title: HAEC, miR-33 mimic, 24h TNF, nLDL, replicate 3

city: New Haven

first: Kathryn

last: Citrin

address: 10 Amistad St

institute: Yale University

description:
Library name: C3MTL3
Processed data file column name: C3MTL3_126_067_S85

data_processing:
Paired-end reads were imported into Partek Flow (Copyright ©; 2018 Partek Inc., St. Louis, MO, USA) and validated to have an average read quality >35. Reads were aligned to the Homo sapiens genome assembly GRCh38 (hg38) with the STAR aligner and annotated with Ensembl in Partek Flow software. Raw FASTQ files and processed data (aligned and annotated raw gene counts) are available at Gene Expression Omnibus. Resultant gene count table imported into R for further analysis
Assembly: hg38
Supplementary files format and content: txt file contains aligned and annotated raw gene counts for each sample

source_name: Primary deidentifeid HAEC

growth_protocol: HAEC from three independent donors were pooled and cultured in technical triplicate in EGM-2 (Lonza) at 37˚C 5% CO2.

extract_protocol:
HAEC were lysed in Trizol and RNA was isolated with the Qiagen miRNeasy mini kit.
Libraries were prepped with KAPA mRNA HyperPrep Kit following manufacturer's instructions.

treatment_protocol: For TNF stimulation, HAEC were treated with 10 ng/mL TNFa for 24h prior to harvest. For native LDL stimulation, HAEC were treated with nLDL to a final cholesterol concentration of 50 mg/dL for 48h prior to harvest. For miR-33 mimicry, HAEC at 50-60% confluency were transfected with a miR-33 mimic or control (Horizon Discovery) for 12h in optimem medium, and cells were harvested 72h post-transfection.

value: Primary deidentifeid HAEC

value: nLDL 48h TNF 24h miR-33 mimicry


title: MPTP+SUEHP+SR141714A_SC_3

status: Public on Jun 10 2026

type: SRA

city: Daejeon

first: jungim

last: Kim

address: 1672, Yuseong-daero, Yuseong-gu

department: KM Convergence Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

description: Library name: G4_3_S_C

library_source: transcriptomic

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Spinal cord

growth_protocol: The animals were housed under controlled environmental conditions, with a temperature of 23 ± 1 °C, a relative humidity of 50%, and a 12-hour light/dark cycle.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: MPTP was administered intraperitoneally at a dose of 20 mg/kg  every 2 hours for a total of 4 injections. One week after the final MPTP injection, SUEHP was administered twice a week until the end of the experiment, for a total of 4 injections. CB1 antagonist (SR141714A, 3mg/kg)  or PPARγ inhibitor (T0070907, 5mg/kg) was co-treated intraperitoneally with SUEHP.

tag: tissue

value: Spinal cord

tag: strain

tag: Sex

value: Male

tag: age

value: 8 Weeks

tag: treatment


title: HAEC, miR-33 mimic, 24h TNF, nLDL, replicate 2

country: USA

description:
Library name: C3MTL2
Processed data file column name: C3MTL2_138_055_S84

organism: Homo sapiens

tag: cell type


title: HAEC, miR-33 mimic, 24h TNF, nLDL, replicate 1

description:
Library name: C3MTL1
Processed data file column name: C3MTL1_150_043_S83


title: CTX combo GEX

city: New York

first: Yacine

last: Marouf

state: NY

address: 413 E 69th St

department: MCC

institute: Weill Cornell Medecine

description: Library name: CTX_combo_mRNA

data_processing:
CellRanger v6.1.1
Assembly: GRCm38-2020-A
Supplementary files format and content: h5 files for GEX and ADT
Supplementary files format and content: csv files for VDJ
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Tumor

growth_protocol: B16-F10  tumor cells were implanted intradermally (i.d.) in the flank at doses of 2 x 105.

extract_protocol:
Mice were implanted with B16-F10 tumors. CTX and ICB treatment was administered as previously described. On day 14 post CTX treatment, all cohorts of mice were sacrificed, tumors were mechanically dissociated to obtain a single-cell suspension. Lymphocytes were separated from tumors using 40% Percoll (GE Healthcare) gradient centrifugation. Cells were treated with saturating anti-CD16/CD32 (BD) in staining buffer (2% fetal bovine serum in PBS) on ice for 15 minutes. Cells were then stained with anti-CD45 APC (BioLegend) for 20 mins on ice, TotalSeq anti-mouse hashtag antibodies (C0301, C0302, C0303, C0304, C0305; BioLegend) for 20 mins on ice followed by CITE-seq antibodies (custom made from BioLegend) for 30 mins on ice. Concentration of antibodies used according to the manufacturer’s instructions. The cells were washed 2-3 times in staining buffer (2% fetal bovine serum in PBS between each staining step. The cells were then resuspended in DAPI and FACS sorted based live CD45+ cells and next-generation TCR coupled with 10x Genomics sequencing was performed.
Following QC, the single cell suspension was loaded onto Chromium Chip A (10X Genomics PN 230027) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 1,700-6,400 cells proceeded using the Chromium Single Cell 5′ Reagent Kit (10X Genomics PN 1000006) according to the manufacturer’s protocol. cDNA amplification included 13-16 cycles and 11-50 ng of the material was used to prepare sequencing libraries with 14-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina). An average of 160 million paired reads was generated per sample.

treatment_protocol: Cyclophosphamide monohydrate (MilliporeSigma) mixed in sterile PBS was administered as a single dose of 250mg/kg intraperitoneally (i.p). On day 8, mice were treated with 200 microgram aPD-1 and 100 microgram  aCTLA-4 i.p. in PBS, administered twice weekly until termination of the experiment.

value: Tumor

tag: cell line


title: MPTP+SUEHP+SR141714A_SC_2

description: Library name: G4_2_S_C


title: cKO 4

city: Guangzhou

first: Yiming

last: Zhu

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-Sen University

description:
Library name: Sample8
Column name in raw_counts.txt: cKO4

data_processing:
FastQC (v0.11.9) package was used to check the quality of raw data, and the Trim-Galore (v0.6.7) for trimming the adapter sequence and filter reads with low quality.
Paired-end sequencing reads were aligned to the mouse genome (GRCm38.primary_assembly.genome) using Spliced Transcripts Alignment to a Reference (STAR) 2.7.10a.
Package featureCounts v.2.0.1 was used to count the read numbers mapped to each gene.
Assembly: mouse genome(GRCm38.primary_assembly.genome)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
Total RNA from 10,000 sorted PCs was extracted using the EZ-press RNA Purification Kit PLUS (EZB, B0004-PLUS-S).
Reverse transcription, PCR preamplification, and purification of PCR products were conducted using the Discover-sc WTA Kit V2 (Vazyme Biotech). The RNA-seq library was generated by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech) using 10 ng amplified cDNAs as input following the manufacturer's protocols.

treatment_protocol: Taciflox/flox and Jchain-CreERT2;Taciflox/flox mice were injected once daily with 100 mg/kg tamoxifen in corn oil for 3 consecutive days. Ten thousand bone marrow plasma cells (PCs,CD138high B220–) were sorted from these mice using BD FACS Aria Ⅲ.

value: Bone marrow

value: Plasma cells

tag: genotype

value: 3-day tamoxifen treatment


title: ExoSpin_Plasma_2

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

description: Library name: RNA022728

data_processing:
BCL files were processed using the Illumina Bcl2fastq (v. 2.20) software to generate and demultiplex fastq files. Raw reads were assessed for quality using FastQC (v. 0.11.9). The unique molecular identifier (UMI) sequences in the Pico v3 SMART UMI adapters were first extracted and added to the read name with UMI-tools (v. 1.0.0). Next, the sequencing data were processed with an in-house developed and validated pipeline using cutadapt (v. 1.16), SAMtools (v. 1.9), and STAR (v. 2.7.3a) to obtain deduplicated, high-quality and aligned RNA counts against the human genome (hg38). Ribosomal contamination was assessed using the BBMap tool (v. 38.87). Additional QC statistics were generated by using multiQC (v. 1.9) software package. Gene counts were determined with HTSeq (v. 0.11.0) in reverse stranded mode, only considering uniquely mapping reads. Ensembl release 91 was used to annotate reads within human genes.
Assembly: hg38
Supplementary files format and content: Tab seperated format, rows are genese, columns are samples, first 3 columns are ensembl ID, hgnc symbol and external gene name extacted from biomart

extract_protocol:
Total and small RNA were isolated from samples using the miRNeasy Micro kit (urine and cell culture medium) and miRNeasy Serum/Plasma Advanced kit (blood plasma) according to manufacturer’s instructions (cat. no. 217084 and 217204, Qiagen, Valencia, CA, USA), and eluted in 12 µL DNase/RNase-free water. To allow for a proper method comparison during RNA sequencing, synthetic spike-in controls were added as previously described 43,44. In short, per initial amount of biofluid input volume, 2 µL Sequin spike-in control [JV1] (Garvan Institute of Medical Research) and 2 µL RNA extraction Control (RC) spike-ins (Integrated DNA Technologies) were added to the lysate. Following RNA isolation, 2 µL of External RNA Control Control Consortium (ERCC) and 2 µL Library Prep (LP) spike-ins were added. RNA samples were stored at -80 °C until further use.
treated to remove residual genomic DNA by adding 1 µL of HL-dsDNase (#70800-202, ArcticZymes, 2 U/µL) and 1 µL reaction buffer (#66001, ArcticZymes) to 12 µL RNA, followed by 10 min incubation at 37 °C, and 10 min incubation at 55 °C to inactivate the DNase. Total RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian (#634487, Takara), including a ribosomal RNA depletion step at the cDNA level, as originally published in 53, with some modifications as reported 54. 8 µL of DNase treated RNA was fragmented for 4 min at 94 °C, followed by the ‘highly degraded RNA’ workflow. Library quality control was performed with the Fragment Analyzer high sense small fragment kit (Agilent Technologies, sizing range 50-1000 bp). Libraries were quantified using the KAPA Library Quantification Kit (#KK4854, Roche), followed by equimolar pooling and Qubit quantification. The loading concentration of the pool was 0.58 nM with 2% phiX on an S2 100 cycles flow cell (paired-end 2 x 50 nucleotides) on a NovaSeq 6000 instrument (Illumina)

value: Breast Cancer

tag: preparation protocol

value: ExoSpin

tag: batch


title: MPTP+SUEHP+SR141714A_SC_1

description: Library name: G4_1_S_C


title: HAEC, control mimic, 24h TNF, nLDL, replicate 3

description:
Library name: CCMTL4
Processed data file column name: CCMTL4_103_090_S79

value: nLDL 48h TNF 24h


title: MPTP+SUEHP_SC_4

description: Library name: G3_4_S_C

value: MPTP+SUEHP


title: HAEC, control mimic, 24h TNF, nLDL, replicate 2

description:
Library name: CCMTL2
Processed data file column name: CCMTL2_115_078_S78


title: MPTP+SUEHP_SC_3

description: Library name: G3_3_S_C


title: Exosome Purification_Plasma_3

description: Library name: RNA022732

value: Exosome Purification


title: HAEC, control mimic, 24h TNF, nLDL, replicate 1

description:
Library name: CCMTL1
Processed data file column name: CCMTL1_127_066_S77


title: MPTP+SUEHP_SC_2

description: Library name: G3_2_S_C


title: MPTP+SUEHP_SC_1

description: Library name: G3_1_S_C


title: HAEC, control mimic, 24h TNF, replicate 2

description:
Library name: CCMTV2
Processed data file column name: CCMTV2_151_042_S75

value: TNF 24h


title: HAEC, control mimic, 24h TNF, replicate 1

description:
Library name: CCMTV1
Processed data file column name: CCMTV1_163_030_S74


title: MPTP_SC_4

description: Library name: G2_4_S_C

value: MPTP


title: MPTP_SC_3

description: Library name: G2_3_S_C


title: HAEC, control mimic, 0h TNF, replicate 2

description:
Library name: CCMVV2
Processed data file column name: CCMVV2_128_065_S69


title: HAEC, control mimic, 0h TNF, replicate 3

description:
Library name: CCMVV3
Processed data file column name: CCMVV3_116_077_S70


title: MPTP_SC_2

description: Library name: G2_2_S_C


title: HAEC, control mimic, 0h TNF, replicate 1

description:
Library name: CCMVV1
Processed data file column name: CCMVV1_140_053_S68


title: MPTP_SC_1

description: Library name: G2_1_S_C


title: TGF-β-2

city: Birmingham

first: Lin

last: Jin

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: Library name: Jin_F4

data_processing:
FASTQ files were generated through BaseSpace using Illumina's bcl2fastq software.
Raw paired-end FASTQ files were quality- and adapter-trimmed using Trimmomatic v0.36 in paired-end mode with parameters: PE -threads 8 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Paired trimmed reads were retained for downstream analysis.
Trimmed paired-end reads were aligned to the human hg38 reference genome using STAR v2.7.3a with parameters: --readFilesCommand zcat --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --quantMode GeneCounts --limitBAMsortRAM 64000000000.
Gene-level read counts were generated from STAR coordinate-sorted BAM files using htseq-count with the hg38 refGene GTF annotation file and parameters: -f bam -r pos -s reverse -t exon -i gene_id -m union -a 10.
Count tables were used for downstream differential gene expression analysis.
Assembly: UCSC hg38
Supplementary files format and content: tab-delimited text file consisting of raw counts (transcript abundances) for each sample for each Ensembl Gene ID

source_name: primary skin fibroblast

growth_protocol: Immortalized human skin fibroblasts or primary human skin fibroblasts (passages 2–5) were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified 5% CO₂ incubator. Cells were maintained by replacing the medium every 2–3 days and subcultured before reaching full confluence to preserve normal morphology and proliferative capacity.

extract_protocol:
Total RNA was extracted from cultured fibroblasts using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and samples were stored at –80°C until further use
Using the NEBNext Ultra II RNA Library Prep Kit for Illumina with poly(A) selection, we begin with high-quality total RNA and enrich mRNA using oligo-dT magnetic beads to capture polyadenylated transcripts, followed by washing and elution; we then fragment the purified mRNA under heat and prime it for reverse transcription to generate first-strand cDNA, after which we perform second-strand synthesis to produce double-stranded cDNA (optionally incorporating strand specificity), and subsequently carry out end repair and dA-tailing to create adapter-compatible ends; we ligate sequencing adapters, purify the library using magnetic beads (with optional size selection), and amplify it by PCR with indexed primers to enrich adapter-ligated fragments, and finally we assess library size distribution and concentration before pooling and sequencing on an Illumina platform.

treatment_protocol: Cells were treated either with or without TGF‑β or with compoound F05650303 for 48 hours.

value: primary skin fibroblast

value: fibroblast

value: wt

value: TGF-β


title: 14-day TGF-β

description:
Library name: D310
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v9.0.1
Assembly: GRCh38-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoid

growth_protocol: Human iPSCs were maintained on Matrigel-coated plates in mTeSR1 medium under feeder-free conditions at 37°C and 5% CO₂. Colonies were passaged every 4–5 days using EDTA when cultures reached ~70–80% confluency. Human iPSC-derived skin organoids were generated following a previously established Nature protocol. Mature organoids were maintained in N2B27 medium consisting of DMEM/F12 and Neurobasal medium.

extract_protocol:
Skin organoids were digested and dissociated into single cell suspension. Cells were stained with 7AAD (BD catalog#559925). 7AAD- viable cells were flow sorted using BD FACSAria flow cytometer.
Sorted single cell suspensions of 4 samples,10x GEM-X OCM 3' Gel Bead v4 (10xGenomics PN 2001126), and partitioning oil (10xGenomics PN 2001213) were loaded into 10x Genomics GEM-X 3' OCM Chip (PN 2001099) to capture single cells in nanoliter-scale oil droplets by 10xChromiumX  instrument and generate Gel Beads-In-EMulsions (GEMs), and each sample was loaded with one set of beads with unique list of barcodes. Four samples were barcoded separately but multiplexed in the same GEMs. About 60% loaded cells can be captured in oil droplets, each with a gel bead containing oligoes bearing a bead-unique barcode and a 3’ end poly T sequence.  individual cells were lysed in droplets, the released mRNA bind to barcoded Poly T, and full length of single strand cDNA from each single nucleus are synthesized by “template switch” mechanism. GEMs containing single cell barcoded-cDNA were broken and all single cell cDNA libraries were pooled together. Pooled cDNA were cleaned up by DynaBeads MyOne™ Silane beads (10xGenomics PN 2000048) and then preamplified by PCR to generate sufficient mass for sequencing library construction. The sequencing libraries were constructed as 3’-biased whole transcriptome libraries by following steps of cDNA fragmentation, end repair & A-tailing adaptor ligation, and sample index PCR amplification.

treatment_protocol: Organoids were treated with TGF-β (10 ng/mL) for 8 or 14 days, with medium changed every other day, prior to transcriptomic analysis.

value: organoid

value: iPSC


title: Normal control_SC_4

description: Library name: G1_4_S_C

value: Spinal cord

value: Male

value: 8 Weeks

value: Saline


title: HT tumor, CART

city: Taipei

first: Yi-Lin

last: Chiu

address: No. 161, Sec. 6, Minquan E. Rd., Neihu Dist.

country: Taiwan

institute: National Defense Medical Center

description: Library name: Sample3

data_processing:
Raw sequencing reads were assessed for quality using FastQC. Adapter sequences and low-quality bases were trimmed using vendor-provided preprocessing workflows.
Transcript-level quantification was performed using Salmon (v1.10.0) and kallisto (v0.46.1), both employing lightweight mapping strategies (quasi-mapping for Salmon and pseudoalignment for kallisto).
Assembly: GRCh38
Supplementary files format and content: Expression values were reported as TPM (transcripts per million) and estimated counts. No read alignment to the genome was performed.

source_name: Tumor tissue

growth_protocol: Human HT B-cell lymphoma cells (1.5 × 10⁷) were implanted subcutaneously into male CAnN.Cg-Foxn1nu/CrlNarl mice (4 weeks old).

extract_protocol:
Tumors were lysed in QIAzol Lysis Reagent(QIAGEN), and RNA purified with RNeasy Mini Kit (QIAGEN).
Total RNA (1 µg) was used for library construction. Poly(A)+ mRNA was isolated using oligo(dT) magnetic beads and fragmented using divalent cations at elevated temperature. First- and second-strand cDNA synthesis was performed using random primers. Double-stranded cDNA underwent end repair, A-tailing, and adaptor ligation. Size selection was performed using magnetic beads, followed by PCR amplification with indexed primers. Library preparation was performed by Genewiz on an Illumina NovaSeq 6000 platform using 2×150 bp paired-end mode.

treatment_protocol: When tumors reached ~100 mm³, animals were randomized to four treatment arms: (i) vehicle control, (ii) ibrutinib (25 mg kg⁻¹ day⁻¹, oral gavage), (iii) intratumoral CD19-directed CAR-T cells (5 × 10⁶ cells), or (iv) the combination of ibrutinib and CAR-T.

value: Tumor tissue

value: HT

value: B-cell lymphoma

value: WT

value: CART


title: JJN3 cells, nontargeting control, rep 3

city: Berlin

first: Stefan

last: Habringer

address: Hindenburgdamm 30

department: Hematology, Oncology and Cancer Immunology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

description:
Library name: Sample 12
JJN3_nt_3

data_processing:
Analysis with usegalaxy.org
Trim Galore
Bowtie 2
htseq-count
DESeq2
Assembly: hg38
Supplementary files format and content: rLog normalized counts

extract_protocol:
Rneasy mini prep kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification (Source: Novogene).

value: plasma cell

value: nontargeting sgRNA control

value: untreated


title: HT tumor, CART+Ibrutinib

description: Library name: Sample4

value: CART+Ibrutinib


title: Normal control_SC_3

description: Library name: G1_3_S_C


title: HT tumor, Ibrutinib

description: Library name: Sample2

value: Ibrutinib


title: HT tumor, control

description: Library name: Sample1

value: control


title: Normal control_SC_2

description: Library name: G1_2_S_C


title: MPTP+SUEHP+T0070907_MB_4

description: Library name: G5_4_midBr

source_name: Midbrain

value: Midbrain


title: 14_day_RA_rep2

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
Library name: D5
10X Genomics

data_processing:
Raw data generated using the 10X Chromium were processed following a standardized pipeline. Libraries were sequenced on an Illumina platform, producing paired-end reads with 28 bp for Read 1 (containing cell and molecular barcode information), 91 bp for Read 2 (cDNA sequences), and an 8 bp index read for sample identification.
The resulting BCL files were converted to FASTQ format using the Cell Ranger mkfastq tool, which also demultiplexed libraries based on sample index barcodes. Reads were then aligned to the human reference genome (GRCh38-200-A) using the STAR aligner embedded within the Cell Ranger software suite.
Transcript quantification was performed by extracting unique molecular identifiers (UMIs), filtering out low-quality reads, and collapsing UMIs to account for amplification artifacts, yielding a digital gene expression (DGE) matrix for each cell.
Assembly: GRCh38
Supplementary files format and content: matrix and tab-separated files

source_name: pluripotent cell

growth_protocol: The reporter H9 embryonic stem cell line H9-hTnnT2-pGZ-TD2 (WiCell, Wisconsin, USA), henceforth abbreviated as H9s, was used for all experiments between passages 40 to 45. These pluripotent stem cells are a modified version of H9 embryonic stem cells (WA09), derived from the epiblast of a post-implantation embryo and engineered to express green fluorescent protein (GFP) when cells are differentiated to cardiomyocytes and express the cardiac marker Troponin T. H9s were maintained in mTeSRTM Plus Medium (StemCell Technologies, Vancouver, Canada) on Matrigel®-coated 6-well plates (Corning, New York, USA). Media was replenished daily, and cells were incubated in a humidified 37°C incubator. For 6- and 72-hr timepoints, H9s at P41 were passaged when they reached 50-70% confluence. Media was aspirated and cells were washed with 1ml Dulbecco's Phosphate Buffered Saline (DPBS) (Gibco, Massachusetts, USA). Thereafter, 1 mL of room temperature ReLeSR (StemCell Technologies, Vancouver, Canada) was added to each well to dissociate the cells and was incubated at ambient temperature for 1 minute, aspirated, then further incubated for 3 minutes at 37°C. Four out of the six wells were used, and cells were sub-cultured or split at 1:6 and returned to the incubator to re-attach and acclimate for 19 hrs until treatment.

extract_protocol:
Following treatment, cells were dissociated into a single cell suspension, cell counts and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter (Nexcelom Biosciences, Lawrence, MA) using Acridine Orange (AO)/Propidium Iodide (PI) stain (Perkin Elmer, Inc., Waltham, MA), following manufacturer’s instructions, and then the cells were processed for single-cell library construction. Cells were initially washed once in 37°C TrypLE (Thermo Fisher Scientific), aspirated, then incubated for ~20-25 min at 37°C in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) with 1 mM DTT, 3 µg/ml actinomycin D, 25 µg/ml anisomycin, and 64 U/ml RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific, Waltham, MA) in 500 µl volume, gently agitating after 10 min of incubation. Using a wide-bore pipette tip, cells were then dissociated by gentle pipetting until no cell clumps were visible. After transferring to a 15 ml conical tube, 2 ml of 37°C base media was added to stop enzymatic activity, gently mixed by pipetting, and cells were pelleted at 200 x g for 3 min at 4°C. After media removal, cells were resuspended in 1 ml ice-cold cell suspension buffer (1X PBS, 0.5% Opti-Prep Density Gradient Medium (Sigma-Aldrich), 0.1% Bovine Serum Albumin Fraction V (Thermo Fisher Scientific, Waltham, MA), 64 U/ml RNaseOUT, 1mM DTT). The cells were pelleted twice more at 200 xg for 3 min at 4°C, washing each time with fresh Cell Suspension Media. After the final wash, cells were filtered through a 40 µm nylon cell strainer, transferred, and stored in a Lo-Bind tube.  Following dissociation, cell were counted and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter.
Single-cell HepaRG suspensions were barcoded and prepped for sequencing using the Chromium Next GEM Single Cell 3’ Reagent Kit A (v3.1; 10X Genomics), following the manufacturer’s instructions, with an input of 10,000 cells per sample. Then nanoliter scaled Gel Beads-in-emulsion (GEMs) were partitioned to capture single cells as well as a master mix of Illumina TruSeq Read 1 primers, 10X barcodes, unique molecule identifiers (UMI), poly(dT) primers, and reverse transcription enzymes, followed by cells lysing and a cDNA synthesis reaction. After contents were released from the GEMs, pooled barcoded cDNA was purified by silane magnetic beads and amplified by PCR. After fragmentation, Illumina Read 2, P5, P7, and a sample index were added to the pooled amplified cDNA before paired-end sequencing on an Illumina NovaSeq 6000, using a S2 flow cell. Sample library prep traces were verified and quantified on a Bioanalyzer High Sensitivity DNA chip (Agilent).

treatment_protocol: To evaluate whether RA exposure might induce differentiation when cells are maintained in pluripotent conditions, cells were treated with 30 nM RA for 6 hrs and 72 hrs. As RA treatment may alter cell-types or their trajectories, we also examined how RA might affect hPSCs undering undirected differentiation.  H9 cells were cultured in medium formulated for non-specified cell lineage differentiation over 14 days. H9s at passage 44 and 70% confluence were sub-cultured as described earlier. To account for the longer duration of culture and prevent over-confluence, the split ratio was 1:15. The following day, cells were fed with differentiation media containing either 30 nM RA or vehicle control.

value: pluripotent cell

value: embryonic stem cell

tag: biological rep

value: all-trans retinoic acid (30nM)

tag: timepoint

value: 14 days


title: Normal control_SC_1

description: Library name: G1_1_S_C

value: Spinal cord

value: Male

value: 8 Weeks

value: Saline


title: WT, dorsal skin, epidermal progenitor cells, 6-month-old telogen, RNA-seq, rep 2

city: Los Angeles

first: Ya-Chen

last: Liang

state: CA

address: 2011 Zonal Ave., HMR 304A

department: Department of Pathology

institute: University of Southern California

description:
Library name: Chuong-875
Column name in Msx2_EpdSC_DESeq2_cKO_vs_WT_counts.txt: Ch-875_S222

data_processing:
RNA-seq Data Processing and Analysis: RNA-seq analysis was conducted using the Partek® Flow® platform (Partek Inc.). Default parameters were applied unless otherwise specified.
Quality Control and Alignment: Pre-alignment quality control (QA/QC) steps were performed prior to read mapping. Reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR version 2.7.3a, followed by post-alignment QA/QC.
Quantification and Normalization: Aligned reads were quantified to the Ensembl release 103 annotation model using the Partek Expectation/Maximization (E/M) method. Gene expression values were normalized using Transcripts Per Million (TPM).
Differential Expression Analysis: Differential gene expression analysis was performed using Partek Gene-Specific Analysis (GSA). Genes with a false discovery rate (FDR) < 0.05 and an absolute fold change > 2 were considered significantly differentially expressed.
Assembly: Emsemble GRCm38/mm10 for all samples.
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text files include GSA result for each sample

source_name: skin

growth_protocol: Mice were maintained under a 12 h light/dark cycle at 21–26 °C and 30–70 % relative humidity in the USC animal facility.

extract_protocol:
Total RNAs of indicated tissues were isolated using the standard AllPrep DNA/RNA Micro Kit protocol (Cat. 80284, Qiagen)
Library preparation using the SMARTer Stranded Total RNA-Seq Kit v3 was performed in Novogen company (CA, USA)

treatment_protocol: No treatment

value: skin

value: epidermal progenitor cell

value: wild-type


title: 14_day_RA_rep1

description:
Library name: D4
10X Genomics


title: MPTP+SUEHP+T0070907_MB_3

description: Library name: G5_3_midBr


title: MPTP+SUEHP+T0070907_MB_2

description: Library name: G5_2_midBr


title: 14_day_control_rep2

description:
Library name: D3
10X Genomics

value: vehicle (DMSO)


title: MPTP+SUEHP+T0070907_MB_1

description: Library name: G5_1_midBr


title: MPTP+SUEHP+SR141714A_MB_4

description: Library name: G4_4_midBr


title: MPTP+SUEHP+SR141714A_MB_3

description: Library name: G4_3_midBr


title: MPTP+SUEHP+SR141714A_MB_2

description: Library name: G4_2_midBr


title: 6_hr_RA_rep2

description:
Library name: 6R2
10X Genomics

value: 6 hrs


title: MPTP+SUEHP+SR141714A_MB_1

description: Library name: G4_1_midBr


title: 6_hr_control_rep2

description:
Library name: 6C2
10X Genomics


title: MPTP+SUEHP_MB_4

description: Library name: G3_4_midBr

value: MPTP+SUEHP


title: 6_hr_control_rep1

description:
Library name: 6C1
10X Genomics


title: MPTP+SUEHP_MB_3

description: Library name: G3_3_midBr


title: 3-months-rep3

status: Public on Jun 11 2026

city: Cambridge

first: Yuancheng Ryan

last: Lu

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: 3-3m-C

library_source: genomic

data_processing:
ATAC-seq data was aligned to the mm10 genome using bowtie2, and duplicate reads were removed using Picard MarkDuplicates. Aligned data was processed using samtools and converted to fragments files with bedtools bamtobed.
Assembly: mm10
Supplementary files format and content: ATAC-seq fragments files (.fastq.gz) : Tab-delimited files with 5 columns corresponding to the chromosome, start, end, sample name, and duplicate count for each paired-end fragment.

molecule: genomic DNA

source_name: Ear Fibroblasts

extract_protocol:
Cells were incubated with custom-loaded Tn5 transposase in high-salt transposition buffer for 30 minutes at 37 °C with agitation. Transposed DNA was purified using the Zymo DNA Clean & Concentrator kit.
Libraries were pre-amplified for 5 cycles, then subjected to qPCR to determine the additional number of cycles needed, minimizing amplification bias. Final libraries were purified, quality-checked by gel electrophoresis, and quantified. Sequencing was performed on an Illumina platform using paired-end reads, targeting ~20 million reads per sample.

value: Ear Fibroblasts


title: MPTP+SUEHP_MB_2

description: Library name: G3_2_midBr


title: CD34+ day7 Transduced - B

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: Library name: S17

data_processing:
Raw fastq data were preprocessed using Cell Ranger (v7.1.0, 10X Genomics) to produce features-barcodes matrices. GRCh38 genome and genes annotations provided by the manufacturer were used as reference data for reads mapping and gene expression quantification. Genes expression matrices were then processed within the R environment (v4.1.3) using the Seurat package (v4.1.1).
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Sparse raw UMI counts matrix ( barcodes + features + .mtx)

source_name: mPB

extract_protocol:
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions.
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions.

value: mPB

value: B


title: F2F3-sorted day7 Transduced

description: Library name: S12


title: MPTP+SUEHP_MB_1

description: Library name: G3_1_midBr

value: Midbrain


title: MPTP_MB_4

description: Library name: G2_4_midBr

value: MPTP


title: CD34+CD38- day7 Transduced

description: Library name: S10


title: MPTP_MB_3

description: Library name: G2_3_midBr


title: CD34+ Untransduced

description: Library name: C04


title: CD34+ day7 Transduced - A

description: Library name: C03

value: A


title: MPTP_MB_2

description: Library name: G2_2_midBr


title: Normal control_MB_4

description: Library name: G1_4_midBr


title: TI72h_rep2

description: Library name: TI72h_exp2022_05

data_processing:
Raw data in fastq format were QC checked and trimmed using TrimGalore (v0.5.0) to get rid of adapters at 3’ of reads. Trimmed reads were then aligned to the GRCh38 reference genome using STAR (v2.7.0d) setting the parameter –outFilterMultimapNmax to the value of 1 to emit only uniquely mapped reads. Gencode genes primary assembly gene transfer file (GTF) v35 was used as reference gene annotation file.
Gene expression quantification was performed by using featurecounts (v1.6.3), setting min overlap of 10bp and discarding chimeric alignments. The reference annotation file used was the same provided to STAR aligner.
Gene counts matrices for the two experimental designs evaluated were then analyzed in the R environment (v4.0.3). Considering the lack of replicates we employed a data analysis workflow that relied on edgeR DEGs identification setting custom biological variation coefficients (BCV) to 0.1-0.3 for the different 1vs1 comparisons performed. Counts were normalized using TMM method and differential test was performed with exactTest function provided by the edgeR package (v3.32).
Assembly: GRCh38 primary assembly
Supplementary files format and content: Raw gene counts matrix in tabular format (.txt)

growth_protocol: CD34+ cells were culture in serum free media supplemented with cytokines in a setting of gene therapy protocol.

extract_protocol: RNA was harvested using miRNeasy Mini kit Qiagen and eluted in RNAse free water.

treatment_protocol: CD34+ cells were expose to different small molecules during cutlure (UM171, SR1, 4HPR) alone or in combination

tag: transduction

value: LV-Transduced


title: TI24h_rep2

description: Library name: TI24h_exp2022_05


title: TI72h_rep1

description: Library name: TI72h_rd062


title: Normal control_MB_1

description: Library name: G1_1_midBr


title: GMP-sorted day7 Transduced

description: Library name: S11

value: GMP+


title: CD34+ day7 Transduced - patient 4

description: Library name: E09

data_processing:
Raw fastq data were preprocessed using Cell Ranger (v7.1.0, 10X Genomics) to produce features-barcodes matrices. GRCh38 genome and genes annotations provided by the manufacturer were used as reference data for reads mapping and gene expression quantification. Genes expression matrices were then processed within the R environment (v4.0.3) using the Seurat package (v4.1.1).
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Sparse raw UMI counts matrix ( barcodes + features + .mtx)

extract_protocol:
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions (v2 chemistry).
Chromium(TM) Single Cell 3' Library (10xGENOMICS) according to manufacturer’s instructions (v2 chemistry).

tag: patient

value: day 7


title: C57BL/6 mouse 3, saline i.p. injection (same volume as subacute MPTP), striatum collected 3 days post-treatment

city: Shanghai

first: Yifei

last: He

email: crestedibistoki@gmail.com, 21301010016@m.fudan.edu.cn, yumei@fudan.edu.cn, 23211520033@m.fudan.edu.cn

address: 138 Yixueyuan Road

department: Institute of Brain Science

institute: Fudan University

description:
Library name: Subacute control_3d_03
Column name in fpkm_counts_MPTP_sub_acute.csv: Control_3_count Control_3_FPKM

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: Species: mus_musculus Origin: ensembl Version: GRCm39.107  Genome: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz Gff3: http://ftp.ensembl.org/pub/release-107/gff3/mus_musculus/Mus_musculus.GRCm39.107.chr.gff3.gz Transcript: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for A53T 12m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for A53T 16m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MitoPark 5m Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MPTP acute 3d Experiment and Control samples
Supplementary files format and content: csv file includes the Sequencing Counts and FPKM values for MPTP subacute 3d Experiment and Control samples

source_name: Striatum

growth_protocol: Male C57BL/6 mice (10-12 weeks old) and C57BL/6Smoc-Tfam(flox)Slc6a3(iCre)Smoc (MitoPark) were obtained from Shanghai Model Organisms Center, Inc. Human alpha-synuclein A53T (α-Syn A53T or A53T) transgenic mice (line G2-3) were acquired from the Jackson Laboratory. Animals were housed in individually ventilated cages with a 12-hour light/dark cycle, maintained at a suitable temperature and circadian rhythm. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Shanghai Medical College, Fudan University (No. 20240712-010) and conducted in accordance with the National Research Council's Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Total RNA from mouse striatum was extracted with Total RNA Isolation Reagent (YY101, epizyme, China) and its concentration was measured by BioTek Microplate Reader (USA).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on the instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: For the acute MPTP model, C57BL/6J mice received four intraperitoneal injections of 15 mg/kg MPTP-HCl (Sigma-Aldrich, USA) at 2-hour intervals in a single day. For the subacute model, mice were injected with 20 mg/kg MPTP-HCl intraperitoneally once daily for five consecutive days. Control mice were administered an equivalent volume of normal saline (NS).

value: Striatum

value: WT


title: TI24h_rep1

description: Library name: TI24h_rd062


title: C57BL/6 mouse 1, saline i.p. injection (same volume as subacute MPTP), striatum collected 3 days post-treatment

description:
Library name: Subacute control_3d_01
Column name in fpkm_counts_MPTP_sub_acute.csv: Control_1_count Control_1_FPKM


title: C57BL/6 mouse 4, 20mg/kg MPTP-HCl i.p. daily for 5 days, striatum collected 3 days post-treatment

description:
Library name: MPTP subacute_3d_04
Column name in fpkm_counts_MPTP_sub_acute.csv: Experiment_4_count Experiment_4_FPKM

value: 20mg/kg MPTP-HCl i.p. daily for 5 days


title: CD34+ dp Transduced - patient 4

description: Library name: E07

value: dp


title: CD34+ day7 Transduced - patient 1

description: Library name: E06


title: C57BL/6 mouse 3, 20mg/kg MPTP-HCl i.p. daily for 5 days, striatum collected 3 days post-treatment

description:
Library name: MPTP subacute_3d_03
Column name in fpkm_counts_MPTP_sub_acute.csv: Experiment_3_count Experiment_3_FPKM


title: C57BL/6 mouse 2, 20mg/kg MPTP-HCl i.p. daily for 5 days, striatum collected 3 days post-treatment

description:
Library name: MPTP subacute_3d_02
Column name in fpkm_counts_MPTP_sub_acute.csv: Experiment_2_count Experiment_2_FPKM


title: CD34+ day4 Transduced - patient 1

description: Library name: E05

value: day 4


title: CD34+ dp Transduced - patient 1

description: Library name: E04


title: C57BL/6 mouse 1, 20mg/kg MPTP-HCl i.p. daily for 5 days, striatum collected 3 days post-treatment

description:
Library name: MPTP subacute_3d_01
Column name in fpkm_counts_MPTP_sub_acute.csv: Experiment_1_count Experiment_1_FPKM


title: pooledinput

city: Boston

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
ChIP-seq analysis was performed as previously reported in ref
ChIP reads were aligned to the hg19 genome assembly using BWA
ChIP-seq peaks were called using MACS 2.0
DEseq2 was used to assign differential intensities and statistics
Differential binding sites was determined by filtering out insignificant peaks (adjusted p-value<0.05) and then determining log2FC values between samples for each region using a log2 FC >0 or <0
Assembly: hg19
Supplementary files format and content: Analysis was done using the CoBRA workflow

source_name: human bladder

extract_protocol:
We started from 10 sections 10 μm thick that were washed 3 times with xylenes to remove paraffin, rehydrated in an ethanol/water series. The tissue was resuspended in lysis buffer as previously described and sonicated for 5 minutes using a Covaris E220 instrument (setting: 140 peak incident power, 5% duty factor, and 200 cycles per burst) in 1 ml adaptive focused acoustics (AFA) fiber millitubes. Soluble chromatin (5 μg) was immunoprecipitated with 10 μg H3K27ac (Diagenode catalog number C15410196)) antibody (Ab).
ChIP-seq libraries were constructed using ThruPLEX-FD kits (Rubicon Genomics) following the manufacturer’s protocols. 75-bp single-end reads were sequenced on a Nextseq instrument (Illumina)

value: human bladder


title: C57BL/6 mouse 3, saline i.p. injection (same volume as acute MPTP), striatum collected 3 days post-treatment

description:
Library name: Acute control _3d_03
Column name in fpkm_counts_MPTP_acute.csv: Control_3_count Control_3_FPKM


title: ucc8, input


title: ucc7, input


title: C57BL/6 mouse 2, saline i.p. injection (same volume as acute MPTP), striatum collected 3 days post-treatment

description:
Library name: Acute control _3d_02
Column name in fpkm_counts_MPTP_acute.csv: Control_2_count Control_2_FPKM


title: C57BL/6 mouse 1, saline i.p. injection (same volume as acute MPTP), striatum collected 3 days post-treatment

description:
Library name: Acute control _3d_01
Column name in fpkm_counts_MPTP_acute.csv: Control_1_count Control_1_FPKM


title: C57BL/6 mouse 3,15mg/kg MPTP-HCl i.p. every 2h for 4 times in one day, striatum collected 3 days post-treatment

description:
Library name: MPTP acute_3d_03
Column name in fpkm_counts_MPTP_acute.csv: Experiment_3_count Experiment_3_FPKM


title: ucc4, input


title: C57BL/6 mouse 2,15mg/kg MPTP-HCl i.p. every 2h for 4 times in one day, striatum collected 3 days post-treatment

description:
Library name: MPTP acute_3d_02
Column name in fpkm_counts_MPTP_acute.csv: Experiment_2_count Experiment_2_FPKM


title: C57BL/6 mouse 1,15mg/kg MPTP-HCl i.p. every 2h for 4 times in one day, striatum collected 3 days post-treatment

description:
Library name: MPTP acute_3d_01
Column name in fpkm_counts_MPTP_acute.csv: Experiment_1_count Experiment_1_FPKM


title: ucc3, input


title: ucc9

tag: antibody


title: ucc8


title: Wild-type control mouse 2, 12 months, striatum

description:
Library name: WT_12m_02
Column name in fpkm_counts_A53T_12m.csv: Control_2_count Control_2_FPKM


title: MPTP_MB_1

description: Library name: G2_1_midBr

value: Male

value: 8 Weeks


title: Wild-type control mouse 1, 12 months, striatum

description:
Library name: WT_12m_01
Column name in fpkm_counts_A53T_12m.csv: Control_1_count Control_1_FPKM


title: ucc7


title: ucc4


title: Alpha-synuclein A53T transgenic mouse 2 (line G2-3), 12 months, striatum

description:
Library name: A53T_12m_02
Column name in fpkm_counts_A53T_12m.csv: Experiment_2_count Experiment_2_FPKM

value: Transgenic, expressing human alpha-synuclein with A53T mutation (line G2-3)


title: ucc3


title: Alpha-synuclein A53T transgenic mouse 1 (line G2-3), 12 months, striatum

description:
Library name: A53T_12m_01
Column name in fpkm_counts_A53T_12m.csv: Experiment_1_count Experiment_1_FPKM


title: Alpha-synuclein A53T transgenic mouse 3 (line G2-3), 12 months, striatum

description:
Library name: A53T_12m_03
Column name in fpkm_counts_A53T_12m.csv: Experiment_3_count Experiment_3_FPKM


title: ucc13


title: ucc, input


title: ucc12


title: Aortic intimal cells; 12 weeks of high-cholesterol diet; ERG control mice

city: Toronto

middle: L

last: Howe

state: Ontario

address: 101 College Street

department: Biomedical Research (Cardiovascular)

country: Canada

institute: Toronto General Hospital Research Institute

description:
Library name: SRB_SCRNA_SEQ_03
10x Genomics

data_processing:
To allow for EC lineage tracing in aortic intimal samples, a custom reference genome was generated by combining the GRCm38 mouse genome assembly (refdata-gex-mm10-2020-A) and a 5,215 base-pair reporter sequence containing Sun1-sfGFP, 6x c-Myc tags, and a bGH poly(A) signal. A reporter exon containing sfGFP and the 6x c-Myc tags was defined from base-pair 2,821 to 4,560 of the reporter sequence. Samples were demultiplexed and aligned to the custom reference genome using 10x Genomics Cell Ranger (v7.2.0) and each sample was subsetted to retain the top 10,000 cells by unique molecular identifier count.
Assembly: Custom reference genome (GRCm38 + reporter sequence; see data processing)
Supplementary files format and content: Filtered matrix files

source_name: Aortic intimal digest

growth_protocol: ERG control (Cdh5CreERT2; Rosa26lox-STOP-lox-Sun1-sfGFP; Erg+/+) and ERG EC-KO mice (Cdh5CreERT2; Rosa26lox-STOP-lox-Sun1-sfGFP; Ergfl/fl) were bred and housed under pathogen-free conditions at the University Health Network Animal Resources Centre (ARC).

extract_protocol:
Aortas were harvested from the aortic arch to renal bifurcation, cleaned, and pinned en face, and aortic intimal cells were isolated following gentle digestion with 0.15 W units/mL collagenase D (Sigma-Aldrich # 11088858001) and 167 units/mL DNAse I (Thermo Fisher Scientific # EN0521) in PBS-/- for 10 minutes at 37°C. Six male and female mice were pooled per sample.
Samples were assessed for viability with Trypan Blue (Thermo Fisher Scientific # 15250061), prepared as described in the 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 user guide, and sequenced paired-end using the 10x Genomics Chromium platform (10x Genomics, USA).

treatment_protocol: Erg knockout was induced in male and female 6-8 week-old mice using five consecutive daily intraperitoneal injections of 2 mg tamoxifen (Sigma-Aldrich # T5648) in 200 µL corn oil (Sigma-Aldrich # C8267). For atherosclerosis experiments, mice were allowed one week of recovery before induction of hypercholesterolemia. Atheroscelrosis was induced in mice with a single tail vein injection of AAV encoding mutant mPCSK9 (rAAV8/D377Y-mPCSK9; Vector Biolabs # 7600; 1x1011 viral genomes in 200 µL PBS-/-) and replacement of normal chow with 4 or 12 weeks of ad libitum semi-synthetic high-cholesterol diet containing 1.25% cholesterol and 40% fat (Research Diets # D12108C).

value: Aortic intimal digest

value: AAV8-PCSK9 + 12 weeks of high-cholesterol diet

value: 20-22 weeks

value: pooled male and female

tag: pooled number_of_mice


title: ucc1


title: Aortic intimal cells; 4 weeks of high-cholesterol diet; ERG EC-KO mice

description:
Library name: SRB_SCRNA_SEQ_02
10x Genomics

value: AAV8-PCSK9 + 4 weeks of high-cholesterol diet

value: 12-14 weeks


title: ucc11


title: ucc5, input


title: ucc10


title: Differ-2

first: Ji

last: Wu

state: Shanghai

address: No. 800, Dongchuan Road

institute: Shanghai Jiao Tong University

description:
Library name: Sample 4
Differ-2

data_processing:
The original image files obtained by high-throughput sequencing must undergo base identification and error filtering to obtain sequence data (Raw data). The HISAT2 software was used to perform corresponding genomic alignment on the filtered clean reads for bioinformatics analysis.
Assembly: GRCm38
Supplementary files format and content: table format include FPKM values for each sample

source_name: spermatogonial stem cells

extract_protocol:
Total RNA was extracted with TRIzol, and rRNA-depleted libraries were prepared using the Epi™ Mini LongRNA-seq Kit (Guangzhou Epibiotek).2ug RNA was used for the construction of sequencing libraries
The EpiTM mini longRNA-seq kit was used for the specific library construction of rRNA strands, and the PCR amplification products were purified at a ratio of 1× using EpiTM DNA Clean Beads. The library was inspected using the Bioptic Qsep100 Analyzer

value: spermatogonial stem cells

value: Differentiation


title: Differ-1

description:
Library name: Sample 3
Differ-1


title: Wild-type control mouse 3, 12 months, striatum

description:
Library name: WT_12m_03
Column name in fpkm_counts_A53T_12m.csv: Control_3_count Control_3_FPKM

value: Striatum


title: Control-2

description:
Library name: Sample 2
Control-2

value: WT


title: MP8, input


title: Control-1

description:
Library name: Sample 1
Control-1


title: ucc5


title: MP6, input


title: MP5, input


title: G16: GCN2KO lung, CD45-

first: Elaine

last: Soon

address: Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge CB2 0XY

country: United Kingdom

institute: Cambridge Institute for Medical Research (CIMR)

description:
Library name: Sample_16
10xGenomics

data_processing:
The raw sequences were aligned with Cell Ranger using the STAR aligner to the reference mouse genome GRCm38.p6. Filtering and quality control assessments were performed using the SCATER R package and dimensionality reduction was performed using the PCA, T-SNE and UMAP algorithms. Cells were clustered into similar types using the Walktrap community detection algorithm, and top marker genes for each cluster were then identified. A gene-set variation analysis was performed with these markers to identify the cell type clusters, using previously-identified cell markers.
Assembly: GRCm38
Supplementary files format and content: CD45N.rds, ‘RDS processed file of CD45-negative populations’
Supplementary files format and content: CD45P.rds, ‘RDS processed file of CD45-positive populations’

source_name: Whole lung

extract_protocol:
Age- and sex-matched gcn2-/- and wild-type littermates from the same cage were sacrificed by cervical dislocation. The lungs were flushed with PBS-heparin (25U/ml), washed thrice in PBS, and finely minced. The lung homogenates were digested (using collagenase, dispase and DNase), filtered through a 100micron sieve, subjected to red blood cell lysis and then passed through a 50micron filter. Flow cytometry was used to isolate single live CD45-positive and CD45-negative cells and 16,000 cells were processed using the Chromium 3’ kit (10xGenomics).
The library was constructed according to manufacturer's instructions (10xGenomics). GCs were resuspended in the master mix and loaded into the chip together with partitioning oil and gel beads to generate the gel bead emulsion. The poly-A RNA derived from the lung cells in each GEM was retrotranscripted to cDNA, containing an Illumina primer, Unique Molecular Identifier and the 10x barcode. The pooled barcoded cDNA was cleaned up with Silane Dynabeads, amplified by PCR and fragments were then selected for library construction. An Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole lung

value: Baseline


title: G15: GCN2KO lung, CD45+

description:
Library name: Sample_15
10xGenomics


title: MP3, input


title: G14: WT lung, CD45-

description:
Library name: Sample_14
10xGenomics


title: Aortic intimal cells; 12 weeks of high-cholesterol diet; ERG EC-KO mice

description:
Library name: SRB_SCRNA_SEQ_04
10x Genomics


title: MP9


title: MP1, input


title: G13: WT lung, CD45+

description:
Library name: Sample_13
10xGenomics


title: G12: GCN2KO lung, CD45-

description:
Library name: Sample_12
10xGenomics


title: MP8


title: G11: GCN2KO lung, CD45+

description:
Library name: Sample_11
10xGenomics


title: MP6


title: G10: WT lung, CD45-

description:
Library name: Sample_10
10xGenomics


title: MP5


title: Aortic intimal cells; 4 weeks of high-cholesterol diet; ERG control mice

description:
Library name: SRB_SCRNA_SEQ_01
10x Genomics


title: 14_day_control_rep1

description:
Library name: D2
10X Genomics

value: pluripotent cell

value: embryonic stem cell

value: vehicle (DMSO)

value: 14 days


title: 72_hr_RA_rep1

description:
Library name: 3R
10X Genomics

value: all-trans retinoic acid (30nM)

value: 72 hrs


title: 72_hr_control_rep1

description:
Library name: 3C
10X Genomics


title: 6_hr_RA_rep1

description:
Library name: 6R1
10X Genomics

value: 6 hrs


title: G9: WT lung, CD45+

description:
Library name: Sample_9
10xGenomics


title: MP3

value: human bladder


title: MP1


title: G7: GCN2KO lung, CD45+

description:
Library name: Sample_7
10xGenomics


title: G8: GCN2KO lung, CD45-

description:
Library name: Sample_8
10xGenomics


title: WT_NK_IL2

first: In-Hwan

last: Jang

address: 125, Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea

department: Immunotherapy Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
HISAT2 software (ver. 2.2.0) was used to index the reference genome and map sequencing reads of samples.
Samtools (ver. 1.15.1) was used to convert BAM files
FeatureCounts (ver. 2.0.1) software was used to calculate the generated BAM files
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes fpkm for each Sample

growth_protocol: NK92 cells were cultured in alpha-MEM supplemented with 12.5% FBS, 12.5% Horse serum, 1% penicillin–streptomycin, 0.2 mM inositol, 0.1 mM 2-mercaptoethanol, 0.02 mM folic acid, and recombinant human IL-2 (hIL-2) (20 ng/ml) at 37 °C and humidified with 5% CO2.

extract_protocol:
RNA was harvested using Rnaseay mini plus kit (Quiagen).
RiboCop rRNA Depletion + CORALL RNA-seq V2 Library Prep kit

value: human natural killer cell line

tag: genetic modification

value: human IL-2 (24 hours before RNA extraction)

tag: sample group

value: Control group


title: G6: WT lung, CD45-

description:
Library name: Sample_6
10xGenomics

tag: tissue


title: dOGT-ISS_NK_IL2

value: ISS deletion of OGT

value: Experimental group


title: G5: WT lung, CD45+

description:
Library name: Sample_5
10xGenomics


title: WT_NK

value: human IL-2 (48 hours before RNA extraction)


title: G4: WT lung, CD45+

description:
Library name: Sample_4
10xGenomics

value: WT


title: dOGT-ISS_NK


title: MP9, input


title: G3: GCN2KO lung, CD45+

description:
Library name: Sample_3
10xGenomics

value: Whole lung


title: CD34+ day4 Transduced

description: Library name: C02

value: mPB


title: L226C-Treg_VDJ

city: London

first: Panicos

last: Shangaris

address: Waterloo Road

institute: King's College London

library_source: other

data_processing:
Data were processed with the 10X cellranger pipeline (cellranger multi and counts)
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files.
Library strategy: VDJ-Seq

molecule: protein

source_name: Blood

extract_protocol:
Blood diluted with PBS-EDTA and 2% Ficoll-Paque PLUS, incubated in 37C for 5 minutes and centerifuged at 300xg for 5 minutes with supernatant discarded. Tregs and CD4+ T cells sorted ina BD FACS Aria III.
Single-cell mRNA, dual-indexed, sequencing libraries were generated following the Chromium Single Cell 5’ v2 protocol with Feature Barcode technology for Cell Surface Protein and Immune Receptor Mapping
For each 10x run, patient samples were hash-tagged and pooled, using one antibody-derived tag per patient following the CITE-Seq protocol (Biolegend) and then flow-sorted to generate separate compartments of CD4+ T-cells and FOXP3+ T-cells before proceeding with the 10x assay.

value: Blood

tag: disease state

value: MIX


title: G2: WT lung, CD45+

description:
Library name: Sample_2
10xGenomics

value: Baseline


title: L226B-Treg_VDJ


title: G1: GCN2KO lung, CD45+

description:
Library name: Sample_1
10xGenomics


title: Normal control_MB_3

first: jungim

last: Kim

address: 1672, Yuseong-daero, Yuseong-gu

institute: Korea Institute of Oriental Medicine

description: Library name: G1_3_midBr

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

value: Midbrain

tag: strain

tag: Sex

value: Male

tag: age

value: 8 Weeks

value: Saline


title: L226A-Treg_VDJ


title: RNA of MPRA in intermediate progenitors from E17 somatosensory mouse cortex rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

description: Library name: MPRA_RNA_IPC_E16_rep2

data_processing:
50xbp paired-end reads from the DNA or RNA libraries were trimmed using cutadapt with the following parameters: -u 1 -a GAATTCTCATTAC -A TCGACCGCAAGTTGG --discard-untrimmed. Count tables for DNA and RNA reads were generated using MPRAflow (--bc-length 12 and –mpranalyze).
Assembly: mm10
Supplementary files format and content: tab-seperated file containing the output from MRPA flow and MPRA analyze

source_name: somatosensory cortex

extract_protocol:
Somatosensory cortices from E13, E14, E15, E16 and E17 mouse embryos (in utero electroporated at E12, E13, E14, E15 and E16, respectively) were isolated after the removal of the meninges and dissociated using a papain-based neural dissociation kit (Miltenyi Biotec, Cat. N.: 130-092-628) according to the manufacturer’s protocol. Single cells were then fixed at RT for 10 minutes in 1% Formaldehyde in PBS (ThermoFisher, Cat. N: 28908) and quenched with final 0.2M Glycine (Invitrogen, Cat. N: 15527013). Fixed cells were spun down with 500g at 4˚C for 5 minutes, washed once with 1% BSA (ThermoFisher, Cat. N: AM2618) in PBS and incubated at 4°C for 10minutes in permeabilization buffer (0.1% Saponin (Sigma-Aldrich, Cat. N: SAE0073), 0.2% BSA and 1% RNAsin plus RNase inhibitor (Promega, Cat. N: N261A) in PBS). Cells were washed at 2500g at 4˚C for 5minutes,  following the staining against Pax6 (1:40, BD 561664), Eomes (1:33, BD 566749) and Tubb3 (1:14, BD 560394) in staining buffer (0.1% saponin, 1% BSA, 0.1% RNAsin plus RNase inhibitor in PBS) at 4˚C for 1h with slow rotation. Cells were washed twice with permeabilization buffer, once with PBS with DAPI (1:1000; ThermoFisher, Cat. N: 62248) and a final wash with PBS containing 0.5% BSA. After the last wash the cells were resuspended in PBS with 1% BSA and 1% RNAsin plus RNase inhibitor, filtered with a 40µM cell strainer (ThermoFisher, Cat. N: 15342931) and FAC-sorted. Sorted Pax6+ cells (NSC) and Tbr2+ cells (IPC) were digested with Proteinase K (Proteinase K (New England Biolabs, Cat. N: P8107S) at 55˚C for 1 h and decrosslinked at 65 ˚C for 15 minutes. DNA and RNA were extracted using the Quick-DNA/RNA Microprep Plus Kit (Zymo Research; Cat. N: D7005). Purified RNA was treated with TURBO DNase (Thermo Fisher; Cat. N: AM1907) and reverse transcribed with Maxima H Minus RT (Thermo Fisher; Cat. N: EP0753) using Oligo(dT)18 Primer (Thermo Fisher; Cat. N: SO131). cDNA was purified with 1.5X vol. AMPure XP magnetic beads (Agencourt, Cat. N: A63881) and stored at -20 °C for later use.
Libraries were prepared from both DNA and cDNA using the same protcol. In brief, UMIs were incorporated by PCR using the primers RV_univ_MPRA (CGACGCTCTTCCGATCT) and FWD_mScar_Tn7_10UMI_3 (0.5 µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG NNNNNNNNNN TCGACCGCAAGTTGGAC) with the following conditions: 98°C 30s; {98°C 10s, 65°C 30s, 72°C 1min} x3; 72°C 3min; Hold at 4°C. P7 and P5 sequencing adapters were added in two separate PCRs using indexed Ad2.X(CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT) and P5NEXTPT5 primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T) with the following conditions: 98°C 30s; {98°C 10s, 65°C 90s} x(10+X); 72°C 5min; Hold at 4°C. The required number of PCR cycles was determined by qPCR, using 1/10 of the second PCR product as input. All amplification steps were carried out using 1X NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544). PCR products were purified using AMPure XP magnetic beads at a volume ration of 0.8X to 1.2X.

value: somatosensory cortex

tag: cell type

value: intermediate progenitors (Tbr2+)

value: C57BL/6JRj (Haplotype H2b)


title: CAF67

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

description: Library name: CAF67

data_processing:
Reads were aligned to the human transcriptome using STAR software (version 2.7.3a) and each mRNA count number was calculated by RSEM (version 1.3.1).  Genes with P-value < 0.05 and FDR < 0.01 were considered as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab delimited files including rsem results for each sample

source_name: Stomach

growth_protocol: CAFs or GIST fibroblasts were maintained in MF medium (Toyobo).

extract_protocol:
Total RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega).
After assessing RNA sample quality by RIN on an RNA ScreenTape System (Agilent Technologies), RNA-seq was conducted using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human and NovaSeq 6000 (TruSeq stranded, paired 100 bases, read depth 60-80 M per sample).

value: Stomach

tag: cell line

value: gastric fibroblasts from cancerous tissues of scirrhous gastric cancer patient

tag: pathological type

tag: tumor stage


title: L215-A-Treg_VDJ


title: Normal control_MB_2

city: Daejeon

description: Library name: G1_2_midBr

tag: treatment


title: CAF63

description: Library name: CAF63


title: CAF66

description: Library name: CAF66


title: RNA of MPRA in intermediate progenitors from E17 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_IPC_E16_rep1

tag: genotype


title: CAF42

description: Library name: CAF42

value: gastric fibroblasts from cancerous tissues of non-scirrhous gastric cancer patient


title: L193-B-Treg_VDJ


title: C57BL/6 mouse 2, saline i.p. injection (same volume as subacute MPTP), striatum collected 3 days post-treatment

description:
Library name: Subacute control_3d_02
Column name in fpkm_counts_MPTP_sub_acute.csv: Control_2_count Control_2_FPKM

value: Striatum


title: CAF30

description: Library name: CAF30


title: L226C-CD4_VDJ


title: M5_male

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Library name: M5_male
counts_matrix_male.txt

data_processing:
Nextflow nf-core/rnaseq (v3.8.1; star alignment then salmon gene-level quantification)
Assembly: GRCm39 genome and gencode.vM30
Supplementary files format and content: salmon merged gene-level counts tabulated file

source_name: hippocampus

extract_protocol:
polyA extraction
mRNA stranded Illumina dual indexing sequenced as paired-end reads 59x10x10x59bp on Illumina NextSeq20000.

value: hippocampus

value: AETA-m

value: male


title: RNA of MPRA in intermediate progenitors from E16 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_IPC_E15_rep2


title: CAF19

description: Library name: CAF19


title: M4_male

description:
Library name: M4_male
counts_matrix_male.txt


title: L226B-CD4_VDJ

value: Blood


title: M3_male

description:
Library name: M3_male
counts_matrix_male.txt


title: RNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep3

description: Library name: MPRA_RNA_IPC_E14_rep3


title: M2_male

description:
Library name: M2_male
counts_matrix_male.txt


title: RNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_IPC_E14_rep2


title: M1_male

description:
Library name: M1_male
counts_matrix_male.txt


title: C5_male

description:
Library name: C5_male
counts_matrix_male.txt

value: WT


title: C4_male

description:
Library name: C4_male
counts_matrix_male.txt


title: C3_male

description:
Library name: C3_male
counts_matrix_male.txt


title: L215-B-CD4_VDJ

value: MIX


title: L215-A-CD4_VDJ


title: RNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep3

description: Library name: MPRA_RNA_IPC_E13_rep3


title: C1_male

description:
Library name: C1_male
counts_matrix_male.txt


title: RNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_IPC_E14_rep1


title: L193-B-CD4_VDJ


title: M5_female

description:
Library name: M5_female
counts_matrix_female.txt

value: female


title: M4_female

description:
Library name: M4_female
counts_matrix_female.txt


title: L226C-Treg_ADT

data_processing:
Data were processed with the 10X cellranger pipeline (cellranger multi and counts)
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files.
Library strategy: ADT-Seq


title: RNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_IPC_E13_rep2


title: RNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_IPC_E13_rep1


title: M3_female

description:
Library name: M3_female
counts_matrix_female.txt


title: L226B-Treg_ADT


title: C4_female

description:
Library name: C4_female
counts_matrix_female.txt


title: RNA of MPRA in intermediate progenitors from E13 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_IPC_E12_rep1


title: M2_female

description:
Library name: M2_female
counts_matrix_female.txt


title: tsc_spen_novus_rip

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

institute: UNC Chapel Hill

description: Library name: tsc_spen_novus_rip

data_processing:
RIP-Seq reads were aligned using STAR v2.5.4b with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools.
Assembly: mm10
Supplementary files format and content: Wiggle tracks were normalized to q30 aligned reads to mm10

source_name: mouse TSCs 6-2

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three to four days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
Both input and immunoprecipitated RNA were purified with the Zymo Clean and Concentrator.
KAPA RNA Hyperprep Kit with RiboErase, 9uL of IP/input RNA + 1uL ERCC RNA spike-in

treatment_protocol: To induce RBP knockdown, TSCs were treated with 1000ng/mL of doxycycline for four days. For all RIP experiments, trypsinized cells were crosslinked with 0.3% formaldehyde (Thermo Fisher, cat #: 28908) in PBS for 30 minutes at 4C with rotation, then quenched with 200mM glycine for 5 minutes at room temperature with rotation. Crosslinked cells were then washed thrice with ice-cold PBS, followed by resuspension in ice-cold PBS and divided into 10-million cell aliquots.

value: SPEN(novus, NBP1-82952)

value: mouse TSCs 6-2


title: C1_female

description:
Library name: C1_female
counts_matrix_female.txt


title: tsc_sfpq_rip

description: Library name: tsc_sfpq_rip

value: SFPQ(GeneTex, GTX114209)


title: L226A-Treg_ADT


title: L193-B-Treg_ADT


title: tsc_safb1-rip_mm

description: Library name: tsc_safb1-rip_mm

value: SAFB(Bethyl, A300-812A)


title: RNA of MPRA in neural stem cells from E17 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_NSC_E16_rep1

value: somatosensory cortex

value: neural stem cells (Pax6+)


title: tsc_safb1-rip_kcab

description: Library name: tsc_safb1-rip_kcab


title: L226C-CD4_ADT


title: tsc_d15_sfpq_rip

description: Library name: tsc_d15_sfpq_rip


title: RNA of MPRA in neural stem cells from E16 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_NSC_E15_rep2

value: C57BL/6JRj (Haplotype H2b)


title: L226B-CD4_ADT


title: tsc_d15_khdrbs1_2_rip

description: Library name: tsc_d15_khdrbs1_2_rip

value: KHDRBS1(Santa Cruz, sc-1238)


title: RNA of MPRA in neural stem cells from E16 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_NSC_E15_rep1


title: tsc_d15_khdrbs1_1_rip

description: Library name: tsc_d15_khdrbs1_1_rip


title: L226A-CD4_ADT


title: tsc_d15_hnrnpl_1_rip

description: Library name: tsc_d15_hnrnpl_1_rip

value: HNRNPL(Aviva Biosystems, ARP40368_P050)


title: RNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep3

description: Library name: MPRA_RNA_NSC_E14_rep3


title: tsc_d15_hnrnpl_2_rip

description: Library name: tsc_d15_hnrnpl_2_rip


title: L215-A-CD4_ADT


title: tsc_d15_ciz1_rip

description: Library name: tsc_d15_ciz1_rip


title: RNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_NSC_E14_rep2


title: tsc_c9_u2af35_rip

description: Library name: tsc_c9_u2af35_rip


title: L215-B-CD4_ADT


title: tsc_c9_srsf1_rip

description: Library name: tsc_c9_srsf1_rip

value: SRSF1(Santa Cruz, sc-33652)


title: RNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_NSC_E14_rep1


title: tsc_c9_spen_rip

description: Library name: tsc_c9_spen_rip


title: L193-B-CD4_ADT


title: tsc_c9_hnrnpu_rip

description: Library name: tsc_c9_hnrnpu_rip

value: HNRNPU (santa cruz)Santa Cruzsc-32315


title: L226C-Treg_mRNA

data_processing:
Data were processed with the 10X cellranger pipeline (cellranger multi and counts)
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files.


title: tsc_c9_hnpnpc_rip

description: Library name: tsc_c9_hnpnpc_rip

value: HNRNPCSanta Cruzsc-32308


title: tsc_c9_hnrnpm_rip

description: Library name: tsc_c9_hnrnpm_rip

value: HNRNPMsanta cruzsc20001


title: RNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_NSC_E13_rep2


title: tsc_c9_ciz1_2_rip

description: Library name: tsc_c9_ciz1_2_rip


title: L226B-Treg_mRNA

value: Blood


title: RNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_NSC_E13_rep1


title: tsc_c3_xrn2_rip

description: Library name: tsc_c3_xrn2_rip

value: WT


title: tsc_c3_u2af35_rip

description: Library name: tsc_c3_u2af35_rip


title: L226A-Treg_mRNA

value: MIX


title: tsc_c3_tia1_2_rip

description: Library name: tsc_c3_tia1_2_rip

value: TIA1(Proteintech, 12133-2-AP)


title: RNA of MPRA in neural stem cells from E13 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_NSC_E12_rep2


title: tsc_c3_tia1_1_rip

description: Library name: tsc_c3_tia1_1_rip


title: tsc_c3_supt16h_rip

description: Library name: tsc_c3_supt16h_rip

value: SUPT16H(Proteintech, 20551-1-AP)


title: RNA of MPRA in neural stem cells from E13 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_NSC_E12_rep1


title: tsc_c3_srsf1_rip

description: Library name: tsc_c3_srsf1_rip

value: mouse TSCs 6-2


title: L193-B-Treg_mRNA


title: tsc_c3_rbm15_rip

description: Library name: tsc_c3_rbm15_rip

value: RBM15(Proteintech, 10587-1-AP)


title: DNA of MPRA in intermediate progenitors from E17 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_IPC_E16_rep2

value: intermediate progenitors (Tbr2+)


title: tsc_c3_ptbp1_rip

description: Library name: tsc_c3_ptbp1_rip

value: PTBP1(Abcam, ab5642)


title: L226C-CD4_mRNA


title: tsc_c3_nudt21_rip

description: Library name: tsc_c3_nudt21_rip

value: nudt21(Proteintech, 10322-1-AP)


title: L226B-CD4_mRNA


title: tsc_c3_lbr_rip

description: Library name: tsc_c3_lbr_rip

value: LBR(Proteintech, 12398-1-AP)


title: DNA of MPRA in intermediate progenitors from E16 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_IPC_E15_rep2

value: somatosensory cortex

value: C57BL/6JRj (Haplotype H2b)


title: RNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep3

description: Library name: MPRA_RNA_NSC_E13_rep3

value: neural stem cells (Pax6+)


title: tsc_c3_hnrnpu_rip

description: Library name: tsc_c3_hnrnpu_rip

value: HNRNPU(Santa Cruz, sc-32315)


title: L226A-CD4_mRNA


title: tsc_c3_hnrnpm_rip

description: Library name: tsc_c3_hnrnpm_rip

value: HNRNPM(santa cruz, sc20001)


title: DNA of MPRA in intermediate progenitors from E16 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_IPC_E15_rep1


title: tsc_c3_hnrnpc_rip

description: Library name: tsc_c3_hnrnpc_rip

value: HNRNPC(Santa Cruz, sc-32308)


title: L215-A-CD4_mRNA

value: Blood


title: tsc_B5_spen-rip

description: Library name: tsc_B5_spen-rip

value: SPEN( Novus, NBP1-82952)

value: WT


title: L215-A-Treg_mRNA

value: MIX


title: DNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep3

description: Library name: MPRA_DNA_IPC_E14_rep3


title: tsc_B5_safb-rip

description: Library name: tsc_B5_safb-rip

value: SAFB(Bethyl, A300-812A)


title: L215-B-CD4_mRNA


title: tsc_B5_matrin3-rip

description: Library name: tsc_B5_matrin3-rip

value: Matrin3(Abcam, ab151715)

value: mouse TSCs 6-2


title: DNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_IPC_E14_rep2

value: intermediate progenitors (Tbr2+)


title: RNA of MPRA in intermediate progenitors from E16 somatosensory mouse cortex rep1

description: Library name: MPRA_RNA_IPC_E15_rep1


title: L226A-CD4_VDJ


title: tsc_B5_aly-ref-rip

description: Library name: tsc_B5_aly-ref-rip

value: ALYREF(Abcam, ab202894)


title: L193-B-CD4_mRNA


title: tsc_c3_pabpn1_rip

description: Library name: tsc_c3_pabpn1_rip

value: PABPN1(Abcam, ab75855)


title: tsc_b15_xrn2_b2_rip

description: Library name: tsc_b15_xrn2_b2_rip


title: C2_male

description:
Library name: C2_male
counts_matrix_male.txt

value: hippocampus

value: male


title: DNA of MPRA in intermediate progenitors from E17 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_IPC_E16_rep1

value: somatosensory cortex

value: C57BL/6JRj (Haplotype H2b)


title: tsc_b15_u2af65_b2_rip

description: Library name: tsc_b15_u2af65_b2_rip

value: U2AF65(Santa Cruz, sc-53942)


title: DNA of MPRA in intermediate progenitors from E15 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_IPC_E14_rep1


title: SEM_MBNL1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
We performed single-end 51-cycle sequencing on the NovaSeq 6000 sequencer (Illumina).
Raw reads were trimmed using TrimGalore (v0.6.3) and aligned to the Homo sapiens reference genome GRCm37.p13(hg19) genome using BWA (v0.7.17-r1198).
Duplicated and low mapping quality reads were removed using “bamsormadup” function from the biobambam2 tool (v2.0.87) and samtools (version 1.9, parameter “-q 1 -F 1024”).
The fragment size in each sample was estimated based on the cross-correlation profile calculated from SPP (v1.11).
Fragments were extended to fragment size and normalized to 15 million reads to generate bigwig files.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: B-ALL

growth_protocol: The SEM and MOLM13 cell lines were cultured in RPMI-1640 medium (Lonza) containing 10 % fetal bovine serum (Hyclone), 2 mM glutamine (Sigma), and 1% penicillin/streptomycin (Thermo Fisher Scientific) in an incubator at 37 °C, 5 % CO2 and 95 % humidity. A high-titer virus for TRE3G-HA-MBNL1-Zeocin was generated using 293 T cells, which were cultured in DMEM (GIBCO, Life Technologies) with 10% heat-inactivated fetal bovine serum (Hyclone) and 2 mM L-glutamine (Sigma) at 37 °C in 5% CO2. All cell lines were validated by STR and verified to be free of mycoplasma by Lookout Mycoplasma PCR Detection Kit (Sigma, #MP0035).

extract_protocol:
ChIP was performed with antibodies against human MBNL1 (cat# MABE70, Millipore) and HA (cat#sc-7392, Santa Cruz). Each ChIP assay was conducted in two biological replicates, as described previously (PMID:33512425), following the slight modifications below. In Brief, about ten million isolated cells were fixed with 1% formaldehyde (cat#? vendor) at 1X106 cells/mL dilution. The fixed cells were aliquoted as 10 million per tube, followed by snap freezing in dry ice. In the MBNL1-antibody and HA-antibody-based ChIP procedure, about 1X107 cross-linked cells were used for immunoprecipitation.
The IP-ed chromatin products were used for sequencing library construction, following the instruction of the NEBNext Ultra II DNA library prep kit (cat# E7645, New England Biolabs) with Trueseq adaptors. QC-validated libraries were sequenced with an Illumina HiSeq 2500 platform. Reproducible ChIP-seq peaks were called using MACS2(2.0.10.20131216) and identified from two biological replicates. Finally, low-confidence peaks were filtered from the blacklist regions defined by ENCODE.

treatment_protocol: MOLM13 ells were transduced with lentivirus expressing TetOn-HA-MBNL1 and selected for stable transduction by Zoecin (100ug/ml, 3 days). The induction of exogenous HA-tagged MBNL1 was conducted with 1 ug/mL doxycycline for 24 hours.

value: B-ALL

value: SEM


title: tsc_b15_u2af35_b2_rip

description: Library name: tsc_b15_u2af35_b2_rip


title: DNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep3

description: Library name: MPRA_DNA_IPC_E13_rep3


title: tsc_b15_supt16h_b1_rip

description: Library name: tsc_b15_supt16h_b1_rip

value: SUPT16H(Proteintech, 20551-1-AP)


title: PKW-B6_6

city: Otsu

first: Shoma

last: Matsumoto

state: Shiga

address: Setatsukinowa-cho

department: Research Center for Animal Life Science

institute: Shiga University of Medical Science

description: Library name: PKW-B6_6

data_processing:
DNA barcode sequences were extracted from fastq files using the plasmid sequence for transgenic mouse generation (pNM1419_iSeq_Reference.fa; supplementary file).
Read count and integration of similar barcode sequences were performed by starcode v1.4 (Zorita et al., 2015).
Assembly: pNM1419_iSeq_Reference.fa

source_name: E11.5 embryo

extract_protocol:
E11.5 mouse embryos with DNA barcode-linked EGFP were minced and enzymatically into single cell. Genomic DNA was extracted and purified using phenol/chloroform.
Genomic DNA was amplified using transgene-specific primers with Illumina index sequences. PCR was performed using KOD One PCR Master Mix -Blue- (Takara). The amplicons were purified by FastGene Gel/PCR Extraction Kit (Nippon Genetics).

value: E11.5 embryo

value: DNA barcode-linked GFP Tg


title: SEM_Input


title: tsc_b15_nudt21_b1_rip

description: Library name: tsc_b15_nudt21_b1_rip

value: nudt21(Proteintech, 10322-1-AP)

value: WT


title: RNA of MPRA in intermediate progenitors from E13 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_IPC_E12_rep2


title: C5_female

description:
Library name: C5_female
counts_matrix_female.txt

value: female


title: tsc_b12_srsf1_rip

description: Library name: tsc_b12_srsf1_rip

value: SRSF1(Santa Cruz, sc-33652)

value: mouse TSCs 6-2


title: DNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_IPC_E13_rep2

value: intermediate progenitors (Tbr2+)


title: Molm13_OE_Millipore

source_name: AML

value: AML


title: tsc_b12_rbm15_rip

description: Library name: tsc_b12_rbm15_rip

value: RBM15(Proteintech, 10587-1-AP)


title: C2_female

description:
Library name: C2_female
counts_matrix_female.txt

value: hippocampus


title: DNA of MPRA in intermediate progenitors from E14 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_IPC_E13_rep1

value: somatosensory cortex


title: tsc_b12_ptbp1_rip

description: Library name: tsc_b12_ptbp1_rip

value: PTBP1(Abcam, ab5642)


title: Molm13_OE


title: L215-A-Treg_ADT

value: Blood

value: MIX


title: tsc_b12_pabpn1_rip

description: Library name: tsc_b12_pabpn1_rip

value: PABPN1(Abcam, ab75855)


title: DNA of MPRA in intermediate progenitors from E13 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_IPC_E12_rep2

value: C57BL/6JRj (Haplotype H2b)


title: 316-34-2, APP mutant, day0

city: Niigata

first: Hideaki

last: Matsui

state: Niigata

address: 1  Bancho-757 Asahimachidori, Chuo Ward

department: Brain Research Institute

institute: Niigata University

data_processing:
TruSeq stranded mRNA LT Sample Prep Kit
Trimmed reads are mapped to reference genome with HISAT2
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: Homo sapiens GRCh38 (NCBI_109.20200522)
Supplementary files format and content: tab-delimited raw file include raw count values for each sample

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM (Nacalai Tesque, Kyoto, Japan) supplemented with 10% FBS (BioWest, Nuaillé, France) and 1% penicillin‒streptomycin solution (Wako, Osaka, Japan) at 37°C under 5% CO2

extract_protocol:
Total cellular RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) and a Direct-zol RNA kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s guidelines.

treatment_protocol:
APP-deficient or mutant HeLa cells were generated using the CRISPR-Cas9 system. The APP gRNA sequence was cloned and inserted into pSpCas9 (BB)-2A-Puro (PX495) v.2.0 (plasmid #62988; Addgene, Cambridge, MA, USA)
After treatment with 2 μg/ml puromycin for 48 hr, the cells were grown and passaged in medium without puromycin for 7 days and then spread in four 96-well plates at 0.75 cells/100 μl.
HeLa and APP mutant cells (316,15 and 316-34) were treated with etoposide (20 μM, 2 days).

value: HeLa

value: APP mutant


title: tsc_b12_matrin3_rip

description: Library name: tsc_b12_matrin3_rip

value: Matrin3(Abcam, ab151715)


title: Molm13_MBNL1


title: tsc_b12_lbr_rip

description: Library name: tsc_b12_lbr_rip

value: LBR(Proteintech, 12398-1-AP)

value: WT


title: DNA of MPRA in intermediate progenitors from E13 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_IPC_E12_rep1


title: RNA of MPRA in neural stem cells from E17 somatosensory mouse cortex rep2

description: Library name: MPRA_RNA_NSC_E16_rep2

value: neural stem cells (Pax6+)


title: Molm13_Input


title: tsc_b12_hnrnpu_rip

description: Library name: tsc_b12_hnrnpu_rip

value: HNRNPU(Santa Cruz, sc-32315)

value: mouse TSCs 6-2


title: DNA of MPRA in neural stem cells from E17 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_NSC_E16_rep2


title: tsc_b12_hnrnpm_rip

description: Library name: tsc_b12_hnrnpm_rip

value: HNRNPM(santa cruz, sc20001)


title: Patient 30 pre treatment scRNA-seq

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Processing of raw reads was performed using the Cell Ranger software provided by 10X genomics and the hg38 human reference genome (GRCm38 v86 and corresponding GENCODE annotation file). During read alignment, PCR duplicates were removed. The UMI (unique molecular identifier) for each gene is counted to measure the gene expression levels. The cell doublet status is inferred by the software DoubletFinder. A number of quality-control metrics are evaluated to control the data quality, including the total UMI count, the total number of genes detected, the mitochondrial gene ratio, log10(gene number) per UMI, and the inferred status of cell doublet.  Low-quality cells with a total UMI count smaller than 500, a total number of genes smaller than 200, and a mitochondrial gene ratio greater than 50% are excluded for further analysis.
Assembly: GRCm38 v86
Supplementary files format and content: Filtered bc matrix from CellRanger and Parse pipelines.

source_name: Tumor biopsy

extract_protocol:
The sample was incubated at 37 °C for 5 min. After dissociation, 2ml of advanced DMEM+10%FBS media was added to the sample and filtered through a 70 μm cell strainer (Fisher Scientific, cat.43-10070-40) into Eppendorf tubes
The filtrate was centrifuged at 500g for 5 min, and the supernatant was removed. If the pellet was bloody, red blood cell (RBC) removal was performed using RBC Lysis Solution (1x) (Miltenyi Biotec, cat. No. 130-094-183) for 10 min at RT. Sample was then centrifuged at 500g for 5 min and pellet was resuspended in 1ml of advanced DMEM, to be combined into one Eppendorf tube.
The single-cell suspension was visualized, counted, and stored at nitrogen until 10x Genomics Single-Cell sequencing was performed.

value: Tumor biopsy

value: Before


title: tsc_b12_alyref_rip

description: Library name: tsc_b12_alyref_rip

value: ALYREF(Abcam, ab202894)


title: tsc_b12_hnrnpc_rip

description: Library name: tsc_b12_hnrnpc_rip

value: HNRNPC(Santa Cruz, sc-32308)


title: DNA of MPRA in neural stem cells from E17 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_NSC_E16_rep1

value: somatosensory cortex


title: DNA of MPRA in neural stem cells from E16 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_NSC_E15_rep2


title: Patient 28 pre treatment scRNA-seq


title: P21_Worthington_rep4

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description:
scRNA_Worthington_P21_raw_counts.dge.txt
scRNA_Worthington_P21_metadata.txt

data_processing:
scRNA-seq sequencing and basecalling were performed with NextSeq 500 instrument (Illumina)
Cellranger mkfastq (10x Genomics v3.0.1) was used to demultiplex bcl files to fastq files using standard parameters
Cellranger count (10x Genomics v3.0.1) was used to produce an aligned single cell feature count matrix, using mm10 genome as a reference.
Seurat (v4.0.0) pipeline including SCTransform was used to normalize and scale the single cell data. Default parameters were used. The following parameters were used for regression: percent.mt, and sample.
PCA and UMAP were used to for dimensionality reduction and visualization of single cells data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: tab-delimited file with the metadata for each sample in the matrix

source_name: S1 cortex

extract_protocol:
Tissue pieces were processed to obtain a single cell suspension using papain digestion  (30-90   min   according   to   the   mice   age),   following   an   adapted   protocol   from   the  Worthington Papain Dissociation System kit  (Worthington Biochemical).  Single cells  were   resuspended   in   ice-cold   Hibernate-A   containing   10%   fetal   bovine   serum.  Oligodendrocytes were isolated by fluorescence activated cells sorting. Sorted cells  were spun down and resuspended into 0.04% BSA in PBS. Cell were counted in a  hemocytometer chamber and immediately processed for single cell GE formation.
Library was performed according to the manufacter’s instructions with the single cell 3’  v2 protocol (or v3 for the second replicate) (10x Genomics).  Approximately 6-8,000  sorted oligodendrocytes were loaded onto  a Chromium™ Single Cell 3’ Chip and  processed   through   the   Chromium   Controller   to   generate   single-cell   gel   beads   in  emulsion.   cDNA   amplification   and   library   construction   were   done   following  10xGenomics instructions. Libraries were quantified in BioAnalyzer and sequenced  with a NextSeq 500 instrument (Illumina).

treatment_protocol: One male and one female Fezf2CreERT2/+; td-Tomato+/-; Plp1-eGFP+/- mice at each time  point were used. We dissected the brain and made 200-400um coronal sections in  Hybernate A (Brainbits) using a vibratome. Sections were transferred to another plate  and somatosensory cortex micro dissected into three sub-cortical regions (layer1-4,  layer5 and layer6) using the fluorescently labeled layer5 cells as landmark. Tissue was  kept in cold Hybernate A with B27 at all times. RNAse free techinique was used

value: S1 cortex

value: All


title: rc139-6-2-tscs-mm-ythdc1_rip

description: Library name: rc139-6-2-tscs-mm-ythdc1_rip


title: Patient 11 pre treatment scRNA-seq


title: P21_Worthington_rep3


title: P21_Worthington_rep1


title: P21_Worthington_rep2


title: DNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep3

description: Library name: MPRA_DNA_NSC_E14_rep3

value: C57BL/6JRj (Haplotype H2b)


title: Patient 4 pre treatment scRNA-seq


title: P7_Worthington_rep3

description:
scRNA_Worthington_P7_raw_counts.dge.txt
scRNA_Worthington_P7_metadata.txt


title: Patient 25 pre treatment scRNA-seq


title: P7_Worthington_rep2


title: P7_Worthington_rep1


title: P90_LayerVI_rep2

description:
scRNA_OL_layers_raw_counts.dge.txt
scRNA_OL_layers_metadata.txt

value: Oligodendrocyte

value: Fezf2 CreERT2 +/- ; td-Tomato +/- ; Plp1-eGFP +/-


title: Patient 1 post treatment scRNA-seq

value: After


title: DNA of MPRA in neural stem cells from E15 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_NSC_E14_rep1


title: P90_LayerV_rep2


title: P90_LayerII-IV_rep2


title: P30_LayerVI_rep2


title: Patient 19 post treatment scRNA-seq


title: DNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep3

description: Library name: MPRA_DNA_NSC_E13_rep3


title: P30_LayerV_rep2


title: DNA of MPRA in neural stem cells from E14 somatosensory mouse cortex rep2

description: Library name: MPRA_DNA_NSC_E13_rep2


title: P30_LayerII-IV_rep2


title: Patient 19 pre treatment scRNA-seq


title: P90_LayerVI_rep1


title: P90_LayerV_rep1


title: P90_LayerII-IV_rep1


title: P30_LayerVI_rep1


title: P30_LayerV_rep1


title: DNA of MPRA in neural stem cells from E13 somatosensory mouse cortex rep1

description: Library name: MPRA_DNA_NSC_E12_rep1


title: Patient 16 pre treatment scRNA-seq


title: P14_LayerVI_rep1