title: PLEKHA7 siRNA knockdown-treat, biological rep 1

address: 南开大学津南校区综合实验楼D413

value: PLEKHA7 siRNA transfection


title: CTL_B

status: Public on Jul 22 2024

type: SRA

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

country: USA

institute: Albert Einstein College of Medicine

library_source: transcriptomic

data_processing:
Raw sequence reads were processed using the nf-core RNA-Seq pipeline (https://nf-co.re/rnaseq/3.10) to obtain gene expression levels.
Gene filtering was performed using the zPKM program.
Count normalization and differential expression testing was performed using the DESeq2 program.
Assembly: hg19
Supplementary files format and content: *.genes.results files are tab-delimmited text files that contain unnormalized gene expression levels for each sample
Supplementary files format and content: counts.filtered.normalized.csv is comma-delimmited textr file that contains filtered and normalized counts for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: lung

growth_protocol: Human IMR-90 primary fibroblasts were obtained from the American Tissue Culture Collection (ATCC; LOT number 70020198). They were cultured in DMEM (Dulbecco’s Modified Eagle Medium, from ATCC) supplemented with 10% fetal bovine serum (FBS, Gibco/Life Technologies) and 1% Penicillin-Streptomycin solution (Gibco/Life Technologies) at 3% oxygen and 37°C. Cells obtained from ATCC were at passage 11 upon arrival and were cultured for an additional 5 passages before the start of the experiment.

extract_protocol:
RNA was extracted from frozen cell pellets using the Zymo DNA/RNA extraction kit (Microprep plus D7005) according to the manufacturer’s instructions and quantified using a Qubit kit (Thermo Fisher Scientific, USA).
Libraries were prepared by using the mRNA-Seq service from Novogene Corp Inc., CA

treatment_protocol: Cells were then treated for a total of 9 times over the course of several months with ENU. Cells were treated with medium containing 50 µg/ml ENU 24 hours after seeding 1 million cells in a 10 cm dish. After 3 days cells were counted, 1 million cells re-seeded, and any remaining cells were collected and stored at -80°C. The same procedure was repeated 7 days after treatment. All downstream analysis was performed on samples collected 7 days after the last treatment unless stated otherwise.

tag: tissue

value: lung

tag: cell line

value: ATCC IMR-90 CCL-192

tag: cell type

value: fibroblast

tag: genotype

value: WT

tag: treatment

value: Control cycle 9

tag: batch

value: Batch B


title: CTL_C

value: Batch C


title: 3.5 hpf embryo, H3K9me3, rep 2

city: Athens

first: Mary

last: Goll

state: GA

address: 130 East Green Street

department: Genetics

institute: University of

description: E coli DNA spike in

library_source: genomic

data_processing:
Short reads (<20 bp) and adaptor sequences were removed using TrimGalore
Trimmed reads were aligned to the zebrafish genome assembly (GRCz.11 Ensemble release 98) using STAR with the following paramters: --readFilesCommand zcat –outSAMtype BAM SortedByCoordinate –outSAMmultNmax 1 –alignEndsType EndToEnd –alignIntronMax 1 –alignMatesGapMax 2000
Alignments were then filtered using SAMtools for a MAPQ score of 1 and PCR duplicates were removed using Picard MarkDuplicates
data was then normalized for library size and DNA spike-in using BEDtools “genomecov”
The Hypergeometric Optimization of Motif EnRichment (HOMER) software package was used to identify peaks over IgG using the following parameters: -style histone -minDist 1000 -gsize 1.5e9 -F 4
replicates were then analyzed using ChIPr with parameter -m 2 to identify reproducible peaks
Assembly: GRCz.11 release 98
Supplementary files format and content: bigwigs, averaged bigwigs, and peak files
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Danio rerio

source_name: embryo

extract_protocol: This is H3K9me3 CUT&RUN data isolated from zebrafish embryos. Genomic DNA libraries were prepared using an illumina protocol.

tag: timepoint

value: AB

tag: antibody

value: H3K9me3 Abcam 8898

value: embryo


title: ENU_A

value: ENU 50 µg/mL cycle 9

value: Batch A


title: CTL_A


title: Brainstem_247_Section_392-Sample_7

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

data_processing:
Fastq files were produced from raw sequencing data or base call files (BCLs) using the bcl2fastq program from Illumina.
Genome sequence indexing and alignment of reads to the Ratticus Norvegicus reference genome were performed using STAR software.
The Subread R package feature count algorithm (featureCounts) was used to generate the count matrix of reads to genomic features, including genes and exons.
Genes that were present in less than 3 cells were filtered out.
Cells that expressed less than 200 genes or more than 10 percent mitochondrial genes were filtered out.
Assembly: mRatBN7
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Tab-delimited text file contains normalized gene expression values for each sample

organism: Rattus norvegicus

source_name: DMV

extract_protocol:
Cell Lysates were directly processed for Reverse Transcription
Smart-3SEQ

tag: strain

value: Sprauge Dawley Rat

value: DMV

tag: age

value: 12 weeks

tag: Sex

value: Female

tag: side

value: Left

tag: connectivity

value: Non-FB

tag: cell state

tag: position

value: Rostral


title: Brainstem_247_Section_398-Sample_11

value: Right

value: FB


title: C1E_C

value: lung

value: ATCC IMR-90 CCL-192

value: fibroblast

value: WT

value: Control cycle 1


title: Brainstem_247_Section_392-Sample_6


title: C1E_B

value: Batch B


title: 3.5 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in

value: AB

value: H3K9me3 Abcam 8898

value: embryo


title: ENU_B

value: ENU 50 µg/mL cycle 9


title: C1E_A

value: Batch A


title: 3.5 hpf embryo, IgG, rep 1

description:
E coli DNA spike in
mIgG.bw (CUTnRUN_timecourse)

value: IgG


title: Brainstem_247_Section_392-Sample_4

value: Sprauge Dawley Rat

value: DMV

value: 12 weeks

value: Female

value: Left


title: Brainstem_247_Section_392-Sample_5

value: Non-FB

value: Rostral


title: 2 hpf embryo, H3K9me3, rep 2

description: E coli DNA spike in


title: 2.5 hpf embryo, H3K9me3, rep 3

description: E coli DNA spike in


title: 2 hpf embryo, IgG, rep 1


title: 2 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in


title: Brainstem_247_Section_392-Sample_15

value: Right


title: Brainstem_247_Section_392-Sample_3

value: FB


title: 2.5 hpf embryo, H3K9me3, rep 2

description: E coli DNA spike in


title: Brainstem_247_Section_392-Sample_1


title: Brainstem_247_Section_392-Sample_2


title: 2.5 hpf embryo, H3K9me3, rep 1

description: E coli DNA spike in


title: Brainstem_247_Section_392-Sample_14


title: 2.5 hpf embryo, IgG, rep 2


title: Brainstem_247_Section_392-Sample_12


title: 2.5 hpf embryo, IgG, rep 1


title: Brainstem_247_Section_392-Sample_13


title: AC109347.1 overexpressed SK-N-SH cells-2

city: Guangzhou

first: Cunyou

last: Zhao

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

country: China

institute: Southern Medical University

data_processing:
The reads were aligned to the UCSC Homo sapiens reference genome hg19 with TopHat version 2.0.4, and multi-aligned reads were removed with SAMtools.
We then used HTSeq to generate mapping counts for the known annotated genes
We used Cuffdiff to convert the counts into total FPKM values, which represented the gene expression levels.
DEGs between AC109347.1 overexpressed and wild type were identified with the edgeR ver. 2.6.12 statistical package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

source_name: SK-N-SH

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

value: SK-N-SH

value: neuroblastoma

value: AC109347.2 overexpressed

value: treated with a recombinant lentivirus carrying lncRNA AC109347.2


title: Brainstem_247_Section_392-Sample_11


title: Whole skin, tamoxifen and streptozotocin, sample 1, scRNAseq

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

description: 10x Genomics; sequenced on Illumina NovaSeq 6000

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were performed using Cell Ranger software (v6.0.1, v6.0.2, v7.2.0)
raw_feature_bc_matrix.h5 and filtered_feature_bc_matrix.h5 contents were used as input to SoupX (v1.6.2) and corrected counts were used as input to Seurat (v5.0.1)
Assembly: GRCm38/mm10
Supplementary files format and content: hdf5 archives each containing 2 tab-separated values (.tsv) files and 1 matrix (.mtx)

organism: Mus musculus

source_name: Whole skin

extract_protocol:
Single-cell suspensions were prepared from 6 mm punch biopsies of full-thickness mouse skin using the Miltenyi Whole Skin Dissociation kit (Miltenyi Biotec). Samples were incubated in enzymes P, D, and A for 3 hours at 37°C. Mechanical dissociation was then performed using the h_skin_01 setting on a Miltenyi gentleMACS dissociator (Miltenyi Biotec) for 20 seconds. Suspension was filtered through a 30 µm filter to remove debris. Cell viability was assessed by staining with ViaStain AOPI Staining Solution (Nexcelom Bioscience), and live/dead cells were counted using a Cellometer Auto 2000 (Nexcelom Bioscience). Volume of each suspension containing 50,000 live cells was centrifuged at 300g at 4°C for 5 minutes and resuspended in 50 mL 0.4% BSA prepared in 1x phosphate-buffered saline.
Library construction was performed per manufacturer specifications (Chromium Next GEM Single Cell 3' Gene expression (GEX) library protocol, v3.1).
Single-cell RNA-sequencing (3' - v3.1)

value: Whole skin

value: male

value: Tamoxifen and streptozotocin


title: AC109347.1 overexpressed SK-N-SH cells-1

value: AC109347.1 overexpressed

value: treated with a recombinant lentivirus carrying lncRNA AC109347.1


title: Brainstem_247_Section_386-Sample_8

value: Sprauge Dawley Rat

value: DMV


title: Brainstem_247_Section_386-Sample_5

value: 12 weeks

value: Female


title: WT SK-N-SH cell-1

value: wild type

value: treated with an empty lentivirus vector with no insert


title: WT SK-N-SH cell-2


title: HSPCs, ADT-derived cDNA 1

city: San Francisco

first: Catherine

last: Smith

state: California

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Mission Bio Tapestri
Experiment 8 Protein
Experiment8.genotypes.hdf5

library_source: other

data_processing:
FASTQ files from single-cell DAbseq samples were processed via an open-source pipeline. This analysis pipeline trims adaptor sequences, demultiplexes DNA panel amplicons and antibody tags into single cells, and aligns panel reads to the hg19 reference genome. Valid cell barcodes were called using the inflection point of the cell-rank plot in addition to the requirement that 60% of DNA intervals were covered by at least eight reads. Variants were called using GATK (v 4.1.3.0) according to GATK best practices. ITDseek was used to detect FLT3 internal tandem duplication (ITD) from amplicon sequencing reads. For each valid cell barcode, variants were filtered according to quality and sequence depth reported by GATK, with low quality variants and cells excluded based on the cutoffs of quality score < 30, read depth < 10, and alternate allele frequency < 20%. Cell-surface protein reads were normalized using centered log ratio transformation.
To de-multiplex individual patients combined into a single sample, we used a novel computational approach incorporating both patient-specific anti-CD45 oligo-conjugated “hash” antibody tags as well as single nucleotide polymorphisms (SNPs) covered by the SC DNA panel. Individual samples were multiplexed together into groups of 3 and all SNPs were treated as binary (mutated or wildtype). For each multiplexed run, to identify SNPs that maximally differ between samples we filtered all SNPs mutated in <10% or >80% of cells. We performed a series of hierarchical clustering steps to further refine antibody hash data.
Assembly: hg19
Supplementary files format and content: hdf5 files
Library strategy: DAbseq

molecule: protein

source_name: Bone Marrow/Peripheral Blood

extract_protocol:
We performed DAbseq on unsorted mononuclear cells using a microfluidic approach with molecular barcode technology using the Tapestri platform (MissionBio) as previously described .
Briefly, cryopreserved cells were blocked and stained with unique anti-CD45 oligo-conjugated antibodies to provide sample-level identifiers, and groups of 2-3 individual patients were pooled together for multiplexed runs. Pooled samples were run through Mission Bio Tapestri platform as previously described. DNA from barcoded cells was amplified via PCR using a targeted panel that included 288 amplicons associated with acute leukemia. DNA PCR products were isolated and purified with standard library preparation protocol. Protein PCR products were isolated from the supernatant from AmpureXP bead purification via incubation with a 5’ Biotin Oligo (ITD), and purified using Streptavidin C1 beads.

value: Bone Marrow/Peripheral Blood

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: Brainstem_247_Section_386-Sample_4

value: Right

value: Non-FB

value: Rostral


title: Brainstem_247_Section_386-Sample_7

value: Left

value: FB


title: Brainstem_247_Section_386-Sample_3


title: Brainstem_247_Section_386-Sample_2


title: T1D, Tscm CD4 T cells, ind T1D4

city: Hinxton

first: Anna

last: Lorenc

address: Genome Campus

department: Human Genetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: sequenced by Adaptive Biotechnologies with TCRB ImmunoSEQ assay. Processing of raw Illumina sequence reads, filtering, demultiplexing, clustering and mapping of CDR3 sequences and annotation of VDJ genes were done by Adaptive Biotechnologies

data_processing:
Processing of raw Illumina sequence reads, filtering, demultiplexing, clustering and mapping of CDR3 sequences and annotation of VDJ genes were done by Adaptive Biotechnologies
Assembly: IMGT
Supplementary files format and content: tab-delimited text files with repertoire characteristics for each sample
Library strategy: TCR-seq

source_name: peripheral blood

extract_protocol:
RNA was isolated using the RNeasy Micro kit (for samples with < 650,000 cells) or RNeasy Mini kit (for all other samples) (QIAGEN. 74004 and 74106, respectively), following the manufacturer’s guidelines, including treatment with DNase (RNase-Free DNase Set, QIAGEN, 79254)
cDNA synthesis using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, 4368814), following steps performed by Adaptive Biotechnology (TCRB sequences using the ImmunoSEQ assay)

value: peripheral blood

tag: health

value: type 1 diabetes

value: CD4-positive, CD95-positive, alpha-beta stem cell memory T cell


title: T1D, Tscm CD4 T cells, ind T1D8


title: T1D, Tscm CD4 T cells, ind T1D3


title: Brainstem_247_Section_386-Sample_6


title: T1D, Tscm CD4 T cells, ind T1D6


title: T1D, Tscm CD4 T cells, ind T1D5


title: T1D, Tscm CD4 T cells, ind T1D7


title: Brainstem_247_Section_380-Sample_8


title: Brainstem_247_Section_380-Sample_9


title: Brainstem_247_Section_386-Sample_1


title: Brainstem_247_Section_392-Sample_10


title: T1D, Treg CD4 T cells, ind T1D8

value: CD4-positive, CD25-positive, alpha-beta regulatory T cell


title: Brainstem_247_Section_380-Sample_6

value: Sprauge Dawley Rat


title: T1D, Treg CD4 T cells, ind T1D6


title: T1D, Treg CD4 T cells, ind T1D7


title: Brainstem_247_Section_380-Sample_5

value: DMV


title: T1D, Treg CD4 T cells, ind T1D5


title: Brainstem_247_Section_380-Sample_4

value: 12 weeks


title: Brainstem_247_Section_380-Sample_3

value: Female


title: T1D, Treg CD4 T cells, ind T1D4


title: Brainstem_247_Section_380-Sample_2


title: T1D, Treg CD4 T cells, ind T1D3


title: T1D, Treg CD4 T cells, ind T1D2


title: T1D, Tscm CD4 T cells, ind T1D2


title: Brainstem_247_Section_380-Sample_1


title: Brainstem_247_Section_380-Sample_12


title: T1D, TN CD4 T cells, ind T1D9

value: CD4-positive, naive alpha beta T cell


title: T1D, Treg CD4 T cells, ind T1D1


title: Brainstem_247_Section_380-Sample_11


title: T1D, TN CD4 T cells, ind T1D7


title: Brainstem_247_Section_374-Sample_8


title: T1D, TN CD4 T cells, ind T1D8


title: T1D, Tscm CD4 T cells, ind T1D1


title: Brainstem_247_Section_380-Sample_10


title: Brainstem_247_Section_374-Sample_9


title: Brainstem_247_Section_374-Sample_7


title: T1D, TN CD4 T cells, ind T1D5


title: Brainstem_247_Section_380-Sample_7


title: Brainstem_247_Section_374-Sample_6


title: T1D, TN CD4 T cells, ind T1D3


title: T1D, TN CD4 T cells, ind T1D4


title: Brainstem_247_Section_374-Sample_4


title: Brainstem_247_Section_374-Sample_5


title: T1D, TN CD4 T cells, ind T1D2


title: T1D, TN CD4 T cells, ind T1D14


title: T1D, TN CD4 T cells, ind T1D6


title: Brainstem_247_Section_374-Sample_2


title: Brainstem_247_Section_374-Sample_3


title: T1D, TN CD4 T cells, ind T1D13


title: Brainstem_247_Section_374-Sample_1


title: T1D, TN CD4 T cells, ind T1D11


title: T1D, TN CD4 T cells, ind T1D12


title: Brainstem_247_Section_374-Sample_14


title: Brainstem_247_Section_374-Sample_12


title: T1D, TN CD4 T cells, ind T1D10


title: Brainstem_247_Section_374-Sample_11


title: T1D, TN CD4 T cells, ind T1D1

value: CD4-positive, CD45RO-positive, CD27-positive central memory alpha-beta  T cell


title: T1D, CM CD4 T cells, ind T1D9


title: Brainstem_247_Section_374-Sample_10


title: T1D, CM CD4 T cells, ind T1D7


title: T1D, CM CD4 T cells, ind T1D8


title: T1D, CM CD4 T cells, ind T1D6


title: Brainstem_247_Section_368-Sample_1


title: T1D, CM CD4 T cells, ind T1D5


title: Brainstem_247_Section_368-Sample_9


title: T1D, CM CD4 T cells, ind T1D3


title: Brainstem_247_Section_368-Sample_8


title: T1D, CM CD4 T cells, ind T1D14


title: Brainstem_247_Section_368-Sample_7


title: Brainstem_247_Section_368-Sample_6


title: Brainstem_247_Section_368-Sample_2


title: Brainstem_247_Section_362-Sample_8


title: Brainstem_247_Section_362-Sample_7


title: T1D, CM CD4 T cells, ind T1D13


title: Brainstem_247_Section_362-Sample_6


title: T1D, CM CD4 T cells, ind T1D11


title: T1D, CM CD4 T cells, ind T1D10


title: T1D, CM CD4 T cells, ind T1D1


title: Brainstem_247_Section_362-Sample_4


title: Brainstem_247_Section_368-Sample_3


title: HD, Tscm CD4 T cells, ind HD8

value: healthy


title: T1D, CM CD4 T cells, ind T1D4


title: Brainstem_247_Section_362-Sample_2


title: HD, Tscm CD4 T cells, ind HD6


title: T1D, CM CD4 T cells, ind T1D2


title: Brainstem_247_Section_362-Sample_3


title: HD, Tscm CD4 T cells, ind HD7


title: Brainstem_247_Section_368-Sample_4


title: Brainstem_247_Section_362-Sample_1


title: HD, Tscm CD4 T cells, ind HD4


title: 3dpl/MTZ

city: Tancha

first: Manana

last: Kutsia

state: Okinawa

address: 1919-1 Tancha, Onna, Kunigami District, Okinawa 904-0495

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v3.1.0
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Telencephalon

extract_protocol:
The telencephalon was dissected in ice-cold Hank’s Balanced Salt Solution (HBSS). Seven telencephalons per each experimental condition were pooled and processed. Isolated telencephalons were chemically dissociated for 30 - 40 min at room temperature in HBSS containing papain (20U/ml) and DNase (2000U/ml) with gentle trituration every 10 minutes. The cell suspension was filtered with a 40 μm cell strainer, then 10% FBS in L-15 medium was added to stop the enzymatic reaction. The dissociated cells were washed with 10% FBS/PBS solution, and the final pellet was resuspended in 10% FBS/PBS for cell sorting. Before cell sorting, cells were again passed through a 40μm cell strainer, and Sytox blue dead cell stain was added to label the dead cells. FACS sorting was performed using BD FACSAria II, and  9000 to 20000 dTomato+ cells were collected in a 10% FBS/PBS precoated tube.
Single-cell RNAseq libraries were prepared using Chromium Single Cell 3' Reagents Kits v3 according to the manufacter’s instructions with 12 cycles of cDNA amplification and 15 cycles of indexing PCR

value: Telencephalon

value: Radial glia cell

value: 3-7 months old

value: Stab lesioned; MTZ


title: T1D, CM CD4 T cells, ind T1D12


title: HD, Tscm CD4 T cells, ind HD3


title: Non-injured/MTZ

description: 10x Genomics


title: HD, Tscm CD4 T cells, ind HD1


title: 3dpl

description: 10x Genomics

value: Stab lesioned


title: RPL22-ZR751-2

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

description: Processed data files on GSMnnnn

data_processing:
The raw CLIP-seq data were parsed via FastQC for quality control. Low-quality sequences, artifacts sequences, contaminated sequences and low-quality reads were filtered out via Clip tool kit (34).
Low-quality sequences before the adapters and universal adapter sequences were removed by Cutadapt trimmer. Reads with sufficient quality were then aligned to the human reference genome (hg38).
The aligned sam file for each biological replicate was parsed and converted to .bed file using parseAlignment.pl, selectRow.pl and bed2rgb.pl.
Using the combined results .bed files, peak calling was performed using Clip tool kit tag2peak.pl and statistical significance was set as p-value = 0.05. Integrative Genomics Viewer (IGV) was used to visualize the peaks (35).
Motif detection was conducted on the called peaks using HOMER (36). Genomic annotations were obtained by extracting the coordinates of the significant peaks using bedtools, followed by gene ontology analysis.

source_name: Breast

extract_protocol:
ZR-75-1 cells were crosslinked with 400mJ/cm2 254nm UV. Crosslinked cells were lysed with ice-cold lysis buffer (1X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% IGEPAL CA-630) supplemented with 1x halt protease inhibitors (Pierce) and SuperaseIN (Invitrogen). After lysis, samples were treated with DNase I (Promega) at 37degC, 1000rpm 5 minutes. Each lysate sample was then split equally, and each portion treated with either a medium or low dilutions of a mix of RNase A and RNase I (Thermo; 3.3ng/ul RNase A and 1units/ul RNase I, and 0.67 RNase A and 0.2units/ul RNase I, respectively) at 37degC for 5 minutes. Lysate was immediately cleared by centrifuging at 21,000xg 4degC 20 minutes. The clarified lysate was added to protein G dynabeads (Invitrogen) that were pre-conjugated to an anti-RPL22 antibody (Santa Cruz sc-136413). Immunoprecipitation was performed at 4degC with end-over-end rotation for 1.5 hours. Beads were then washed 2X with ice-cold high salt wash buffer (5X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% IGEPAL CA-630), 2X with ice-cold lysis buffer (1X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% IGEPAL CA-630), and 2X with ice-cold PNK buffer (10mM Tris-HCl pH 7.5, 0.5% IGEPAL CA-630, 10mM MgCl2).
The RNA was then end-repaired and poly(A) tailed on-bead by treatment with T4 PNK (NEB) and then treatment with yeast poly(A) polymerase (Jena Bioscience). The RNA was 3’-end-labeled with azide-dUTP (TriLink biotechnologies) using yeast poly(A) polymerase (Jena Bioscience). The protein-RNA complexes were then labelled with IRDye800-DBCO (LiCor). The protein-RNA complexes were then eluted from beads in 1XLDS sample buffer (Invitrogen), resolved by running on a 4-12% Bis-Tris NuPAGE gel (Invitrogen), transferred to nitrocellulose, and imaged using an Odyssey Fc instrument (LiCor). The regions of interest were excised from the membrane and the RNA was isolated by Proteinase K (Invitrogen) digestion and subsequent pulldown with oligodT dynabeads (Invitrogen). After eluting from the oligodT beads, the RNA was immediately used for library preparation using the SMARTer smRNA-Seq Kit (Takara), with the following modifications. The poly(A) tailing step was omitted, and reverse transcription was performed with a custom RT primer. The PCR step was performed with indexed forward (i5) primers and a universal reverse (i7) primer. The libraries were PAGE purified and then sequenced on an Illumina HiSeq4000 instrument at the UCSF Center for Advanced Technologies.

value: Breast

value: epithelial cell

value: Selection for RPL22 bound RNA


title: Non-injured

description: 10x Genomics


title: RPL22-ZR751-1

data_processing:
The raw CLIP-seq data were parsed via FastQC for quality control. Low-quality sequences, artifacts sequences, contaminated sequences and low-quality reads were filtered out via Clip tool kit (34).
Low-quality sequences before the adapters and universal adapter sequences were removed by Cutadapt trimmer. Reads with sufficient quality were then aligned to the human reference genome (hg38).
The aligned sam file for each biological replicate was parsed and converted to .bed file using parseAlignment.pl, selectRow.pl and bed2rgb.pl.
Using the combined results .bed files, peak calling was performed using Clip tool kit tag2peak.pl and statistical significance was set as p-value = 0.05. Integrative Genomics Viewer (IGV) was used to visualize the peaks (35).
Motif detection was conducted on the called peaks using HOMER (36). Genomic annotations were obtained by extracting the coordinates of the significant peaks using bedtools, followed by gene ontology analysis.
Assembly: hg38
Supplementary files format and content: called peaks RPL22-ZR751_clearCLIP.pool.tag.uniq.del.CIMS.fdr10.f10.bed (statistically significant peaks) and RPL22-ZR751_clearCLIP.pool.tag.uniq.rgb.bedgraph (all called peaks) as the processed files

value: anti-RPL22 antibody (Santa Cruz sc-136413)


title: Brainstem_247_Section_362-Sample_5

value: Left

value: FB

value: Rostral


title: HD, Treg CD4 T cells, ind HD8

value: peripheral blood

value: CD4-positive, CD25-positive, alpha-beta regulatory T cell


title: Primary Hepatic stellate cells, TILAM LNA 3

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

institute: Massachusetts General Hospital

data_processing: Reads were quality assessed using the FASTQC (v 0.11.9) and aligned to the human reference genome (GRCh38_release_37) from GENCODE with Star aligner (v2.7.10a) using RSEM (v1.3.3) with default parameters. First, the human reference genome was indexed using the GENCODE annotations (gencode.vGRCh38_release_43) with rsem-prepare-reference from RSEM software. Next, rsem-calculate-expression was used to align the reads and quantify the gene abundance. The output of rsem-calculate-expression gives separately the read count and transcripts per million (TPM) value for each gene. Differential expression analysis was performed using gene read counts with DESeq2 package (v 1.38.3) to produce LFC values and corresponding p-values (FDR) applying a Benjamini–Hochberg correction for multiple testing, with a minimum of 5 reads required for a differentially-expressed gene.

source_name: The primary human hepatic stellate cells (HSCs) from donor 4 (Lonza, HUCLS, ID: 201951)

growth_protocol: Primary human hepatic stellate cells (HSCs) were purchased from Lonza and cultured as described previously (PMID 35617485).

extract_protocol:
HSCs from donor 4 (Lonza, HUCLS, ID: 201951) were transfected with NTC, PML si17, LNA-CTA, and LNA-TILAM2 in triplicate. Cells were harvested and RNA was extracted using Qiagen RNeasy Mini Kit (74104). RNA quality number (RQN) greater than 9 (Agilent 4200 TapeStation System) underwent polyA-selection and stranded library preparation for sequencing (Genewiz from Azenta Life Sciences).
Libraries were prepared with the NEB Directional Ultra II RNA library preparation kit. After library preparation, the libraries were sequenced on the HiSeq platform.

treatment_protocol: HSCs were reverse transfected with siRNAs or locked nucleic acids (LNAs) as indicated using Dharmafect-1 transfection reagent (Horizon Discovery, cat# T-2001) according to the manufacturer's instructions. For 12-well plates, 60µL of 3µM siRNAs or LNAs were added to 180µL Opti-MEM (Gibco, cat# 31985070) for the final concentration of 150nM and then mixed with diluted Dharmafect-1 in Opti-MEM (2.4 µL Dharmafect-1 in 237.6µL Opti-MEM). After 30 min, HSCs resuspended in transfection medium (DMEM supplemented with 16% FBS) were seeded in the wells containing the siRNA or LNA/Dharmafect-1 mixture at 70,700 cells/mL in 720µL/well. Transfection in other plate formats were scaled up or down accordingly based on surface area. Cells were incubated with siRNAs or LNAs and transfection reagents for 72 hours before analysis. The siRNAs were purchased from Horizon Discovery, and the LNAs were purchased from Qiagen

value: The primary human hepatic stellate cells (HSCs) from donor 4 (Lonza, HUCLS, ID:201951)

value: WT

value: LNA transfection


title: Primary Hepatic stellate cells, TILAM LNA 2

value: The primary human hepatic stellate cells


title: HD, Treg CD4 T cells, ind HD5

value: healthy


title: Primary Hepatic stellate cells, TILAM LNA 1


title: Primary Hepatic stellate cells, siRNA control #5 3

value: siRNA transfection


title: HD, Treg CD4 T cells, ind HD4


title: HD, Tscm CD4 T cells, ind HD5

value: CD4-positive, CD95-positive, alpha-beta stem cell memory T cell


title: HD, Treg CD4 T cells, ind HD3


title: Primary Hepatic stellate cells, siRNA control #5 2


title: HD, Treg CD4 T cells, ind HD2


title: Primary Hepatic stellate cells, siPML 17# 2


title: Primary Hepatic stellate cells, siPML 17# 3


title: HD, TN CD4 T cells, ind HD9

value: CD4-positive, naive alpha beta T cell


title: ZR751_RPL22-4A1_2

data_processing:
Demultiplexed pair-end FASTQ files were aligned to hg19 reference genome using STAR
We used kallisto for transcript expression quantification. GRCh37 cDNA sequences for constructing the Kallisto indices were downloaded from the Ensembl FTP archives at ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.75.cdna.all.fa.gz.
Assembly: hg19
Supplementary files format and content: tsv file containing kallisto output for each sample

extract_protocol:
Total RNA was isolated using an RNAeasy Kit (Qiagen) according to the manufacturer's instructions. At least 10,000 ng total RNA dissolved in ddH2O was extracted and sent to NovoGene.
Libraries were prepared externally by NovoGene, sequenced on a NovaSeq 6000 PE150.

value: Breast

value: RPL22 knockdown


title: HD, Tscm CD4 T cells, ind HD2


title: HD, TN CD4 T cells, ind HD8


title: HD, Treg CD4 T cells, ind HD7


title: ZR751_RPL22-4A1_3

value: epithelial cell


title: Primary Hepatic stellate cells, siPML 17# 1


title: HD, TN CD4 T cells, ind HD7


title: ZR751_RPL22-4A1_1


title: ZR751_RPL22-1A1_3


title: ZR751_GFP_3

value: GFP knockdown


title: Primary Hepatic stellate cells, LNA control A 3


title: Primary Hepatic stellate cells, LNA control A 2


title: ZR751_RPL22-1A1_1


title: ZR751_RPL22-1A1_2


title: HD, Treg CD4 T cells, ind HD6


title: HD, TN CD4 T cells, ind HD6


title: ZR751_GFP_1


title: Primary Hepatic stellate cells, LNA control A 1


title: HD, TN CD4 T cells, ind HD5


title: NCIH2110_RPL22-4A1_3

source_name: Lung

value: Lung

value: epithelial-like


title: Primary Hepatic stellate cells, siRNA control #5 1


title: HD, Treg CD4 T cells, ind HD1


title: NCIH2110_RPL22-4A1_2


title: NCIH2110_RPL22-4A1_1


title: HD, TN CD4 T cells, ind HD4


title: NCIH2110_RPL22-1A1_3


title: BMAC, fresh, leptin receptor positive FACS-sorted [SR019_BMAC_MSC]

city: La Jolla

first: Samuel

middle: Richard

last: Ward

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

description:
10x Genomics Chromium Single Cell RNA sequencing 3' v3
bmac_mscs_barcodes.tsv.gz
bmac_mscs_features.tsv.gz
bmac_mscs_matrix.mtx.gz
library_ids.csv

data_processing:
Space Ranger 1.2.0
Loupe Browser v.6.0.0
Ensembl release 104 (Oryctolagus_cuniculus.OryCun2.0.104.chr.gtf)
Assembly: OryCun2.0 (Oryctolagus_cuniculus.OryCun2.0.dna.toplevel.fa
Supplementary files format and content: tsv: barcodes, features
Supplementary files format and content: mtx: matrix

source_name: Bone marrow

extract_protocol:
Permeabilization protocol by 10x Genomics CG000238 Rev E. 18 min incubation time.
10x Genomics Protocol CG000239 Rev E

treatment_protocol: snapfrozen in liquid nitrogen-cooled isopentane and stored at -80°C

value: Bone marrow

value: mixed

value: Concentrated using Arthrex Angel System at 7% hematocrit, LEPR+ FACS-sorted fraction


title: NCIH2110_RPL22-1A1_2


title: NCIH2110_RP122-1A1_1


title: HD, TN CD4 T cells, ind HD2

value: peripheral blood


title: ZR751_GFP_2


title: BMAC, fresh, leptin receptor positive FACS-sorted [SR018_BMAC_MSC]


title: NCIH2110_GFP_3


title: HD, TN CD4 T cells, ind HD14


title: NCIH2110_GFP_2


title: BMAC, fresh [SR020_BMAC]

description:
10x Genomics Chromium Single Cell RNA sequencing 3' v3
bmac_barcodes.tsv.gz
bmac_features.tsv.gz
bmac_matrix.mtx.gz
library_ids.csv

value: Concentrated using Arthrex Angel System at 7% hematocrit


title: LNCaP_shLuc_3

source_name: Prostate

value: Prostate

value: LNCaP

value: Luciferase knockdown


title: HD, TN CD4 T cells, ind HD13

value: healthy


title: NCIH2110_GFP_1


title: LNCaP_shLuc_1


title: BMAC, fresh [SR018_BMAC]


title: BMAC, fresh [SR019_BMAC]


title: LNCaP _shLuc_2


title: HD, TN CD4 T cells, ind HD12


title: LNCaP_sh705_3

value: RPL22L1 knockdown


title: LNCaP_sh705_1


title: Cultured MSCs, passage 3 [Lonza_MSCs_p3]

description:
10x Genomics Chromium Single Cell RNA sequencing 3' v3
lonza_mscs_barcodes.tsv.gz
lonza_mscs_features.tsv.gz
lonza_mscs_matrix.mtx.gz
library_ids.csv

value: Mesenchymal stem cells

value: Purchased from Lonza and measured at passage 3


title: BMAC, fresh [SR017_BMAC]


title: HD, TN CD4 T cells, ind HD11

value: CD4-positive, naive alpha beta T cell


title: LNCaP_sh705_2

value: epithelial cell


title: BMAC, fresh [SR015_BMAC]


title: HD, TN CD4 T cells, ind HD10


title: LNCaP_sh704_3


title: LNCaP_sh704_2


title: HD, TN CD4 T cells, ind HD3


title: LNCaP_sh704_1


title: BMAC, fresh [SR014_BMAC]


title: HD, TN CD4 T cells, ind HD1


title: LNCaP_RPL22_3

value: RPL22 overexpression


title: HD, CM CD4 T cells, ind HD9

value: CD4-positive, CD45RO-positive, CD27-positive central memory alpha-beta  T cell


title: LNCaP_RPL22_2


title: BMAC, fresh [SR013_BMAC]


title: LNCaP_RPL22_1


title: HD, CM CD4 T cells, ind HD8


title: BMAC, fresh [SR011_BMAC]


title: BMAC, fresh [SR012_BMAC]


title: LNCaP_GFP_2

value: GFP overexpression


title: CAL851_RPL22L1_3

value: Breast

value: RPL22L1 overexpression


title: BMAC, fresh [SR010_BMAC]

value: Bone marrow

value: mixed


title: LNCaP_GFP_1


title: HD, CM CD4 T cells, ind HD7

value: peripheral blood


title: CAL851_RP122L1_1


title: HD, CM CD4 T cells, ind HD6


title: CAL851_GFP_3


title: CAL851_GFP_1


title: CAL85_ RPL22L1_2


title: HD, CM CD4 T cells, ind HD5


title: CAL851_GFP_2


title: HD, CM CD4 T cells, ind HD4


title: BMAC, fresh [SR003_BMAC]

value: Concentrated using Arthrex Angel System at 7% hematocrit


title: BMAC, fresh [SR008_BMAC]


title: SMARCB1-neg_PTCL-NOS_4

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children’s Hospital Münster

description: 10X Genomics, Chromium Next GEM Single Cell Fixed RNA, Multiplex

data_processing:
NovaSeq 6000 binary base call (bcl) files were demultiplexed into individual library fastq files using the mkfastq program from the Cellranger v7.1.0  Suite (10X Genomics). Feature-barcode matrices were obtained for each sample by aligning the raw fastq files to the GRCh38 reference genome using the cellranger multi pipeline (10X Genomics).
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor, FFPE sample

extract_protocol:
Isolation of cells for Chromium Fixed RNA profiling was done according to protocol CG000632_RevB (10X Genomics). Briefly, after deparaffinization and rehydration the tissue sections were dissociated using a heated gentleMACS Octo dissociator for FFPE tissue (130-096-427; Miltenyi Biotec) with freshly prepared Dissociation Enzyme Mix containing Liberase TH (5401151001; Millipore Sigma). After sample filtration, single-nuclei suspensions were counted using Invitrogen Countess 3 Automated Cell Counter (16842556; Thermo Fisher Scientific).
To generate fixed RNA gene expression libraries, we used the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, 16 rxn (PN-1000414). Single-nuclei suspensions were mixed with human transcriptome probes and hybridized for 20 h at 42°C and then further processed according to protocol CG000527_RevE (10X Genomics). One million cells per sample were used for probe hybridization, with an expected recovery of 80,000 cells per library (5,000 cells per individual barcode in a 16-plex library).

value: Tumor, FFPE sample


title: BMAC, fresh [SR009_BMAC]


title: SMARCB1-neg_PTCL-NOS_5


title: SMARCB1-neg_PTCL-NOS_3


title: HD, CM CD4 T cells, ind HD3


title: LNCaP_GFP_3

value: Prostate

value: LNCaP


title: ADSVF, fresh [SR020_FAT]

description:
10x Genomics Chromium Single Cell RNA sequencing 3' v3
fat_barcodes.tsv.gz
fat_features.tsv.gz
fat_matrix.mtx.gz
library_ids.csv

source_name: Adipose

value: Adipose

value: ADSVF enzymatically released from adipose to obtain single cell suspension


title: HD, CM CD4 T cells, ind HD2

value: healthy


title: SMARCB1-neg_PTCL-NOS_1


title: ADSVF, fresh [SR019_FAT]


title: HCC-LM3 cells, apigenin, biol rep3

city: hefei

first: Wanying

last: Zhang

address: JinZhai Road 96, Hefei, Anhui, China

institute: University of Science and Technology of China

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the GRCh38/hg38 using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include FPKM for each sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: hepatocellular carcinoma cells

value: apigenin treatment


title: SMARCB1-neg_PTCL-NOS_2


title: HD, CM CD4 T cells, ind HD14


title: HCC-LM3 cells, apigenin, biol rep2


title: HCC-LM3 cells, apigenin, biol rep1


title: heart sample, control patient 20

city: Munich

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

department: Institute for Stroke and Dementia (ISD)

institute: LMU Hospital

data_processing:
Libraries were sequenced 2x60 reads base pairs paired-end on an Illumina NextSeq 1000 to a depth of 300,000-600,000 reads/sample.
FastQC was used to check the quality of fastq files.
Low-quality reads and adapters were trimmed using Cutadapt using the following parameters: (1) reads <20 bp, and (2) quality cutoff of 20.
The trimmed FASTQ files were mapped to the mm10 reference genome using STAR.
The mapped reads (of lesion tissue sections) belonging to the same slide were merged using the merge BAM files tool in Galaxy version 4.
To quantify the number of reads mapping to the exons of each gene,featureCounts programwas used. Data was further analyzed in R (DESeq2 package).
Assembly: mm10 reference (mouse)
Supplementary files format and content: counts matrix with filtered counts, as follow: samples with a high percentage of mitochondrial genes (>20%) and samples with a high percentage of ribosomal genes (>8%) were excluded.

source_name: human heart

extract_protocol:
Human heart paraffin sections were used to retrieve the PFA-cross-linked mRNA as previously described (reference below). In brief, PFA-fixed paraffin-embedded hearth tissue sections were scratched from each slide using a stereomicroscope (Olympus SZ51, Model# 1111260100), collected in cold PKD buffer supplemented with proteinase K solution and snap-frozen in liquid nitrogen until further use. To prepare the Smartseq2 libraries, samples were thawed at RT for 3 min and incubated at 56°C in a thermal cycler (lid temperature 66°C), for 4 h or until tissue was completely dissolved. Samples were then placed on ice and incubated at 56°C for 1 min with dT25 magnetic beads to reverse crosslinked samples. Samples were incubated at RT to allow mRNA hybridization and washed with 1x hybridization buffer (HB), containing 2x SSPE, 0.05% Tween-20 and 0.05% RNase Inhibitor. Samples were then washed with PBS with 0.1% RNase Inhibitor and incubated with RNase-free water for 2 min at 80°C to elute mRNA. Smartseq2 libraries were prepared from 1 ng mRNA, as previously described (reference below).  (Reference: Ji, H., Besson-Girard, S., Androvic, P., Bulut, B., Liu, L., Wang, Y., and Gokce, O. (2023). High-Resolution RNA Sequencing from PFA-Fixed Microscopy Sections. In Neural Repair Methods in Molecular Biology., V. T. Karamyan and A. M. Stowe, eds. (Springer US), pp. 205–212. 10.1007/978-1-0716-2926-0_16)
Smart-seq2 libraries

value: human heart

tag: disease state

value: control


title: heart sample, control patient 19

tag: tissue


title: HD, CM CD4 T cells, ind HD13

value: CD4-positive, CD45RO-positive, CD27-positive central memory alpha-beta  T cell


title: ADSVF, fresh [SR017_FAT]


title: HD, CM CD4 T cells, ind HD12


title: HD, CM CD4 T cells, ind HD11


title: heart sample, control patient 18


title: HCC-LM3 cells, DMSO, biol rep3

tag: cell line

value: DMSO control


title: HD, CM CD4 T cells, ind HD10

tag: cell type


title: HCC-LM3 cells, DMSO, biol rep1


title: ADSVF, fresh [SR014_FAT]


title: heart sample, control patient 17


title: HD, CM CD4 T cells, ind HD1


title: heart sample, IS patient 16

value: ischemic stroke


title: Cells overexpressing FOSL1, donor 3  MS6

city: Oxford

first: Simon

last: Davis

address: MRC Weatherall Institute of Molecular Medicine

department: Radcliffe Department of Medicine

institute: University of Oxford

data_processing:
FASTQ files were aligned using STAR version 2.7.3a and quantified using featureCounts version 2.0.6. Ensembl Homo sapiens GRCh38.86 was used as the reference genome.
Assembly: GRCh38.86
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample

source_name: CD8+ T cells

extract_protocol:
RNA was extracted from naive or activated CD8+ T cells using RNeasy Kit following manufacturer's instructions.
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Naive CD8+ T cells were isolated from PBMCs using Naive CD8+ T Cell Isolation Kit from Miltenyi using manufacturers instructions. Approximately 1 million cells were used for activation using anti-CD3/anti-CD28 beads from Miltenyi T Cell Activation/Expansion Kit. The bead to cell ratio was 3:1.

value: CD8+ T cells


title: ADSVF, fresh [SR013_FAT]

value: mixed


title: ADSVF, fresh [SR012_FAT]


title: Donor 3  MS5


title: heart sample, IS patient 13


title: ADSVF, fresh [SR010_FAT]


title: ADSVF, fresh [SR018_FAT]


title: heart sample, IS patient 14


title: ADSVF, fresh [SR011_FAT]


title: Line_6_hiPSC_Rep_1

city: New York

first: Stefan

last: Irion

state: New York

address: 415 E 29th St

institute: BlueRock Therapeutics

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software cellranger-4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hiPSC-derived microglia

extract_protocol:
Cryogenic vials were transferred to a 37°C water bath for ~2 minutes resuspended in either RPMI-1640 or StemPro-34 SFM medium in a drop-wise fashion. Cells were counted on the NC-200 and quenched with an additional 3mL of its respective medium. Cells were centrifuged at 250g for 5 minutes and resuspended in the appropriate assay or culture medium.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3, 10x Genomics).

value: hiPSC-derived microglia


title: Cells overexpressing FOSL1, donor 2  MS4


title: Line_6_MG01_Rep_A9

description: 10x Genomics

value: microglial differentiation


title: ADSVF, fresh [SR015_FAT]


title: Line_6_MG01_Rep_A4

description: 10x Genomics


title: HCC-LM3 cells, DMSO, biol rep2


title: heart sample, IS patient 12


title: Donor 2  MS3


title: Cells overexpressing FOSL1, donor 1  MS2


title: heart sample, IS patient 11


title: heart sample, IS patient 10


title: Donor 1 MS1


title: ADSVF, fresh [SR008_FAT]


title: 28-EtOH-OP-Veh-Liv

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Kallisto with index generated from GRCm39
Protein_coding transcripts were summed to get the gene expression levels
Assembly: GRCm39
Supplementary files format and content: Estimated counts and TPM

source_name: Liver

extract_protocol:
Lower right lobe of the lung tissues was immediately placed in RNAlater solution, then held on ice for 4–5 hours, and then stored at -80ºC until the RNA extraction procedure. RNA extraction was performed using RNeasy Mini Kits from Qiagen (Valencia, CA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on flowcells. After clustering, the flowcells were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: Liver

value: EtOH (14D)


title: Line_6_MG01_Rep_A1

description: 10x Genomics


title: SEC3

first: Revathi

last: Balasubramanian

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

data_processing:
fpkm counts
Assembly: mm10
Supplementary files format and content: .txt counts file

source_name: Anterior segment of mouse eye

extract_protocol:
Qiagen RNAeasy micro kits according to manufactures protocol plus otional DNAse treatment
Nugen Ovation RNA-seq system V

value: Anterior segment of mouse eye

value: SEC


title: heart sample, IS patient 9


title: 27-EtOH-OP-Veh-Liv


title: heart sample, control patient 15


title: SEC1


title: Parental control, unstimulated EN11

description: Parental control, unstimulated

source_name: Jurkat T cells

value: Jurkat T cells


title: LEC3

description: CONTROLLY3_GES14_00900_accepted_hits.bam

value: LEC


title: 26-EtOH-OP-Veh-Liv


title: Parental control, unstimulated EN10

description: Parental control, unstimulated


title: heart sample, control patient 7


title: Parental control, stimulated EN09

description: Parental control, stimulated


title: ADSVF, fresh [SR009_FAT]

value: Adipose

value: ADSVF enzymatically released from adipose to obtain single cell suspension


title: SEC2


title: LEC2

description: CONTROLLY2_GES14_00899_accepted_hits.bam


title: heart sample, IS patient 6

value: human heart


title: LEC1

description: CONTROLLY1_GES14_00898_accepted_hits.bam


title: 15-EtOH-24-H-Liv

value: EtOH (24H)


title: Parental control, stimulated EN08

description: Parental control, stimulated


title: Parental control, unstimulated EN12

description: Parental control, unstimulated


title: 14-EtOH-24-H-Liv


title: Parental control, stimulated EN07

description: Parental control, stimulated


title: BEC3

value: BEC


title: 11-EtOH-24-H-Liv


title: heart sample, IS patient 4


title: BEC2


title: Cells overexpressing FOSL1, unstimulated EN06


title: BEC1


title: Cells overexpressing FOSL1, unstimulated EN04


title: heart sample, control patient 2

value: control


title: Zc3h14_KO_testis_mRNA

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: Testis

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.

value: Testis

tag: genotype

value: ZC3H14 KO


title: 25-EtOH-OP-Veh-Liv

tag: treatment


title: heart sample, IS patient 8

value: ischemic stroke


title: 6-EtOH-9-H-Liv

value: EtOH (9H)


title: Cells overexpressing FOSL1, unstimulated EN05


title: 10-ETOH-24h-Liv


title: Cells overexpressing FOSL1, stimulated EN03

description: Cells overexpressing FOSL1, stimulated


title: Cells overexpressing FOSL1, stimulated EN02

description: Cells overexpressing FOSL1, stimulated


title: Zc3h14_WT_testis_mRNA

value: WT


title: Mouse Colon, DSS, KO, rep3

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

description:
KO_DSS_rep3
raw_counts.tsv
logcpm.tsv

data_processing:
Raw sequencing reads were aligned to the mouse reference genome, mm10, and processed using Kallisto v0.46 with default parameters
Normalized counts, log2(CPM+1), are calculated using raw counts from Kallisto.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes log2(CPM+1) values for each Sample

source_name: Colon

extract_protocol:
Colon tissues were harvested at day 8 and processed for downstream analysis. Total RNA was extracted from the colon tissues using Trizol reagent and RNAs were purified using RNeasy Mini Kit. 1µg RNA was used for cDNA reaction using Maxima first-strand cDNA synthesis kit
RNA-seq library was prepared using Illumina Truseq Total RNA sequencing kit according to the manufacturer's guidelines

treatment_protocol: 8–12-week-old TERT+/+, TERTVAA, and TERT-/- mice were fed with drinking water supplemented with 3% DSS for 4 days, followed by another 4 days of normal drinking water

value: Colon

value: TERT Knockout

value: DSS treated


title: heart sample, IS patient 1


title: 5-EtOH-9-H-Liv

value: Liver


title: 3-EtOH-9-H-Liv


title: Mouse Colon, DSS, KO, rep2

description:
KO_DSS_rep2
raw_counts.tsv
logcpm.tsv


title: 4-EtOH-9H-Liv


title: Cells overexpressing FOSL1, stimulated EN01

description: Cells overexpressing FOSL1, stimulated

value: Jurkat T cells


title: Mouse Colon, DSS, VAA, rep3

description:
VAA_DSS_rep3
raw_counts.tsv
logcpm.tsv

value: TERT VAA Knockin


title: 21-LD-OP-Veh-Liv

value: Pair-Fed (14D)


title: heart sample, IS patient 5


title: Zc3h14_KO_polyA-tail

source_name: Germ cells

value: Germ cells


title: Mouse Colon, DSS, VAA, rep2

description:
VAA_DSS_rep2
raw_counts.tsv
logcpm.tsv


title: Mouse Colon, DSS, KO, rep1

description:
KO_DSS_rep1
raw_counts.tsv
logcpm.tsv


title: 7 days post activation + 10 days resting B_36

value: CD8+ T cells


title: Zc3h14_WT_polyA-tail


title: 20-LD-OP-Veh-Liv


title: heart sample, IS patient 3

value: human heart


title: 7 days post activation + 10 days resting B_35


title: ZC3H14_iCLIP_germ_cells

description: Mouse_ZC3H14_iCLIP_crosslinked_nucleotide.txt.gz


title: 19-LD-OP-Veh-Liv


title: 7 days post activation + 10 days resting B_34


title: Mouse Colon, DSS, VAA, rep1

description:
VAA_DSS_rep1
raw_counts.tsv
logcpm.tsv


title: Mouse Colon, DSS, WT, rep2

description:
WT_DSS_rep2
raw_counts.tsv
logcpm.tsv


title: 7 days post activation + 7 days resting B_30

description: 7 days post activation + 7 days resting


title: Mouse Colon, DSS, WT, rep3

description:
WT_DSS_rep3
raw_counts.tsv
logcpm.tsv


title: 13-LD-24-H-Liv

value: Pair-Fed (24H)


title: 7 days post activation + 7 days resting B_29

description: 7 days post activation + 7 days resting


title: 16-LD-24-H-Liv


title: 7 days post activation + 2 days resting B_27

description: 7 days post activation + 2 days resting


title: 12-LD-24-H-Liv


title: 9-LD-9-H-Liv

value: Pair-Fed (9H)


title: Mouse Colon, DSS, WT, rep1

description:
WT_DSS_rep1
raw_counts.tsv
logcpm.tsv


title: 7 days post activation + 7 days resting B_28

description: 7 days post activation + 7 days resting


title: Mouse Colon, Untreated, KO, rep1

description:
KO_UT_rep1
raw_counts.tsv
logcpm.tsv

value: Untreated


title: Mouse Colon, Untreated, KO, rep2

description:
KO_UT_rep2
raw_counts.tsv
logcpm.tsv


title: Mouse Colon, Untreated, VAA, rep2

description:
VAA_UT_rep2
raw_counts.tsv
logcpm.tsv


title: 1-LD-9H-Liv


title: 7 days post activation + 2 days resting B_25

description: 7 days post activation + 2 days resting


title: Mouse Colon, Untreated, VAA, rep1

description:
VAA_UT_rep1
raw_counts.tsv
logcpm.tsv


title: Neonatal esophagus P0

first: Lana

last: Kostic

address: 61 Biopolis Dr, Proteos

department: IMCB

institute: A*STAR

description: 10x Genomics

data_processing:
cellranger-6.0.2
Assembly: mm10-2020-A
Supplementary files format and content: RData object containing merged, normalized, and clustered data from the h5 matrices

source_name: esophagus

extract_protocol:
The esophagi were microdissected at E13.5/E16.5/P0 from 12, 9, and 7 embryos/neonates, respectively, and dissected tissues pooled for each time point. Samples for each time point were isolated and pooled from 2 to 3 litters. Single- cell dissociation was done by cold active protease digestion. Dissected tissues were transferred to ice-cold PBS with 5 mM CaCl2, 10 mg/ml of Bacillus Licheniformis protease (Sigma, P5380-250MG), and 125 U/ml DNAse I (Qiagen, #79256), and incubated on ice with mixing by pipet every 2 min. Samples were incubated on ice for 7min (E13.5), 9min (E16.5) and 12min (P0) and single-cell dissociation was confirmed under a brightfield microscope.
Single-cell RNA- Seq libraries for high-throughput sequencing were prepared using the Chromium Single Cell 5′ Library and Gel Bead Kit (10x Genomics).

value: esophagus


title: Embryonic esophagus E13.5

description: 10x Genomics


title: Embryonic esophagus WT E13.5

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw sequencing data were processed by 10x Genomic using the 10x Genomic Space Ranger pipeline(version-2.0.0) to generate fastq files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger default settings
Gene expression level of Refseq coding genes were quanitified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: scalefactors_json.json scalefactors in json format
Supplementary files format and content: tissue_hires_image.png hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png low-res image of tissue
Supplementary files format and content: tissue_positions.csv list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene IDs
Supplementary files format and content: matrix.mtx.gz gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial transcriptomics

source_name: mouse embryo

extract_protocol:
Fresh frozen tissues were OCT embedded and 8um frozen sections were cut using cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides and Reagent Kit according to manufacture's instructions

value: mouse embryo

tag: developmental stage

value: not treated


title: Embryonic esophagus E16.5

description: 10x Genomics

value: WT


title: Embryonic esophagus WT E16.5


title: Neonatal Esophagus WT P0_1


title: Neonatal Esophagus WT P0_2


title: 7 days post activation B_24

description: 7 days post activation


title: Mouse Colon, Untreated, WT, rep2

description:
WT_UT_rep2
raw_counts.tsv
logcpm.tsv

value: Colon


title: 28-EtOH-OP-Veh

value: Lung

value: EtOH (14D)


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, FRT, CD103, TRM3

city: Providence

first: Geongoo

last: Han

address: 171 Meeting St.

institute: Brown University

data_processing:
Adapter and low-quality sequences were trimmed from the raw sequence reads using Trimmomatic v0.36
STAR v2.7.3a was used to align the trimmed sequences to the mm10 mouse genome and to estimate the number of reads per gene.
Gene count was normalized in DESeq2 v1.38.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file raw counts for all samples
Supplementary files format and content: tab-delimited text file normalized counts by DESeq2 for all samples

source_name: CD103+ CD8 TRM

extract_protocol:
RNA was extracted from CD8 T cells using the RNeasy Plus Micro Kit (Qiagen)
The RNA library was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

value: female

value: CD103+ CD8 TRM

value: HSV-2 infection


title: 7 days post activation + 2 days resting B_26

description: 7 days post activation + 2 days resting


title: 8-LD-9-H-Liv

value: Liver


title: 27-EtOH-OP-Veh

source_name: Lung


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, FRT, CD103, TRM2


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, FRT, CD103, TRM1


title: 7 days post activation B_22

description: 7 days post activation


title: Mouse Colon, Untreated, WT, rep1

description:
WT_UT_rep1
raw_counts.tsv
logcpm.tsv


title: Hepatic stellate cells (Lrat-cre_zsgreen) CCl4 3

data_processing:
Raw RNA-seq data were mapped to the mouse  reference genome (mm10) with tophat (V2.0.8). The mapped reads were futher assemblied into transcriptomes using CUFFLINK (v2.2.1) and SCRIPTURE (v.beta2). CUFFMERGE was used to merge the transcripts assemblied by CUFFLINK and SCRIPTURE into one list of transcripts through cuffmerge
mm10
Control.plus.bw and Control.minus.bw: All reads from all control replicates mapped to sens (plus) and antisense (minus) strand of the genome
CCl.plus.bw and CCl4.minus.bw: All reads from all CCl4 replicates mapped to sens (plus) and antisense (minus) strand of the genome

source_name: Isolated from liver

extract_protocol:
Hepatic stellate cells isolated through digestion and cell sorting
Total RNA was isolated by RNeasy column (Qiagen). RNA-seq libraries were prepared according to instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing

treatment_protocol: Mice (LratCre mice crossed to ZsGreen reporter mice) receiving 4 weeks of CCl4 (intraperitoneal injection) verses control mice without treatment

value: Isolated from liver

value: Hepatic stellate cell

value: 4 weeks CCl4


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, spleen, TCM3

source_name: CD8 TCM

value: CD8 TCM


title: 72 hours post activation B_20

description: 72 hours post activation

value: CD8+ T cells


title: 15-EtOH-24H

value: EtOH (24H)


title: 72 hours post activation B_21

description: 72 hours post activation


title: 26-EtOH-OP-Veh


title: 14-EtOH-24H


title: 7 days post activation B_23

description: 7 days post activation


title: Hepatic stellate cells (Lrat-cre_zsgreen) CCl4 1


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, spleen, TCM2


title: 72 hours post activation B_19

description: 72 hours post activation


title: Hepatic stellate cells (Lrat-cre_zsgreen) CCl4 2


title: 48 hours post activation B_18

description: 48 hours post activation


title: Hepatic stellate cells (Lrat-cre_zsgreen) control 3

value: control; no treatment


title: Hepatic stellate cells (Lrat-cre_zsgreen) control 2


title: HSV-2 infected mice, 30 dpi, gBT-I transgenic CD8 T cell, spleen, TCM1


title: 11-EtOH-24H


title: 25-EtOH-OP-Veh


title: 48 hours post activation B_17

description: 48 hours post activation


title: Hepatic stellate cells (Lrat-cre_zsgreen) control 1


title: 10-EtOH-24h


title: 6-EtOH-9H

value: EtOH (9H)


title: In vivo young, biol rep 7 [S76]

first: Rong

last: Li

address: 5A Engineering Drive 1

department: Mechanobiology Institute (MBI)

institute: National University of Singapore

data_processing:
Reads were aligned to reference mm39 with STAR (2.7.8a) and quantified with HTSeq (0.11.0) using PartekFlow software (v10.0.22.1005) with default parameters.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes # values for each Sample

source_name: Oocytes

extract_protocol:
Single oocytes were collected with NEBNext Single Cell Lysis Module (NEB #E5530S) in 8μl volume and flash-frozen and stored at -80°C.
NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB #E6420) was used for cDNA synthesis, amplification and library generation. Manufacturer's protocol for cells was followed with these specifications: 16 PCR cycles for cDNA amplification, 8 PCR cycles for enrichment of adaptor-ligated DNA with unique dual index primer pairs from NEB.

value: Oocytes

value: young


title: 48 hours post activation B_16

description: 48 hours post activation


title: In vivo young, biol rep 5 [S73]


title: 24 hours post activation B_15

description: 24 hours post activation


title: In vivo young, biol rep 6 [S74]


title: 5-EtOH-9H


title: In vivo young, biol rep 8 [S77]


title: 24 hours post activation B_14

description: 24 hours post activation


title: In vivo young, biol rep 4 [S72]


title: 4-EtOH-9H


title: Calu3_WT_rep1

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were mapped to the human genomes using STAR.
FeatureCounts was used to summarize and count mapped RNA-seq reads for genomic features.
Assembly: hg19
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).

source_name: airway

growth_protocol: Cells were grown in recommended media supplemented with 10% FBS. STING knockout cells were generated by CRISPR editing.

extract_protocol:
Trizol extraction
Truseq stranded mRNA kit was used to generate libraries following manufacturer's protocol.

treatment_protocol: No treatments

value: airway

value: airway-derived cells

value: WT


title: Detroit562_STING KO_rep4

value: Detroit 562

value: STING knockout


title: Calu3_WT_rep2


title: 3-EtOH-9H

value: Lung


title: 12 hours post activation B_12

description: 12 hours post activation


title: Detroit562_STING KO_rep3


title: Reconstituted chimeric follicle (RCF) AA, biol rep 12 [S279]

value: RCF, aged + aged


title: 21-LD-OP-Veh

value: Pair-Fed (14D)


title: Detroit562_STING KO_rep2


title: In vivo young, biol rep 3 [S71]


title: 20-LD-OP-Veh


title: 12 hours post activation B_11

description: 12 hours post activation


title: Reconstituted chimeric follicle (RCF) AA, biol rep 11 [S278]


title: 19-LD-OP-Veh


title: Detroit562_WT_rep4


title: 12 hours post activation B_10

description: 12 hours post activation


title: Reconstituted chimeric follicle (RCF) AA, biol rep 10 [S277]


title: 16-LD-24H

value: Pair-Fed (24H)


title: Detroit562_WT_rep3


title: Reconstituted chimeric follicle (RCF) AA, biol rep 9 [S276]


title: Reconstituted chimeric follicle (RCF) AA, biol rep 8 [S275]


title: 3 hours post activation B_8

description: 3 hours post activation


title: 12-LD-24H


title: 13-LD-24H


title: Detroit562_STING KO_rep1


title: 3 hours post activation B_7

description: 3 hours post activation


title: Reconstituted chimeric follicle (RCF) AA, biol rep 7 [S274]


title: 30 mins post activation B_6

description: 30 mins post activation


title: OE21_STING KO_rep4


title: Reconstituted chimeric follicle (RCF) AA, biol rep 6 [S273]


title: 24 hours post activation B_13

description: 24 hours post activation


title: Reconstituted chimeric follicle (RCF) AA, biol rep 5 [S272]


title: 30 mins post activation B_5

description: 30 mins post activation


title: OE21_STING KO_rep3


title: 3 hours post activation B_9

description: 3 hours post activation


title: 1-LD-9H

value: Pair-Fed (9H)


title: Detroit562_WT_rep2


title: OE21_STING KO_rep2


title: 9-LD-9H


title: Detroit562_WT_rep1


title: Naive CD8+ T cells B_3

description: Naive CD8+ T cells


title: 8-LD-9H


title: Lung Trms Sample 3

city: Iowa City

first: Stephanie

last: van de Wall

address: 500 Newton Road

institute: University of Iowa

description: raw counts.txt

data_processing:
library strategy: Ultra-low input RNA-seq
Hi Seq Control Software (HCS)
Sequence reads were trimmed to remove possible adapter sequences and nucleotides of poor quality using Trimmomatic v.0.36.
Trimmed sequenced reads were mapped to the Mus musculus reference genome available on ESEMBL usig the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
The gene hit counts table was using for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA was extracted from cells following the Trizol Reagent User Guide (Thermo Fisher Scientific). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). Extracted RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA libraries for ultra-low RNA-seq were prepared using the SMARTSeq HR Ultra Low Input Kit for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA. Illumina Nextera XT library was used for sequencing library preparation.

value: Transgenic T cells


title: OE21_STING KO_rep1


title: Lung Trms Sample 2

description: raw counts.txt


title: Reconstituted chimeric follicle (RCF) AA, biol rep 3 [S270]


title: Naive CD8+ T cells B_2

description: Naive CD8+ T cells

value: CD8+ T cells


title: OE21_WT_rep4


title: 30 mins post activation B_4

description: 30 mins post activation


title: Reconstituted chimeric follicle (RCF) AA, biol rep 2 [S269]


title: Lung Trms Sample 1

description: raw counts.txt


title: Spleen 1M P14s Sample 3

description: raw counts.txt

source_name: Spleen

value: Spleen


title: OE21_WT_rep3


title: Day 0 ESC, BRAT1 KO 2, Biol Rep C

city: Rochester

first: Eric

middle: John

last: Wagner

address: 575 Elmwood Avenue

department: Biochemistry and Biophysics

institute: University of Rochester Medical Center

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.20.0. Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters:  "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r".
Processed/cleaned reads were then mapped to the GRCh38/gencode42 Human reference using STAR_2.7.9a with the following parameters: "-twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted - outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical -outReadsUnmapped Fastx".
Gene level read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file GRCh38/gencode42 and the following parameters for stranded RNA libraries  "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).
Assembly: GRCh38/gencode42
Supplementary files format and content: raw gene counts

source_name: embryonic stem cell

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen, #15596026) following the manufacturer’s instructions
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490S); Click-Seq Library Preparation as described in Jaworski and Routh, 2018 (10.1007/978-1-4939-7514-3_6)

value: embryonic stem cell

value: H7 hESC

value: H7 BRAT1 KO 2


title: Reconstituted chimeric follicle (RCF) AY, biol rep 6 [S244]

value: Oocytes

value: RCF, aged + young


title: OE21_WT_rep1

value: airway

value: airway-derived cells


title: H596_STING KO_rep4


title: Day 0 ESC, BRAT1 KO 2, Biol Rep B


title: Day 0 ESC, BRAT1 KO 2, Biol Rep A


title: Reconstituted chimeric follicle (RCF) AY, biol rep 4 [S242]


title: SiNostril+IFNγ [BR3]

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

description: Gene expression

data_processing:
Base-calling sofeware, version, parameters:
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequencing data filtering:this project uses the filtering software SOAPnuke developed by BGI independently for filtering. Software Information:  SOAPnuke:Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05
Data filtering steps; 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Read alignment: Align to the reference genome: After getting clean reads, used HISAT to align the clean reads to the reference genome. Software Information: HISAT2;  Version：v2.0.4; Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: mm10; Reference species: Species：Mus_musculus; Source：NCBI;  Reference Genome Version：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include gene expression  RPKM values level  for each Sample

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using DNBSEQ platform

value: intestinal epithelial

value: Nostril knockdown

value: Nostril targeted SiRNA transfection+ IFNγ

tag: time


title: Naive CD8+ T cells B_1

description: Naive CD8+ T cells

source_name: CD8+ T cells


title: Day 0 ESC, BRAT1 KO 1, Biol Rep C

value: H7 BRAT1 KO 1


title: SiNostril+IFNγ [BR2]

description: Gene expression


title: Day 0 ESC, BRAT1 KO 1, Biol Rep B


title: Spleen 1M P14s Sample 2

description: raw counts.txt


title: H596_STING KO_rep2

value: STING knockout


title: OE21_WT_rep2

value: WT


title: Reconstituted chimeric follicle (RCF) AY, biol rep 3 [S241]


title: Reconstituted chimeric follicle (RCF) AY, biol rep 2 [S240]


title: Reconstituted chimeric follicle (RCF) AY, biol rep 5 [S243]


title: Spleen 1M P14s Sample 1

description: raw counts.txt


title: Day 0 ESC, BRAT1 KO 1, Biol Rep A


title: Reconstituted chimeric follicle (RCF) AY, biol rep 1 [S234]


title: SiNostril+IFNγ [BR1]

description: Gene expression


title: SiNostril [B3]

description: Gene expression

value: Nostril targeted SiRNA transfection


title: H596_STING KO_rep1


title: H596_WT_rep4


title: Reconstituted chimeric follicle (RCF) YY, biol rep 11 [S231]

value: RCF, young + young


title: SiNostril [B2]

description: Gene expression


title: H596_STING KO_rep3


title: Day 0 ESC, Control Line 2, Biol Rep B

value: H7 Control 2


title: H596_WT_rep3


title: SiNostril [B1]

description: Gene expression


title: Day 0 ESC, Control Line 2, Biol Rep A


title: H596_WT_rep2


title: Reconstituted chimeric follicle (RCF) YY, biol rep 9 [S229]


title: SiNegative control+IFNγ [CR3]

description: Gene expression

value: Scrambled SiRNA transfection + IFNγ


title: Day 0 ESC, Control Line 1, Biol Rep C

value: embryonic stem cell

value: H7 Control 1


title: Reconstituted chimeric follicle (RCF) YY, biol rep 8 [S228]


title: SiNegative control+IFNγ [CR2]

description: Gene expression


title: SiNegative control+IFNγ [CR1]

description: Gene expression


title: H596_WT_rep1


title: Reconstituted chimeric follicle (RCF) YY, biol rep 6 [S225]


title: Day 0 ESC, Control Line 1, Biol Rep B

value: H7 hESC


title: SCC25_STING KO_rep4


title: Day 0 ESC, Control Line 1, Biol Rep A


title: Reconstituted chimeric follicle (RCF) YY, biol rep 5 [S202]

value: Oocytes


title: Day 0 ESC, Control Line 2, Biol Rep C


title: SCC25_STING KO_rep3


title: Day 14 neuroprog., BRAT1 KO 2, Biol Rep C

value: H7 BRAT1 KO 2

value: Differentiated


title: Reconstituted chimeric follicle (RCF) YY, biol rep 4 [S201]


title: Day 14 neuroprog., BRAT1 KO 2, Biol Rep B


title: SCC25_STING KO_rep1

value: airway

value: airway-derived cells


title: SiNegative control [C1]

description: Gene expression

value: intestinal epithelial

value: Scrambled SiRNA transfection


title: SiNegative control [C2]

description: Gene expression


title: SCC25_STING KO_rep2


title: SiNegative control [C3]

description: Gene expression


title: Day 14 neuroprog., BRAT1 KO 2, Biol Rep A


title: SCC25_WT_rep4


title: Reconstituted chimeric follicle (RCF) YY, biol rep 10 [S230]


title: Reconstituted chimeric follicle (RCF) YY, biol rep 3 [S200]


title: Reconstituted chimeric follicle (RCF) YY, biol rep 7 [S226]


title: Section_160-Sample_8

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

address: 1 University of New Mexico

institute: University of New Mexico

description: RNA extracted from a single microdissected neuron

data_processing: Initial quality control included melt-curve analysis and removal of samples and genes with >30% failed reactions. Genes with >75% working reactions were used to generate a median expression level across all samples. Raw Ct values were normalized against this median expression level to obtain DCt values. DCt values were generated for each gene according to the following equation: DCt_gene = Ct_gene - (median sample Ct). The median across all samples within a gene was then used to calculate -DDCt from DCt values by use of the following equation: -DDCt_gene = -(DCt_gene - DCt_median_across_samples).

label: Evagreen

source_name: Rat brainstem

label_protocol: The reverse transcriptase reaction was performed using SuperScript VILO Master Mix (Thermo Fisher Scientific, Waltham, MA). cDNA samples were processed for 22 cycles of specific target amplification of 96 genes using TaqMan PreAmp Master Mix as per the manufacturer’s protocol (Applied Biosystems, Foster City, CA, USA) followed by real-time PCR using Evagreen intercalated dye-based approach to detect the PCR-amplified product. Intron-spanning PCR primers were designed for every assay using Primer3 and BLAST. Real-time PCR reactions were performed using 96x96 BioMark Dynamic Arrays (Fluidigm, South San Francisco, CA, USA) of 81 samples and 173 genes enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions. Each run consisted of 30 amplification cycles (15 s at 95C, 5 s at 70C, 60 s at 60C). Two 96x96 BioMark Arrays were used to measure gene expression across all the 96 samples before QC. The same serial dilution sample set was included in each chip to verify reproducibility and test for technical variability. This 6-point dilution series also serves to detect any over-amplification that may lead to a bias in the data. Samples from each animal were run across the two chips to obtain data on 173 genes per sample. Each set of chip runs contained overlapping assays that served as technical replicates to evaluate chip-to-chip variability.

extract_protocol: Cell Lysates were directly processed for Reverse Transcription

value: Sprague Dawley

value: 12 weeks

value: Male

tag: region

value: DMV

value: Non-FB

value: Rostral

tag: cluster

value: A

value: Left


title: Day 14 neuroprog., BRAT1 KO 1, Biol Rep C

value: embryonic stem cell

value: H7 BRAT1 KO 1


title: Reconstituted chimeric follicle (RCF) YY, biol rep 2 [S199]

value: Oocytes

value: RCF, young + young


title: SCC25_WT_rep3

value: WT


title: Section_160-Sample_7

tag: strain

tag: age

value: G


title: Day 14 neuroprog., BRAT1 KO 1, Biol Rep B

value: H7 hESC

value: Differentiated


title: Reconstituted chimeric follicle (RCF) YY, biol rep 1 [S198]


title: SCC25_WT_rep2

value: airway

value: airway-derived cells


title: Section_160-Sample_6

value: Sprague Dawley

value: 12 weeks

tag: Sex

value: FB

value: E

tag: side


title: SCC25_WT_rep1


title: Section_160-Sample_5

value: Male

value: DMV

tag: connectivity

value: Rostral


title: Day 14 neuroprog., BRAT1 KO 1, Biol Rep A

value: embryonic stem cell


title: In vivo young, biol rep 2 [S18]

value: young


title: Reconstituted chimeric follicle (RCF) AA, biol rep 4 [S271]

value: Oocytes

value: RCF, aged + aged


title: Day 14 neuroprog., Control Line 2, Biol Rep C

value: H7 Control 2


title: MG01 Line 6 post-thaw Sample 3

description: NextSeq 500/550 High Output Kit (75 Cycles)

data_processing:
Reads were filtered and trimmed using Cutadapt v3.4
Trimmed sequence reads were aligned with STAR v2.7.8a to hg38 and mm39.
Aligned reads were sorted and indexed using SAMtools v1.12
Aligned reads were  filtered to detect only human-specific reads using XenofilteR
Human reads aligning to expressed genes were counted using HTSeq v0.13.5
Assembly: hg38/mm39
Supplementary files format and content: tab-delimited text file

source_name: hiPSC-derived Microglia (MG01)

extract_protocol:
RNA was isolated from micro-dissected fixed histology sections using the RNeasy FFPE kit (Qiagen Cat#73504) or extracted post-thaw of cryopreserved cells.
cDNA libraries for sequencing were generated using the Collibri 3’ mRNA Library Prep Kit for Illumina (ThermoFisher Cat#A38110024) following manufacturer's protocol

value: hiPSC-derived Microglia (MG01)

value: post-thaw MG01


title: In vivo young, biol rep 1 [S17]


title: MG01 Line 6 post-thaw Sample 1


title: Section_160-Sample_4

value: Non-FB

tag: position

value: A

value: Left


title: Day 14 neuroprog., Control Line 2, Biol Rep A

value: H7 hESC

value: Differentiated


title: Section_160-Sample_2

value: Sprague Dawley

value: 12 weeks

value: FB


title: In vitro young, biol rep 7 [S164]

value: in vitro culture, young


title: Section_160-Sample_1

value: Male

value: Rostral


title: LS513, COMBO, 3

first: Amy

middle: E

last: Schade

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description:
LS513 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 3
LS513_gene_count.xlsx
LS513_COMBO_3

data_processing:
Raw reads were processed through fastp. Reads were aligned using Hisat2 v2.0.5. Data were then further processed using DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts are uploaded and processed using DESeq2 with count files as input.

growth_protocol: Cells were cultured in growth medium supplemented with 10% FBS and 1% glutamine, and grown at 37 degree incubators with 5% CO2.

extract_protocol:
Total RNA was isolated after 16-24 hours of vehicle, single agent, or combination treatment using the RNeasy Plus Mini kit (Qiagen, #74136). Cells were scraped and collected in RLT plus buffer, homogenized using Qiagen QIAshredder, and gDNA was removed with gDNA eliminator columns.
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.  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.

treatment_protocol: Cells were treated with the indicated agents for 16-24 hours before RNA collection. Cells were pretreated with DMSO or EZH2i (tazemetostat at 5uM) for 5 days, and then seeded into 6cm plates of 300,000 to 350,000 cells per plate. The following day, cells were treated with DMSO, MEKi (trametinib) or KRASi (MRTX1133) for LS513 cells, with and without EZH2i.

value: Colorectal cancer

value: COMBO


title: Section_160-Sample_3

value: B


title: MG01 Line 6 post-thaw Sample 2


title: In vitro young, biol rep 5 [S162]

value: Oocytes


title: Day 14 neuroprog., Control Line 1, Biol Rep C

value: embryonic stem cell

value: H7 Control 1


title: In vitro young, biol rep 8 [S165]


title: In vitro young, biol rep 6 [S163]


title: Day 14 neuroprog., Control Line 1, Biol Rep B


title: Tumor patient 17 (peritumoral_fat), scRNAseq

city: Paris

first: Fabien

last: Quinquis

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
Alignment with cellranger (v3.0.0 to v6.0.0 according to sample), default options
Ambient RNA correction with SoupX v1.5.2
Doublet removal with DoubletFinder (v2.0.3), scDblFinder (v1.4.0) and scds (v1.6.0) in hybrid mode, default options, union of the three methods
Remove cells with more than 20% of reads mapping mitochondrial genes
Apply additional coverage based filters to remove low quality cells
Normalization and downstream analysis with Seurat v4.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text and MatrixMarket files containing raw counts generated by CellRanger and corresponding normalized counts generated by Seurat v3

extract_protocol:
Fresh tumor samples were cut in small pieces then dissociated 30 min at 37C in CO2-independent medium (Gibco) containing 150 mg/ml of Liberase TL (Roche) and DNase 1 (Sigma Aldrich). Dissociated cells were then filtered with a cell strainer and washed in PBS. Debris were removed by centrifugation (3,000 xg for 10 min at 4C), using the debris removal solution (Miltenyi Biotech). Cells were then resuspended in PBS, counted and adjusted at 10⁶ cells/ml. 6,000 cells were loaded on a 10X Chromium (10X Genomics) and libraries were prepared using a Single Cell 30 Reagent Kit (NextGem kit, 10X Genomics), according to the manufacturer’s protocol, targeting 3,000 recovered cells per cell type and sample. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
NA
NA

tag: age at_diagnosis

value: F

tag: location

value: retroperitoneum

tag: tumour size_(mm)

tag: tumour grade


title: Section_157-Sample_9

value: A

value: Left


title: LS513, COMBO, 2

city: Boston

description:
LS513 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 2
LS513_gene_count.xlsx
LS513_COMBO_2

tag: cell line

tag: cell type


title: Day 14 neuroprog., Control Line 2, Biol Rep B

tag: tissue

value: H7 hESC

tag: genotype

value: H7 Control 2

tag: treatment

value: Differentiated


title: Day 14 neuroprog., Control Line 1, Biol Rep A


title: Section_157-Sample_7

value: Sprague Dawley

value: 12 weeks

tag: region

value: FB


title: In vitro young, biol rep 4 [S149]

value: in vitro culture, young


title: Section_157-Sample_2

value: Male

value: DMV

value: Non-FB

value: Rostral

tag: cluster

value: E

value: Right


title: In vitro young, biol rep 1 [S128]

value: Oocytes


title: LS513, EZH2i, 1

description:
LS513 cell line treated with 5 uM tazemetostat (EZH2i), replicate 1
LS513_gene_count.xlsx
LS513_EPZ_1

value: Colorectal cancer


title: LS513, COMBO, 1

description:
LS513 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 1
LS513_gene_count.xlsx
LS513_COMBO_1

value: COMBO


title: LS513, EZH2i, 3

description:
LS513 cell line treated with 5 uM tazemetostat (EZH2i), replicate 3
LS513_gene_count.xlsx
LS513_EPZ_3


title: Whole skin, tamoxifen and streptozotocin, sample 3, scRNAseq

city: Bethesda

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

institute: NIAMS/NIH

description: 10x Genomics; instrument model: Illumina NovaSeq X

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were performed using Cell Ranger software (v6.0.1, v6.0.2, v7.2.0)
raw_feature_bc_matrix.h5 and filtered_feature_bc_matrix.h5 contents were used as input to SoupX (v1.6.2) and corrected counts were used as input to Seurat (v5.0.1)
Assembly: GRCm38/mm10
Supplementary files format and content: hdf5 archives each containing 2 tab-separated values (.tsv) files and 1 matrix (.mtx)

source_name: Whole skin

extract_protocol:
Single-cell suspensions were prepared from 6 mm punch biopsies of full-thickness mouse skin using the Miltenyi Whole Skin Dissociation kit (Miltenyi Biotec). Samples were incubated in enzymes P, D, and A for 3 hours at 37°C. Mechanical dissociation was then performed using the h_skin_01 setting on a Miltenyi gentleMACS dissociator (Miltenyi Biotec) for 20 seconds. Suspension was filtered through a 30 µm filter to remove debris. Cell viability was assessed by staining with ViaStain AOPI Staining Solution (Nexcelom Bioscience), and live/dead cells were counted using a Cellometer Auto 2000 (Nexcelom Bioscience). Volume of each suspension containing 50,000 live cells was centrifuged at 300g at 4°C for 5 minutes and resuspended in 50 mL 0.4% BSA prepared in 1x phosphate-buffered saline.
Library construction was performed per manufacturer specifications (Chromium Next GEM Single Cell 3' Gene expression (GEX) library protocol, v3.1).
Single-cell RNA-sequencing (3' - v3.1)

value: Whole skin

value: male

value: Tamoxifen and streptozotocin


title: Section_157-Sample_6

tag: strain

value: B


title: Tumor patient 15 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: F

value: retroperitoneum


title: Tumor patient 17 (DDLPS_DD), scRNAseq

description: 10x Genomics


title: In vitro young, biol rep 3 [S148]


title: LS513, KRASi, 2

description:
LS513 cell line treated with 5 nM trametinib (MEKi) after 16 hours, replicate 2
LS513_gene_count.xlsx
LS513_MRTX_2

value: KRASi


title: LS513, EZH2i, 2

description:
LS513 cell line treated with 5 uM tazemetostat (EZH2i), replicate 2
LS513_gene_count.xlsx
LS513_EPZ_2


title: Section_157-Sample_5

value: Sprague Dawley

tag: age

value: 12 weeks

value: FB

value: Left


title: In vitro young, biol rep 2 [S129]

value: in vitro culture, young


title: LS513, KRASi, 3

description:
LS513 cell line treated with 5 nM trametinib (MEKi) after 16 hours, replicate 3
LS513_gene_count.xlsx
LS513_MRTX_3


title: Tumor patient 14 (DDLPS_DDK), scRNAseq

description: 10x Genomics

tag: Sex


title: Tumor patient 16 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: M


title: Tumor patient 15 (DDLPS_WD), scRNAseq

description: 10x Genomics


title: Whole skin, tamoxifen and streptozotocin, sample 2, scRNAseq

description: 10x Genomics; sequenced on Illumina NovaSeq 6000 and Illumina NextSeq 2000


title: LS513, DMSO, 3

description:
LS513 cell line treated with DMSO, replicate 3
LS513_gene_count.xlsx
LS513_DMSO_3

value: DMSO


title: LS513, KRASi, 1

description:
LS513 cell line treated with 5 nM trametinib (MEKi) after 16 hours, replicate 1
LS513_gene_count.xlsx
LS513_MRTX_1


title: Reconstituted chimeric follicle (RCF) AA, biol rep 1 [S268]

value: Oocytes

value: RCF, aged + aged


title: Tumor patient 14 (DDLPS_DD), scRNAseq

description: 10x Genomics


title: Whole skin, vehicle and streptozotocin, sample 4, scRNAseq

value: Vehicle and streptozotocin


title: Section_124-Sample_4

value: Male

value: Non-FB

value: Caudal

value: G

tag: side


title: Tumor patient 14 (DDLPS_WD), scRNAseq

description: 10x Genomics

value: F


title: Section_124-Sample_1

value: DMV

tag: connectivity

value: C


title: Section_124-Sample_3

value: Sprague Dawley

tag: position

value: D


title: Whole skin, vehicle and streptozotocin, sample 1, scRNAseq

description: 10x Genomics; sequenced on Illumina NovaSeq 6000

value: Whole skin

value: male


title: Section_157-Sample_1

value: 12 weeks

value: Rostral

value: Right


title: SKCO1, COMBO, 3

description:
SK-CO1 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 3
SKCO1_gene_count.xlsx
SKCO1_COMBO_3

value: Colorectal cancer

value: COMBO


title: Whole skin, vehicle and streptozotocin, sample 3, scRNAseq

value: Vehicle and streptozotocin


title: LS513, DMSO, 2

description:
LS513 cell line treated with DMSO, replicate 2
LS513_gene_count.xlsx
LS513_DMSO_2

value: DMSO


title: Section_124-Sample_2

description: RNA extracted from a single microdissected neuron

value: Male

value: Non-FB

value: Left


title: Tumor patient 16 (DDLPS_WD), scRNAseq

description: 10x Genomics

tag: age at_diagnosis

value: M

value: retroperitoneum


title: Whole skin, vehicle and streptozotocin, sample 2, scRNAseq


title: Whole skin, tamoxifen, sample 2, scRNAseq

value: Tamoxifen


title: Section_113-Sample_2

value: Sprague Dawley

value: Caudal

value: G


title: Section_124-Sample_5

value: FB

value: H


title: Section_113-Sample_4

value: 12 weeks

value: C


title: Tumor patient 13 (WDLPS), scRNAseq

description: 10x Genomics

source_name: WDLPS

value: WDLPS

value: F

tag: location


title: Section_113-Sample_1

value: Right


title: Whole skin, tamoxifen, sample 1, scRNAseq

value: Whole skin

value: male


title: Whole skin, tamoxifen, sample 3, scRNAseq


title: Tumor patient 12 (peritumoral_fat), scRNAseq

description: 10x Genomics

tag: tumour size_(mm)


title: Section_148-Sample_9

value: Male

value: Non-FB

value: Middle

value: B


title: SKCO1, EZH2i, 3

description:
SK-CO1 cell line treated with 5 uM tazemetostat (EZH2i), replicate 3
SKCO1_gene_count.xlsx
SKCO1_EPZ_3

value: Colorectal cancer


title: Tumor patient 10 (DDLPS_DD), scRNAseq

description: 10x Genomics

value: retroperitoneum

tag: tumour grade


title: Tumor patient 12 (DDLPS_WD), scRNAseq

description: 10x Genomics


title: SKCO1, COMBO, 1

description:
SK-CO1 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 1
SKCO1_gene_count.xlsx
SKCO1_COMBO_1

tag: cell line

value: COMBO


title: Section_148-Sample_8

value: Sprague Dawley

value: A


title: SKCO1, EZH2i, 1

description:
SK-CO1 cell line treated with 5 uM tazemetostat (EZH2i), replicate 1
SKCO1_gene_count.xlsx
SKCO1_EPZ_1

tag: cell type


title: LS513, DMSO, 1

description:
LS513 cell line treated with DMSO, replicate 1
LS513_gene_count.xlsx
LS513_DMSO_1

value: DMSO


title: Tumor patient 11 (lipoma), scRNAseq

description: 10x Genomics

source_name: lipoma

tag: tissue

value: lipoma

value: M

value: trunk


title: Whole skin, vehicle, sample 4, scRNAseq

tag: genotype

value: Vehicle


title: Whole skin, vehicle, sample 3, scRNAseq

tag: treatment


title: SKCO1, EZH2i, 2

description:
SK-CO1 cell line treated with 5 uM tazemetostat (EZH2i), replicate 2
SKCO1_gene_count.xlsx
SKCO1_EPZ_2


title: Section_148-Sample_4

value: 12 weeks

tag: region

value: DMV

value: C

value: Left


title: SKCO1, COMBO, 2

description:
SK-CO1 cell line treated with a combination of trametinib and tazemetostat for 16 hours, replicate 2
SKCO1_gene_count.xlsx
SKCO1_COMBO_2


title: Section_148-Sample_7

value: Male

value: Non-FB

tag: cluster


title: Tumor patient 8 (WDLPS), scRNAseq

description: 10x Genomics

value: WDLPS

value: limb


title: Whole skin, vehicle, sample 2, scRNAseq

value: Whole skin

value: male


title: Tumor patient 9 (WDLPS), scRNAseq

description: 10x Genomics

value: F

value: retroperitoneum


title: SKCO1, MEKi, 3

description:
SK-CO1 cell line treated with 2.5 nM trametinib (MEKi) after 16 hours, replicate 3
SKCO1_gene_count.xlsx
SKCO1_TRAM_3

value: Colorectal cancer

value: MEKi


title: Whole skin, vehicle, sample 1, scRNAseq


title: Section_148-Sample_6

tag: strain

value: Sprague Dawley

value: FB

value: Middle

value: A


title: SKCO1, DMSO, 3

description:
SK-CO1 cell line treated with DMSO, replicate 3
SKCO1_gene_count.xlsx
SKCO1_DMSO_3

value: DMSO


title: SKCO1, MEKi, 2

description:
SK-CO1 cell line treated with 2.5 nM trametinib (MEKi) after 16 hours, replicate 2
SKCO1_gene_count.xlsx
SKCO1_TRAM_2


title: H3K4ME1_MONOCYTES_STROKE_2

first: Arthur

last: Liesz

address: Feodor-Lynen-Straße 17

institute: LMU Hospital

data_processing:
*library strategy: CUT&tag
Libraries werepooled together andsequenced on anNovaseq 600 SP 300 flowcellusing paired-end sequencing(2*150).
CUT&Tag-seq datawas mapped using CUT&RUNTools 2.0
Differentially accessible peaks (3 groups - control, shared,stroke)wereidentified using csaw.8Motif enrichment analysis was performed usingmonaLisa.The plotting of the Cut&tagsignal at genomic features was performed using SeqPlots.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: bone marrow

extract_protocol:
Bone marrows (from femurs) were homogenized and filtered through 40 μm cell strainers to obtain single cell suspensions. BM monocytes(CD11b+Ly6C+Ly6G-)andthelineage-(CD3, CD4, CD8a, CD19,Ter119)and Ly6G)negative myeloid fraction of BM (HSPC-enriched population)weresorted using aFACS Aria II cell sorter (BD Biosciences, Inc.).
nuclei were extracted from 1·10^5 cells, washed twice and incubated with 10 μL of activated concanavalin A beads (ThermoFisher) for 10 min atRT. The beads were thenresuspended in cold antibody buffer containing primary antibodies(against H3K27ac, H3K4me1 or H3K4me3)and the mixture was incubated overnight at 4°C on anutator. Then, the beads were washed twice and resuspended in secondaryH+Lantibody(NovusBio)dilutedin 50 μL digitonin buffer, followed by incubation for 30 min atRTon a rotator. Samples were then incubated with 2.5 µL CUTANA pAG-Tn5 (EpiCypher) for 1 h at RT on a nutator. DNA was tagmented for 1 hat 37°C using tagmentation buffer and tagmented chromatin fragments were released for 1 h at 58°C. 13 ul of tagged DNA was used to prepare the library using NEBNext® High-Fidelity 2X PCR Master Mix(NEB)with CUT&Tag specific PCR cycling parameters. DNA was purified using AMPureXP Beads (Beckman Coulter). The quality of the CUT&Tag libraries was assessed using the Agilent 2100 Bioanalyzer System (Agilent).

treatment_protocol: Freshly isolated cells, as described below, from control mice and mice one month after experimental ischemic stroke

value: bone marrow

value: monocytes

tag: disease state

value: stroke

tag: chip antibody

value: Histone H3K4me1 antibody (pAb), Active Motif, cat#39297