2018.A369). Females were paired in the evening and checked for seminal plugs early the next morning ~6-8h post-copulation.

value: uterus

value: WT

value: post-copulation with intact male


title: H3K115ac_peChIP_mESC_Rep1_INPUT

description: INPUT library


title: PJH1079, Stag2-KO mouse urothelium, 1 week after TMX induction

description:
Library name: PJH1079_ko
gene_expression_htseqcount_1week.txt


title: H3K115ac_peChIP_mESC_Rep1

description: ChIP library


title: PJH1018, Stag2-WT mouse urothelium, 1 week after TMX induction

description:
Library name: PJH1018_wt
gene_expression_htseqcount_1week.txt


title: N2 C elegans, control, L4 stage, rep3

city: Galway City

first: Jose

middle: Carlos

last: Casas-Martinez

state: Galway County

address: Human Biology Building, University Road

department: Physiology

country: Ireland

institute: University of Galway

description: Library name: C3

data_processing:
Data Quality Control. Raw data (raw reads) in fastq format was firstly processed through in-house perl scripts. In this step, clean data (clean reads) was obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content were calculated. All the downstream analyses were based on the clean data with high quality.
Novel transcripts prediction. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis. (For DESeq2[5] with biological replicates) Differential expression[6] analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR[7] without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: Mapping reads to the reference genome. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and generate a better mapping result than other non-splice mapping tools.
Supplementary files format and content: gene_fpkm_group.txt

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: C. elegans were maintained in Nematode Growth Medium (NGM) at 20 ºC in the laboratory

extract_protocol:
Age-synchronised worms from a single NGM plate were incubated with TRIZol (500 ml per NGM plate), samples were mixed by vortexing for 30 sec. Chloroform was added to each tube (100 μL for a 12-well plate and 1 ml for a C. elegans 60 mm Ø plate), and the tube shaken vigorously by hand for 15 sec before incubation for 5 min at room temperature. RNA precipitation was achieved by adding 100% isopropanol to the aqueous phase (250 μL for a 12-well plate) and incubating at -20ºC overnight. RNA pellet was washed by adding 100 μL of 80% ethanol, supernatant was discarded and the tubes were allowed to air dry for 5-10 min at room temperature. The RNA was reconstituted in 10 μL of RNase-free H2O. Samples were analysed using the NanoDrop2000 spectrophotometer to quantify nucleic acid content and purity.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Tunicamycin treatment of C. elegans on a worm population synchronized by bleaching. Several plates of adult worms carrying embryos were subjected to a chemical (bleach-NaOH solution) and mechanical (by vortexing) procedure. The resulting embryos, for the embryonic stage, were treated with TM diluted in S Medium, for 24 h on a rocker at 20 °C. The resulting embryos, for the L4 stage, were transferred to NGM plates until they reached the L4 developmental stage and then treated with TM diluted in S Medium, for 24 h on a rocker at 20 °C. After treatment worms were transferred to NGM plates and allow to grow until adulthood.

value: Whole organism

value: wildtype

value: control

tag: Stage

value: L4 Stage


title: PJH1131, Stag2-KO mouse urothelium, 1 week after TMX induction

description:
Library name: PJH1131_ko
gene_expression_htseqcount_1week.txt


title: N2 C elegans, control, L4 stage, rep2

description: Library name: C2


title: H3K27ac_peChIP_mESC_Rep2

description: ChIP library


title: 4438-010-60

description: Library name: 4438-010-60

value: Yes

value: Male


title: MOLM-13 cells TSN-3

city: Guiyang

first: Xianchao

last: He

state: Guizhou

address: Huaxi

country: China

institute: Guizhou University

description: Library name: Samples 6

data_processing:
Differential gene expression analysis was performed using DESeq2 v1.26.0 (FDR < 0.05, |log₂FC| > 0.584).
Gene Set Enrichment Analysis (GSEA) was conducted using the MSigDB Hallmark 2023 gene set (FDR < 0.25), and the analysis was performed on the OmicShare platform v6.2.
Assembly: GRCh38
Supplementary files format and content: xlsx file contains the gene expression of all samples

source_name: cell line

growth_protocol: MOLM-13 cell was cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) mixture.

extract_protocol:
Total RNA was extracted from TSN/DMSO treated cells using RNAiso Plus reagent
Libraries were constructed and sequenced using the NovaSeq™ X Plus platform

treatment_protocol: MOLM-13 cells were treated with 20 nM TSN or DMSO for 48 h (n=3 biological replicates).

value: cell line

tag: cell type

value: Acute myeloid leukemia

value: DMSO


title: 4438-025-60

description: Library name: 4438-025-60

value: Nasal brushing

value: Former Smoker (not even a puff for >= 1 month)


title: N2 C elegans, tunicamycin treated, embryo stage, rep2

description: Library name: B2

value: tunicamycin 1.25 μg/ml

value: Embryo Stage


title: N2 C elegans, tunicamycin treated, embryo stage, rep1

description: Library name: B1


title: 4438-021-60

description: Library name: 4438-021-60


title: 4796-027-60

description: Library name: 4796-027-60

value: Current Smoker (one puff in the last month)


title: N2 C elegans, tunicamycin treated, embryo stage, rep3

description: Library name: B3


title: MOLM-13 cells TSN-2

description: Library name: Samples 5


title: N2 C elegans, control, L4 stage, rep1

description: Library name: C1


title: PJH1020, Stag2-WT mouse urothelium, 1 week after TMX induction

description:
Library name: PJH1020_wt
gene_expression_htseqcount_1week.txt

value: peeled urothelium

value: 1 week after TMX induction


title: PJH1013, Stag2-WT mouse urothelium, 1 week after TMX induction

description:
Library name: PJH1013_wt
gene_expression_htseqcount_1week.txt


title: N2 C elegans, tunicamycin treated, embryo stage, rep4

description: Library name: B4


title: MOLM-13 cells TSN-1

description: Library name: Samples 4

value: WT


title: N2 C elegans, control, embryo stage, rep3

description: Library name: A3

value: Whole organism


title: 4795-055-60

description: Library name: 4795-055-60

value: No


title: CCR9 KO_MC38 tumor_3 weeks

city: Chiba

first: YANGSONG

last: WANG

state: Chiba

address: 1-8-1, Inohana,

department: Experimental Immunology

country: Japan

institute: Chiba University

description: Library name: CCR9_KO_MC38 tumor_3 weeks

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using Cell Ranger v7.1.0 (10x Genomics)
Assembly: refdata-gex-mm10-2020-A (10X Genomics)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Thymus

extract_protocol:
A FACSAria III cell sorter (BD) was used for live Thymic CD11c+ cell sorting.
Libraries were prepared following the manufacturer's instructions using the Chromium Next GEM Single-Cell 5’ Reagent Kit v2 (10× Genomics).

value: Thymus

value: Thymic CD11c+ cells

value: CD11c+ cells

value: MC38_3 weeks


title: N2 C elegans, control, embryo stage, rep4

description: Library name: A4

value: wildtype

value: control


title: 4795-018-60

description: Library name: 4795-018-60

value: Female


title: CCR9 WT_MC38 tumor_2 weeks

description: Library name: CCR9_WT_MC38 tumor_2 weeks

value: MC38_2 weeks


title: 4796-034-60

description: Library name: 4796-034-60

value: Nasal brushing

value: Yes

value: Former Smoker (not even a puff for >= 1 month)


title: MOLM-13 cells DMSO-3

description: Library name: Samples 3

value: cell line

value: Acute myeloid leukemia

value: DMSO


title: Leaves, GmNRPE1-RNAi-T-sRNA-r6

status: Public on Feb 02 2026

city: Riverside

first: Brandon

last: Le

state: CA

address: 3401 Watkins Drive

department: Institute for Integrative Genome Biology

institute: University of California, Riverside

data_processing:
Raw reads were subjected to adapter trimming using a custom Perl script. Reads without an adapter or shorter than 18-nt after trimming were discarded from further processing.
Trimmed reads (≥ 18-nt) aligned to rRNA/tRNA/snoRNA regions were then removed using Bowtie v1.1.0 (Langmead et al., 2009) with the parameters '-v 2 k1', and reads that were assigned to the 45S rRNA regions were counted. The remaining reads were aligned to the soybean genome using ShortStack v3.4 with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were separated by size and normalization was performed by calculating the RPMR value (reads per million of 45S rRNA reads) (Li, Le et al. 2016; PMID: 27938667).
Genome_build: Soybean (Glycine max) genome; Gmax_275_v2.0 (Phytozome 10)
Supplementary_files_format_and_content: Tab-delimited text file containing the raw and normalized read counts per 100-bp non-overlapping windows for each sample. The column headers for each file are as follows: Window_ID, chromosome, start position, end position, raw read count, reads per million (RPM) normalization, reads per million of 45S rRNA reads (RPMR) normalization,  read size. Windows without any raw read count are omitted. The start and end positions are 0-based coordinates and can be formatted into bed files for further downstream analysis.

organism: Glycine max

source_name: Leaves, GmNRPE1-RNAi-T-sRNA

extract_protocol:
Mature leaf tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using TRI Reagent from the Molecular Research Center (MRC, TR118) following the manufacturer's protocol.
Small RNA library was constructed as previously described (Li, Le et al. 2016; PMID: 27938667). Briefly, 10 µg of total RNA from mature leaf was resolved on a 15% urea-PAGE gel, and the ~15-40 bp RNAs were recovered by gel purification.  Small RNA libraries were constructed following instructions from the NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300S). The libraries were pooled and sequenced on an Illumina HiSeq 2500 at the UC Riverside IIGB Genomics Core.

tag: cultivar

value: Mustang

tag: RNAi

tag: transgene

value: T

tag: replicate

value: Leaves


title: 4795-023-60

description: Library name: 4795-023-60

value: No


title: Adult, long bone, bone marrow

city: Okayama

first: Ikue

last: Tosa

state: Okayama

address: Shikata-cho2-5-1, Kita-ku

institute: Okayama University

description:
Library name: Adult, long bone, bone marrow
10x Genomics

data_processing:
The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger.
Assembly: GRCm39
Supplementary files format and content: Tab-sepalated values files and matrix files

source_name: long bone, bone marrow

extract_protocol:
Cells were collected from C57BL6J mice for stromal cell analyses. Hematopoietic cells were depleted using the autoMACS Pro Separator (Miltenyi Biotec). FCM analyses were carried out using the FACS Diva 8.0.1 software (BD Biosciences). Dead cells and debris were excluded using FSC, SSC, and DAPI staining. Cells were sorted using a FACSAria III Cell Sorter (BD Biosciences).
Sorted cells were processed with Chromium Next GEM Single Cell 3ʹ GEM kit v.3.1 (10X Genomics) according to the manufacturer’s instruction.

value: long bone, bone marrow

tag: strain

value: Stromal cells

value: WT

tag: age

value: adult


title: Leaves, GmNRPE1-RNAi-T-sRNA-r4

tag: tissue


title: Leaves, GmNRPE1-RNAi-T-sRNA-r5


title: Cellular diversity of the developing chick trigeminal ganglion at single-cell resolution

city: San Francisco

first: Erica

middle: J

last: Hutchins

address: 513 Parnassus Ave

department: Cell and Tissue Biology

institute: University of California San Francisco

description:
Library name: All_TG_samples
Parse Biosciences

data_processing:
FASTQ files underwent barcode correction, read alignment, read deduplication, and transcript quantification using Parse Biosciences Trailmaker Pipeline Module (v1.6.2)
Additional data processing was done using the Parse Biosciences Trailmaker Insights Module. A cell size distribution filter using default settings was first applied to filter out cells with fewer than 331, 290, 365, and 374 transcripts in left TG sample #1, left TG sample #2, right TG sample #1, and right TG sample #2, respectively. These values were determined using barcode rank plots for each sample to identify cells with low transcript counts. Cells were next filtered based on the number of genes vs transcripts using the default third-order spline regression model where the prediction interval for defining outliers in the distribution was set to 0.999. A doublet filter using scDblFinder was then used to remove doublets with a probability threshold of 0.7. Resulting data was further processed in R (v4.4.0) with Seurat package (v4).
Assembly: GRCg7b
Supplementary files format and content: Tab separated values files and matrix files

organism: Gallus gallus

source_name: Trigeminal Ganglia

growth_protocol: Fertilized chicken eggs (Gallus gallus, Rhode Island Red breed) were purchased locally from Petaluma Farms (Petaluma, CA). Embryos were incubated in a humidified incubator set to 100°F until desired Hamburger-Hamilton (HH) stage was reached (~66 hours).

extract_protocol:
Live embryos were excised from eggs at HH17 on Whatman filter paper and stored in Ringer’s solution until further processing. Pooled left and right trigeminal ganglia (TG) samples were generated by microdissection of 20 TG from separate embryos (left and right ganglia were never collected from the same embryo). Ganglia were collected and stored on ice in pre-chilled Ringer’s solution until two duplicate pooled left and right samples of 20 TG each were collected. Tissues were washed three times in pre-chilled DPBS and then enzymatically dissociated in 500µl 1X Accumax (Cat# AM105) supplemented with 25U RQ1 DNase (Cat# M6101) and 250U SUPERase-In (Cat# AM2694) at 37ºC for 21 minutes with gentle pipette mixing every 5 minutes. Single cell suspensions were stored on ice while briefly manually counting cells on hemocytometer and checking viability with trypan blue staining before proceeding to cell fixation for Parse Biosciences Split Pool Barcoding described below. Each 20 TG sample was confirmed to contain approximately 300,000 viable cells after dissociation and prior to fixation. Single cell suspensions were processed with Parse Biosciences Evercode Cell Fixation v3 kits per manufacturer’s instructions. All centrifugation steps were performed at 300xG in a swinging bucket rotor at 4°C and all cell straining steps were conducted using PluriSelect pluriStrainer mini with 20µm mesh size (Cat# 43-10020-40). Fixed samples were frozen in a Mr. Frosty Freezing Container at -80°C until sufficient sample numbers were generated to proceed with barcoding.
Fixed whole cell single cell suspensions were thawed and processed for combinatorial barcoding  using the Parse Biosciences Evercode WT 100K v3 kit per manufactuerer's protocols. To target a total of ~100,000 barcoded cells output from the kit, we loaded approximately ~87,000 fixed and viable cells per sample into round 1 of split pool barcoding (~350,000 cells total across all 4 samples). Libraries were size selected using SPRIselect Reagent (Cat# B23317) when instructed. Library size distribution QC was conducted using Agilent Bioanalyzer High Sensitivity DNA Kit (Cat# UFUCOP-5067-4626) and quantified using Qubit dsDNA HS (High Sensitivity) Assay kit (Cat# Q33230). A total of 8 final sublibraries were generated and sequenced at a sequencing depth of 2 billion paired-end reads (20,000 reads/cell for 100,000 cells).

value: Trigeminal Ganglia

value: pooled male and female


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r6

source_name: Leaves, GmNRPE1-RNAi-NT-sRNA

value: NT


title: CCR9 WT_MC38 tumor_3 weeks

description: Library name: CCR9_WT_MC38 tumor_3 weeks

value: Thymus

value: Thymic CD11c+ cells

value: CD11c+ cells

tag: genotype

tag: treatment

value: MC38_3 weeks


title: Leaves, GmNRPE1-RNAi-T-sRNA-r1


title: MOLM-13 cells DMSO-1

description: Library name: Samples 1

value: cell line

value: Acute myeloid leukemia


title: 4796-037-60

description: Library name: 4796-037-60

value: Nasal brushing

tag: mp score

value: Yes

value: Former Smoker (not even a puff for >= 1 month)

value: Female


title: CCR9 WT_PBS_2 weeks

description: Library name: CCR9_WT_PBS_2 weeks

value: PBS

tag: batch


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r5

value: Mustang

value: Leaves


title: MOLM-13 cells DMSO-2

description: Library name: Samples 2

value: WT

value: DMSO


title: N2 C elegans, control, embryo stage, rep2

description: Library name: A2

value: Whole organism

value: wildtype

value: control

value: Embryo Stage


title: N2 C elegans, control, embryo stage, rep1

description: Library name: A1


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r3

value: NT


title: Old, long bone, bone marrow

description:
Library name: Old, long bone, bone marrow
10x Genomics

value: long bone, bone marrow

value: Stromal cells

value: old


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r4

source_name: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r6


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r1

source_name: Leaves, GmNRP(D/E)2-RNAi-T-sRNA

value: T


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r1


title: Leaves, GmNRPE1-RNAi-T-sRNA-r3


title: Leaves, GmNRPD1-RNAi-T-sRNA-r3

source_name: Leaves, GmNRPD1-RNAi-T-sRNA

value: Jack


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r3


title: Leaves, GmNRPE1-RNAi-T-sRNA-r2


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r2


title: Leaves, GmNRPD1-RNAi-T-sRNA-r2


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r5


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r4


title: H3K27ac_peChIP_mESC_Rep1

description: ChIP library

value: mESC (46C)


title: Leaves, GmNRPE1-RNAi-NT-sRNA-r1


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r6


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r5


title: Leaves, GmNRPE1-RNAi-T-mRNA-r5

data_processing:
Raw 100-nt single-end reads were quality controlled using FASTQC v0.11.5 (Robinson, McCarthy et al. 2010) and mapped to the soybean genome (Gmax_275_v2.0; Phytozome 10) using the STAR aligner v 2.5.3a (Dobin, Davis et al. 2013) with parameter --quantMode GeneCounts to generate read counts for each gene. Differential expression analysis was carried out using EdgeR (Robinson, McCarthy et al. 2010) with a two-fold change and a FDR ≤ 0.05.
Genome_build: Soybean (Glycine max) genome; Gmax_275_v2.0 (Phytozome 10)
Supplementary_files_format_and_content: Tab-delimited text file containing the mapped reads count for each gene from the STAR aligner. The column headers for each file are as follows: Gene_ID, number of mapped reads

source_name: Leaves, GmNRPE1-RNAi-T-mRNA

extract_protocol:
Mature leaf tissues were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Total RNA was isolated from the powder using TRI Reagent from the Molecular Research Center (MRC, TR118) following the manufacturer's protocol.
Poly(A) mRNA was isolated from five µg of mature leaf total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490), and the purified mRNA was used to construct the mRNA-seq library using the NEBNext® mRNA Library Prep Reagent Set for Illumina® (NEB, E6100L). The libraries were sequenced on an Illumina Illumina HiSeq 2500 at the UC Riverside IIGB Genomics Core.


title: Leaves, GmNRPE1-RNAi-T-mRNA-r6


title: Leaves, GmNRPE1-RNAi-T-mRNA-r4


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r4


title: Leaves, GmNRP(D/E)2-RNAi-T-sRNA-r2


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r5

source_name: Leaves, GmNRPE1-RNAi-NT-mRNA


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r1


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r6


title: Leaves, GmNRPE1-RNAi-T-mRNA-r2


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r2


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r5

source_name: Leaves, GmNRP(D/E)2-RNAi-T-mRNA


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r4


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r4


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r3


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r3


title: Leaves, GmNRPD1-RNAi-T-sRNA-r1


title: Leaves, GmNRP(D/E)2-RNAi-NT-sRNA-r2


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r6

source_name: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r5


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r1


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r1


title: Leaves, GmNRPD1-RNAi-NT-sRNA-r2

source_name: Leaves, GmNRPD1-RNAi-NT-sRNA


title: Leaves, GmNRPD1-RNAi-NT-sRNA-r1


title: Leaves, GmNRPD1-RNAi-NT-sRNA-r3


title: Leaves, GmNRPD1-RNAi-NT-mRNA-r2

source_name: Leaves, GmNRPD1-RNAi-NT-mRNA


title: Leaves, GmNRPD1-RNAi-NT-mRNA-r1


title: senescent rMSCs, TSA and phenamil extracs treat, Day1

city: Cheonan

first: Cheng Ji

last: Li

address: 119 Dandea-ro, Dongnam-gu

country: South Korea

institute: ITREN

description:
Library name: nB_TP
Single sample for this condition (no biological replicates)

data_processing:
Adapter and low-quality sequence trimming was performed using BBDuk v39.01.
The processed reads were aligned to the NCBI Rattus norvegicus reference genome (mRatBN7.2) using STAR v2.7.10b.
Gene-level raw read counts were generated using HTSeq-count v2.0.2.
A log2-normalized expression matrix was generated using TMM-normalized CPM values with a pseudocount of 1: log2(CPM + 1).
Assembly: mRatBN7.2 (GCF_015227675.2)
Supplementary files format and content: Tab-delimited text file (.tsv) containing gene-level raw counts. Columns: Entrez ID, gene symbol, and integer read counts for each sample (Ctrl, nB, nB_T, nB_TP).
Supplementary files format and content: Tab-delimited text file (.tsv) containing log2-normalized gene expression values. Columns: Entrez ID, gene symbol, and log2-normalized expression values for each sample (Ctrl, nB, nB_T, nB_TP).

organism: Rattus norvegicus

source_name: femurs

growth_protocol: Cells were cultured in osteogenic induction medium under standard conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted using TRIzol following the manufacturer’s instructions; RNA integrity was assessed by Bioanalyzer/TapeStation.
Libraries were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD according to the manufacturer’s protocol; single-end libraries were sequenced on Illumina NextSeq 500 (SE 100 bp).

treatment_protocol: Cells were treated with TSA and/or phenamil according to group assignment for 24 h; control received vehicle only.

value: femurs

value: mesenchymal stem cells

value: osteogenic differentiation with TSA and phenamil


title: senescent rMSCs, TSA extracs treat, Day1

description:
Library name: nB_T
Single sample for this condition (no biological replicates)

value: osteogenic differentiation with TSA


title: young rMSCs, control, Day1

description:
Library name: Ctrl
Single sample for this condition (no biological replicates)

value: osteogenic differentiation


title: scATAC, PBMC, Healthy Control_3

city: Seoul

first: Minseok

last: Kim

address: 103 Daehak-ro, Jongno-gu, Seoul

institute: Seoul National University College of Medicine

description:
Library name: HC_6_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
Data were aligned to the human reference genome using Cellranger v7.1.0, and further analysis was conducted using the Seurat package in R and Scanpy package in Python. Samples were demultiplexed based on SNP.
Assembly: hg38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: h5ad

source_name: Blood

extract_protocol:
Peripheral blood was obtained from vaccine recipients and mononuclear cells were isolated from 16 ml of peripheral blood using Vacutainer® CPT™ Mononuclear Cell Preparation Tube (Becton, Dickinson and Company, NJ, USA). After collecting 4 ml of plasma, the white opaque layer containing PBMCs was isolated and washed with RPMI supplemented with 10% FBS twice. The isolated PBMCs were frozen in CELLBANKER®1 Cell Freezing Media (Zenogen Pharma, Fukushima, Japan) for liquid nitrogen storage. After, PBMC was thawed and suspended in a 2 ml tube, then centrifuged at 4°C for 5 min at 500 x g in a swinging bucket centrifuge. The pellet was resuspended in 100 ul of Lysis Buffer and incubated for 3 min on ice. After incubation, 1 ml chilled Wash Buffer was added to lysed cells and mixed with pipetting. The sample was centrifuged at 4°C for 5 min at 500 x g. The supernatant was removed without disrupting the nuclei pellet, and this washing step was repeated two more times for a total of 3 times.
For vaccinated samples, nuclei from four donors were multiplexed per GEM, with 12,500 nuclei loaded per donor. For non-vaccinated samples, 15,000 nuclei were loaded per GEM without multiplexing. All samples were processed on the Chromium Next GEM Chip J (PN-1000230) according to the manufacturer’s recommendations. All single-cell libraries were produced using the 10x Chromium Single Cell ATAC + Gene Expression workflow following the manufacturer's instructions (PN-1000283). Final libraries were sequenced using Illumina NovaSeq 6000(Illumina, Inc., San Diego, CA, USA), for both GEX and ATAC sequencing.

value: Blood

value: PBMC

tag: vaccine type


title: Leaves, GmNRPE1-RNAi-NT-mRNA-r3

value: Mustang

value: Leaves


title: scRNA, PBMC, Healthy Control_2

description:
Library name: HC_4_GEX
10x Genomics


title: Leaves, GmNRPE1-RNAi-T-mRNA-r3


title: Leaves, GmNRPE1-RNAi-T-mRNA-r1


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r6


title: Leaves, GmNRPD1-RNAi-T-mRNA-r3

source_name: Leaves, GmNRPD1-RNAi-T-mRNA


title: Leaves, GmNRP(D/E)2-RNAi-T-mRNA-r2


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r4


title: scRNA, PBMC, Healthy Control_3

description:
Library name: HC_6_GEX
10x Genomics


title: scRNA, PBMC, protein vaccinated_3

description:
Library name: RC9_GEX
10x Genomics

value: SARS-CoV-2 vaccine

value: protein subunit


title: Leaves, GmNRPD1-RNAi-T-mRNA-r2


title: scATAC, PBMC, protein vaccinated_3

description:
Library name: RC9_ATAC
10x Genomics


title: scRNA, PBMC, mixed vaccinated

description:
Library name: BC1_GEX
10x Genomics

value: mixed (viral vector / protein)


title: Leaves, GmNRPD1-RNAi-T-mRNA-r1


title: Leaves, GmNRPD1-RNAi-NT-mRNA-r3

value: NT


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r3


title: senescent rMSCs, control, Day1

description:
Library name: nB
Single sample for this condition (no biological replicates)


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_5

description:
Library name: RB5_GEX
10x Genomics

value: viral vector + mRNA


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_5

description:
Library name: RB5_ATAC
10x Genomics


title: scATAC, PBMC, Healthy Control_1

description:
Library name: HC_3_ATAC
10x Genomics


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_3

description:
Library name: RB3_GEX
10x Genomics


title: scRNA, PBMC, Healthy Control_1

description:
Library name: HC_3_GEX
10x Genomics


title: Leaves, GmNRP(D/E)2-RNAi-NT-mRNA-r2


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_2

description:
Library name: RB2_ATAC
10x Genomics


title: scATAC, PBMC, mRNA vaccinated_6

description:
Library name: RA6_ATAC
10x Genomics

value: mRNA


title: scRNA, PBMC, mRNA vaccinated_6

description:
Library name: RA6_GEX
10x Genomics


title: scRNA, PBMC, protein vaccinated_2

description:
Library name: RC5_GEX
10x Genomics


title: scATAC, PBMC, protein vaccinated_2

description:
Library name: RC5_ATAC
10x Genomics


title: scATAC, PBMC, mixed vaccinated

description:
Library name: BC1_ATAC
10x Genomics


title: scRNA, PBMC, protein vaccinated_1

description:
Library name: RC1_GEX
10x Genomics


title: scATAC, PBMC, protein vaccinated_1

description:
Library name: RC1_ATAC
10x Genomics


title: scATAC, PBMC, Healthy Control_2

description:
Library name: HC_4_ATAC
10x Genomics


title: scRNA, PBMC, mRNA vaccinated_5

description:
Library name: RA5_GEX
10x Genomics


title: scATAC, PBMC, mRNA vaccinated_4

description:
Library name: RA4_ATAC
10x Genomics


title: scATAC, PBMC, mRNA vaccinated_3

description:
Library name: RA3_ATAC
10x Genomics


title: scRNA, PBMC, mRNA vaccinated_2

description:
Library name: RA2_GEX
10x Genomics


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_6

description:
Library name: RB6_ATAC
10x Genomics


title: scRNA, PBMC, mRNA vaccinated_1

description:
Library name: RA1_GEX
10x Genomics


title: scATAC, PBMC, mRNA vaccinated_1

description:
Library name: RA1_ATAC
10x Genomics


title: RLS3-NC3

city: shanghai

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

description:
Library name: RLS3-NC3
FPKM

data_processing:
Image processing and base calling were performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8). The sequencing quality of reads was assessed with FastQC, followed by removal of 3' and 5' adapters using cutadapt. Reads were aligned to the reference genome using Hisat2 software. Transcript abundance was estimated with StringTie software based on official database annotation information. Gene level FPKM values were calculated as expression values.
Assembly: hg19
Supplementary files format and content: FPKM in excel

growth_protocol: SNU-668 Erastin-resistant cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
We have completed your RNA sequencing experimental project. After concentration measurement using NanoDrop ND-1000,  1-2ug of total RNA was selected per sample for RNA sequencing library construction. The specific procedure is as follows: total RNA samples underwent oligo dT enrichment (rRNA removal), followed by library preparation using the KAPA Stranded RNA-Seq Library Prep Kit (Roche). During library construction, double-stranded cDNA synthesis employed the dUTP method in combination with subsequent high-fidelity PCR polymerase, ensuring that the final RNA sequencing library is strand-specific. The constructed libraries were assessed for quality using the Agilent 2100 Bioanalyzer and quantified via qPCR. The pooled libraries from different samples were sequenced on the Illumina NovaSeq 6000 sequencing platform, which included steps such as NaOH alkaline single-strand generation, in-situ amplification on the Illumina flow cell, and 150-cycle paired-end sequencing.

treatment_protocol: SNU-668 Erastin-resistant cells were transfected with shRNA-SPIN1 or shRNA-NC

value: gastric cancer cell line

value: SPIN1 knockdown


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_6

description:
Library name: RB6_GEX
10x Genomics


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_1

description:
Library name: RB1_GEX
10x Genomics


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_4

description:
Library name: RB4_GEX
10x Genomics


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_3

description:
Library name: RB3_ATAC
10x Genomics


title: RLS3-SPIN1-1

description:
Library name: RLS3-SPIN1-1
FPKM

value: WT


title: scRNA, PBMC, cross (viral vector + mRNA) vaccinated_2

description:
Library name: RB2_GEX
10x Genomics


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_4

description:
Library name: RB4_ATAC
10x Genomics


title: RLS3-3-input

description: Library name: RLS3-3-input

data_processing:
Sequencing images were processed and sequence data were obtained using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Raw sequences were quality-checked with FastQC (v0.11.7) and filtered using Trimmomatic (v0.32). The filtered high-quality data were aligned to the reference genome from the Ensembl database (using HISAT2 v2.1.0). Modification peaks for each sample and differentially modified peaks for each comparison were then identified using exomePeak2 (v1.8.1). Peaks were annotated based on the Ensembl database annotation, and the presence of peaks in each transcript region across samples was statistically analyzed.
Assembly: hg19
Supplementary files format and content: enriched peaks in excel

extract_protocol:
RNA was harvested using Trizol reagent. 120 ug of total RNA for the construction of sequencing libraries.
After quantifying the total RNA using NanoDrop ND-1000, intact mRNA was purified and fragmented into approximately 300nt segments. RNA fragments containing m1A modification sites were enriched via immunoprecipitation using an anti-N1-methyladenosine (m1A) antibody. Sequencing libraries for both m1A-enriched mRNA and input mRNA were constructed using the KAPA Stranded mRNA-seq Kit. The library mRNA was pooled and denatured into single-stranded DNA. After adapter ligation, it was bound to Illumina flow cells for in situ amplification, followed by 150bp sequencing on the Illumina NovaSeq 6000.

treatment_protocol: SNU-668 Erastin-resistant cells were transfected with shRNA-ALKBH3 or shRNA-NC


title: RLS3-ALKBH3-1-input

description: Library name: RLS3-ALKBH3-1-input

value: ALKBH3 knockdown


title: RLS3-2-input

description: Library name: RLS3-2-input


title: RLS3-1-input

description: Library name: RLS3-1-input


title: scATAC, PBMC, cross (viral vector + mRNA) vaccinated_1

description:
Library name: RB1_ATAC
10x Genomics


title: scRNA, PBMC, mRNA vaccinated_4

description:
Library name: RA4_GEX
10x Genomics


title: scRNA, PBMC, mRNA vaccinated_3

description:
Library name: RA3_GEX
10x Genomics


title: RLS3-3-IP

description:
Library name: RLS3-3-IP
enriched peaks

data_processing:
Sequencing images were processed and sequence data were obtained using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Raw sequences were quality-checked with FastQC (v0.11.7) and filtered using Trimmomatic (v0.32). The filtered high-quality data were aligned to the reference genome from the Ensembl database (using HISAT2 v2.1.0). Modification peaks for each sample and differentially modified peaks for each comparison were then identified using exomePeak2 (v1.8.1). Peaks were annotated based on the Ensembl database annotation, and the presence of peaks in each transcript region across samples was statistically analyzed.
Assembly: hg19
Supplementary files format and content: enriched peaks in excel
Library strategy: MeRIP-Seq


title: scATAC, PBMC, mRNA vaccinated_5

description:
Library name: RA5_ATAC
10x Genomics


title: scATAC, PBMC, mRNA vaccinated_2

description:
Library name: RA2_ATAC
10x Genomics


title: RLS3-NC2

description:
Library name: RLS3-NC2
FPKM


title: RLS3-SPIN1-3

description:
Library name: RLS3-SPIN1-3
FPKM


title: RLS3-SPIN1-2

description:
Library name: RLS3-SPIN1-2
FPKM


title: RLS3-ALKBH3-3-input

description: Library name: RLS3-ALKBH3-3-input

value: ALKBH3  knockdown


title: RLS3-NC1

description:
Library name: RLS3-NC1
FPKM


title: RLS3-ALKBH3-1-IP

description:
Library name: RLS3-ALKBH3-1-IP
enriched peaks


title: ribo Ribo_RLS3

description:
Library name: Ribo_RLS3
raw count and RPKM

data_processing:
Reads were assessed for sequencing quality using FastQC. To ensure consistency with the Ribo-Seq data, only the R1 single-end portion (150bp) of the RNA-Seq results was used in this analysis. The software cutadapt was used to remove 3' and 5' adapters and filter out reads shorter than 22bp or longer than 34bp. First, rRNA/tRNA/snRNA/snoRNA were filtered out using the bowtie software, and then the reads were aligned to the reference genome using the STAR software. All downstream analyses used uniquely mapped reads. RPF quality control (QC) was performed directly using RiboTish software, generating plots including RPF length distribution, RPF density distribution across CDS regions, RPF frame distribution, and RPF density distribution around start/stop codons. Translation abundance in the gene CDS regions was estimated and RPKM values were calculated using Plastid software, based on the annotation information from the official ENSEMBL database.
Assembly: hg19
Supplementary files format and content: count and RPKM in excel
Library strategy: Ribo-Seq

extract_protocol:
Lysing cells to obtain a cell lysate; digesting RNA not protected by ribosomes using RNase; performing high-density sucrose centrifugation to isolate monosomes (single ribosomes); extracting and purifying the short, undigested mRNA fragments from the ribosomes; ligating specific sequence adapters; constructing a library via PCR.
By enriching for monosomes, short undigested mRNA fragments bound to ribosomes were obtained. Adapters were ligated to the 3' and 5' ends of the mRNA, followed by reverse transcription to synthesize cDNA and subsequent PCR amplification, resulting in the final sequencing library. After quality inspection, the library was subjected to sequencing.


title: RLS3-ALKBH3-2-input

description: Library name: RLS3-ALKBH3-2-input


title: RLS3-ALKBH3-3

description:
Library name: RLS3-ALKBH3-3
raw read counts and DESeq2 normalized counts

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg19). featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile.
Assembly: hg19
Supplementary files format and content: raw read counts and DESeq2 normalized counts in excel

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
total RNA samples underwent oligo dT enrichment (rRNA removal), followed by library preparation using the KAPA Stranded RNA-Seq Library Prep Kit (Roche). During library construction, double-stranded cDNA synthesis employed the dUTP method in combination with subsequent high-fidelity PCR polymerase, ensuring that the final RNA sequencing library is strand-specific. The constructed libraries were assessed for quality using the Agilent 2100 Bioanalyzer and quantified via qPCR. The pooled libraries from different samples were sequenced on the Illumina NovaSeq 6000 sequencing platform, which included steps such as NaOH alkaline single-strand generation, in-situ amplification on the Illumina flow cell, and 150-cycle paired-end sequencing.


title: RLS3-ALKBH3-3-IP

description:
Library name: RLS3-ALKBH3-3-IP
enriched peaks


title: RLS3-2-IP

description:
Library name: RLS3-2-IP
enriched peaks


title: RLS3-ALKBH3-2-IP

description:
Library name: RLS3-ALKBH3-2-IP
enriched peaks


title: RLS3-1-IP

description:
Library name: RLS3-1-IP
enriched peaks


title: group3 MKRN2 KO SHSY5Y cells, Overexpression of CSDE1

city: Shanghai

first: Zi

last: Wang

address: 600 South Wanping Road, Xuhui District, Shanghai, China

institute: Shanghai Mental Health Center

description: Library name: 3-F-C

data_processing:
1. Raw data processing: Base calling and demultiplexing were performed using bcl2fastq (v2.20.0.422). 2. Quality control & filtering: Raw reads were assessed with FastQC (v0.10.1) and trimmed using Cutadapt (v1.9.1) to remove adapters and low-quality bases (Q<20). 3. Alignment: Clean reads were aligned to the human reference genome (hg38) using HISAT2 (v2.0.1) with default parameters. 4. Quantification: Gene-level expression (FPKM) was calculated using RSEM (v1.2.6). 5. Differential expression: Differential expression analysis was performed using edgeR or DESeq2 (as specified in the report for respective comparisons). 6. Advanced analysis: The pipeline also included transcript assembly (StringTie), lncRNA identification, and functional enrichment analysis (GO and KEGG).
Assembly: hg38 (GRCh38)
Supplementary files format and content: txt files include FPKM values  for each Sample
Supplementary files format and content: csv file includes DE results (e.g., log2FC, p-value, FDR) for each comparison.

source_name: Cell line

growth_protocol: The MKRN2 knock-out SHSY5Y cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose), supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin (all from Gibco, USA) in a 37◦C humidified atmosphere of 5% CO2.

extract_protocol:
The MKRN2 knock-out SHSY5Y cells transfected with Flag, CSDE1-Flag, and MKRN2-Myc plasmids were collected after 48hrs, and the cells pellet were resuspended with an approximately equal volume of polysome lysis buffer[100 mM KCl, 5 mM MgCl2, 10 mM HEPES(pH 7.0), 0.5% NP40, 1mM DTT, 100 units/ml RNase inhibitor (Vazyme), 400 μM vanadyl ribonucleoside complexes (VRC, NEB, USA) and Protease inhibitor cocktail(1:100, Roche)]. Incubated on ice for 10 min, centrifuged at 15 000 g for 15 min to clear lysate of large particles. anti-FLAG M2 Affinity gels (Sigma, USA) were washed with NT2 buffer (50 mM Tris–HCl, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40 pH 7.4) before using for immunoprecipitation. 50μl of pre-cleared supernatant lysate were saved as the total cellular mRNA(input), and the rest of RNA-protein complexes were immunoprecipitated with anti-FLAG M2 Affinity gels (Sigma, USA) in 850μl of NT2 buffer supplemented with 100 units/ml RNase inhibitor, 400 μM VCR, 10μl of 100mM DTT and 20mM EDTA, and incubated for 4hours at 4℃ with tumbling end over end. Beads were washed with 1.0 ml of ice-cold NT2 buffer for five times supplemented with 0.5 M urea and 0.1% SDS, and then resuspended the beads in 100 μl of NT2 buffer supplemented with 30 μg of proteinase K (Roche) to release the RNP components. RNAs were extracted using Trizol (Invitrogen), and subjected to RIP-seq analysis.
Strand-specific sequencing libraries were constructed using the Ribo-off rRNA Depletion Kit to remove ribosomal RNA, followed by the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina. The procedure included RNA fragmentation, reverse transcription, end repair, A-tailing, adapter ligation, and PCR amplification. The final libraries were quantified and sequenced on an Illumina NovaSeq 6000 platform.

value: Cell line

value: Human Neuroblastoma Cell

value: MKRN2 KO

value: transfection with CSDE1


title: group3 MKRN2 KO SHSY5Y cells, Co-expression of CSDE1 and MKRN2

description: Library name: 3-C-M

value: transfection with CSDE1+MKRN2


title: group2 MKRN2 KO SHSY5Y cells, Co-expression of CSDE1 and MKRN2

description: Library name: 2-C-M


title: RLS3-ALKBH3-2

description:
Library name: RLS3-ALKBH3-2
raw read counts and DESeq2 normalized counts


title: RLS3-ALKBH3-1

description:
Library name: RLS3-ALKBH3-1
raw read counts and DESeq2 normalized counts


title: ribo Ribo_RLS3-ALKBH3

description:
Library name: Ribo_RLS3-ALKBH3
raw count and RPKM


title: RLS3-3

description:
Library name: RLS3-3
raw read counts and DESeq2 normalized counts


title: RLS3-2

description:
Library name: RLS3-2
raw read counts and DESeq2 normalized counts


title: RLS3-1

description:
Library name: RLS3-1
raw read counts and DESeq2 normalized counts


title: RNA RNA_RLS3

description:
Library name: RNA_RLS3
raw count and RPKM

data_processing:
Reads were assessed for sequencing quality using FastQC. To ensure consistency with the Ribo-Seq data, only the R1 single-end portion (150bp) of the RNA-Seq results was used in this analysis. The software cutadapt was used to remove 3' and 5' adapters and filter out reads shorter than 22bp or longer than 34bp. First, rRNA/tRNA/snRNA/snoRNA were filtered out using the bowtie software, and then the reads were aligned to the reference genome using the STAR software. All downstream analyses used uniquely mapped reads. RPF quality control (QC) was performed directly using RiboTish software, generating plots including RPF length distribution, RPF density distribution across CDS regions, RPF frame distribution, and RPF density distribution around start/stop codons. Translation abundance in the gene CDS regions was estimated and RPKM values were calculated using Plastid software, based on the annotation information from the official ENSEMBL database.
Assembly: hg19
Supplementary files format and content: count and RPKM in excel


title: Visium FFPE, T1190_RCA

city: St Louis

first: Junedh

last: Amrute

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: T1190_RCA

data_processing:
Can be found in Methods Amrute et al, 2025
Assembly: GRCh38
Supplementary files format and content: .rds
Supplementary files format and content: mtx, image
Library strategy: Spatial Transcriptomics

source_name: human coronary artery

extract_protocol:
Visium FFPE: Fresh coronary tissue was fixed in 4% PFA overnight, washed with PBS, and embedded in FFPE blocks. FFPE blocks were sectioned onto Visium slides and underwent H&E staining before imaging.  Libraries were generated using the Visium FFPE v1 kit (#1000188; #1000362; #1000364) and sequenced on a NextSeq2000 according to manufacturer’s recommendations. Libraries were sequenced on a NovaSeq 6000. Xenium in situ: A custom gene panel was designed (Supplementary Table 4) based on the CITE-seq reference map and combined with the Xenium Human Multi-Tissue and Cancer Panel (#1000626, 10x Genomics). FFPE blocks and sectioned and the 10x Genomics Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide protocol (10x Genomics, Protocol number CG000749) used for sample (#1000661; #1000460; #1000487. 10x Genomics,).
Visium FFPE: Fresh coronary tissue was fixed in 4% PFA overnight, washed with PBS, and embedded in FFPE blocks. FFPE blocks were sectioned onto Visium slides and underwent H&E staining before imaging.  Libraries were generated using the Visium FFPE v1 kit (#1000188; #1000362; #1000364) and sequenced on a NextSeq2000 according to manufacturer’s recommendations. Libraries were sequenced on a NovaSeq 6000. Xenium in situ: A custom gene panel was designed (Supplementary Table 4) based on the CITE-seq reference map and combined with the Xenium Human Multi-Tissue and Cancer Panel (#1000626, 10x Genomics). FFPE blocks and sectioned and the 10x Genomics Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide protocol (10x Genomics, Protocol number CG000749) used for sample (#1000661; #1000460; #1000487. 10x Genomics,).

value: human coronary artery


title: group3 MKRN2 KO SHSY5Y cells, Control

description: Library name: 3-F

value: transfection with empty vector


title: Visium FFPE, T1171_LM

description: Library name: T1171_LM


title: group2 MKRN2 KO SHSY5Y cells, Overexpression of CSDE1

description: Library name: 2-F-C


title: Visium FFPE, T1183_RCA

description: Library name: T1183_RCA


title: Visium FFPE, T1163

description: Library name: T1163


title: RNA RNA_RLS3-ALKBH3

description:
Library name: RNA_RLS3-ALKBH3
raw count and RPKM


title: Visium FFPE, T1161

description: Library name: T1161


title: group2 MKRN2 KO SHSY5Y cells, Control

description: Library name: 2-F


title: Visium FFPE, T1186_RCA

description: Library name: T1186_RCA


title: Visium FFPE, T1167_LAD

description: Library name: T1167_LAD


title: CITE-seq, WashU2, GEX

description: Library name: GEX_WashU2

data_processing:
Can be found in Methods Amrute et al, 2025
Assembly: GRCh38
Supplementary files format and content: .rds
Library strategy: CITE-seq

extract_protocol:
Human single cell isolation for CITE-seq Fresh human coronary arteries from explanted hearts at the time of transplantation or donors declared dead after cardiac death (DCD) or brain death (DBD) at Washington University School of Medicine and Mid America Transplant Service were harvested, perfused with cardioplegia, and transported on ice. Starting at the coronary sinus, the left main, left anterior descending, and left circumflex arteries were dissected removing any epicardial fat while preserving the adventitia. Sections were partitioned for histopathology, spatial transcriptomics, single cell isolation, and flash frozen. Cells were isolated as before (17). Briefly: Coronaries were minced using a razor blade on ice and transferred to a 15 mL conical tube containing 3 mL DMEM with 170 µL Collagenase IV (250 U mL-1 final concentration), 35 µL DNAse1 (60 U mL-1), and 75 µL Hyaluronidase (60 U mL-1, all purchased from Sigma Aldrich) and incubated at 37 °C for 45 min with agitation. After 45 min, the digestion reaction was quenched with 6 mL of HBB buffer (2% FBS and 0.2% BSA in HBSS), filtered through 40 µm filters into a 50 mL conical tube and transferred back into a 15 mL conical tube to obtain tighter pellets. Samples were then centrifuged at 4°C, 1,200 rpm for 5 min, and the supernatant was discarded. The pellets were resuspended in 1 mL ACK Lysis buffer (#A10492-01, Gibco) and incubated at room temperature for 5 min followed by the addition of 9 mL DMEM and centrifugation at 4°C, 1,200 rpm for  5 min. Supernatant was discarded and the pellet was resuspended in 2 mL FACS buffer (2% FBS and 2 mM EDTA in calcium/magnesium free PBS), and centrifugation was repeated in above conditions and supernatant aspirated. The TotalSeq A 277 panel (BioLegend) antibody cocktail was resuspended in 100 µL of FACS buffer and 1 µL each of custom oligo-labeled FAP (Amgen) and LRRC15 (Amgen) were added.  The combined 102 µL were used to resuspend the pellet with the addition of 1 µL of DRAQ5 (#564907, Thermo Fisher Scientific) and incubated on ice for 30 min. Solution was washed with FACS buffer three times following same centrifugation as above and then resuspended in 500 µL of FACS buffer and 1 µL DAPI (#564907, BD Biosciences), then filtered into filter-top FACS tubes. First singlets were gated and subsequent DRAQ5+/DAPI- events were collected in 300 µL cell resuspension buffer (0.04% BSA in PBS). The collected cells were centrifuged as above and resuspended in collection buffer to a target concentration of 1,000 cells µL-1. Cells were counted on a hemocytometer before proceeding with the 10x protocol.
CITE-seq Library Preparation Collected cells were processed using the single Cell 3’ Kit v 3.1 (#1000268, 10x Genomics). 10,000 cells were loaded onto ChipG (#1000121) for GEM generation. Reverse transcription, barcoding, and complementary DNA amplification of the RNA and ADT tags were performed as recommended in the 3’ v3.1 chromium protocol. Custom conjugated FAP antibodies were generated using TotalSeqA barcodes by Biolegend. sequenced on a NovaSeq6000. CITEseq libraries were generated using TotalSeqA reagents and Chromium Next GEM Single Cell 3ʹ Kit v3.1 reagents (#1000268, 10x Genomics) following the 10x Genomics protocol (Document CG000185) modified to capture the TotalSeqA barcodes.  Briefly, during cDNA amplification, 1 µl of 0.2 µM ADT Additive Primer (CCTTGGCACCCGAGAATT*C*C) was added to the reaction.   5 µl of purified ADT fraction was indexed with SI-PCR primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC*T*C) and RPI Primer (CAAGCAGAAGACGGCATACGAGAT[i7index]GTGACTGGAGTTCCTTGGCACCCGAGAATTC*C*A) at a final concentration of 2.5 µM each using 2x Kapa Hifi Master Mix. Libraries were sequenced on a NovaSeq 6000.


title: Visium FFPE, T1079

description: Library name: T1079


title: Visium FFPE, D1118_LAD

description: Library name: D1118_LAD


title: Visium FFPE, T1170_LAD

description: Library name: T1170_LAD


title: Visium FFPE, T1111

description: Library name: T1111


title: CITE-seq, WashU1, GEX

description: Library name: GEX_WashU1


title: Visium FFPE, T1099R

description: Library name: T1099R


title: CITE-seq, sample47, GEX

description: Library name: GEX_sample47


title: Visium FFPE, T1077

description: Library name: T1077


title: CITE-seq, sample45, GEX

description: Library name: GEX_sample45


title: CITE-seq, sample48, GEX

description: Library name: GEX_sample48


title: Visium FFPE, T1071

description: Library name: T1071


title: CITE-seq, sample43, GEX

description: Library name: GEX_sample43


title: Visium FFPE, LCA

description: Library name: LCA


title: Visium FFPE, T1153R

description: Library name: T1153R


title: CITE-seq, sample50, GEX

description: Library name: GEX_sample50


title: CITE-seq, sample51, GEX

description: Library name: GEX_sample51


title: CITE-seq, sample35, GEX

description: Library name: GEX_sample35


title: CITE-seq, sample46, GEX

description: Library name: GEX_sample46


title: CITE-seq, sample40, GEX

description: Library name: GEX_sample40


title: CITE-seq, sample44, GEX

description: Library name: GEX_sample44


title: CITE-seq, sample49, GEX

description: Library name: GEX_sample49


title: CITE-seq, sample37, GEX

description: Library name: GEX_sample37


title: CITE-seq, sample25, GEX

description: Library name: GEX_sample25


title: CITE-seq, sample36, GEX

description: Library name: GEX_sample36


title: CITE-seq, sample20, GEX

description: Library name: GEX_sample20


title: CITE-seq, sample31, GEX

description: Library name: GEX_sample31


title: CITE-seq, sample38, GEX

description: Library name: GEX_sample38


title: CITE-seq, sample23, GEX

description: Library name: GEX_sample23


title: CITE-seq, sample26, GEX

description: Library name: GEX_sample26


title: CITE-seq, sample19, GEX

description: Library name: GEX_sample19


title: CITE-seq, sample24, GEX

description: Library name: GEX_sample24


title: CITE-seq, WashU2, ADT

description: Library name: Ab_WashU2

library_source: other

molecule: protein


title: CITE-seq, sample21, GEX

description: Library name: GEX_sample21


title: CITE-seq, sample51, ADT

description: Library name: Ab_sample51


title: CITE-seq, WashU1, ADT

description: Library name: Ab_WashU1


title: CITE-seq, sample11, GEX

description: Library name: GEX_sample11


title: CITE-seq, sample18, GEX

description: Library name: GEX_sample18


title: CITE-seq, sample22, GEX

description: Library name: GEX_sample22


title: CITE-seq, sample14, GEX

description: Library name: GEX_sample14


title: CITE-seq, sample49, ADT

description: Library name: Ab_sample49


title: CITE-seq, sample16, GEX

description: Library name: GEX_sample16


title: CITE-seq, sample48, ADT

description: Library name: Ab_sample48


title: CITE-seq, sample46, ADT

description: Library name: Ab_sample46


title: CITE-seq, sample47, ADT

description: Library name: Ab_sample47


title: CITE-seq, sample45, ADT

description: Library name: Ab_sample45


title: CITE-seq, sample44, ADT

description: Library name: Ab_sample44


title: CITE-seq, sample40, ADT

description: Library name: Ab_sample40


title: CITE-seq, sample43, ADT

description: Library name: Ab_sample43


title: CITE-seq, sample37, ADT

description: Library name: Ab_sample37


title: CITE-seq, sample38, ADT

description: Library name: Ab_sample38


title: CITE-seq, sample50, ADT

description: Library name: Ab_sample50


title: CITE-seq, sample36, ADT

description: Library name: Ab_sample36


title: Treated Tumor- anti-Semaphorin4D #2

type: RNA

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: Myeloid Innate Immunity

hyb_protocol: The CodeSet of each NanoString panel was hybridized to approximately 100 ng of RNA according to the manufacturer's protocol and the bound probes were immobilized to cartridge on the nCounter PrepStation following the vendor protocol.

scan_protocol: Each cartridge was scanned on the NanoString Digital Analyzer at 555 fields of view (FOV).

data_processing:
Gene expression data was analysed using nSolver™ Analysis Software version 4.0 from NanoString Technologies (NanoString Technologies, WA, USA).
Default parameters were used for QC. Normalizations were done by using selected housekeeping genes with low CV at different data ranges.
Selected house keeping genes are as follows: GPL30557 (Cog7,Oaz1,Sap130,Sdha,Ubb); GPL31165 (Alas1,Eef1g,Eif2b4,Nubp1,Oaz1,Polr1b);GPL32407 (Alas1,Eef1g,Gapdh,G6pdx,Oaz1,Ppia); GPL32728 (Abcf1,G6pdx,Eef1g,Polr1b,Hprt,Sdha).
Differential expression was analyzed using Limma package.

source_name: Soft Tissue

label_protocol: Not applicable

growth_protocol: TUBO tumor cell lines were cultured in standard complete media before injected into BALB/c mice

extract_protocol: Mice were euthanized at the same timepoint and the tumors were dissected. Tumor samples were flash frozen in liquid nitrogen, then stored at -80C before RNA sequencing

treatment_protocol: TUBO bearing mice were treated with a combination of spmaphorin4D blocking antibody and intratumoral dendritic cell therapy for 3 weeks before analysis

tag: gender

value: Female

value: BALB/c

tag: tissue type

value: Tumor


title: Treated Tumor- HER2 DC1+aSEMA4D #3

description: Myeloid Innate Immunity


title: Treated Tumor- HER2 DC1+aSEMA4D #2

description: Myeloid Innate Immunity


title: CITE-seq, sample26, ADT

description: Library name: Ab_sample26


title: CITE-seq, sample31, ADT

description: Library name: Ab_sample31


title: CITE-seq, sample35, ADT

description: Library name: Ab_sample35


title: Treated Tumor- HER2 DC1 Treatmen #1

description: Myeloid Innate Immunity


title: Treated Tumor- HER2 DC1+aSEMA4D #1

description: Myeloid Innate Immunity


title: Treated Tumor- Untreated Control #1

description: Myeloid Innate Immunity


title: Treated Tumor- Untreated Control #2

description: Myeloid Innate Immunity


title: CITE-seq, sample24, ADT

description: Library name: Ab_sample24


title: Treated Tumor- HER2 DC1 Treatment #2

description: Myeloid Innate Immunity


title: CITE-seq, sample25, ADT

description: Library name: Ab_sample25


title: CITE-seq, sample23, ADT

description: Library name: Ab_sample23


title: Untreated Tumor- HER2 DC1+aSEMA4D #3

description: Myeloid Innate Immunity


title: Treated Tumor- anti-Semaphorin4D #1

description: Myeloid Innate Immunity


title: Untreated Tumor- anti-Semaphorin4D #2

description: Myeloid Innate Immunity


title: CITE-seq, sample20, ADT

description: Library name: Ab_sample20


title: CITE-seq, sample19, ADT

description: Library name: Ab_sample19


title: CITE-seq, sample18, ADT

description: Library name: Ab_sample18


title: Untreated Tumor- HER2 DC1+aSEMA4D #1

description: Myeloid Innate Immunity


title: CITE-seq, sample22, ADT

description: Library name: Ab_sample22


title: CITE-seq, sample16, ADT

description: Library name: Ab_sample16


title: Untreated Tumor- anti-Semaphorin4D #1

description: Myeloid Innate Immunity


title: CITE-seq, sample14, ADT

description: Library name: Ab_sample14


title: Untreated Tumor- HER2 DC1 Treatment #2

description: Myeloid Innate Immunity


title: CITE-seq, sample21, ADT

description: Library name: Ab_sample21


title: Untreated Tumor- HER2 DC1+aSEMA4D #2

description: Myeloid Innate Immunity


title: Untreated Tumor- HER2 DC1 Treatmen #1

description: Myeloid Innate Immunity


title: CITE-seq, sample11, ADT

description: Library name: Ab_sample11


title: Untreated Tumor- Untreated Control #1

description: Myeloid Innate Immunity


title: FMO54-ECGI10-DMSO-KinA71

city: Brussels

first: Xavier

last: Bisteau

address: Route de Lennik 808

country: Belgium

institute: Université Libre de Bruxelles

description: Library name: Sample 86

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases using "Trimmomatic v.0.36".
Clean paired sequences were aligned to the human reference genome GRCh38 using “STAR” software v.2.5.3.
The number of reads per gene were obtained using "HTSeq" v.0.9.1.
Raw counts were normalized to obtain counts per 20 millions of reads (CP20M) that were used for differential expression analysis with DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing matrix of counts normalized to 20 millions of reads for all genes in all samples.

source_name: Esophagus

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS,  sodium pyruvate (1mM) and antibiotics. They were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated using  the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality was checked using a Fragment Analyzer 5200.
cDNA libraries were prepared from 100 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Englands Biolabs) following manufacturer's recommendations.

treatment_protocol: Cells were maintained for 6 days in the presence of 0,1 % DMSO or 1uM of Palbociclib

value: Esophagus

tag: cell line

value: eSCC

value: 0,1 % DMSO


title: FMO53-ECGI10-DMSO-KinA60

description: Library name: Sample 85


title: FMO56-ECGI10-6D-PD-KinA71

description: Library name: Sample 88

value: palbociclib 1uM


title: ORG-0062 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: RNA extracted from FFPE tissue sections of histologically normal breast lobules.

hyb_protocol: NanoString nCounter protocol

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer (555 fields of view).

data_processing: Raw RCC files were imported into NanoString nSolver. Counts were background-corrected using negative controls and normalized using standard positive-control and housekeeping normalization. Normalized linear counts for endogenous targets are provided as processed data; internal control probe counts are available in the RCC files.

label: NanoString bar coding

source_name: histologically normal breast lobules (FFPE)

label_protocol: Not applicable (nCounter uses reporter and capture probes; no separate labeling step).

growth_protocol: Benign breast tissue was obtained from reduction mammoplasty or contralateral prophylactic mastectomy specimens. Histologically normal lobules were identified on H&E-stained sections.

extract_protocol: From each FFPE block, three consecutive 10 µm sections were collected and RNA was isolated using the Qiagen RNeasy FFPE kit (cat. 73504) according to the manufacturer’s protocol. RNA quantity and quality were assessed; samples meeting QC thresholds were used for NanoString hybridization.

treatment_protocol: No treatment; ex vivo tissue.

tag: race

value: non-Hispanic White

tag: bmi

tag: surgical procedure

tag: menopausal status

value: pre

tag: parity

value: yes


title: FMO51-TE15-6D-PD-KinA60

description: Library name: Sample 83

tag: cell type


title: FMO55-ECGI10-6D-PD-KinA60

description: Library name: Sample 87


title: FMO52-TE15-6D-PD-KinA71

description: Library name: Sample 84


title: ORG-0059_L normal breast lobule RNA (non-Hispanic White); PanCancer IO 360


title: ORG-0022 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360


title: Untreated Tumor- Untreated Control #2

description: Myeloid Innate Immunity

tag: strain


title: FMO50-TE15-DMSO-KinA71

description: Library name: Sample 82


title: FMO49-TE15-DMSO-KinA60

description: Library name: Sample 81


title: FMO47-TE11-6D-PD-KinA60

description: Library name: Sample 79


title: ORG-0016 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

tag: age


title: ORG-0090 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

value: prophylactic mastectomy

value: postmenopausal

value: Yes


title: FMO48-TE11-6D-PD-KinA71

description: Library name: Sample 80

tag: tissue


title: ORG-0128_R normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

value: reduction mammoplasty


title: FMO44-TE9-6D-PD-KinA71

description: Library name: Sample 76


title: ORG-0130_R1 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

value: premenopausal


title: FMO43-TE9-6D-PD-KinA60

description: Library name: Sample 75


title: FMO46-TE11-DMSO-KinA71

description: Library name: Sample 78


title: ORG-0159 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360

value: Mastect/Prophy


title: ORG-0103 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360


title: FMO45-TE11-DMSO-KinA60

description: Library name: Sample 77


title: ORG-0018 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360

value: non-Hispanic Black


title: ORG-0100 normal breast lobule RNA (non-Hispanic White); PanCancer IO 360


title: ORG-0147_R4 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: ORG-0064 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: FMO42-TE9-DMSO-KinA71

description: Library name: Sample 74


title: FMO37-TE8-DMSO-KinA60

description: Library name: Sample 69


title: FMO41-TE9-DMSO-KinA60

description: Library name: Sample 73


title: FMO36-TE5-6D-PD-KinA71

description: Library name: Sample 68


title: ORG-0097 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: ORG-0095 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: ORG-0051 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: ORG-0146_R1 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: FMO40-TE8-6D-PD-KinA71

description: Library name: Sample 72


title: FMO38-TE8-DMSO-KinA71

description: Library name: Sample 70


title: ORG-0093 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: FMO35-TE5-6D-PD-KinA60

description: Library name: Sample 67


title: FMO34-TE5-DMSO-KinA71

description: Library name: Sample 66


title: uterine_fluid_3

city: Madrid

description:
Library name: UF3
Column name in miRNAs_expressed_all_samples.txt: UF3

data_processing:
Raw read files were evaluated, filtered and trimmed by the sequencing provider (Novogene Corporation Inc). Quality of the clean (processed) small RNAseq reads was confirmed using FASTQC (Babraham Bioinformatics) prior to the downstream analyses.
The processed small RNAseq reads were mapped to the rabbit reference genome (OryCun2.0), annotated and quantified using the program miRDeep2 based on rabbit precursor and mature miRNAs available from the mirBase database (release 22)
Assembly: OryCun2.0
Supplementary files format and content: tab delimited text file contains raw counts and mirDeep2 normalized counts for each sample

organism: Oryctolagus cuniculus

source_name: uterine extracellular vesicles

growth_protocol: A total of 21 sexually mature female California x New Zealand white rabbits (Oryctolagus cuniculus), multiparous (with 4-6 parturitions), with 4.7±0.4 kg of live body weight were used. All of them were housed in individual cages under standard environmental conditions (16 hours/8 hours light/dark cycle, 22-24 ºC and 55-60 % relative humidity) and ad libitum access to food and water.

extract_protocol:
After at least 14-15 hours, all animals were euthanized (with barbituric overdose previous sedation), and after a laparotomy, ovaries and the rest of the reproductive tract were extracted. The presence and number of corpus luteum on ovarian surface were determined to confirm that all females had ovulated, and a mean of 11.8±2.3 corpus luteum/doe was observed.
Both oviducts and uteri from female rabbits were transported to the laboratory on ice. The oviducts and uteri were carefully trimmed to remove associated tissues and washed in cold Ca2+ and Mg2+- free phosphate-buffered saline (PBS−). Each oviduct was flushed (1 mL cold PBS−) from ampulla to isthmus, while each uterus was flushed (2.2 mL cold PBS−) towards the uterine tubal junction. All manipulations were performed at 4 °C. To remove cells and cellular debris, each oviduct and uterine flush sample was centrifuged once at 300 × g for 7 min. Subsequently, the supernatant was centrifuged again at 10,000 × g for 30 minutes. The resulting supernatants were individually passed through a 0.22-μm filter and stored at 4°C until the isolation of EVs. Subsequently, the method of  Cañón-Beltrán et al. [https://doi.org/10.1007/978-1-0716-1246-0_16], based on PURE-EV (HansaBioMed Life Sciences) size exclusion chromatography (SEC), followed by centrifugation was used.
Five replicates of OF-EVs (n=3 animals/per replicate) and three replicates of UF-EVs (n=5 animals/per replicate) of each experimental group (OF and UF, respectively) were used and the miRNeasy Micro Kit (Qiagen, Hilden, Germany) was used to isolate total RNA, following the manufacturers instructions. The RNA concentration and size distribution were evaluated using an Agilent RNA 6000 Pico kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ ends of small RNA, respectively. Then, the first strand cDNA was synthesized after hybridization with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing on the Illumina sequencing platform Novaseq6000 with SE50. The library was checked with Qubit 2.0 and real-time PCR for quantification and a bioanalyzer 2100 for size distribution detection. Quantified libraries were pooled and sequenced on the Illumina platform Novaseq6000, according to effective library concentration and data amount (20M reads per sample). The sequencing strategy was Single-end 50 bp (SE50). The index-coded samples were clustered according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on the Illumina platform Novaseq6000, and single-end reads were generated.

treatment_protocol: Does were synchronized with 25 IU of eCG (Serigán, Lab. Ovejero, León, Spain) 48 h before the day of induction of ovulation with 20 µg of a synthetic analogue of GnRH (Cystoreline, Ceva, Spain) via i.m. (time 0).

value: uterine extracellular vesicles

tag: genotype

value: WT

value: synchronized and ovulation induced


title: ORG-0111 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: oviductal_fluid_2

description:
Library name: OF2
Column name in miRNAs_expressed_all_samples.txt: OF2

source_name: oviductal extracellular vesicles

value: oviductal extracellular vesicles

tag: treatment


title: uterine_fluid_12

description:
Library name: UF1
Column name in miRNAs_expressed_all_samples.txt: UF1


title: FMO39-TE8-6D-PD-KinA60

description: Library name: Sample 71

value: Esophagus

value: eSCC


title: FMO31-TE4-6D-PD-KinA60

description: Library name: Sample 63

value: palbociclib 1uM


title: oviductal_fluid_1

description:
Library name: OF1
Column name in miRNAs_expressed_all_samples.txt: OF1


title: uterine_fluid_4

description:
Library name: UF4
Column name in miRNAs_expressed_all_samples.txt: UF4


title: FMO27-KYSE-520-6D-PD-KinA95

description: Library name: Sample 59


title: ORG-0163 normal breast lobule RNA (non-Hispanic Black); PanCancer IO 360


title: FMO33-TE5-DMSO-KinA60

description: Library name: Sample 65

value: 0,1 % DMSO


title: FMO25-KYSE-520-DMSO-KinA95

description: Library name: Sample 57


title: FMO26-KYSE-520-DMSO-KinA136

description: Library name: Sample 58


title: FMO32-TE4-6D-PD-KinA71

description: Library name: Sample 64


title: oviductal_fluid_4

description:
Library name: OF4
Column name in miRNAs_expressed_all_samples.txt: OF4


title: In_WT_1

city: Fuzhou

first: Sun

last: Minghui

address: Cangshan

institute: Fujian Agriculture and Forestry University

description:
Library name: Sample 3
bre2 ChiP

data_processing:
Trimmomatic (version 0.38) was used to filter out low-quality reads. Clean reads were mapped to the genome by Bwa (version 0.7.15) . Samtools (version 1.3.1) was used to remove potential PCR duplicates.MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters (bandwidth,300 bp; model fold, 5, 50;q value, 0.05).
Assembly: NRRL_3357
Supplementary files format and content: tab-delimited text files include Bre2_H3K4me3_vs_WT.peak_annotation
Supplementary files format and content: tab-delimited text files include gene fpkm for each sample

organism: Aspergillus flavus

source_name: mycelium

growth_protocol: For ChIP experiments, WT and Δbre2 fungal strains (10^4 spores/mL) was grown in YES medium at 180r/mim for 24 h. Then the cultures were transferred to a cross-linking solution for ChIP experiments.

extract_protocol:
For ChiP-seq, the mycelium were cross-linked with 1% formaldehyde for 10 min at room temperature, after which 0.125 mol/L glycine was added, and the mixture was rested for 5 min to terminate the cross-linking reaction. Nuclei were collected by centrifuging the samples at 2,000 g for 5 min at 4 °C after being treated with lysis buffer (ECOTOP, ES-8523-500). To fragment chromatin DNA, nuclei were treated with nucleus lysis buffer and sonicated. For the lysis-sonicated chromatin, 20 μL of chromatin was stored at -20 ° C and used as input DNA， 100 μL chromatin Immunoprecipitation with H3K4me3 antibody (CST, 9751) ，10 μg H3K4me3 antibody (CST, 9751) was used to immunize 100 μL of chromatin Precipitation reaction, 4 ° C overnight.After adding 30 μL protein magnetic beads, the samples were further incubated for 3 hours to form magnetic beads/antibody/protein/DNA complex.
For ChiP-seq, high-throughput DNA sequencing libraries were prepared using a I NEXTFLEX® ChIP-Seq Library Prep Kit (NOVA-514120, Bioo Scientific). The library products corresponding to 200-500 bp were enriched, quantified, and sequenced on Illumina® Sequencing（NOVA-514120，Bioo Scientific） and sequenced on Illumina Xten with PE 150 method.

value: mycelium

tag: chip antibody

value: none (input)


title: oviductal_fluid_5

description:
Library name: OF5
Column name in miRNAs_expressed_all_samples.txt: OF5


title: FMO29-TE4-DMSO-KinA60

description: Library name: Sample 61


title: oviductal_fluid_3

description:
Library name: OF3
Column name in miRNAs_expressed_all_samples.txt: OF3


title: FMO28-KYSE-520-6D-PD-KinA136

description: Library name: Sample 60


title: FMO30-TE4-DMSO-KinA71

description: Library name: Sample 62


title: FMO19-KYSE-410-6D-PD-KinA95

description: Library name: Sample 51


title: cKO-PR

city: Solna

first: Saida

last: Hadjab

address: Solnavägen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Library name: P36003_102
10x Genomics

data_processing:
Data were processed using Cell Ranger v9.0.1 software.
Assembly: Mouse mm10
Supplementary files format and content: Count matrices in .h5 format

source_name: DRG

extract_protocol:
Isolation of nuclei from frozen tissue was performed as described by the Allen Institute for Brain Science. All steps performed in 4°C. Briefly, tissues were homogenized in 2ml chilled homogenization buffer (10 mM Tris pH 8, 250 mM Sucrose, 25 mM KCl, 5 mM MgCl2, 0.1 mM DTT, 1x Protease inhibitor cocktail, 0.2 U/μl Protector RNase Inhibitor, 0.1% Triton X-100) and filtered through 70 µm and 30 µm cell strainers. Nuclei pellets were collected by 10 min, 900 x g suspension, and then resuspended in 250 μl chilled homogenization buffer. Finally, debris was removed by Iodixanol 25-29%, and nuclei pellet was resuspended. For neuron specific- single nuclei RNA-sequencing, nuclei pellet was resuspended in 500 μl blocking buffer (1x PBS, 1% BSA, 0.2 U/μl RNase inhibitor) for fluorescent-activated nuclei sorting.
Library was performed according to manufacture's description (single-cell 3' protocol, 10x genomics).

value: DRG

value: 3x100mg/kg Tamoxifen i.p.


title: FMO20-KYSE-410-6D-PD-KinA136

description: Library name: Sample 52


title: In_KObre2_2

description:
Library name: Sample 2
bre2 ChiP


title: FMO16-KYSE-150-6D-PD-KinA136

description: Library name: Sample 48


title: FMO18-KYSE-410-DMSO-KinA136

description: Library name: Sample 50


title: IP_WT_2

description:
Library name: Sample 8
WT ChiP

value: anti-H3K4me3 (CST, 9751)


title: Liver, LKO, HFD, rep3

city: Toronto

first: Carolyn

middle: L

last: Cummins

state: ON

address: 144 College St Room 1101

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

description:
Library name: L23
Column Name in hfd2_rnaseq_counts.csv: L23

data_processing:
Sequence reads were aligned to the mouse reference genome (mm10) using Bowtie2. DESeq2 analysis was used to determine differentially expressed genes between the conditions.
Assembly: mm10
Supplementary files format and content: CSV file including RPKM values for each sample.
Supplementary files format and content: Tab-deliminated Txt file containing RPKM values for each sample.

source_name: Liver

growth_protocol: Female mice were aged to 9 months on a chow diet.

extract_protocol:
Total RNA was extracted from liver samples collected from female WT and LKO mice fed chow or HFD for 12 weeks using TRIzol® (ThermoFisher).
Samples were processed for quality control, mRNA library preparation with Poly A enrichment by NEBNext Ultra II RNA, and sequencing of 20 million NovaSeq Paired-End150 reads by Illumina (Novogene, Sacramento, CA). Fastq files were provided, and analysis was performed using a previously optimized workflow.

treatment_protocol: Mice were either grouped in high-fat diet (TD. 88137) or continuation of chow diet for 12 weeks.

value: Liver

tag: Sex

value: Female

value: LKO

tag: diet

value: HFD


title: FMO24-KYSE-450-6D-PD-KinA136

description: Library name: Sample 56


title: IP_KObre2_2

description:
Library name: Sample 6
WT ChiP


title: FMO23-KYSE-450-6D-PD-KinA95

description: Library name: Sample 55


title: In_WT_2

description:
Library name: Sample 4
bre2 ChiP


title: FMO17-KYSE-410-DMSO-KinA95

description: Library name: Sample 49


title: FMO15-KYSE-150-6D-PD-KinA95

description: Library name: Sample 47


title: IP_WT_1

description:
Library name: Sample 7
WT ChiP


title: FMO14-KYSE-150-DMSO-KinA136

description: Library name: Sample 46


title: Liver, WT, HFD, rep3

description:
Library name: L15
Column Name in hfd2_rnaseq_counts.csv: L15


title: FMO12-KYSE-140-6D-PD-KinA136

description: Library name: Sample 44


title: FMO22-KYSE-450-DMSO-KinA136

description: Library name: Sample 54


title: FMO11-KYSE-140-6D-PD-KinA95

description: Library name: Sample 43


title: Liver, WT, HFD, rep2

description:
Library name: L14
Column Name in hfd2_rnaseq_counts.csv: L14


title: FMO10-KYSE-140-DMSO-KinA136

description: Library name: Sample 42


title: IP_KObre2_1

description:
Library name: Sample 5
WT ChiP


title: FMO9-KYSE-140-DMSO-KinA95

description: Library name: Sample 41


title: FMO13-KYSE-150-DMSO-KinA95

description: Library name: Sample 45


title: FMO21-KYSE-450-DMSO-KinA95

description: Library name: Sample 53


title: In_KObre2_1

description:
Library name: Sample 1
bre2 ChiP


title: Control

description:
Library name: P36003_101
10x Genomics


title: Liver, LKO, Chow, rep3

description:
Library name: L9
Column Name in hfd2_rnaseq_counts.csv: L9

value: Chow


title: Liver, LKO, Chow, rep1

description:
Library name: L7
Column Name in hfd2_rnaseq_counts.csv: L7


title: Liver, LKO, HFD, rep4

description:
Library name: L24
Column Name in hfd2_rnaseq_counts.csv: L24


title: FMO7-KYSE-70-6D-PD-KinA95

description: Library name: Sample 39


title: Liver, WT, Chow, rep3

description:
Library name: L5
Column Name in hfd2_rnaseq_counts.csv: L5

value: WT


title: Liver, WT, Chow, rep1

description:
Library name: L1
Column Name in hfd2_rnaseq_counts.csv: L1


title: FMO2-KYSE-30-DMSO-KinA136

description: Library name: Sample 34


title: FMO8-KYSE-70-6D-PD-KinA136

description: Library name: Sample 40


title: Liver, WT, HFD, rep4

description:
Library name: L16
Column Name in hfd2_rnaseq_counts.csv: L16


title: Liver, LKO, HFD, rep2

description:
Library name: L20
Column Name in hfd2_rnaseq_counts.csv: L20


title: Liver, LKO, HFD, rep1

description:
Library name: L19
Column Name in hfd2_rnaseq_counts.csv: L19


title: FMO4-KYSE-30-6D-PD-KinA136

description: Library name: Sample 36


title: Liver, WT, HFD, rep1

description:
Library name: L13
Column Name in hfd2_rnaseq_counts.csv: L13


title: Liver, LKO, Chow, rep2

description:
Library name: L8
Column Name in hfd2_rnaseq_counts.csv: L8


title: Liver, LKO, Chow, rep4

description:
Library name: L10
Column Name in hfd2_rnaseq_counts.csv: L10


title: FMO6-KYSE-70-DMSO-KinA136

description: Library name: Sample 38


title: FMO1-KYSE-30-DMSO-KinA95

description: Library name: Sample 33


title: TF_D7_TF_L

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

description: Library name: D7_TF

data_processing:
Single-cell RNA-seq data were generated using a combinatorial indexing–based protocol and processed with split-pipe (v1.4.2). Raw sequencing reads were aligned to the Mus musculus GRCm39 reference genome using STAR (v2.7.11b), and gene–cell expression matrices were generated following barcode correction and filtering. Filtered count matrices were imported into R and analyzed using Seurat (v 5.0.2) . Cells with fewer than 200 detected genes and genes detected in fewer than three cells were excluded. Low-quality cells were further removed based on mitochondrial and ribosomal transcript content, library size, and gene complexity, retaining cells with 200-6,000 detected genes and <25% mitochondrial transcripts. Putative doublets were identified and removed on a per-sample basis using DoubletFinder (v 2.22.0) after standard preprocessing.
Assembly: mm10
Supplementary files format and content: barcode, features, matrixs files from split-pipe

source_name: Lung

extract_protocol:
Briefly, lungs were harvested from mock and influenza-infected WT and TFAM+/− mice (n=4 mice per group) and processed into single-cell suspensions. Viable cells were isolated and approximately 25k cells per sample were used for library preparation. Single-cell libraries were generated using Parse Biosciences split-pool combinatorial barcoding chemistry, which enables cell fixation, barcoding, and library construction through successive rounds of molecular indexing. Cell fixation, reverse transcription, barcoding, and library amplification were performed according to the Parse protocol. Barcoded libraries were pooled and sequenced on an Illumina platform to a depth of approximately 56,891 read per cell.
Cells were fixed and processed for sequencing using the Evercode WT single-cell whole-transcriptome kit (Parse Biosciences, Seattle WA) according to the manufacturer’s guidelines. Resulting nucleic acid sublibraries were evaluated for adequacy on an Agilent Bioanalyzer (RNA integrity number >8), pooled, and sequenced on an Illumina Novaseq 6000 sequencer using 100 base pair (bp) paired-end reads (Iowa Institute of Human Genetics, University of Iowa).

value: Lung

value: TFAMfl/fl


title: FMO29-TE14-DMSO-KinA60

description: Library name: Sample 29

value: Esophagus


title: FMO5-KYSE-70-DMSO-KinA95

description: Library name: Sample 37

value: eSCC


title: Liver, WT, Chow, rep4

description:
Library name: L6
Column Name in hfd2_rnaseq_counts.csv: L6


title: FMO3-KYSE-30-6D-PD-KinA95

description: Library name: Sample 35

value: palbociclib 1uM


title: FMO28-TE10-6D_PD-KinA66

description: Library name: Sample 28


title: Liver, WT, Chow, rep2

description:
Library name: L4
Column Name in hfd2_rnaseq_counts.csv: L4


title: TF_D14_WT_L

description: Library name: D14_WT


title: FMO31-TE14-DMSO-KinA60

description: Library name: Sample 31


title: FMO32-TE14-6D_PD-KinA66

description: Library name: Sample 32


title: TF_D14_TF_L

description: Library name: D14_TF