title: PVR3

city: nanchang

first: shengxiang

last: zhang

state: Jiangxi Province

address: 463 Bayi Avenue, Donghu District, Nanchang City, Jiangxi Province, China

institute: nanchang university

description: Library name: Sample6

data_processing:
Illumina Casava1.7 software used for basecalling.
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 reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GCF_009806435.1_UM_NZW_1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

organism: Oryctolagus cuniculus

source_name: retina

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: retina


title: ON_Old2C

status: Public on Dec 06 2025

type: SRA

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

library_source: transcriptomic

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
Ultra-low input RNA Seq directly

tag: tissue

value: Bone marrow

tag: cell line

value: Primary HSPCs patient sample

tag: cell type

value: hematopoietic stem and progenitor cells

tag: genotype

value: WT

tag: treatment

value: cell culture over night


title: A4_C0_3_paired-end

city: Turku

first: Miriam

last: Goetting

address: Yliopistonmäki

department: Dept of Biology

country: Finland

institute: University of Turku

data_processing:
The base calling was done using bcl2fastq (v. 1.8.4)
Read alignment was done using Tophat (v2.1.0) to  salmon genome reference
Genewise read counts were calculated using subreads package (v. 1.5.1)
Genome_build: ICSASG v2 (International Cooperation to Sequence the Atlantic Salmon Genome from NCBI)
Supplementary_files_format_and_content: files are tab delimited text files containing the genewise read counts for each sample

molecule: total RNA

organism: Salmo salar

source_name: blood

growth_protocol: Blood was sampled from landlocked salmon by caudal puncture and stored on ice.

extract_protocol:
Erythrocyte samples were  homogenized in TissueLyser (Qiagen, Austin, USA) and RNA was isolated using NucleoZol (Macherey-Nagel).
Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047). Same samples were paired-end and single-end sequenced (paired-end: 3 biological replicates). For the single-end sequencing there are additional biological replicates for the treatments (single-end: 5 biological replicates).

treatment_protocol: Blood samples were centrifuged and top layer containing white blood cells and plasma was removed. Samples were immediately frozen in liquid nitrogen.

tag: acclimation condition

value: cold, 8 C, 3 weeks

tag: environmental stress

value: control

value: erythrocyte

tag: developmental stage

value: juvenile


title: PVR2

country: China

description: Library name: Sample5


title: retinal organoid, RDH12_AD_6

city: LONDON

first: Mariya

last: Moosajee

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

description: Library name: AD_A1_02_03

data_processing:
Raw reads were quality and adapter trimmed using cutadapt (version 3.4) before alignment.
Reads were mapped and subsequent gene-level counted using RSEM 1.3.1 and STAR 2.7.10a against the human genome GRCh38 using annotation release 95, both from Ensembl.
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.38.3) within the R programming environment (version 4.2.2).
Assembly: GRCh38
Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.

source_name: Organoid

extract_protocol:
RNA was isolated, quantified and cDNA generated from 2 pooled organoids at day 303 week 44 (Qiagen, UK).
cDNA libraries were sequenced on a HiSeq 2500 with paired-end reads of 150 bp using Illumina Stranded Total RNA with Ribo-Zero Plus (Illumina, UK)

value: Organoid


title: colon, WTNAM-4

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

country: USA

institute: NIEHS

data_processing:
RNA-SEQ reads (30-60M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Assembly: mm10
Supplementary files format and content: excel table; log2 transformed and normalized abundance measurements by DESeq2

organism: Mus musculus

source_name: colon

extract_protocol:
Total RNA was isolated using TRIzol™ Plus RNA Purification Kit (Thermo Fisher Scientific) from frozen colon tissue after pulverization in liquid nitrogen with mortar and pestle.
The integrity of the total RNA was determined using a Tapestation (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  Libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina, San Diego, CA) with Ribo-Zero technology. The indexed samples were sequenced on the Nova-seq 6000 (Illumina) employing a 75-bp single-end protocol

treatment_protocol: Eight to twelve-week-old WT or NAPRT KO female mice were treated with or without 2.5% DSS in drinking water together with 3 g/L nicotinamide (NAM) for 7 days.

value: colon

value: 2.5% DSS+ 3g/l NAM


title: HIGH1

description: Library name: HIGH1

library_source: genomic

data_processing:
Reads were trimmed with Trim Galore, aligned with BWA-MEM (release 0.7.17-r1188), to the human genome (GRCh38 primary assembly).
Mus musculus (GRCm39) and Bos taurus (GCF_002263795.3) genomes were used for sequential disambiguation to remove potential contaminant reads from FBS and host DNA of the in-vivo experiment.
Bam files were filtered for mitochondrial, Y chromosome and PCR duplicated reads with Picard (2.25.0-0). Blacklisted regions were filtered using as reference ENCODE blacklist  (hg38 v2). Soft-clipped reads were filtered out with gatk when the ratio of clipped over the total bases exceeded 0.25.  Finally, only properly paired reads, with non-secondary alignment and mapping quality of at least 15 and length > 45 bp were retained.
To quantify open chromatin regions, bedtools multibamcov (with parameters -q 10) was used against the Rank6 signatures regions unique of old and young conditions, generated from the previous experiment.
Differential accessibility was computed with DESeq2, filtering regions with less then 10 counts, and testing for the contrast High vs Low dose (FDR 0.05).
The analysis of known motif enriched in DARs was conducted with Homer software115 (parameters -size 200 -mask)
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

molecule: genomic DNA

extract_protocol:
Purify transposed DNA using a QUIAGEN MinElute Reaction Cleanup kit (28204)
customized Nextera PCR primer mix 1/2

value: in vivo after cell culture over night


title: cmd-1(E140V) 3rd biological replicate

city: St Louis

first: Hieu

last: Hoang

state: MO

address: 660 South Euclid Avenue, 4th floor entry 1

department: Pediatrics

institute: Washington University in St Louis

description:
Library name: udn74-3
cmd-1(E140V) mRNA seq 3rd replicate

data_processing:
Demultiplexing with Illumina BCLconvert
Fastq files were combined and aligned with STAR 2.7.11b
Gene counts quantitated with Subread:featureCount 2.0.8 with CPM and RPKM transformations added with custom Rscripting.
Isoform counts quantitated with Salmon 1.10.0
Assembly: Ensembl WBcel235.108
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

organism: Caenorhabditis elegans

source_name: Whole worms mixed stages, mostly adults

growth_protocol: C. elegans mix staged mostly adults grown in Nematode Growth Medium plates at 20oC

extract_protocol: Trizol chroloform extraction with isopropanol precipitation and ethanol wash

value: Whole worms mixed stages, mostly adults

value: all cell types from whole worms

tag: batch


title: retinal organoid, WT_5

description: Library name: WT_35_03_03


title: ON_Young2C


title: normal2

description: Library name: Sample2


title: retinal organoid, WT_2

description: Library name: WT_35_01_02


title: colon, WTNAM-2


title: wild type (VC2010) 3rd biological replicate

description:
Library name: VC2010-3
wild-type mRNA seq 3rd replicate

value: wild type (VC2010)


title: ON_Young2A


title: wild type (VC2010) 2nd biological replicate

description:
Library name: VC2010-2
wild-type mRNA seq 2nd replicate


title: ON_Young2B


title: retinal organoid, RDH12_AD_2

description: Library name: AD_A1_01_02


title: normal3

description: Library name: Sample3

value: retina


title: retinal organoid, RDH12_AD_1

description: Library name: AD_A1_01_01


title: colon, KONAM-2

value: NAPRT KO


title: retinal organoid, WT_8

description: Library name: WT_35_05_03


title: colon, KONAM-1


title: MCF7_iCas9_sgAAVS1_rep3

status: Public on Dec 05 2025

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description: Library name: sample52

data_processing:
Basecalled FASTQ reads were adaptor-, quality-, and length-trimmed using Cutadapt v1.9.1.  Trimmed reads were aligned to the hg38 reference genome using STAR v2.7.2b with the following parameters to maximize multi-mapping read alignment: --runThreadN 30 --outSAMtype BAM SortedByCoordinate --runMode alignReads --outFilterMultimapNmax 10000 --alignTranscriptsPerReadNmax 1000000 --outSAMmultNmax 1 --outMultimapperOrder Random --winAnchorMultimapNmax 20000 --alignEndsType EndToEnd.
The output BAM files were converted to BED format using the “bamtobed” command from BEDtools v.2.30.0. BED files were then converted to a normalized wiggle file using a custom python script. The normalized wiggle files were further converted to bigwig format using wigToBigWig with the “-clip” parameter.
Gene expression counts were tabulated using HTSeq v0.6.1 and differential expression analyses performed using DESeq2. Repeat expression counts were tabulated using featureCounts with the following parameters: -M -F SAF -T 8 -p -s 2.
Assembly: hg38
Supplementary files format and content: txt format

source_name: cell line

extract_protocol:
Subcellular RNA fractionation – cell lines  RNA fractionation was performed as described previously (Conrad, et al. Methods in Molecular Biology, 2017). Briefly, cells were grown to 80% confluency in 10-cm plates (8-10 million total per replicate) followed by trypsinization and spinning at 800×g for 5 min at 4°C. All buffers were prepared ahead of time, freshly supplemented with 20 U of RiboLock RNase inhibitor (Thermo) per mL, and pre-incubated on ice. Cell pellets were resuspended gently in 400 μL cell lysis buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.15% v/v IGEPAL CA-630) freshly supplemented with 20 U of RiboLock RNase inhibitor (Thermo) and incubated on ice for 2 min. Lysed cells were gently layered atop 1 mL sucrose nuclei isolation buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 24% w/v sucrose) within a 15-mL conical tube and spun at 1500×g for 10 min at 4°C. The supernatant containing the cytoplasmic fraction was transferred to a 2-mL tube and spun again for 2 min at 16,000×g at 4°C to clarify residual nuclei; clarified supernatant was transferred to fresh tubes. The remaining nuclei pellet after the sucrose spin was washed twice with 1 mL PBS-EDTA buffer, resuspended in 250 μL glycerol buffer (20 mM Tris-HCl pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% v/v glycerol), then 250 μL urea nuclear lysis buffer (10 mM Tris-HCl pH 7.5, 1 M urea, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1% v/v IGEPAL CA-630) was immediately added and incubated on ice for 2 min; isolation of intact nuclei can be confirmed if no chromatin debris is seen upon glycerol buffer resuspension. Nuclear lysates were spun at 16,000×g for 5 min at 4°C to fractionate insoluble chromatin. The supernatant containing the nuclear soluble (nucleoplasmic) fraction was transferred to a new tube. The isolated chromatin pellet was rinsed twice with 1 mL PBS-EDTA. Once all three fractions have been isolated, 1 mL TRIzol was added to each lysate and mixed by thorough inversion. The insoluble chromatin fraction was further solubilized by pipetting thru a 1-mL pipette tip then passed at least ten times through a 25-gauge syringe needle or once the liquid can be resuspended by the syringe without resistance.  Subcellular RNA fractionation – primary tissues  RNA fractionation of primary human tissue samples were performed similarly to cell lines with the following modifications to pre-processing steps. Fresh frozen tissues were retrieved from liquid nitrogen storage and transferred on dry ice. Tissue were cut on dry ice into smaller specimens of 15-50 mg and submerged immediately into pre-chilled RNAlater™ ICE Frozen Tissue Transition Solution (Thermo Scientific, AM7030) and incubated overnight at -20°C following manufacturer’s recommendations. Transitioned tissue were minced with a scalpel blade and resuspended gently in 400 μL cell lysis buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.15% v/v IGEPAL CA-630) freshly supplemented with 20 U of RiboLock RNase inhibitor (Thermo) and incubated on ice for 2 min. Tissues were homogenized using a glass dounce homogenizer (Kimble, 885300-0001). Homogenized tissues were filtered thru a Falcon™ 40-μm cell strainer then gently layered atop 1 mL sucrose nuclei isolation buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 24% w/v sucrose) within a 15-mL conical tube and spun at 1500×g for 10 min at 4°C. The nuclei pellets were processed as described above.
Library Prep: For chromatin RNA-sequencing (chrRNA-seq) libraries, 1 µg purified fractionated chromatin RNAs were depleted for highly abundant ribosomal RNAs using the NEBNext® rRNA depletion kit v2 (New England Biolabs, E7400L) and purified using Agencourt RNA Cleanup XP magnetic beads. For mRNA sequencing (mRNA-seq) libraries, 1 µg purified total RNAs were enriched for polyadenylated messenger RNAs using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Ribo-depleted chrRNA-seq and polyA-enriched mRNA-seq libraries were both prepared using the NEBNext® Ultra II Directional RNA-sequencing Library Prep kit for Illumina® (New England Biolabs, E7775L); RNA fragmentation steps were omitted with the chrRNA-seq samples to preserve transcript lengths.

value: cell line

value: human adenocarcinoma cells

value: stably expressing Cas9-IRES-TagBFP, TetOn3G-2A-PuroR, sgRNAs targeting AAVS1 safe harbor


title: ON_Young1A

value: Bone marrow

value: Primary HSPCs patient sample

value: hematopoietic stem and progenitor cells

value: WT

value: cell culture over night


title: MCF7_iCas9_L1HS_274_KO_rep1

description: Library name: sample47

value: stably expressing Cas9-IRES-TagBFP, TetOn3G-2A-PuroR, sgRNAs targeting LINE-1 locus


title: MCF7_iCas9_L1HS_175_KO_rep3

description: Library name: sample46


title: cmd-1(E141G) 1st biological replicate

description:
Library name: udn96-1
cmd-1(E141G) mRNA seq 1st replicate


title: MCF7_iCas9_L1HS_175_KO_rep1

description: Library name: sample44


title: retinal organoid, WT_6

description: Library name: WT_35_05_01

value: Organoid


title: ON_Old2B


title: NativeSkin, IL-22, 24h, biol rep 5

city: Davos Wolfgang

first: Yasutaka

last: Mitamura

state: Graubünden

address: Herman-Bruchard-Strasse 9

department: Immunology

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research

description:
Library name: IL22_5
Column name in raw_exon_counts_all.txt.gz: IL22_5_24h_mg23_5

data_processing:
Sequence reads were shortened to a length of 101 bp from the end, adapter and low-quality sequences were trimmed off, as well as dark cycles appearing as high-quality G bases using Cutadapt (v 2.5).
Processed reads were aligned to the CRCh38 human genome assembly and annotated with the GRCh38.109 gtf file using STAR (v 2.7.9a).
Exons were counted using the featureCounts read summarization program from the Subread package (v 2.0.1).
Assembly: GRCh38 (hg38) human genome assembly
Supplementary files format and content: Tab-delimited text file includes raw exon counts for each sample.

source_name: skin

growth_protocol: Upon arrival, NativeSkin samples were incubated with Genoskin xeno-free medium at 37°C and 5% CO2 overnight for an equilibration period.

extract_protocol:
One-eighth of the 15 mm diameter ex-vivo human skin was minced and digested in Trizol and processed with Precellys devices (Precellys 24 homogenizer) at 4°C to extract RNA from the tissue. The RNA was then purified using an RNAeasy Plus Micro Kit (Qiagen) following the manufacturer’s guidelines.
For sequencing_batch 1: Illumina Stranded mRNA Prep kit following the manufacturer’s protocol. For sequencing_batch 2: Illumina TruSeq Stranded mRNA kit following the manufacturer’s protocol.

treatment_protocol: After equilibration time, NativeSkin samples were treated with IL4 (100 ng/mL), IL-13 (100 ng/mL), IL-4+IL-13 (100 ng/mL each), IL-22 (100 ng/mL), or PBS with 0.1% BSA. The stimulation media was exchanged after 12 hours of stimulation and samples were collected after a total stimulation time of 24 hours.

value: skin

tag: time

tag: donor

tag: experiment batch

tag: rna extraction_batch

tag: sequencing batch


title: NativeSkin, IL-13, 24h, biol rep 5

description:
Library name: IL13_5
Column name in raw_exon_counts_all.txt.gz: IL13_5_24h_mg23_3


title: NativeSkin, IL-4, 24h, biol rep 5

description:
Library name: IL4_5
Column name in raw_exon_counts_all.txt.gz: IL4_5_24h_mg23_2


title: NativeSkin, IL-4 + IL-13, 24h, biol rep 5

description:
Library name: IL13_IL4_5
Column name in raw_exon_counts_all.txt.gz: IL4_IL13_5_24h_mg23_4


title: cmd-1(E140V) 2nd biological replicate

description:
Library name: udn74-2
cmd-1(E140V) mRNA seq 2nd replicate


title: retinal organoid, WT_4

description: Library name: WT_35_03_02


title: NativeSkin, Control, 24h, biol rep 5

description:
Library name: CTRL_5
Column name in raw_exon_counts_all.txt.gz: CTRL_5_24h_mg23_1

value: PBS with 0.1% BSA


title: PVR1

description: Library name: Sample4


title: retinal organoid, WT_3

description: Library name: WT_35_01_03


title: ON_Old2A


title: ON_Old1B


title: cmd-1(E140V) 1st biological replicate

description:
Library name: udn74-1
cmd-1(E140V) mRNA seq 1st replicate

value: Whole worms mixed stages, mostly adults


title: Inlet 2 Forward and Reverse reads samples 5-8 (5-24h_sibmac, 6-24h_sibmac, 7-24h_mutmac, 8-24h_mutmac)

city: Chapel Hill

first: Celia

middle: E

last: Shiau

state: NC

address: 2159 Genome Sciences Building

institute: UNC Chapel Hill

description:
Library name: Raw Data 2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.0.
Custom transgenes (EGFP and TagBFP) were appended to the zebrafish reference genome (GRCz11, from 10x Genomics). The modified annotations were merged into the existing GTF, and a custom reference was built using cellranger mkref. Gene expression matrices were generated using Cell Ranger Multi with sample demultiplexing guided by configuration CSVs specifying sample IDs, reference paths, and OCM barcodes.
Downstream analysis was performed in R using Seurat (v5). Cells were filtered using miQC with a posterior cutoff of 0.80, mitochondrial content column set as "percent.mt", and nFeature_RNA as the gene feature input. Cells marked as "discard" by miQC were removed from the dataset.
SCTransform was used for normalization and variance stabilization (SCT assay), followed by dimensionality reduction via PCA using the first 30 principal components. UMAPs were computed from these PCs, and clustering was performed using shared nearest neighbor (SNN) graph-based clustering across multiple resolutions ranging from 0.02 to 0.6, using Seurat’s FindClusters function. A resolution of 0.4 was selected as the final clustering resolution for downstream analyses based on biological interpretability.
Cells with expression >0 were classified as positive for each gene.  Gene expression summaries were computed by averaging normalized expression per cluster and condition, as well as calculating the fraction of gene-positive cells (expression >0) per cluster per sample. For statistical comparison between conditions, pairwise t-tests with FDR correction were applied to both gene-positive fractions and average expression values, stratified by cluster. Differential expression analysis between conditions was performed using a pseudobulk DESeq2 approach.
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files for barcodes, features, gene counts and meta data for all cells, and matrix file.

organism: Danio rerio

source_name: Macrophages

extract_protocol:
All irg1-KI:GFP+ cells expressing any detectable level of GFP were isolated using FACS on a BD FACSMelody across four conditions: control uncut, control 24 hpa, control 48 hpa, and nlrc3l mutant 24 hpa. Two biological replicates were collected per condition, each consisting of pooled cells from 90 embryos, resulting in a total of eight samples. To maintain cell viability and quality, embryos were dissociated and sorted in batches of 30, with three such batches pooled to constitute a single sample of cells used for scRNA-sequencing.
Cells were stained with acridine orange and propidium iodide and assessed for viability, concentration, and singleness using the LUNA-FX7 Dual Fluorescence Cell Counter (Logos Biosystems). Cells were then processed using the 10x Genomics Chromium X Controller and the Chromium GEM-X Single Cell 3' Kit v4 (PN-1000686) following the manufacturer’s user guide (https://tinyurl.com/2kz2bcs4). Samples were loaded onto the GEM-X 3’ Chip with a target recovery of 20,000 cells per inlet for library preparation. Single cells, reverse transcription reagents and gel beads coated with barcoded oligos were encapsulated together in an oil droplet to produce gel beads in emulsion (GEMs). Reverse transcription was performed using a C1000 thermal cycler (Bio-Rad) to generate complementary DNA (cDNA) libraries tagged with a cell barcode and unique molecular index (UMI). GEMs were then broken and purified using Dynabeads MyOne SILANE beads (Invitrogen) prior to 11 cDNA amplification cycles. Amplified cDNA libraries were purified with SPRIselect magnetic beads (Beckman Coulter) and quantified using an Agilent Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). Fragmentation, end repair, A-tailing and double-sided size selection using SPRIselect beads were then performed. Illumina-compatible adapters were ligated onto the size-selected cDNA fragments. Adapter-ligated cDNA was then purified using SPRIselect beads. Uniquely identifiable indexes were added during 12 amplification cycles. The completed sequencing libraries were then purified using SPRIselect beads, visualized using the TapeStation D5000 High Sensitivity DNA ScreenTape, and pooled in an equimolar ratio. Pooled libraries were sequenced on a DNBSEQ-T7 machine (MGI Tech) at the UNC High Throughput Sequencing Facility in paired-end format (Read 1: 28 cycles, i7 index: 10 cycles, i5 Index: 10 cycles, Read 2: 90 cycles).

value: Macrophages

value: WT AB or nlrc3l-/-

value: 24 hours post tail amputation

tag: age

value: 3 days post fertilization


title: NativeSkin, IL-13, 24h, biol rep 4

description:
Library name: IL13_4
Column name in raw_exon_counts_all.txt.gz: IL13_4_24h_mg21_14


title: ON_Old1C


title: ON_Old1A


title: Inlet 1 Forward and Reverse reads samples 1-4 (1-uncut_sibmac, 2-uncut_sibmac, 3-48h_wtmac, 4-48h_wtmac)

description:
Library name: Raw Data 1
10x Genomics

value: WT AB

value: uncut or 48 hours post tail amputation (hpa)

value: 3 days post fertilization or 4 days post fertilization (48 hpa)


title: retinal organoid, WT_1

description: Library name: WT_35_01_01


title: normal1

description: Library name: Sample1

value: retina


title: MCF7_iCas9_sgAAVS1_rep2

description: Library name: sample51

value: cell line

value: human adenocarcinoma cells

value: stably expressing Cas9-IRES-TagBFP, TetOn3G-2A-PuroR, sgRNAs targeting AAVS1 safe harbor


title: MCF7_iCas9_sgAAVS1_rep1

description: Library name: sample50


title: MCF7_iCas9_L1HS_274_KO_rep3

description: Library name: sample49


title: MCF7_iCas9_L1HS_274_KO_rep2

description: Library name: sample48


title: Tconv Rep4

city: Bethesda

first: Tovah

last: Markowitz

state: MD

address: 10 Center Dr, Building 29B

department: Integrated Data Sciences Section (IDSS)

institute: NIAID

description: Library name: 12_Eos15_Tconvs

data_processing:
The sequencing reads were trimmed adapters and low-quality bases using Cutadapt (version 1.18). The trimmed reads were mapped to mouse reference genome (mm10) and Gencode annotation M21 using STAR aligner (version 2.7.0f) with two-pass alignment option. RSEM (version 1.3.1) was used for gene and transcript quantification based on GENCODE annotation file.
Assembly: mm10
Supplementary files format and content: raw RSEM counts

source_name: Thymus

extract_protocol:
RNA was extracted from sorted cells using TRIzol (Thermo Fisher Scientific) and RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s instruction.
The SMARTer Ultra Low Input RNA Kit was used to generate high-quality cDNA directly from 1 ng of Total RNA using their patented SMART (Switching Mechanism at 5’ End of RNA Template) technology. The cDNA is then made into a sequencing ready library using the Nextera® XT DNA Sample Preparation Kit from Illumina.

treatment_protocol: Eos+ Tregs (CD4+Foxp3+Ccr6+Cxcr4+), Eos- Tregs (CD4+Foxp3+Ccr6-Cxcr4-) and Tconvs (CD4+Foxp3-) were sorted from thymus of CD4-Cre x Foxp3-GFP mice.

value: Thymus

value: Tconv


title: Eosplus Treg Rep3

description: Library name: 7_Eos203_Eosplus_Tregs

value: Treg

value: Eos+


title: Eosminus Treg Rep3

description: Library name: 8_Eos203_Eosminus_Tregs

value: Eos-


title: Tconv Rep2

description: Library name: 6_Eos199_Tconvs


title: Lung Control PBS 2

type: RNA

city: Honolulu

first: Juwon

last: Park

state: HI

address: 651 Ilalo St.

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: University of Hawaii at Manoa

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902934) expression matrix

hyb_protocol: Following fragmentation, 2.3 ug of ss-cDNA were hybridized for 16 hr at 45C on Clariom S arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were processed using the oligo (v1.66.0) and the Linear Model for Microarray Analysis (limma) package (v3.58.1) in R (v4.3.3).

label: biotin

source_name: Lung tissue from control mouse exposed to PBS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: RNA samples with higher quality and yield were extracted by TRIzol method

treatment_protocol: Mice were treated with either PBS or House Dust Mite (HDM) extract 25microg every other day for 5 weeks.

tag: pdgfrα+

value: Control

tag: condition

value: PBS

tag: gender

value: Male

tag: date of birth

tag: body weight

tag: hdm treatment date


title: Lung Control HDM 3

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902941) expression matrix

source_name: Lung tissue from control mouse exposed to HDM

value: HDM


title: Lung Control PBS 3

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902935) expression matrix


title: Lung Control HDM 1

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902939) expression matrix


title: Lung Ablated PBS 1

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902930) expression matrix

source_name: Lung tissue from PDGFRα+ fibroblast-ablated mouse exposed to PBS

value: Ablated

value: Female


title: Lung Control PBS 1

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902933) expression matrix


title: Eosminus Treg Rep2

description: Library name: 5_Eos199_Eosminus_Tregs

tag: tissue

tag: cell type

tag: genotype


title: Lung Ablated HDM 3

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902938) expression matrix

source_name: Lung tissue from PDGFRα+ fibroblast-ablated mouse exposed to HDM


title: Tconv Rep1

description: Library name: 3_Eos198_Tconvs


title: Eosminus Treg Rep1

description: Library name: 2_Eos198_Eosminus_Tregs


title: Eos KO anti-Eos

description: Library name: EosKO_aEos

data_processing:
Reads were processed using chrom-seek (1.2.0) pipeline. [https://github.com/OpenOmics/chrom-seek]
Reads were trimmed with Cutadapt v4.4 and then aligned to mm10 GRCm38.p6 using BWA v0.7.1. All reads aligning to the mm10 v2 blacklist regions were identified and removed with Picard SamToFastq. Reads with a mapQ score less than 6 were removed with SAMtools v1.17 and PCR duplicates were removed with Picard MarkDuplicates.
Data was converted into bigwigs for viewing and normalized by reads per genomic content (RPGC) using deepTools v3.5.1.
Narrow peaks were called using macs v 2.2.7.1 treating matching Eos cKO samples as controls.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak

source_name: Spleen

extract_protocol:
Tregs were purified using CD4+CD25+ Regulatory T Cell Isolation Kit (Miltenyi Biotec) from the spleens of WT or Eos-flox x Foxp3-Cre (Eos cKO) mice and fixed for 10 min at room temperature with 1% Formaldehyde (Millipore Sigma). Cross-linking reaction was stopped by adding 125 mM Glycine (Millipore Sigma). Cells were washed twice in ice-cold PBS and cell pellets were flash-frozen and stored at -80 °C. Cross-linked DNA was fragmentated by sonication using Digital Sonicator (Diagenode). The lysates was incubated overnight at 4 °C with 50 uL Protein A/G magnetic beads (Thermo Fisher Scientific) that had been pre-incubated with 6 ug appropriate antibodies. Samples were washed, eluted, reverse cross-linked at 65 °C for 24 h, and purified using ChIP DNA Clean & Concentrator (Zymo Research). For each ChIP analysis, 5 x106 – 10 x 106 cells were used. Antibodies used were anti-Eos 18H2 (this study) and anti-Helios D8W4X (Cell Signaling).
library was prepared using NEBNext Ultra II End repair/dA-Tailing Module (New England Biolabs) and NEBNext Ultra II Ligation Module (NEB#E7595S/L) according to manufacturer’s instructions.

value: Spleen

value: Eos-flox x Foxp3-Cre


title: MCF7_iCas9_L1HS_175_KO_rep2

description: Library name: sample45

tag: cell line

value: stably expressing Cas9-IRES-TagBFP, TetOn3G-2A-PuroR, sgRNAs targeting LINE-1 locus


title: Eosplus Treg Rep2

description: Library name: 4_Eos199_Eosplus_Tregs


title: WT anti-Eos

description: Library name: WT_aEos


title: AML_PDX1

description:
Library name: sample25
chromatin fractionated RNA

library_source: other

molecule: other

source_name: Acute myeloid leukemia

value: Acute myeloid leukemia


title: T47D_LINE1_ASO2_RNA_rep3

description: Library name: sample24

value: cell line

value: epithelial cells

value: wild-type


title: AML_PDX2

description:
Library name: sample26
chromatin fractionated RNA


title: mice thymus, scRNAseq

city: Daejeon

first: Young Seok

last: Ju

address: 291 Daehakro

country: South Korea

institute: KAIST

description: 10x genomics

data_processing:
The library was sequenced using HiSeq X Ten platform (Illumina). Raw reads were processed by standard pipelines of Cell Ranger (v.2.10); aligning reads to the mouse reference genome (mm10), generating feature-barcode matrices, and calling cell barcodes.
Assembly: mm10
Supplementary files format and content: tsv and matrix files

source_name: thymus

extract_protocol:
Thymi of seven mice were dissected and finely chopped followed by enzymatic digestion in 5ml digestion solution-RPMI1640 (Gibco #11875127) with 0.5mg/ml of Collagenase type 2 (Worthington #LS004177), 0.25mg/ml of Dispase (Gibco #17105-041), and 0.1mg/ml of DNase I (Roche #10104159001) in 37℃ for 15 min with gentle pipetting every 5 minutes. After spinning down, supernatants were washed and suspended in albumin buffer (PBS, 0.5% BSA, and 2mM EDTA). Then, RBC lysis was done by treating 2ml ACK lysis buffer (Gibco #A1049201) for 5 minutes at room temperature followed by PBS washing. Leukocytes were stained with CD45 antibody (Miltenyi Biotec #130-045-801) and depleted with autoMACS Pro Separator (Miltenyi Biotec).
After washing, a single-cell RNA sequencing library was generated by standard protocols of Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics)

value: thymus

tag: strain

value: FVB


title: T47D_LINE1_ASO2_RNA_rep1

description: Library name: sample22


title: NativeSkin, IL-22, 24h, biol rep 4

description:
Library name: IL22_4
Column name in raw_exon_counts_all.txt.gz: IL22_4_24h_mg21_16

value: skin

tag: treatment

tag: time


title: T47D_LINE1_ASO2_RNA_rep2

description: Library name: sample23


title: T47D_SCR_ASO_RNA_rep3

description: Library name: sample21


title: NativeSkin, IL-4 + IL-13, 24h, biol rep 4

description:
Library name: IL4_IL13_4
Column name in raw_exon_counts_all.txt.gz: IL4_IL13_4_24h_mg21_15

tag: donor

tag: experiment batch


title: NativeSkin, IL-4, 24h, biol rep 4

description:
Library name: IL4_4
Column name in raw_exon_counts_all.txt.gz: IL4_4_24h_mg21_13

tag: rna extraction_batch

tag: sequencing batch


title: NativeSkin, Control, 24h, biol rep 4

description:
Library name: CTRL_4
Column name in raw_exon_counts_all.txt.gz: CTRL_4_24h_mg21_12

value: PBS with 0.1% BSA


title: Lung Control HDM 2

description:
None
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902940) expression matrix

tag: pdgfrα+

value: Control


title: Huh7_SCR_ASO_RNA_rep2

description: Library name: sample14

value: hepatocyte-derived carcinoma cell line


title: H460_LINE1_ASO2_RNA_rep2

description: Library name: sample11

value: hypotriploid human cell line


title: CaCo2_LINE1_ASO2_RNA_rep3

description: Library name: sample6

value: human colorectal adenocarcinoma cells


title: Eosminus Treg Rep4

description: Library name: 11_Eos15_Eosminus_Tregs

value: Thymus

value: Treg

value: Eos-


title: Lung Ablated HDM 1

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902936) expression matrix

value: Ablated

tag: condition

value: HDM

value: Male


title: Lung Ablated PBS 2

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902931) expression matrix

value: PBS

tag: gender


title: Eosplus Treg Rep4

description: Library name: 10_Eos15_Eosplus_Tregs

value: Eos+


title: Lung Ablated PBS 3

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902932) expression matrix

tag: date of birth


title: Tconv Rep3

description: Library name: 9_Eos203_Tconvs

value: Tconv


title: Huh7_SCR_ASO_RNA_rep1

description: Library name: sample13

value: cell line

value: wild-type


title: Eosplus Treg Rep1

description: Library name: 1_Eos198_Eosplus_Tregs


title: CaCo2_SCR_ASO_RNA_rep3

description: Library name: sample3


title: Eos KO anti-Helios

description: Library name: EosKO_aHelios

value: Spleen

value: Eos-flox x Foxp3-Cre


title: WT anti-Helios

description: Library name: WT_aHelios


title: GBM_tumor_patient2

description:
Library name: sample28
chromatin fractionated RNA

source_name: Glioblastoma

value: Glioblastoma


title: GBM_tumor_patient1

description:
Library name: sample27
chromatin fractionated RNA


title: K562_cyto_Takara_rep1

description: Library name: sample42

molecule: cytoplasmic RNA

value: lymphoblast cells


title: T47D_SCR_ASO_RNA_rep2

description: Library name: sample20

value: epithelial cells


title: Lung Ablated HDM 2

description:
tdTomato
RMA expression value derived from Clariom S Assay mouse microarray (Thermo Fisher Scientific, 902937) expression matrix

tag: body weight


title: T47D_SCR_ASO_RNA_rep1

description: Library name: sample19


title: K562_chr_Takara_rep2

description:
Library name: sample41
chromatin fractionated RNA


title: T47D_cyto_Takara_rep1

description: Library name: sample38


title: K562_chr_Takara_rep1

description:
Library name: sample40
chromatin fractionated RNA


title: T47D_chr_Takara_rep2

description:
Library name: sample37
chromatin fractionated RNA


title: Huh7_LINE1_ASO2_RNA_rep3

description: Library name: sample18

value: hepatocyte-derived carcinoma cell line


title: Huh7_SCR_ASO_RNA_rep3

description: Library name: sample15


title: H460_LINE1_ASO2_RNA_rep3

description: Library name: sample12

value: hypotriploid human cell line


title: Huh7_LINE1_ASO2_RNA_rep1

description: Library name: sample16


title: MCF7_cyto_Takara_rep1

description: Library name: sample35

value: human adenocarcinoma cells


title: Huh7_LINE1_ASO2_RNA_rep2

description: Library name: sample17


title: H460_LINE1_ASO2_RNA_rep1

description: Library name: sample10


title: TNBC_tumor_patient1

description:
Library name: sample32
chromatin fractionated RNA

source_name: Triple-negative breast cancer

value: Triple-negative breast cancer


title: H460_SCR_ASO_RNA_rep3

description: Library name: sample9


title: MCF7_LINE1_ASO2_RNA_rep3

description: Library name: sample26


title: MCF7_LINE1_ASO2_RNA_rep2

description: Library name: sample25


title: MCF7_LINE1_ASO2_RNA_rep1

description: Library name: sample24


title: H460_SCR_ASO_RNA_rep2

description: Library name: sample8


title: CaCo2_LINE1_ASO2_RNA_rep2

description: Library name: sample5

value: human colorectal adenocarcinoma cells


title: H460_SCR_ASO_RNA_rep1

description: Library name: sample7


title: MCF7_LINE1_ASO1_RNA_rep3

description: Library name: sample23


title: MCF7_LINE1_ASO1_RNA_rep2

description: Library name: sample22


title: CaCo2_SCR_ASO_RNA_rep2

description: Library name: sample2


title: CaCo2_SCR_ASO_RNA_rep1

description: Library name: sample1


title: MCF7_LINE1_ASO1_RNA_rep1

description: Library name: sample21


title: T47D_chrRNA_rep1

description:
Library name: sample17
chromatin fractionated RNA


title: T47D_cyto_Takara_rep2

description: Library name: sample39


title: K562_cyto_Takara_rep2

description: Library name: sample43


title: T47D_chr_Takara_rep1

description:
Library name: sample36
chromatin fractionated RNA


title: CaCo2_LINE1_ASO2_RNA_rep1

description: Library name: sample4


title: MCF7_chr_Takara_rep1

description:
Library name: sample34
chromatin fractionated RNA


title: TNBC_tumor_patient2

description:
Library name: sample33
chromatin fractionated RNA


title: ER_tumor_patient1

description:
Library name: sample30
chromatin fractionated RNA

source_name: ER+ breast cancer

value: ER+ breast cancer


title: K562_chrRNA_rep2

description:
Library name: sample10
chromatin fractionated RNA


title: MCF7_SCR_ASO_RNA_rep3

description: Library name: sample29


title: H460_chrRNA_rep2

description:
Library name: sample6
chromatin fractionated RNA


title: GM12878_chrRNA_rep2

description:
Library name: sample4
chromatin fractionated RNA

value: lymphoblastoid cells

value: Scrambled ASO


title: MCF7_SCR_ASO_RNA_rep2

description: Library name: sample28


title: MCF7_SCR_ASO_RNA_rep1

description: Library name: sample27


title: CaCo2_chrRNA_rep1

description:
Library name: sample1
chromatin fractionated RNA


title: MCF7_ChIRPseq_ORF1_rep2

description: Library name: sample4

data_processing:
Basecalled FASTQ reads were adaptor-, quality-, and length-trimmed using Cutadapt v1.9.1.  Trimmed reads were aligned to the hg38 reference genome using STAR v2.7.2b with the following parameters to maximize multi-mapping read alignment: --runThreadN 30 --outSAMtype BAM SortedByCoordinate --runMode alignReads --outFilterMultimapNmax 10000 --alignTranscriptsPerReadNmax 1000000 --outSAMmultNmax 1 --outMultimapperOrder Random --winAnchorMultimapNmax 20000 --alignEndsType EndToEnd.
The output BAM files were converted to BED format using the “bamtobed” command from BEDtools v.2.30.0. BED files were then converted to a normalized wiggle file using a custom python script. The normalized wiggle files were further converted to bigwig format using wigToBigWig with the “-clip” parameter.
Assembly: hg38
Supplementary files format and content: bigwig format

extract_protocol:
15-20 million cells were harvested per biological replicate by trypsinization. Cells were rinsed once with 1X PBS and spun at 800xg for 3 min at 4°C. Cells were resuspended in 10 mL 1X PBS and crosslinked with 1% v/v glutaraldehyde (EM-grade, Sigma-Aldrich) at RT with gentle rocking for 10 min. Crosslinking was quenched with 500 µL of 2.5 M glycine and rocked for 5 min at RT, washed once with 10 mL 1X PBS, transferred into 1.5 mL Eppendorf tube with 1 mL 1X PBS, and pelleted at 2000xg for 3 min. Cell pellets were weighed and snap frozen in liquid nitrogen and stored at -80°C. Chromatin Preparation: Cell pellets were lysed (1 mL per 100 mg pellet) with ChIRP cell lysis buffer (50 mM Tris-Cl pH 7.0, 10 mM EDTA, 1% SDS) freshly supplemented with 1X protease inhibitor cocktail (APExBIO, K1010), 1 mM final PMSF, and RiboLock RNase inhibitor (Thermo Scientific, EO0382). Cell lysates were sonicated on wet ice using a Branson Sonifier S-450 at 15% power, 0.5 sec ON/1.0 sec, for 60 sec; sonication was repeated until lysate was visibly clear. To check shearing efficiency, a 5 µL aliquot of lysate was diluted with 95 µL ChIRP proteinase K buffer (100 mM NaCl, 10 mM Tris-Cl pH 7.0, 1 mM EDTA, 0.5% SDS) and added 5 uL of 20 mg/mL proteinase K (Invitrogen). The proteinase K treated aliquot was incubated on a thermal mixer at 50°C for 45 min shaking at 1200 rpm followed by purification through a spin column using a standard PCR purification kit. Purified sheared DNA was ran on a 2% agarose gel to assess the size distribution of sheared fragments. If the bulk of DNA is >500 bp, repeat sonication as necessary. Once sheared to <500 bp, lysates were spun down at 16,000xg for 10 min at 4°C. The clarified supernatant was transferred to a new tube. ChIRP Probe Hybridization: ChIRP probes were designed against the 5’ UTR promoter of the full-length L1Hs consensus sequence (RepBase78) using the LGC BioSearch Technologies ChIRP Probe Designer (Masking Level set to 0). To all samples, add freshly made 2 vol ChIRP hybridization buffer (750 mM NaCl, 1% SDS, 50 mM Tris-Cl pH 7.0, 1 mM EDTA, 15% formamide, 1 mM PMSF, 1X protease inhibitor cocktail, RiboLock RNase inhibitor) and 1 µL of 100 µM ChIRP probe set (aliquoted and stored at -80°C long-term). Hybridization was performed at 37 °C overnight in a hybridization oven. To capture hybridized chromatin, 100 µL Streptavidin MyOne C1 Dynabeads (Thermo Scientific) per 1 µL probe were pre-washed with ChIRP cell lysis buffer three times. Naked washed beads were resuspended directly with 1 mL of hybridization sample and transferred back into the hybridization solution and mixed for 30 min at 37°C. Captured beads were washed five times with 5 vol of ChIRP wash buffer (2X SSC, 0.5% SDS, 1mM PMSF), rotating at 37°C for 5 min per wash. After final wash, aliquot 10% of captured beads to separate tube for RNA extraction to check for capture efficiency. DNA Extraction: The remaining 90% of captured beads were resuspended in 150 µL ChIRP DNA elution buffer (50 mM NaHCO3, 1% SDS) and treated with 10 µL 10 mg/mL RNase A (Thermo Scientific) and 100 units RNase H (New England Biolabs) at 37°C for 30 min with shaking at 1200 rpm. Beads were separated on a magnetic rack and the clear supernatant containing eluted DNA was transferred to a new tube. RNase extraction was repeated for a second elution and combined with the first. The pooled eluate was treated with 15 µL of 20 mg/mL proteinase K at 50°C for 45 min with shaking at 1200 rpm. Treated samples were transferred to a phase-lock gel tube with 1 vol of 25:24:1 phenol/chloroform/isoamyl alcohol, mixed thoroughly by inverting until emulsified, and spun at 16,000xg for 10 min at 4°C. The aqueous upper layer was transferred to a new 1.5 mL Eppendorf tube, added with 3 µL GlycoBlue™ co-precipitant (Thermo Scientific, AM9516), 30 µL 3 M sodium acetate (10% v/v) and 2.5 vol 100% ethanol. Ethanol precipitation was incubated at -20°C overnight or at least 1 h at -80°C. Precipitated DNA was spun down at 16,000xg for 20 min at 4°C, washed once with 80% v/v ethanol, spun again for 5 min at 4°C, and air-dried for 10 min at RT. DNA pellets were resuspended in 30 µL nuclease-free water. Concentration of DNA was measured using a Qubit 4 fluorometer (Thermo Scientific). DNA capture efficiency can be measured by qPCR.
ChIRP-seq libraries were prepared from the isolated DNA using the NEBNext Ultra II DNA library prep kit (New England Biolabs, E7645L) following manufacturer’s protocol.

value: human breast cancer cell line


title: MCF7_ChIRPseq_ORF2_rep2

description: Library name: sample6


title: MOLM13_chrRNA_rep2

description:
Library name: sample16
chromatin fractionated RNA

value: human acute myeloid leukemia cells


title: THP1_chrRNA_rep1

description:
Library name: sample19
chromatin fractionated RNA

value: cell line

value: human leukemia monocytic cells


title: ER_tumor_patient2

description:
Library name: sample31
chromatin fractionated RNA


title: K562_chrRNA_rep1

description:
Library name: sample9
chromatin fractionated RNA

value: wild-type


title: MOLM13_chrRNA_rep1

description:
Library name: sample15
chromatin fractionated RNA


title: MCF7_ChIRPseq_5UTR_rep1

description: Library name: sample1


title: THP1_chrRNA_rep2

description:
Library name: sample20
chromatin fractionated RNA


title: MDA-MB-231_chrRNA_rep2

description:
Library name: sample14
chromatin fractionated RNA

value: epithelial adenocarcinoma


title: T47D_chrRNA_rep2

description:
Library name: sample18
chromatin fractionated RNA


title: M_38169_S12_R1_001

city: Montpellier CEDEX 4

first: Malik

last: Kahli

address: Parc Euromédecine - CAP DELTA - 1682 Rue de la Valsière

country: France

institute: Sys2Diag UMR9005 CNRS - ALCEN

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed and filtered with phred score > 20. Reads were mapped to GRCh38.p14 and annotated with miRRBase v20 using the miRDeep2 pipeline. miRNA expression quantification and differential analysis were performed with DEseq2.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw count of htseq-count

source_name: saliva

extract_protocol:
Unstimulated whole saliva was collected in the morning (9:00–10:00 AM) from healthy male volunteers (18–40 years old) who had refrained from eating, drinking, or smoking for at least 1 hour. Participants passively drooled into sterile tubes, and a minimum of 4 mL was collected per individual. Samples showing visible blood contamination were excluded. Saliva was placed on ice and processed within 1 hour: first centrifuged at 300 × g for 10 min at 4 °C to remove cells, followed by 3000 × g for 30 min at 4 °C to eliminate residual debris. The resulting supernatant was used for EV isolation.
Total small RNA was extracted from EV and WS samples using the miRNeasy Serum/Plasma Kit (Qiagen, #217184) and eluted in 14 µL of RNase-free water. RNA yield was quantified using the Qubit™ microRNA Assay Kit (ThermoFisher, #Q32881), and size distribution was assessed via the LabChip GX system (Caliper-PerkinElmer) using the Small RNA Assay (#CLS153530) to confirm the presence of miRNAs. Small RNA libraries were prepared from 10 ng of miRNA using the TruSeq Small RNA Library Prep Kit (Illumina, #RS-200-0012). After adapter ligation, cDNA synthesis, and PCR amplification (11 cycles), libraries were purified with Ampure XP beads (Beckman Coulter, #A63880), assessed on the LabChip GX system, and quantified via Qubit™ dsDNA HS Assay (#Q32851). Equimolar pooling was followed by sequencing on the NextSeq 500 platform using the high output v2.5 kit (1.8 pM, #20024906).

value: saliva

value: miletnyi kit


title: Q_38169_S11_R1_001

description: Library name: Sample 11

value: qiagen kit


title: MCF7_ChIRPseq_5UTR_rep2

description: Library name: sample2


title: UC_12114_S6_R1_001

description: Library name: Sample 6

value: ultracentrifugation


title: MDA-MB-231_chrRNA_rep1

description:
Library name: sample13
chromatin fractionated RNA


title: MCF7_chrRNA_rep2

description:
Library name: sample12
chromatin fractionated RNA


title: WS_12114_S5_R1_001

description: Library name: Sample 5

value: whole saliva


title: MCF7_chrRNA_rep1

description:
Library name: sample11
chromatin fractionated RNA

value: human adenocarcinoma cells


title: Q_11113_S3_R1_001

description: Library name: Sample 3


title: Huh7_chrRNA_rep1

description:
Library name: sample7
chromatin fractionated RNA

value: hepatocyte-derived carcinoma cell line


title: CaCo2_chrRNA_rep2

description:
Library name: sample2
chromatin fractionated RNA

value: human colorectal adenocarcinoma cells


title: H460_chrRNA_rep1

description:
Library name: sample5
chromatin fractionated RNA

value: hypotriploid human cell line

value: LINE-1 targeting ASO


title: GM12878_chrRNA_rep1

description:
Library name: sample3
chromatin fractionated RNA

value: lymphoblastoid cells


title: MCF7_ChIRPseq_ORF1_rep1

description: Library name: sample3

value: human breast cancer cell line


title: LMM03 recurrent LMM invasive component [WES]

city: Melbourne

first: Mark

last: Shackleton

state: VIC

address: Level 4, Paula Fox Melanoma and Cancer Centre 545 St Kilda Rd

department: School of Translational Medicine

country: Australia

institute: Monash University

description: Library name: LMM03C_S12

data_processing:
Fastq files were trimmed (SurecallTrimmer v.4.0.1) and aligned to the reference human genome hg38 using bwa-mem (v.0.7.17).
Somatic single nucleotide variants (SNVs) and small insertions and deletions (indels) in each LM/LMM were called with Mutect2 (GATK v.4.1.2.0) tumour-normal mode. Output variant calls were filtered with FilterMutectCalls (GATK v.4.1.2.0).
Assembly: GRCh38
Supplementary files format and content: VCF file of each sample called and filtered by Mutect2
Supplementary files format and content: csv files of filtered somatic varaints annotated with Ensembl VEP (v.95)

source_name: FFPE

extract_protocol:
DNA from tissue and blood samples was extracted using the QIAamp DNA FFPE Tissue Kit or the QIAamp DNA Mini Kit respectively, following manufacturer’s protocols. DNA was quantified using the Invitrogen Qubit Fluorometer and dsDNA High Sensitivity Assay Kit.
Libraries were constructed using the Agilent SureSelectXT HS Target Enrichment System and Agilent SureSelect Clinical Research Exome V2 67.3Mb capture panel according to manufacturer’s protocols.

value: FFPE

value: melanoma

value: lentigo maligna melanoma

tag: sample group

value: recurrent LMM invasive component


title: LMM03 recurrent LMM in situ component [WES]

description: Library name: LMM03B_S11

tag: tissue

value: recurrent LMM in situ component


title: LMM02 incident LM [WES]

description: Library name: LMM02A_S6

tag: cell type

value: lentigo maligna

value: incident LM


title: Q_12114_S7_R1_001

description: Library name: Sample 7

value: saliva

value: qiagen kit


title: LMM01 recurrent LMM invasive component [WES]

description: Library name: LMM01C_S4


title: Huh7_chrRNA_rep2

description:
Library name: sample8
chromatin fractionated RNA

value: cell line

tag: genotype

value: wild-type


title: LMM01 recurrent LMM in situ component [WES]

description: Library name: LMM01B_S3

tag: cell line


title: UC_38169_S10_R1_001

description: Library name: Sample 10

value: ultracentrifugation


title: WS_38169_S9_R1_001

description: Library name: Sample 9

value: whole saliva


title: M_12114_S8_R1_001

description: Library name: Sample 8

value: miletnyi kit


title: MCF7_ChIRPseq_ORF2_rep1

description: Library name: sample5


title: M_11113_S4_R1_001

description: Library name: Sample 4


title: UC_11113_S2_R1_001

description: Library name: Sample 2


title: LMM03 incident LM [WES]

description: Library name: LMM03A_S10


title: WS_11113_S1_R1_001

description: Library name: Sample 1


title: LM02 recurrent LM [WES]

description: Library name: LM02B_S6

value: recurrent LM


title: LMM02 recurrent LMM invasive component [WES]

description: Library name: LMM02C_S8


title: Healthy control 24

city: Chiba

first: Takeshi

last: Kawasaki

address: 1-8-1, Inohana, Chuoku

department: Respirology

country: Japan

institute: Chiba University

description:
Library name: DK22269_13
all.rpm_DK22269.xlsx

data_processing:
Removal of poly A tail and adapter sequences were performed using BBDuk (BBMap version 38.96) with the following settings (k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Trimmed reads were mapped to hg38 using STAR version 2.7.6a with the following settings (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000).
Read counts for each gene were obtained using HTSeq-count version 1.99.2 with the following settings (-m intersection-nonempty -s yes).
Assembly: hg38
Supplementary files format and content: xlsx files include RPM values for each sample

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from 1.0-2.0 × 10^6 PBMCs dissolved in 1.0 mL of Isogen reagent.
Purified total RNA (200 ng) was used for RNA library preparation, following the Quant-Seq 3′ mRNA-seq library preparation kit FWD protocol for Illumina (Lexogen, Vienna, Austria). The RNA libraries were sequenced on an Illumina NextSeq 500 system with 75-nucleotide-long reads.

value: Peripheral blood

value: Healthy control

value: Mononuclear cells


title: LM04 recurrent LM [WES]

description: Library name: LM04B_S12

value: FFPE

value: melanoma


title: Healthy control 23

description:
Library name: DK22269_12
all.rpm_DK22269.xlsx


title: LMM01 incident LM [WES]

description: Library name: LMM01A_S2


title: LM04 incident LM [WES]

description: Library name: LM04A_S11


title: Healthy control 20

description:
Library name: DK22269_09
all.rpm_DK22269.xlsx


title: Healthy control 21

description:
Library name: DK22269_10
all.rpm_DK22269.xlsx


title: Healthy control 19

description:
Library name: DK22269_08
all.rpm_DK22269.xlsx


title: Healthy control 18

description:
Library name: DK22269_07
all.rpm_DK22269.xlsx


title: Healthy control 13

description:
Library name: DK22269_02
all.rpm_DK22269.xlsx


title: LMM02 recurrent LMM in situ component [WES]

description: Library name: LMM02B_S7

value: lentigo maligna melanoma


title: LM01 recurrent LM [WES]

description: Library name: LM01B_S3


title: Healthy control10

description:
Library name: DK20193B_10
all.rpm_DK20193B.xlsx


title: Healthy control 11

description:
Library name: DK20193B_11
all.rpm_DK20193B.xlsx


title: LM03 incident LM [WES]

description: Library name: LM03A_S8


title: LM03 recurrent LM [WES]

description: Library name: LM03B_S9


title: Healthy control 5

description:
Library name: DK20193B_05
all.rpm_DK20193B.xlsx


title: LM02 incident LM [WES]

description: Library name: LM02A_S5


title: LM01 incident LM [WES]

description: Library name: LM01A_S2


title: Healthy control 26

description:
Library name: DK22269_15
all.rpm_DK22269.xlsx


title: Healthy control 1

description:
Library name: DK20193B_01
all.rpm_DK20193B.xlsx


title: Sarcoidosis/without extrapulmonary lesions 3

description:
Library name: DK21066B_03
all.rpm_DK21066B.xlsx


title: Sarcoidosis/without extrapulmonary lesions 2

description:
Library name: DK21066B_02
all.rpm_DK21066B.xlsx


title: Healthy control 25

description:
Library name: DK22269_14
all.rpm_DK22269.xlsx


title: Healthy control 7

description:
Library name: DK20193B_07
all.rpm_DK20193B.xlsx


title: Healthy control 22

description:
Library name: DK22269_11
all.rpm_DK22269.xlsx


title: Healthy control 16

description:
Library name: DK22269_05
all.rpm_DK22269.xlsx


title: Healthy control 17

description:
Library name: DK22269_06
all.rpm_DK22269.xlsx


title: Healthy control 2

description:
Library name: DK20193B_02
all.rpm_DK20193B.xlsx


title: Sarcoidosis/with extrapulmonary lesions 3

description:
Library name: DK21066B_01
all.rpm_DK21066B.xlsx

value: Sarcoidosis/with extrapulmonary lesions


title: Sarcoidosis/with extrapulmonary lesions 1

description:
Library name: DK20141B_01
all.rpm_DK20141B.xlsx


title: Effector CD8+ T cells from mice on dietary restriction, replicate #2

city: New York

first: Charles

last: Carr

state: NY

department: Medicine

institute: Weill Cornell

description:
Library name: DR_effector_CD8_T_cells_2
effector_CD8_T_RNA_seq_counts.tsv

data_processing:
Primary processing of RNA-Seq reads in FastQ format was performed using nf-core/rnaseq and Nextflow.  Strandedness was inferred by subsampling and pseudoalignment using fq and Salmon. Read QC was performed with FastQC, adapter and quality trimming was performed with Trim Galore!, and pseudoalignment and quantification were performed with STAR and Salmon.
Assembly: mm10
Supplementary files format and content: raw counts per sample

source_name: Effector CD8+ T cells

extract_protocol:
Micro RNA Isolation Kit (Qiagen), according to the manufacturer’s instructions.
For naïve and effector CD8+ T cells, cDNA was synthesized with the Ultralow V4 kit (Clonetech) and sequencing libraries were prepared with the Nextera XT DNA prep kit (Illumina). For neutrophils, cDNA libraries was synthesized with the NEB Ultra II Directional RNA Library Prep (plus Poly A isolation module) and sequencing libraries were prepared with the Illumina NovaSeq X Plus kit.

value: Effector CD8+ T cells

value: dietary restriction


title: Effector CD8+ T cells from mice fed ad libitum, replicate #3

description:
Library name: AL_effector_CD8_T_cells_3
effector_CD8_T_RNA_seq_counts.tsv

value: ad libitum


title: Effector CD8+ T cells from mice fed ad libitum, replicate #2

description:
Library name: AL_effector_CD8_T_cells_2
effector_CD8_T_RNA_seq_counts.tsv


title: Effector CD8+ T cells from mice on dietary restriction, replicate #1

description:
Library name: DR_effector_CD8_T_cells_1
effector_CD8_T_RNA_seq_counts.tsv


title: Healthy control 9

description:
Library name: DK20193B_09
all.rpm_DK20193B.xlsx


title: Healthy control 6

description:
Library name: DK20193B_06
all.rpm_DK20193B.xlsx


title: Effector CD8+ T cells from mice fed ad libitum, replicate #1

description:
Library name: AL_effector_CD8_T_cells_1
effector_CD8_T_RNA_seq_counts.tsv


title: Healthy control 4

description:
Library name: DK20193B_04
all.rpm_DK20193B.xlsx


title: Healthy control 3

description:
Library name: DK20193B_03
all.rpm_DK20193B.xlsx


title: Sarcoidosis/with extrapulmonary lesions 9

description:
Library name: DK21223_06
all.rpm_DK21223.xlsx


title: Healthy control 15

description:
Library name: DK22269_04
all.rpm_DK22269.xlsx


title: Naive CD8+ T cells from mice on dietary restriction, replicate #2

description:
Library name: DR_naive_CD8_T_cells_2
naive_CD8_T_RNA_seq_counts.tsv

source_name: Naive CD8+ T cells

value: Naive CD8+ T cells


title: Naive CD8+ T cells from mice on dietary restriction, replicate #1

description:
Library name: DR_naive_CD8_T_cells_1
naive_CD8_T_RNA_seq_counts.tsv


title: Sarcoidosis/with extrapulmonary lesions 2

description:
Library name: DK20141B_04
all.rpm_DK20141B.xlsx


title: Neutrophils from mice on dietary restriction, replicate #2

description:
Library name: DR_neutrophils_rep_2
neutrophil_RNA_seq_counts.tsv

source_name: Neutrophils

value: Neutrophils


title: Healthy control 12

description:
Library name: DK22269_01
all.rpm_DK22269.xlsx


title: Effector CD8+ T cells from mice on dietary restriction, replicate #3

description:
Library name: DR_effector_CD8_T_cells_3
effector_CD8_T_RNA_seq_counts.tsv


title: Healthy control 14

description:
Library name: DK22269_03
all.rpm_DK22269.xlsx


title: Neutrophils from mice on dietary restriction, replicate #1

description:
Library name: DR_neutrophils_rep_1
neutrophil_RNA_seq_counts.tsv


title: Neutrophils from mice fed ad libitum, replicate #3

description:
Library name: AL_neutrophils_rep_3
neutrophil_RNA_seq_counts.tsv


title: Sarcoidosis/without extrapulmonary lesions 4

description:
Library name: DK21066B_04
all.rpm_DK21066B.xlsx


title: Sarcoidosis/with extrapulmonary lesions 8

description:
Library name: DK21223_05
all.rpm_DK21223.xlsx


title: scRNASeq Mouse Thymus (hAPC): Wild type, P14, Bio Rep 1, Batch D

city: Nashville

first: Bryan

middle: Robert

last: Helm

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

description:
Library name: P14_WT_1_D
P14_WT_1_D

data_processing:
FASTQ files were processed with Cellranger v 6.0.1 to derive filtered feature count matrices. Reads were aligned against mm10 and filtered feature matrices were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger: barcodes, features, and count matrices

source_name: Thymus

extract_protocol:
To sort hAPCs for scRNA-sequencing, thymi were harvested and enzymatically digested with an enzymatic solution comprising LiberaseTM (Roche) and DNAse I in PBS at 37°C. Isolated cells were centrifuged and immunostained with a panel of fluorescently-labeled antibodies prior to resuspension in FWB+ EDTA  + propidium iodide (Enzo). HAPCs were FACS purified as MHCII lo to + CD45+ Thy1.2- non-thymic epithelial cells (Epcam+CD11c-). Purified hAPCs  were then centrifuged and resuspended in FWB without EDTA, counted and resuspended at a concentration of 700-1200 cells/µL prior to submission to the University of Texas Genomic Sequencing and Analysis Facility.
Cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics). Libraries were examined for size and quality using the Bioanalyzer High Sensitivity DNA Kit (Agilent) and their concentrations were measured using the KAPA SYBR Fast qPCR kit (Roche).

value: Thymus

value: Antigen Presenting Cells

value: WT

tag: age (days)

tag: batch

value: D


title: Healthy control 8

description:
Library name: DK20193B_08
all.rpm_DK20193B.xlsx


title: Sarcoidosis/with extrapulmonary lesions 7

description:
Library name: DK21223_04
all.rpm_DK21223.xlsx


title: scRNASeq Mouse Thymus (hAPC): Wild type, P07, Bio Rep 2, Batch F

description:
Library name: P07_WT_2_F
P07_WT_2_F

value: F


title: scRNASeq Mouse Thymus (hAPC): Wild type, P10, Bio Rep 1, Batch C

description:
Library name: P10_WT_1_C
P10_WT_1_C

value: C


title: Sarcoidosis/with extrapulmonary lesions 6

description:
Library name: DK21223_03
all.rpm_DK21223.xlsx

value: Peripheral blood


title: Sarcoidosis/with extrapulmonary lesions 4

description:
Library name: DK21223_01
all.rpm_DK21223.xlsx

value: Mononuclear cells


title: scRNASeq Mouse Thymus (hAPC): Wild type, P03, Bio Rep 1, Batch D

description:
Library name: P03_WT_1_D
P03_WT_1_D


title: Sarcoidosis/without extrapulmonary lesions 5

description:
Library name: DK21066B_05
all.rpm_DK21066B.xlsx


title: scRNASeq Mouse Thymus (hAPC): Wild type, P10, Bio Rep 2, Batch C

description:
Library name: P10_WT_2_C
P10_WT_2_C


title: scRNASeq Mouse Thymus (hAPC): Wild type, P00, Bio Rep 2, Batch E

description:
Library name: P00_WT_2_E
P00_WT_2_E

value: E


title: Sarcoidosis/without extrapulmonary lesions 1

description:
Library name: DK20141B_07
all.rpm_DK20141B.xlsx


title: Naive CD8+ T cells from mice fed ad libitum, replicate #2

description:
Library name: AL_naive_CD8_T_cells_2
naive_CD8_T_RNA_seq_counts.tsv

tag: treatment


title: Naive CD8+ T cells from mice fed ad libitum, replicate #1

description:
Library name: AL_naive_CD8_T_cells_1
naive_CD8_T_RNA_seq_counts.tsv


title: Sarcoidosis/with extrapulmonary lesions 5

description:
Library name: DK21223_02
all.rpm_DK21223.xlsx


title: Neutrophils from mice fed ad libitum, replicate #1

description:
Library name: AL_neutrophils_rep_1
neutrophil_RNA_seq_counts.tsv


title: poolD-95

city: Essen

first: Florian

last: Rambow

department: IKIM

country: Germany

institute: University Hospital Essen

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
The merged gene expression matrix (raw counts) containing all samples was analyzed with the Seurat3 package in R. Cells were filtered by nFeature_RNA (genes detected) >3000 and <7000, percent.mt (percentage of mitochondria genes) < 10. This resulted in n=306 valid cells for downstream analysis. After filtering cells, log-normalization was performed using the default NormalizeData function in Seurat. The scaled data was regressed for cell cycle phases (S.Score and G2M.Score) and number of genes per cell (nFeature_RNA) before performing UMAP based dimension reduction (dims=1:20, resolution =0.4).
Assembly: mm10
Supplementary files format and content: csv

source_name: tumor

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000g for 1min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
SMART-seq2 based scRNA-seq; Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).

value: tumor


title: scRNASeq Mouse Thymus (hAPC): Wild type, P14, Bio Rep 2, Batch D

description:
Library name: P14_WT_2_D
P14_WT_2_D


title: scRNASeq Mouse Thymus (hAPC): Wild type, P07, Bio Rep 1, Batch F

description:
Library name: P07_WT_1_F
P07_WT_1_F


title: poolD-96


title: scRNASeq Mouse Thymus (hAPC): Wild type, P00, Bio Rep 1, Batch D

description:
Library name: P00_WT_1_D
P00_WT_1_D


title: poolD-87


title: scRNASeq Mouse Thymus (hAPC): Wild type, P03, Bio Rep 2, Batch D

description:
Library name: P03_WT_2_D
P03_WT_2_D


title: poolD-92


title: poolD-94


title: poolD-93


title: poolD-89


title: Neutrophils from mice fed ad libitum, replicate #2

description:
Library name: AL_neutrophils_rep_2
neutrophil_RNA_seq_counts.tsv


title: poolD-91


title: poolD-88


title: poolD-79


title: poolD-85


title: poolD-82


title: poolD-77


title: poolD-86


title: poolD-90


title: poolD-83


title: poolD-80


title: poolD-73


title: poolD-70


title: poolD-78


title: poolD-71


title: poolD-76


title: poolD-75


title: poolD-69


title: poolD-68


title: poolD-67


title: poolD-74


title: poolD-65


title: poolD-72


title: poolD-66


title: poolD-81


title: poolD-84


title: NHA Rep 3

city: Dallas

first: Samuel

middle: Kent

last: McBrayer

state: Texas

address: 6000 Harry Hines Boulevard, NL11.110K

department: Children's Research Institute

institute: UT Southwestern Medical Center

description:
Library name: NHA Rep 3
NHA_3

data_processing:
The sequencing read were filtered to remove adapter contamination and low quality reads and processed reads were aligned by HiSat2 to the human (UCSC hg38) reference for quantification.
Assembly: UCSC hg38
Supplementary files format and content: xls file contains raw reads for each sample
Supplementary files format and content: xls file contains FPKM values for each sample

source_name: Brain

growth_protocol: BT054, HK157, TS516, TS603, UTSW5, UTSW63, and UTSW71 cells were cultured in NeuroCult NS-A Basal Medium (Human) with Proliferation Supplement (STEMCELL Technologies 05751), supplemented with EGF (20 ng/mL, GoldBio 1150-04-100), bFGF (20 ng/mL, GoldBio 1140-02-10), heparin (2 µg/mL, STEMCELL Technologies 07980), penicillin/streptomycin (100 U/mL and 100 μg/mL, respectively, Thermo Fisher 15140148), amphotericin B (250 ng/mL, Gemini Bio-Products 400104), and Plasmocin (250 ng/mL, InvivoGen ant-mpp). HK157 (when used for RNA sequencing assays), HK211, HK252, and HK308 cells were cultured in DMEM-F12 medium (Thermo Fisher 11320033) supplemented with glutamine (3mM, Thermo Fisher 25030081), B27 (1×, Thermo Fisher 17504044), EGF (20 ng/mL, GoldBio 1150-04-100), bFGF (20 ng/mL, GoldBio 1140-02-10), heparin (2 µg/mL, STEMCELL Technologies 07980), penicillin/streptomycin (50 U/mL and 50 μg/mL, respectively, Thermo Fisher 15140148), amphotericin B (125 ng/mL, Gemini Bio-Products 400104), and Plasmocin (250 ng/mL, InvivoGen ant-mpp). MGG152 cells were cultured in Neurobasal Medium (Thermo Fisher 21103049) supplemented with glutamine (3mM, Thermo Fisher 25030081), B27 (1×, Thermo Fisher 17504044), N2 (0.25×, Thermo Fisher 17502048), EGF (20 ng/mL, GoldBio 1150-04-100), bFGF (20 ng/mL, GoldBio 1140-02-10), heparin (2 µg/mL, STEMCELL Technologies 07980), penicillin/streptomycin (50 U/mL and 50 μg/mL, respectively, Thermo Fisher 15140148), amphotericin B (125 ng/mL, Gemini Bio-Products 400104), and Plasmocin (0.25 µg/mL, InvivoGen ant-mpp). Cells were cultured in 5% CO2 and at ambient oxygen at 37°C. All cells were routinely evaluated for mycoplasma contamination and confirmed to be negative.

extract_protocol:
RNA was harvested using the RNEasy Plus Mini Kit (QIAGen). 2 µg of total RNA served as input for polyA RNA capture and rRNA removal.
Strand-specific libraries were prepared by Novogene.

value: Brain

value: NHA

value: Immortalized astrocyte


title: poolD-63


title: poolD-64


title: NHA Rep 1

description:
Library name: NHA Rep 1
NHA_1


title: poolD-60


title: poolD-62


title: poolD-59


title: NHA Rep 2

description:
Library name: NHA Rep 2
NHA_2


title: LM07 incident LM [WES]

description: Library name: LM07A_S7

value: FFPE

value: melanoma

value: lentigo maligna

value: incident LM


title: poolD-61


title: LMM04 incident LM [WES]

description: Library name: LMM04A_S13


title: LM05 recurrent LM [WES]

description: Library name: LM05B_S2

value: recurrent LM


title: poolD-55


title: LM06 recurrent LM [WES]

description: Library name: LM06B_S5


title: LM07 recurrent LM [WES]

description: Library name: LM07B_S8


title: LM06 incident LM [WES]

description: Library name: LM06A_S4


title: poolD-58


title: Ctrl_2 location y [WES]

description: Library name: Ctrl_2y


title: poolD-54


title: poolD-56


title: LM05 incident LM [WES]

description: Library name: LM05A_S1


title: poolD-57


title: Ctrl_1 location x sample 2 [WES]

description: Library name: Ctrl_1x2


title: Ctrl_2 location x [WES]

description: Library name: Ctrl_2x


title: LMM04 recurrent LMM in situ component [WES]

description: Library name: LMM04B_S14

value: lentigo maligna melanoma

value: recurrent LMM in situ component


title: poolD-53


title: Ctrl_1 location y [WES]

description: Library name: Ctrl_1y


title: Ctrl_1 location x sample 1 [WES]

description: Library name: Ctrl_1x1


title: ΔmmpE BCG infected THP-1 macrophages, 24h, rep3

city: Wuhan

first: Liu

last: Chen

address: No.1 Shizishan Street, Hongshan District

department: College of Animal Science & Technology

institute: Huazhong Agricultural University

description:
Library name: KoMmpE_24h_rep3
K25773
FPKMs_KO2577vsWT.csv

data_processing:
Raw reads were filtered using fastp to remove adapter sequences, poly-N reads, and low-quality reads (Qphred < 5).
Clean reads were aligned to the reference genome using HISAT2 (2.0.5).
Gene-level quantification was performed using featureCounts from the Subread package.
Differential expression analysis was conducted using DESeq2 depending on experimental design.
Functional enrichment analysis (GO, KEGG), splicing analysis, novel transcript prediction, and WGCNA (if sample size ≥ 15) were also performed.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: gene expression matrices with gene IDs and raw counts per sample.
Supplementary files format and content: Differential expression results including gene ID, log2FoldChange, p-value, and adjusted p-value (padj).

source_name: Peripheral blood (monocyte)

growth_protocol: THP-1 human monocytic cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C in a 5% CO₂ incubator. Cells were differentiated into macrophage-like cells by treatment with 100 ng/mL PMA for 48 h.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using Agilent 2100 Bioanalyzer.
mRNA was enriched using Oligo(dT) magnetic beads, fragmented, and converted to cDNA using the NEBNext Ultra II Directional RNA Library Prep Kit. Second-strand cDNA was synthesized incorporating dUTP. After end repair, A-tailing, and adapter ligation, libraries were treated with USER enzyme and PCR-amplified. Library quality was assessed by Qubit and Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads (PE150).

treatment_protocol: After differentiation, cells were infected with wild-type (WT) or mutant BCG strains (ΔmgdE or ΔmmpE) at MOI of 10:1, and incubated for 24 h.

value: Peripheral blood (monocyte)

value: Human monocytic leukemia cell line

value: THP-1 cells infected with ΔmmpE BCG mutant at MOI 10:1 for 24 h


title: poolD-52


title: poolD-51


title: poolD-50


title: ΔmmpE BCG infected THP-1 macrophages, 24h, rep2

description:
Library name: KoMmpE_24h_rep2
K25772
FPKMs_KO2577vsWT.csv


title: poolD-49


title: poolD-48


title: poolD-47


title: ΔmmpE BCG infected THP-1 macrophages, 24h, rep1

description:
Library name: KoMmpE_24h_rep1
K25771
FPKMs_KO2577vsWT.csv


title: poolD-46


title: poolD-45


title: ΔmgdE BCG infected THP-1 macrophages, 24h, rep3

description:
Library name: KoMgdE_24h_rep3
K10753
FPKMs_KO1075vsWT.csv

value: THP-1 cells infected with ΔmgdE BCG mutant at MOI 10:1 for 24 h


title: poolD-44


title: poolD-43


title: WT BCG infected THP-1 macrophages, 24h, rep3

description:
Library name: WT_24h_rep3
W3
FPKMs_KO1075vsWT.csv
FPKMs_KO2577vsWT.csv

value: WT

value: THP-1 cells infected with BCG WT at MOI 10:1 for 24 h


title: poolD-42

value: tumor


title: poolD-40


title: WT BCG infected THP-1 macrophages, 24h, rep1

description:
Library name: WT_24h_rep1
W1
FPKMs_KO1075vsWT.csv
FPKMs_KO2577vsWT.csv


title: WT BCG infected THP-1 macrophages, 24h, rep2

description:
Library name: WT_24h_rep2
W2
FPKMs_KO1075vsWT.csv
FPKMs_KO2577vsWT.csv


title: poolD-39


title: iPSC-derived neural progenitors, line P4, replicate 4

city: Genova

first: Paolo

last: Scudieri

state: Genova

address: Largo Daneo 3

department: DINOGMI

institute: University of Genoa

description:
Library name: sample 24
column name in raw_counts_all samples.xls: P4_4

data_processing:
Raw sequencing data were analyzed using the proprietary NEGEDIA Digital mRNA-seq pipeline (v2.0) provided by Next Generation Diagnostic srl. The pipeline includes quality filtering and trimming, alignment to the reference genome, and gene-level read counting.
Normalization and differential expression analysis were performed using the NEGEDIA degsanalysis pipeline (v1.2.0). Specifically, sequence reads were trimmed using BBDuk software to remove adapter sequences, poly-A tails, and low-quality end bases.
Alignment was performed with STAR 2.6.0a on hg38 reference genome assembly.
Gene expression levels were determined using HTseq-counts 0.9.1. Differentially expressed genes (DEGs) were identified using the following thresholds: log₂(Fold Change) ≥ 1.5 or ≤ −1.5 and adjusted p-value (pAdj) ≤ 0.05.
Assembly: hg38
Supplementary files format and content: Excel file with raw counts
Supplementary files format and content: Excel file with normalized counts

growth_protocol: iPSC-derived neural progenitors were generated via dual inhibition of SMAD signaling using the STEMdiff Neural System (STEMCELL Technologies), following the manufacturer’s instructions.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (74104, Qiagen), following the manufacturer’s protocol.
Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service v2.0 (Next Generation Diagnostic srl) which included library preparation, quality assessment, and sequencing.

value: iPSC-derived neural progenitors

value: ZEB2 mutation


title: iPSC-derived neural progenitors, line P4, replicate 3

description:
Library name: sample 23
column name in raw_counts_all samples.xls: P4_3


title: ΔmgdE BCG infected THP-1 macrophages, 24h, rep1

description:
Library name: KoMgdE_24h_rep1
K10751
FPKMs_KO1075vsWT.csv


title: poolD-38


title: poolD-41


title: iPSC-derived neural progenitors, line P4, replicate 2

description:
Library name: sample 22
column name in raw_counts_all samples.xls: P4_2


title: iPSC-derived neural progenitors, line P4, replicate 1

description:
Library name: sample 21
column name in raw_counts_all samples.xls: P4_1


title: poolD-37


title: iPSC-derived neural progenitors, line P3, replicate 4

description:
Library name: sample 20
column name in raw_counts_all samples.xls: P3_4


title: poolD-36


title: iPSC-derived neural progenitors, line P3, replicate 3

description:
Library name: sample 19
column name in raw_counts_all samples.xls: P3_3


title: iPSC-derived neural progenitors, line P3, replicate 2

description:
Library name: sample 18
column name in raw_counts_all samples.xls: P3_2


title: poolD-34


title: iPSC-derived neural progenitors, line P3, replicate 1

description:
Library name: sample 17
column name in raw_counts_all samples.xls: P3_1


title: ΔmgdE BCG infected THP-1 macrophages, 24h, rep2

description:
Library name: KoMgdE_24h_rep2
K10752
FPKMs_KO1075vsWT.csv


title: poolD-33


title: iPSC-derived neural progenitors, line P2, replicate 4

description:
Library name: sample 16
column name in raw_counts_all samples.xls: P2_4


title: poolD-32


title: poolD-31


title: poolD-30


title: iPSC-derived neural progenitors, line P2, replicate 2

description:
Library name: sample 14
column name in raw_counts_all samples.xls: P2_2


title: iPSC-derived neural progenitors, line P1, replicate 3

description:
Library name: sample 11
column name in raw_counts_all samples.xls: P1_3


title: iPSC-derived neural progenitors, line P2, replicate 1

description:
Library name: sample 13
column name in raw_counts_all samples.xls: P2_1


title: poolD-29


title: poolD-28


title: iPSC-derived neural progenitors, line P1, replicate 4

description:
Library name: sample 12
column name in raw_counts_all samples.xls: P1_4


title: poolD-26


title: poolD-27


title: poolD-35


title: iPSC-derived neural progenitors, line C2, replicate 4

description:
Library name: sample 8
column name in raw_counts_all samples.xls: C2_4


title: iPSC-derived neural progenitors, line C2, replicate 1

description:
Library name: sample 5
column name in raw_counts_all samples.xls: C2_1


title: iPSC-derived neural progenitors, line C2, replicate 3

description:
Library name: sample 7
column name in raw_counts_all samples.xls: C2_3


title: poolD-25


title: poolD-24


title: poolD-22


title: iPSC-derived neural progenitors, line P2, replicate 3

description:
Library name: sample 15
column name in raw_counts_all samples.xls: P2_3


title: poolD-19


title: iPSC-derived neural progenitors, line C2, replicate 2

description:
Library name: sample 6
column name in raw_counts_all samples.xls: C2_2


title: iPSC-derived neural progenitors, line C1, replicate 4

description:
Library name: sample 4
column name in raw_counts_all samples.xls: C1_4


title: iPSC-derived neural progenitors, line C1, replicate 2

description:
Library name: sample 2
column name in raw_counts_all samples.xls: C1_2


title: iPSC-derived neural progenitors, line P1, replicate 1

description:
Library name: sample 9
column name in raw_counts_all samples.xls: P1_1


title: poolD-20


title: poolD-23


title: iPSC-derived neural progenitors, line C1, replicate 1

description:
Library name: sample 1
column name in raw_counts_all samples.xls: C1_1


title: iPSC-derived neural progenitors, line C1, replicate 3

description:
Library name: sample 3
column name in raw_counts_all samples.xls: C1_3


title: poolD-17


title: poolD-15


title: poolD-14


title: iPSC-derived neural progenitors, line P1, replicate 2

description:
Library name: sample 10
column name in raw_counts_all samples.xls: P1_2


title: Naive CD8+ T cells from mice on dietary restriction, replicate #3

description:
Library name: DR_naive_CD8_T_cells_3
naive_CD8_T_RNA_seq_counts.tsv

value: Naive CD8+ T cells

value: dietary restriction


title: poolD-10


title: poolD-16


title: 293T_wt_clone 67_control shRNA_1

city: Innsbruck

first: Sebastian

last: Herzog

address: Innrain 80-82

department: Institute of Developmental Immunology

country: Austria

institute: Medical University of Innsbruck, Biocenter

description:
Library name: 293T_wt_clone 67_control shRNA_1
67_812F

data_processing:
For data analysis, BAM files were converted into FASTQ files using Samtools, and adaptor trimming, mapping against a reference of all mature miRNAs and read counting were done using miRDeep2. For spike-in control RNA read counts, FASTQ files were mapped against a reference file using bbmap/bbduk.
Assembly: In the course of data analysis, reads were mapped against the latest annotation of human miRNAs in mirbase.org (release 22.1).
Supplementary files format and content: tab-delimited text file containing raw read counts including reference spike-in controls for each sample

growth_protocol: 293T cells were cultured in RPMI medium containing 7.5% FCS, 100 U/ml penicillin and 100 U/ml streptomycin in humidified atmosphere with 5% Co2 at 37C.

extract_protocol:
Total RNA was isolated using TRIZOL, and 400 ng of total RNA were spiked with a defined mix of the following reference small RNAs: spike-in 1 pNNNNACGATCGGCTCTANNNN; spike-in 2 pNNNNTGAACGTCCGTACNNNN; spike-in 3 pNNNNTCTCGCGCGCGTTNNNN; spike-in 4 pNNNNCGAGTAATGAACGNNNN. 100 ng of this total RNA + spike-in mix was then used for library preparation.
Libraries were constructed with the QIAGEN QIAseq miRNA Library Kit according to the manufacturers recommendation.

treatment_protocol: Cells were transiently transfected with vectors encoding two non-targeting shRNAs (control_shRNA_1 and control_shRNA_2) as well as two shRNAs targeting ERH (shERH_1 and shERH_2) and selected with puromycin (2 µg/ml) beginning at 24 hrs after transfection. Transfected cells were sorted on day 5 based on expression of a fluorescent marker encoded on the shRNA constructs and were directly subjected to total RNA isolation.

value: kidney, epithelial-like

value: control shRNA_1

value: clone 67


title: 293T_wt_clone 67_shERH_1

description:
Library name: 293T_wt_clone 67_shERH_1
67_1895F


title: 293T_wt_clone 57_shERH_1

description:
Library name: 293T_wt_clone 57_shERH_1
57_1895F

value: clone 57


title: 293T_wt_clone 67_shERH_2

description:
Library name: 293T_wt_clone 67_shERH_2
67_1896F


title: poolD-18


title: 293T_wt_clone 55_shERH_2

description:
Library name: 293T_wt_clone 55_shERH_2
55_1896F

value: clone 55


title: 293T_wt_clone 67_control shRNA_2

description:
Library name: 293T_wt_clone 67_control shRNA_2
67_813F

value: control shRNA_2


title: poolD-13


title: 293T_wt_clone 57_shERH_2

description:
Library name: 293T_wt_clone 57_shERH_2
57_1896F


title: poolD-11


title: poolD-21


title: 293T_wt_clone 55_control shRNA_2

description:
Library name: 293T_wt_clone 55_control shRNA_2
55_813F


title: poolD-12


title: poolD-06


title: 293T_wt_clone 55_control shRNA_1

description:
Library name: 293T_wt_clone 55_control shRNA_1
55_812F


title: 293T_wt_clone 57_control shRNA_1

description:
Library name: 293T_wt_clone 57_control shRNA_1
57_812F


title: 293T_wt_clone 52_shERH_2

description:
Library name: 293T_wt_clone 52_shERH_2
52_1896F

value: clone 52


title: poolD-04


title: 293T_wt_clone 57_control shRNA_2

description:
Library name: 293T_wt_clone 57_control shRNA_2
57_813F


title: 293T_wt_clone 52_shERH_1

description:
Library name: 293T_wt_clone 52_shERH_1
52_1895F


title: 293T_wt_clone 52_control shRNA_2

description:
Library name: 293T_wt_clone 52_control shRNA_2
52_813F


title: poolD-03


title: poolD-09


title: poolD-02


title: poolD-08


title: 293T_wt_clone 55_shERH_1

description:
Library name: 293T_wt_clone 55_shERH_1
55_1895F


title: poolC-96


title: poolD-01


title: poolD-05


title: 293T_ERH_BSdel_clone 43_shERH_1

description:
Library name: 293T_ERH_BSdel_clone 43_shERH_1
43_1895F

value: DGCR8 delta103-126Q

value: clone 43


title: 293T_ERH_BSdel_clone 43_control shRNA_2

description:
Library name: 293T_ERH_BSdel_clone 43_control shRNA_2
43_813F


title: 293T_ERH_BSdel_clone 43_shERH_2

description:
Library name: 293T_ERH_BSdel_clone 43_shERH_2
43_1896F


title: poolD-07


title: 293T_ERH_BSdel_clone 42_shERH_2

description:
Library name: 293T_ERH_BSdel_clone 42_shERH_2
42_1896F

value: clone 42


title: poolC-94


title: 293T_wt_clone 52_control shRNA_1

description:
Library name: 293T_wt_clone 52_control shRNA_1
52_812F

value: WT


title: 293T_ERH_BSdel_clone 43_control shRNA_1

description:
Library name: 293T_ERH_BSdel_clone 43_control shRNA_1
43_812F


title: poolC-95


title: poolC-90


title: poolC-93


title: 293T_ERH_BSdel_clone 42_control shRNA_1

description:
Library name: 293T_ERH_BSdel_clone 42_control shRNA_1
42_812F


title: poolC-89


title: 293T_ERH_BSdel_clone 34_shERH_1

description:
Library name: 293T_ERH_BSdel_clone 34_shERH_1
34_1895F

value: clone 34


title: poolC-86

value: tumor


title: poolC-92


title: poolC-91


title: 293T_ERH_BSdel_clone 42_control shRNA_2

description:
Library name: 293T_ERH_BSdel_clone 42_control shRNA_2
42_813F


title: 293T_ERH_BSdel_clone 42_shERH_1

description:
Library name: 293T_ERH_BSdel_clone 42_shERH_1
42_1895F


title: poolC-82


title: 293T_ERH_BSdel_clone 34_shERH_2

description:
Library name: 293T_ERH_BSdel_clone 34_shERH_2
34_1896F


title: poolC-81


title: 293T_ERH_BSdel_clone 30_shERH_1

description:
Library name: 293T_ERH_BSdel_clone 30_shERH_1
30_1895F

value: clone 30


title: poolC-88


title: 18weekB

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

institute: University of Rochester

description:
Library name: 18Wks_83_062712
10X Genomics

data_processing:
The resulting barcoded libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) and aligned to GRCh38-2020-A and quantified using the standard Spaceranger workflow (v2.0.1) using default settings.
Assembly: GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz list of barcodes
Supplementary files format and content: Features.tsv.gz list of gene IDs
Supplementary files format and content: aligned_fiducials.jpg aligned fiducials of tissue image
Supplementary files format and content: matrix.mtx.gz gene expression count data in Matrix market exchange format
Supplementary files format and content: detected_tissue_image.jpeg image of tissues and spots
Supplementary files format and content: scalefactors_json.json.gz scale factors 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
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
5-micron tissue sections from individual samples were placed onto Visium Gene Expression Slides (10X Genomics), stained with H&E using Visium chemistry (v1) and scanned, in two batches.
The tissue samples were permeabilized to release ligated probe pairs from the cells, that are bound to the spatially barcoded oligonucleotides present on the spots. Spatial transcriptomics libraries were prepared using 10X Genomics reagents kit according to the manufaturer's recommended protocol.

treatment_protocol: Lungs were fixed in 4% PFA for immunohistochemical analyses.

value: lung

tag: Stage

value: Canalicular

tag: pathology

value: No Lung Disease


title: 19weekA

description:
Library name: ABR5747_19Weeks
10X Genomics

value: Trisomy 21


title: 18weekA

description:
Library name: 18Wks_69_062714
10X Genomics


title: poolC-87


title: 293T_ERH_BSdel_clone 34_control shRNA_2

description:
Library name: 293T_ERH_BSdel_clone 34_control shRNA_2
34_813F

value: kidney, epithelial-like


title: poolC-83


title: 16weekC

description:
Library name: 3076_16_3Weeks
10X Genomics

value: Pseudoglandular


title: 293T_ERH_BSdel_clone 34_control shRNA_1

description:
Library name: 293T_ERH_BSdel_clone 34_control shRNA_1
34_812F

value: control shRNA_1


title: poolC-85


title: poolC-73


title: 293T_ERH_BSdel_clone 30_shERH_2

description:
Library name: 293T_ERH_BSdel_clone 30_shERH_2
30_1896F


title: poolC-84


title: 293T_ERH_BSdel_clone 30_control shRNA_2

description:
Library name: 293T_ERH_BSdel_clone 30_control shRNA_2
30_813F


title: 293T_ERH_BSdel_clone 30_control shRNA_1

description:
Library name: 293T_ERH_BSdel_clone 30_control shRNA_1
30_812F


title: poolC-70


title: 20weekA

description:
Library name: 140_20Weeks
10X Genomics


title: 13weekA

description:
Library name: 13Wks_1264_022616
10X Genomics


title: CUT&Tag seq of MOLM13:DMSO-treated rep3_IgG

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: sun yat sen university

description: Library name: dmso_3_IgG

data_processing:
Trim-galore (v0.6.10) was used to trim adapters and filter for sequences, remaining reads were then aligned to the Hg19  using Bowtie2 (v2.5.0) Hisat2 aligner (v2.1.0)
m6A peaks were identified using exomePeak2 R package (v1.6.1) under parameters: “FRAGMENT_LENGTH=140,p_cutoff = 1e-05,paired_end = TRUE” ; for epz_meRIP data , called peaks under parameters:"FRAGMENT_LENGTH=140, log2FC_cutoff = 1,p_cutoff = 1e-05,paired_end = TRUE" for shRBM15B_meRIP data.
CUT&Tag peaks were  identified using MACS2 (v2.2.7.1) under parameters:"-f BAMPE -g hs --keep-dup all -B -q 0.05 -m 5 50"
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include values for each Sample
Library strategy: Cut&Tag

source_name: Bone Marrow

extract_protocol:
For Cut&Tag, 5 × 104 MOLM13 cells were sorted and washed once in 0.5 mL wash buffer (20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; and 1 × protease inhibitors) and were incubated with 10 μL pre-washed concanavalin A–coated magnetic beads in a 1.5 mL microtube at 25 °C for 10 min. Cells were resuspended in 80 μL ice-cold antibody incubation buffer with 1 μg RBM15B antibody per sample (22249-1-AP, proteintech) and then rotated end-over-end at 4 °C overnight. The cells were resuspended in 100 μL of dig-wash buffer [20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.025% digitonin) with rabbit anti-mouse IgG (1:100 dilution, Ab6709; ThermoFisher) and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer (20 mM Hepes pH 7.5; 300 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.01% digitonin) were added to the samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, the cells were resuspended in 300 μL fragmentation buffer (dig-300 buffer with 10 mM MgCl2) and incubated at 37 °C for 1 h. After extraction with phenol–chloroform and ethanol precipitation, the libraries were amplified by PCR.  For m6A-RIP, Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 10μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018).
For Cut&Tag sequencing, the barcoded libraries were pooled and sequenced on the Illumina HiSeq X™ Ten platform to generate 150 bp paired-end reads. For m6A-RIP sequencing, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: For Cut&Tag sequencing, the MOLM-13 cells treated by 1uM epz5676 or DMSO(negative control)  for 72 hours.

value: Bone Marrow

value: acute myeloid leukemia cells

value: Negative control


title: poolC-68


title: poolC-75


title: poolC-80


title: poolC-77


title: poolC-78


title: CUT&Tag seq of MOLM13:DMSO-treated rep2_IgG

description: Library name: dmso_2_IgG


title: poolC-67


title: CUT&Tag seq of MOLM13:DMSO-treated rep1_IgG

description: Library name: dmso_1_IgG


title: poolC-79


title: 17weekB

description:
Library name: 3237_17_6Weeks
10X Genomics


title: poolC-76


title: poolC-69


title: 17weekA

description:
Library name: 1421_17_6Weeks
10X Genomics


title: CUT&Tag seq of MOLM13:DMSO-treated rep3

description: Library name: dmso_3


title: poolC-61


title: CUT&Tag seq of MOLM13:DMSO-treated rep2

description: Library name: dmso_2


title: poolC-62


title: poolC-74


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep2

description: Library name: epz5676_2

value: epz5676, 1uM for 72 hours


title: 16weekB

description:
Library name: H28790_113Days
10X Genomics


title: poolC-64


title: poolC-72


title: 16weekA

description:
Library name: 1784_16_3Weeks
10X Genomics


title: 15weekA

description:
Library name: H28758_108Days
10X Genomics


title: poolC-71


title: GBM28_OncoD-0J1 2

city: Augusta

first: Balveen

last: Kaur

state: GA

address: CN-3205, 1410 Laney-Walker Blvd

institute: Augusta University

description: Library name: GBM28.14

data_processing:
cutadapt (for adapter trimming and quality filtering)
Alignment using STAR aligner
Normalization, quality control, and differential gene expression analysis were performed in R using DESeq2.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Count matrix in CSV format with rows as genes and columns as samples, values represent raw read counts.

source_name: cell line

growth_protocol: Primary GBM cells GBM12 and GBM28 were maintained in 150 mm TC-treated Culture Dishes with 2%FBS DMEM.

extract_protocol:
Total RNA was isolated using the Rneasy Plus kit from Qiagen and samples were submitted for bulk RNA sequencing
Library preparation was performed with the SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio USA, Inc., cat# 634878). This process incorporated RiboGone™ and SMART® (Switching Mechanism at the 5' end of RNA Template) technologies, along with PCR amplification, to generate Illumina-compatible libraries without adapter ligation. RiboGone efficiently depleted rRNA from total RNA before library construction. Library quality was assessed using the TapeStation 2000 (Agilent Technologies), and concentrations were measured with Qubit (Thermo Fisher Scientific) before sequencing. Dual-indexed i5/i7 paired-end libraries were sequenced on the NovaSeq 6000 system (Illumina) with a minimum coverage of 50-60 million reads per sample.

value: cell line

value: glioblastoma


title: 13weekB

description:
Library name: 13_2Wks_3376_071119
10X Genomics


title: poolC-54


title: GBM28_OncoD 3

description: Library name: GBM28.7


title: poolC-52


title: poolC-49


title: poolC-66


title: GBM28_PBS 4

description: Library name: GBM28.4


title: GBM28_OncoD-0J1 1

description: Library name: GBM28.13


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep3_IgG

description: Library name: epz5676_3_IgG


title: poolC-48


title: poolC-65


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep2_IgG

description: Library name: epz5676_2_IgG


title: GBM28_PBS 3

description: Library name: GBM28.3


title: GBM28_PBS 2

description: Library name: GBM28.2


title: poolC-63


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep1_IgG

description: Library name: epz5676_1_IgG


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep3

description: Library name: epz5676_3


title: poolC-60


title: CUT&Tag seq of MOLM13:EPZ5676-treated rep1

description: Library name: epz5676_1


title: poolC-46


title: GBM28_OncoD-0J1 4

description: Library name: GBM28.16


title: CUT&Tag seq of MOLM13:DMSO-treated rep1

description: Library name: dmso_1


title: poolC-57


title: poolC-59