title: REST-ChIP in Rest conditional knockout

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: Library name: KO_REST

data_processing:
Base calling was performed using the Illumina bcl2fastq2 Conversion Software v2.20
Read quality assessment using FastQC. Adapter trimming using Cutadapt.
Reads were mapped to the mouse reference genome (GRCm38) using the Bowtie2 software.
Peak calling was performed using the MACS2 software.
Assembly: GRCm38
Supplementary files format and content: alignment bigWig files

source_name: mouse uterus

extract_protocol:
Uteri from Restf/f and Restf/f PRCre/+ mice (3 of each genotype, in diestrus) at 6 months of age were minced on ice and cross-linked using 1% formaldehyde. Chromatin IP for PGR and REST were performed according to published protocols (Varghese et al., PNAS, 2010. Rubel et al., Mol Endocrinol, 2012.)
An unbiased whole genome profiling of REST and PGR binding was obtained by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq). ChIP-Seq data was generated from REST-ChIP in control (Restfl/fl), REST-ChIP in Rest conditional knockout (Restfl/fl PR+/Cre), PR-ChIP in control (Restfl/fl), and PR-ChIP in Rest conditional knockout (Restfl/fl PR+/Cre) samples. We used corresponding input DNA controls from WT and KO samples to measure total chromatin before IP. ChIP-Sequencing was performed in an Illumina NovaSeq 6000 sequencing machine (Illumina, San Diego, CA) at a 100-base paired-end read resolution. After read quality assessment (FastQC [Andrews 2010]) and adapter trimming (Cutadapt [Martin, EMBnet.journal, 2011 ]), the sequenced reads were mapped to the mouse reference genome (GRCm38) using the Bowtie2 [Langmead et al., Nat Methods, 2012] software. Sequencing produced between 31.5 and 56.5 million reads per sample of which 97% to 99% mapped to the reference genome. Significantly enriched ChIP regions (relative to the corresponding Input sample) were detected using the Model-based Analysis of ChIP-Seq (MACS2 [Zang et al., Genome Biol, 2008]) software. The analysis was run under default settings in the paired-end mode with the q-value cutoff for calling significant regions set at 0.05. The peak regions were scanned for RE-1 and Pgre binding motifs with a position weight matrix (PWM) similarity cutoff set at 70%. The number of significantly enriched regions (enrichment FC ≥ 1.5, q-value ≤ 0.05) detected for each antibody is given in Figure 4C. The mapped regions were visualized using the Integrative Genome Viewer (IGV [Thorvaldsdottir et al., Brief Bioform, 2013]). A motif analysis for known transcription factor binding sites in the enriched regions was performed using the HOMER [Heinz et al., Mol Cell, 2010] software. The heatmaps of sequencing-depth-normalized read coverage around 3 kb up-stream and down-stream from the transcription start site (TSS) of all genes were generated using the deepTools [Ramirez et al., Nucleic Acids Res, 2014] software.

value: mouse uterus

value: KO

value: REST


title: Control Subject 2

status: Public on Jan 21 2026

type: RNA

city: Angers

first: Benoit

last: BRILLAND

address: 4 rue Larrey

country: France

institute: Angers University Hospital

hyb_protocol: 100 ng of the resulting RNA was then hybridised to probes from the nCounter XT autoimmune profiling panel (NS_Hs_AI_Pro_v1.1, NanoString Technologies, 750 genes involved in 35 pathways and processes + 20 housekeeping genes + 14 internal controls), according to the manufacturer’s guidelines using an 19-hour hybridisation.

scan_protocol: Sample slides were prepared, and absolute counts generated using the nCounter FLEX analysis system.

data_processing:
Raw gene expression data were analyzed using nSolver Analysis Software v4.0 (NanoString Technologies) with the Advanced Analysis Module v2.0. The software first identifies and checks standard quality controls such as imaging, binding density, and positive controls to ensure the samples were read and reported properly.
For gene expression data, raw counts were normalized to the positive controls and then log2 transformed. To reduce technical bias, background thresholding was performed using the eight negative controls included within the panel. Genes with counts below a threshold of three standard deviations above the mean background signal were excluded from subsequent analysis. Data normalization was performed on background-thresholded samples using internal positive controls and selected housekeeping genes that were identified using the geNorm algorithm. Data were normalized for hybridization and counting efficiency and kept within the range of 0.3–3 (Nanostring recommended).

molecule: total RNA

organism: Homo sapiens

source_name: kidney biopsy

extract_protocol: Kidney biopsies containing at least 4 glomeruli and sufficient tissue after clinical use were selected for subsequent mRNA extraction. This pragmatic cutoff was chosen to reflect the broad range of biopsies encountered in clinical practice. Ten-micrometer sections were cut from the formalin-fixed paraffin-embedded (FFPE) blocks and placed in 2 ml microcentrifuge tubes after discarding the first two sections (to avoid collecting RNA that would have been damaged by contact with air). Whole sections, including glomeruli and tubulo-interstitium were used. The number of sections per sample was dependent on the size of the FFPE tissue. Preliminary studies allowed us to determine that 3 to 6 sections were necessary to obtain a minimum of 100 ng of total RNA.  Extraction of total RNA from FFPE specimens was performed using the High Pure FFPE RNA Isolation Kit (Roche Molecular Diagnostics, Rotkreuz, Switzerland) according to the manufacturer’s instructions. Extraction of RNA was either performed immediately after FFPE sectioning or sections were frozen at -20°C until the extraction was performed.  RNA purity and quantification were assessed by spectrophotometry (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA): RNA with a 260/280 ratio of 1.7–2.0 as well as a 260/230 ratio in the range of 1.8–2.3 were considered to be of acceptable quality for downstream assays). RNA quality analysis (fragmentation analysis) was performed to assess the integrity of RNA by measuring the proportion of RNA fragments greater than 200 base pairs (DV200) (TapeStation; Agilent, Santa Clara, CA). The resulting data were used to calculate the corrected RNA input for each NanoString hybridization reaction following the manufacturer’s instructions. Only samples with DV200 > 30% were considered for subsequent analyses. RNA was stored at −80 °C prior to NanoString assays. RNA was diluted in nuclease free water at a concentration of 20 ng/μL immediately before the assay, and 100 ng (5 µL) of total RNA per sample were used for quantification.

tag: tissue

value: kidney

tag: disease group

value: CTRL

tag: batch


title: DDKC_9750_plus_rDKK3_S164328

type: SRA

city: Ulm

first: Alexander

last: Kleger

address: Albert einstein allee 23

department: Institute for Molecular Oncology and Stem Cell biology

country: Germany

institute: Universitaetsklinikum Ulm

description:
Library name: DDKC_9750_plus_rDKK3_S164328
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9750_plus_rDKK3_S164328

library_source: transcriptomic

data_processing:
Illumina NovaSeq Control Software (NVCS) 1.8.1 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm39 (UCSC Genome Browser mm39) and GENCODE reference transcriptome M32 (February 2023) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.16 package DESeq2 1.38.0, running under R 4.2.2.
Assembly: UCSC mm39 based on GRCm39
Supplementary files format and content: tsv file includes raw counts for each sample

organism: Mus musculus

source_name: Pancreas

growth_protocol: Pancreatic tumor cells were cultured using Dulbecco's Modified Eagle Medium supplemented with 10% FBS  and 1% Pencillin/ streptomycin

extract_protocol:
RNA isolation was done using Rneasy Plus Mini kit from Qiagen
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

treatment_protocol: Dkk3 null tumor cells were treated with recombinant form of soluble DKK3 commercially available to assess its oncogenic properties

value: Pancreas

tag: cell type

value: Pancreatic cancer cells

tag: genotype

value: DKK3 knockout

tag: treatment

value: recombinant DKK3


title: PR-ChIP in Rest conditional knockout

country: USA

description: Library name: KO_PR

library_source: genomic

molecule: genomic DNA

tag: chip antibody

value: PR


title: Input DNA for REST KO

description: Library name: KO_Input


title: Control Subject 5


title: primary GBM patient 51 corpus callosum

city: Seongnam-si

first: Jaejoon

last: Lim

address: 59 Yatap-ro, Bundang-gu

department: College of Medicine

country: South Korea

institute: CHA University

data_processing:
At first, reads for each sample were mapped to the reference genome(Mouse mm10) by Tophat(v2.0.13) . The aligned results were added to Cuffdiff(v2.2.1)  to report differentially expressed genes. For library normalization and dispersion estimation, geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods  were applied.
Assembly: mm10
Supplementary files format and content: gz format

source_name: Brain tissue

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop8000 spectrophotometer. RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value.
Total RNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq Stranded Total RNA Sample prep kit with Ribo-zero Human/mouse/rat).  Total RNA 400ng was subjected to ribosomal RNA depletion, with Ribo-zero Human/mouse/rat reagent using biotinylated probes that selectively bind rRNA species. Following purification, the rRNA-depleted total RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand. cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final cDNA library. The quality of the amplified libraries was verified by automated electrophoresis (Tapestation, Agilent). After QPCR using KAPA SYBR FAST qPCR Master Mix(Kapa Biosystems), we combined libraries that index tagged in equimolar amounts in the pool. RNA sequencing is performed using an Illumina NovaSeq 6000 system following provided protocols for 2x100 sequencing.

value: Brain tissue

value: IDH1 wild type


title: Control Subject 13


title: AAV-GN Patient 199

value: AAV-GN


title: primary GBM patient 51 tumor core region


title: REST-ChIP in control

description: Library name: Ctrl_REST

value: Ctrl


title: AAV-GN Patient 198


title: Control Subject 14


title: primary GBM patient 50


title: AAV-GN Patient 197


title: AAV-GN Patient 195


title: Control Subject 1


title: primary GBM patient 48 peripheral region


title: AAV-GN Patient 196


title: Mus CD8+ T cell, C57BL/6J , active 48h, IgG, (INPUT)

city: Beijing

first: Yushan

last: YI

address: No.38 Xueyuan Road, Haidian District, Beijing

department: Department of Immunology

country: China

institute: Peking University

description: Library name: Ig5,  INPUT

data_processing:
CUT&RUN sequencing reads were processed using the nf-core/cutanrun pipeline (v3.2.2),raw reads were assessed for quality using FastQC (v0.12.1).Adapter sequences and low-quality bases were trimmed with Trim Galore! (v0.6.10).Processed reads were aligned to the GRCm39 mouse reference genome using Bowtie2 (v2.5.1). Alignments were filtered to retain uniquely mapped reads using SAMtools (v1.17), and PCR duplicates were marked with Picard (v3.2.0). Fragment size distributions and library complexity were evaluated using deepTools (v3.5.4) and preseq (v3.2.0), respectively. Final quality metrics were aggregated with MultiQC (v1.21).Peaks were identified using MACS2 (v2.2.9.1) with a P-value threshold of 0.01. Differential peaks between the Atf4 treatment and IgG control groups were determined using DiffBind (v3.12.0). Due to the availability of only one control replicate in the 48-hour group, three pseudo-controls were generated by random subsampling of the control data. This approach simulated additional control replicates, enabling statistical analysis in DiffBind and allowing for a valid comparison of treatment-induced changes in the 48-hour CUT&RUN data. Location features of differential peaks were annotated using ChIPseeker (v1.38.0).
Assembly: GRCm39
Supplementary files format and content: Peaks and annotation
Library strategy: CUT&Run

source_name: lymph node

extract_protocol:
For CUT & RUN,cell nuclei were isolated and incubated with an anti-ATF4 antibody (Cell Signaling, 11815S) and normal Rabbit IgG (Cell Signaling, 2729S) overnight at 4ºC while shaking. The nuclei were incubated with protein A-micrococcal (pA-MNase) nuclease for 1 h at 4ºC. Nuclei were equilibrated to 0ºC, and MNase digestion was allowed to proceed for 30 min. Soluble chromatin CIT&RUN fragments were isolated and purified by AMPure XP beads (Beckman, Brea, CA, USA).
CUT&RUN libraries were prepared using NEBNext Ultra II DNA (Biolab: Lot 10211572) and its accompanying instructions.

value: lymph node

tag: strain

value: CD8+ T cells

value: WT

value: active 48h


title: primary GBM patient 49


title: DDKC_9750_S164342

description:
Library name: DDKC_9750_S164342
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9750_S164342


title: PR-ChIP in control

description: Library name: Ctrl_PR

value: mouse uterus


title: AAV-GN Patient 193


title: AAV-GN Patient 191


title: Input DNA for control

description: Library name: Ctrl_Input


title: AAV-GN Patient 186


title: AAV-GN Patient 185


title: AAV-GN Patient 190


title: primary GBM patient 48 tumor core region


title: primary GBM patient 44


title: AAV-GN Patient 194


title: AAV-GN Patient 187


title: AAV-GN Patient 188


title: primary GBM patient 47


title: Mus CD8+ T cell, C57BL/6J , active 12h, IgG, biol rep 4, (INPUT)

description: Library name: Ig4,  INPUT

value: active 12h


title: AAV-GN Patient 189

value: kidney


title: primary GBM patient 45


title: Mus CD8+ T cell, C57BL/6J , active 12h, IgG, biol rep 2, (INPUT)

description: Library name: Ig2,  INPUT


title: Mus CD8+ T cell, C57BL/6J , active 12h, IgG, biol rep 3, (INPUT)

description: Library name: Ig3,  INPUT


title: Mus CD8+ T cell, C57BL/6J , active 48h, ATF4, biol rep 2, (ChIP)

description: Library name: A8,  ChIP


title: AAV-GN Patient 184


title: primary GBM patient 42 tumor normal region


title: AAV-GN Patient 180


title: Mus CD8+ T cell, C57BL/6J , active 12h, IgG, biol rep 1, (INPUT)

description: Library name: Ig1,  INPUT


title: AAV-GN Patient 179


title: primary GBM patient 43


title: AAV-GN Patient 178


title: AAV-GN Patient 192


title: AAV-GN Patient 183


title: primary GBM patient 42 peripheral region


title: AAV-GN Patient 182


title: AAV-GN Patient 177


title: Mus CD8+ T cell, C57BL/6J , active 48h, ATF4, biol rep 1, (ChIP)

description: Library name: A7,  ChIP


title: AAV-GN Patient 174


title: Mus CD8+ T cell, C57BL/6J , active 12h, ATF4, biol rep 2, (ChIP)

description: Library name: A5,  ChIP


title: AAV-GN Patient 176


title: Mus CD8+ T cell, C57BL/6J , active 48h, ATF4, biol rep 3, (ChIP)

description: Library name: A9,  ChIP


title: AAV-GN Patient 175


title: primary GBM patient 42 tumor core region


title: AAV-GN Patient 181


title: AAV-GN Patient 173


title: Mus CD8+ T cell, C57BL/6J , active 12h, ATF4, biol rep 3, (ChIP)

description: Library name: A6,  ChIP


title: primary GBM patient 42 subventricular zone


title: Mus CD8+ T cell, C57BL/6J , active 12h, ATF4, biol rep 1, (ChIP)

description: Library name: A4,  ChIP


title: primary GBM patient 41 tumor core region


title: AAV-GN Patient 171


title: AAV-GN Patient 167


title: Locus coeruleus, untreated control, replicate 5

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

description: Library name: S_k_5

data_processing:
Raw reads processed using nf-core/rnaseq pipeline v3.14.0 with standard parameters. Reads aligned to mouse reference genome GRCm39/mm39 using STAR aligner, followed by transcript quantification with Salmon.
Assembly: GRCm39/mm39
Supplementary files format and content: Processed data files format and content: Comma-separated values (CSV) files with gene identifiers and gene names in the first two columns, followed by TPM expression values. TPM values generated by Salmon quantification against mouse GRCm39/mm39 reference genome.

molecule: polyA RNA

source_name: brainstem

growth_protocol: C57BL/6 male mice housed under standard laboratory conditions at 22°C with 12h light/dark cycle, fed standard laboratory chow ad libitum, 7-day adaptation period before treatment

extract_protocol:
Locus coeruleus tissue collected 24h post-treatment, snap-frozen in liquid nitrogen. RNA extracted using ExtractRNA reagent (Evrogen) with bead-beating homogenization, chloroform purification, and isopropanol precipitation. DNA contamination removed with TURBO DNase.
Poly(A) mRNA was isolated from total RNA using NEB-Next Poly(A) mRNA Magnetic Isolation Module, followed by library preparation with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer's protocols. Libraries were indexed with NEBNext Multiplex Oligos and quality controlled using TapeStation 2200 (Agilent Technologies).

treatment_protocol: Both vindeburnol and its derivative VB-127 were administered at 20 mg/kg dissolved in water, given once daily by oral gavage (0.1 ml volume) for 5 consecutive days using steel cannula.

value: brainstem

tag: specific region

value: locus coeruleus


title: AAV-GN Patient 169


title: AAV-GN Patient 172


title: Locus coeruleus, untreated control, replicate 6

description: Library name: S_k_6


title: primary GBM patient 41 peripheral region


title: AAV-GN Patient 168


title: primary GBM patient 42 cortex


title: AAV-GN Patient 166


title: primary GBM patient 46


title: AAV-GN Patient 165


title: AAV-GN Patient 163


title: primary GBM patient 39 peripheral region


title: primary GBM patient 40


title: AAV-GN Patient 164


title: Locus coeruleus, untreated control, replicate 3

description: Library name: S_k_3


title: Locus coeruleus, untreated control, replicate 2

description: Library name: S_k_2


title: AAV-GN Patient 159


title: AAV-GN Patient 161


title: AAV-GN Patient 162


title: Locus coeruleus, untreated control, replicate 4

description: Library name: S_k_4


title: primary GBM patient 38 peripheral region


title: AAV-GN Patient 160


title: primary GBM patient 39 tumor core region


title: primary GBM patient 41 subventricular zone


title: AAV-GN Patient 158


title: AAV-GN Patient 157


title: Locus coeruleus, Vindeburnol treated, replicate 5

description: Library name: S_v_5

value: Vindeburnol


title: AAV-GN Patient 156


title: AAV-GN Patient 155


title: Locus coeruleus, untreated control, replicate 1

description: Library name: S_k_1


title: AAV-GN Patient 153


title: primary GBM patient 37 peripheral region


title: Locus coeruleus, Vindeburnol treated, replicate 4

description: Library name: S_v_4


title: AAV-GN Patient 170


title: Locus coeruleus, Vindeburnol treated, replicate 3

description: Library name: S_v_3


title: AAV-GN Patient 152


title: primary GBM patient 36


title: AAV-GN Patient 150


title: Locus coeruleus, Vindeburnol treated, replicate 1

description: Library name: S_v_1


title: primary GBM patient 37 tumor core region


title: AAV-GN Patient 149


title: AAV-GN Patient 143


title: Locus coeruleus, VB-127 treated, replicate 6

description: Library name: S_127_6


title: Locus coeruleus, VB-127 treated, replicate 5

description: Library name: S_127_5


title: AAV-GN Patient 151


title: primary GBM patient 35


title: AAV-GN Patient 146


title: AAV-GN Patient 147


title: primary GBM patient 34


title: AAV-GN Patient 142


title: AAV-GN Patient 145


title: AAV-GN Patient 144


title: primary GBM patient 38 tumor core region


title: primary GBM patient 28


title: AAV-GN Patient 140


title: AAV-GN Patient 141


title: Locus coeruleus, VB-127 treated, replicate 3

description: Library name: S_127_3


title: Locus coeruleus, Vindeburnol treated, replicate 2

description: Library name: S_v_2


title: AAV-GN Patient 139


title: Locus coeruleus, VB-127 treated, replicate 4

description: Library name: S_127_4


title: Locus coeruleus, VB-127 treated, replicate 2

description: Library name: S_127_2


title: Locus coeruleus, VB-127 treated, replicate 1

description: Library name: S_127_1


title: AAV-GN Patient 137


title: primary GBM patient 27


title: AAV-GN Patient 138


title: primary GBM patient 31


title: AAV-GN Patient 148


title: AAV-GN Patient 136


title: AAV-GN Patient 135


title: AAV-GN Patient 133


title: primary GBM patient 29


title: AAV-GN Patient 134


title: primary GBM patient 26


title: NIHHL group3

city: Xi'an

first: Yang

last: Fu

address: No.169, Changle West Road

department: School of Aerospace Medicine

institute: Air Force Medical university

description: Library name: NIHHL3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach
RNAs differential expression analysis was performed by DESeq2 software between two different groups
Assembly: Ensembl_release109
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: hippocampus

value: Noise exposure(110 dB,2 hours)


title: NIHHL group4

description: Library name: NIHHL4


title: AAV-GN Patient 132


title: NIHHL group2

description: Library name: NIHHL2


title: AAV-GN Patient 131


title: AAV-GN Patient 154


title: primary GBM patient 25


title: primary GBM patient 24


title: primary GBM patient 23


title: primary GBM patient 32


title: AAV-GN Patient 128


title: Control group3

description: Library name: Ctrl3

value: Blank control


title: AAV-GN Patient 126


title: NIHHL group1

description: Library name: NIHHL1


title: AAV-GN Patient 130


title: AAV-GN Patient 129


title: primary GBM patient 21

value: Brain tissue


title: AAV-GN Patient 124


title: primary GBM patient 22

value: IDH1 wild type


title: Control group1

description: Library name: Ctrl1


title: AAV-GN Patient 125

value: AAV-GN


title: AAV-GN Patient 120


title: primary GBM patient 15


title: primary GBM patient 18


title: TercPuma rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Library name: S_3486

data_processing:
Low-quality reads and adapter sequences were trimmed with Trimmomatic  (v0.38), employing the following parameters: HEADCROP:3 TRAILING:10 MINLEN:25
Alignment and quantification was done using STAR  (v2.5.2b)
Assembly: mm10
Supplementary files format and content: raw read count per genes in tab delimited files

source_name: bone marrow cells

extract_protocol:
RNA was extracted from BM-derived lineage marker negative cells with the RNeasy Micro kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: isolation of BM cells from femur of 2nd recipients; MACS sorting of lineage marker negative cells

value: bone marrow cells

value: lin-

value: G3 mTerc-/-Puma-/-

value: 2nd recipients


title: AAV-GN Patient 117


title: AAV-GN Patient 118


title: Control group2

description: Library name: Ctrl2


title: AAV-GN Patient 123


title: TercPuma rep2

description: Library name: S_3446


title: AAV-GN Patient 122


title: primary GBM patient 14


title: TercPuma rep1

description: Library name: S_3468


title: primary GBM patient 20


title: AAV-GN Patient 116


title: AAV-GN Patient 127


title: AAV-GN Patient 115


title: AAV-GN Patient 119


title: TercPuma rep4

description: Library name: S_3443


title: AAV-GN Patient 121


title: primary GBM patient 13


title: AAV-GN Patient 110


title: AAV-GN Patient 109


title: AAV-GN Patient 107


title: TERC rep4

description: Library name: S_3488

value: G3 mTerc-/-Puma+/+


title: Puma rep4

description: Library name: S_3456

value: puma-/-


title: AAV-GN Patient 113


title: AAV-GN Patient 112


title: AAV-GN Patient 114


title: Puma rep3

description: Library name: S_3453


title: AAV-GN Patient 102


title: AAV-GN Patient 108


title: primary GBM patient 12


title: AAV-GN Patient 103


title: TERC rep3

description: Library name: S_3457


title: primary GBM patient 11


title: TERC rep2

description: Library name: S_3436


title: AAV-GN Patient 111


title: primary GBM patient 10


title: Puma rep1

description: Library name: S_3447


title: TERC rep1

description: Library name: S_3481


title: primary GBM patient 7


title: AAV-GN Patient 98


title: AAV-GN Patient 104


title: primary GBM patient 5


title: AAV-GN Patient 105


title: AAV-GN Patient 101


title: SD016/10_BA46

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: CGND-HRA-04238

data_processing:
Demultiplex with bcl2fastq
Align to hg38 with STAR
Count using ENSEMBL v98 annotations with htseq-count
Assembly: hg38
Supplementary files format and content: BA44_BA46_COUNT_DATA.tsv.gz Raw integer count data in compressed TSV
Supplementary files format and content: BA44_BA46_TPM_DATA.tsv.gz Standardized TPM count data in compressed TSV
Supplementary files format and content: BA44_BA46_RNASEQ_PROCESSED.h5ad Combined RNAseq analysis in h5ad

extract_protocol:
Trizol
KAPA Stranded RNA-Seq Kit with RiboErase

tag: donor id

tag: Sex

value: Female

tag: age

tag: als phenotype

value: Control

tag: pmi


title: AAV-GN Patient 100

value: kidney


title: primary GBM patient 6


title: Puma rep2

description: Library name: S_3485


title: primary GBM patient 4


title: AAV-GN Patient 95


title: WT rep1

description: Library name: S_3466

value: wt


title: AAV-GN Patient 106


title: AAV-GN Patient 99


title: SD014/13_BA46

description: Library name: CGND-HRA-04237


title: WT rep3

description: Library name: S_3459


title: AAV-GN Patient 97


title: AAV-GN Patient 96


title: SD013/23_BA44

description: Library name: CGND-HRA-03763


title: AAV-GN Patient 91


title: WT rep2

description: Library name: S_3455


title: AAV-GN Patient 94


title: AAV-GN Patient 93


title: SD013/17_BA46

description: Library name: CGND-HRA-04236

value: Male


title: METTL4CK2_IP

first: Peihua

middle: Second Affiliated Hospital of Xi'an Jiaotong

last: Zhang

state: shannxi

address: NO.157 Xiwu Rd

department: National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy

institute: Xi'an Jiaotong University Second Affiliated Hospital

description: Library name: METTL4CK2_IP

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4), remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: A. lPVSA input peak.xlsx,8 lPVS8 input peak.xlsx,which contained methy lation site information of m6A
Supplementary files format and content: 4_genes fpkm expression.xlsx,which contained the expression information of various genes in various samples (Expression prof le)
Library strategy: MeRIP-seq

source_name: Bone marrow

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.Approximately more than 1μg of total RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) at 94℃ for 5 min.Then the cleaved RNA fragments（including rRNA fragments） were incubated with m6A antibody - dynabead compounds. Then the IP RNA was reverse-transcribed to create the first-strand cDNA by SMARTScribe™ Reverse Transcriptase (CloneTech，cat.634414，Japan)which were next used to add adapter and synthesise second-stranded DNAs with PCR by the following conditions:initial denaturation at 94℃ for 1 min; denaturation at 98℃ for 15 sec, annealing at 55℃ for 15 sec, and extension at 68℃ for 30 sec; and then final extension at 68℃ for 2 min,5 cycles. Then the amplified DNA-seq library is purified by immobilization onto pure beads. The cDNA sequences originating from rRNA reverse transcription were cut by ZapR v2 and R-Probes v2（for mammal） under the condition :incubation at 72℃ for 2 min,4℃ for 2 min，37℃ for 1h,72℃ for 10 min，4℃ forever.
The final library was amplified by second round PCR which consistent with the first round PCR program,and the number of PCR cycles increased to 12-16. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Bone marrow

value: Lin-ckit+ cells

value: Mettl14 fl/fl;Mx1-Cre; KrasLSL G12D/+


title: AAV-GN Patient 92


title: AAV-GN Patient 87


title: METTL4CK1_input

description: Library name: METTL4CK1_input


title: METTL4CK2_input

description: Library name: METTL4CK2_input


title: AAV-GN Patient 89


title: AAV-GN Patient 86


title: AAV-GN Patient 82


title: AAV-GN Patient 83


title: Detroit562, control treatment, sample 2

city: Cambridge

first: Vanessa

middle: Martine

last: Kelley

state: MA

address: 300 Binney

department: Gerstner Center for Cancer Diagnostics

institute: The Broad Institute

description:
Library name: DCNT2
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).

data_processing:
All analysis was performed by the Yale Center for Genome analysis. Reads were aligned to index sequences using the Bowtie aligner, and a maximum of one mismatch was allowed in the 20bp sgRNA sequence.  The number of uniquely aligned reads for each library sequence was calculated after alignment for each of the three biologically independent replicates.  Differential sgRNA expression was analyzed in R using the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout method.  FDR-corrected p-value <0.05 was considered statistically significant.
Assembly: GRCh38
Supplementary files format and content: The processed data file contains one tab explaining the global statistics regarding gRNA representation and differential expression between control and irradiated samples.   The second tab contains the gRNA Brunello ID, the gene that gRNA targets, and the gRNA counts for that gRNA detected in each sample.  The third tab contains differential expression data between gRNA counts in the control and irradiated samples, such as which gRNAs were significantly enriched or depleted in the irradiated samples vs. the control samples.

growth_protocol: Cells were grown in DMEM + 10% FBS.

extract_protocol:
Genomic DNA isolation was performed using QIAamp DNA Blood Midi kit (Cat# 51104. Qiagen, Hilden, Germany) and sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A).
Samples were sent to the Yale Center for Genome Analysis (RRID:SCR_027324).  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).

treatment_protocol: For each replicate of the pooled screen ~10 x 106 Cas9-expressing cells were transduced at a MOI of ~0.3 with lentivirus [Cat#75312, RRID:Addgene_75312 (gRNAs 1-4) and Cat#75313, RRID:Addgene_75313 (gRNAs 5-8)] library and selected with 2 µg/mL puromycin (Gibco) for 7 days.  After puromycin selection, pooled cells were irradiated (2 Gy daily for 4 consecutive days) with a Precision X-Ray 320kV orthovoltage unit. Fourteen days after the final radiation treatment, cells were collected with unirradiated cells from the same experiment used as a control.

tag: cell line

value: Head and Neck Cancer cell line

value: WT

value: Control treatment


title: Detroit562, radiation, sample 1

description:
Library name: DXRT1
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).

value: Radiation (2Gy X4)


title: Detroit562, radiation, sample 2

description:
Library name: DXRT2
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: METTL4CK1_IP

description: Library name: METTL4CK1_IP


title: CK1_IP

description: Library name: CK1_IP

value: Mx1-Cre; KrasLSL G12D/+


title: AAV-GN Patient 90

value: AAV-GN


title: CK2_IP

description: Library name: CK2_IP


title: AAV-GN Patient 85


title: AAV-GN Patient 84


title: AAV-GN Patient 81


title: CK2_input

description: Library name: CK2_input


title: CK1_input

description: Library name: CK1_input


title: AAV-GN Patient 77


title: Cal27, radiation, sample 3

description:
Library name: CXRT3
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).

data_processing:
All analysis was performed by the Yale Center for Genome analysis. Reads were aligned to index sequences using the Bowtie aligner, and a maximum of one mismatch was allowed in the 20bp sgRNA sequence.  The number of uniquely aligned reads for each library sequence was calculated after alignment for each of the three biologically independent replicates.  Differential sgRNA expression was analyzed in R using the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout method.  FDR-corrected p-value <0.05 was considered statistically significant.
Assembly: GRCh38
Supplementary files format and content: The processed data file contains one tab explaining the global statistics regarding gRNA representation and differential expression between control and irradiated samples.   The second tab contains the gRNA Brunello ID, the gene that gRNA targets, and the gRNA counts for that gRNA detected in each sample.  The third tab contains differential expression data between gRNA counts in the control and irradiated samples, such as which gRNAs were significantly enriched or depleted in the irradiated samples vs. the control samples.
Library strategy: CRISPR screen


title: AAV-GN Patient 80


title: Detroit562, control treatment, sample 3

description:
Library name: DCNT3
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: AAV-GN Patient 78


title: Detroit562, control treatment, sample 1

description:
Library name: DCNT1
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: Detroit562, radiation, sample 3

description:
Library name: DXRT3
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: Cal27, radiation, sample 2

description:
Library name: CXRT2
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: AAV-GN Patient 73


title: AAV-GN Patient 76


title: AAV-GN Patient 72


title: primary GBM patient 3

value: Brain tissue

value: IDH1 wild type


title: WT2_IP

description: Library name: WT2_IP


title: WT1_IP

description: Library name: WT1_IP


title: AAV-GN Patient 71


title: WT2_input

description: Library name: WT2_input


title: AAV-GN Patient 68


title: AAV-GN Patient 88


title: AAV-GN Patient 74


title: heart, E18.5, pkm1-KO, rep3

city: Shanghai

first: zhang

last: dandan

address: 1239 Siping Road, Shanghai, P.R. China

department: School of  Life Sciences and Technology

institute: Tongji University

description: Library name: Sample 6

data_processing:
Cutadapt (V1.18) was used to remove adaptor sequences and low-quality bases.
Clean sequencing reads were aligned to the reference genome using the Hisat2 alignment tool.
Transcript assembly was performed using StringTie.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using TRIzol reagent (TaKaRa). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RiboErase Kit and KAPA RNA HyperPrep Kit following manufacturer's instructions.

value: heart


title: AAV-GN Patient 79


title: AAV-GN Patient 75


title: AAV-GN Patient 65


title: AAV-GN Patient 66


title: Detroit562, JAK1 knockout gRNA, sample 3

description: Library name: Det_JAK1KO_3

data_processing:
FASTQ file trimming and data analysis was performed in accordance with standard protocols at the Yale Center for Genome Analysis.
Assembly: GRCh38
Supplementary files format and content: The processed data file contains the gene name, Ensembl gene code, gene name, average differential expression between control and JAK1 KO samples, and raw read counts for each gene for all three replicates for each cell type.

growth_protocol: Cells were grown in DMEM + 10% FBS with puromycin selection (1ug/ml) for the gRNA plasmid and blasticidin selection (7.5ug/ml) for the Cas9 plasmid.

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit (Cat#74104) according to manufacturer’s instructions.
Samples were sent to the Yale Center for Genome Analysis (RRID:SCR_027324) for poly-A RNA sequencing (HiSeq paired-end, 100bp) using NovaSeq (RRID:SCR_024569).

treatment_protocol: Cells were split at passage 2 into three T75 flasks, one for each biological replicate.  Two million cells from each T75 flask were then plated into 10cm dishes on separate, subsequent days.  Forty-eight hours after seeding, cells were washed with PBS, tyrpsinized, and counted for RNA isolation.

value: JAK1 KO

value: No treatment, baseline assessment


title: AAV-GN Patient 70

value: kidney


title: AAV-GN Patient 69


title: Detroit562, JAK1 knockout gRNA, sample 2

description: Library name: Det_JAK1KO_2


title: Cal27, control treatment, sample 2

description:
Library name: CCNT2
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: Cal27, control treatment, sample 3

description:
Library name: CCNT3
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: AAV-GN Patient 61


title: WT1_input

description: Library name: WT1_input


title: Cal27, control treatment, sample 1

description:
Library name: CCNT1
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: heart, E18.5, WT, rep2

description: Library name: Sample 2

value: wildtype


title: AAV-GN Patient 64


title: Cal27, radiation, sample 1

description:
Library name: CXRT1
sgRNA sequence were amplified using a PCR reaction according to the manufacturer’s protocol (Addgene/Broad Institute) with maintenance of ~400x coverage of the human Kinome library.  All PCR reactions were performed using Ex Taq DNA polymerase (Clontech, RR001A). Primers and barcode sequence are listed in the Supplemental Methods Tables 2-3.  Sequencing was performed with NovaSeq paired-end 100bp reads (Illumina NovaSeq X, RRID:SCR_024569).


title: Detroit562, non-targeting control gRNA, sample 2

description: Library name: Det_NT2_2


title: heart, E18.5, pkm1-KO, rep1

description: Library name: Sample 4


title: AAV-GN Patient 67


title: heart, E18.5, WT, rep3

description: Library name: Sample 3


title: AAV-GN Patient 63


title: AAV-GN Patient 60


title: AAV-GN Patient 53


title: Detroit562, non-targeting control gRNA, sample 1

description: Library name: Det_NT2_1


title: AAV-GN Patient 62


title: Detroit562, JAK1 knockout gRNA, sample 1

description: Library name: Det_JAK1KO_1


title: heart, E18.5, WT, rep1

description: Library name: Sample 1


title: E16.5_Wt1creER_Myrf_tdTom_mutant_rep1

city: La Jolla

first: Gidsela

last: Luna

state: California

address: 9500 Gilman Dr

institute: UC San Diego

description: Library name: E16.5_Mutant_rep1

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cell Ranger 6.0.2 (10x Genomics) and reads were aligned. with the mm10-2020-A transcriptome to generate the filtered feature barcode matrix
Assembly: Mouse mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Lung

extract_protocol:
For Single Cell RNA-Sequencing, timed Myrf Fl/Fl;R26TdTomato/R26TdTomato x Wt1creERT2;Myrf Fl/Fl mating’s were set up and pregnant females were injected with Tamoxifen I.P at E12.5. Females were euthanized at E16.5 and mutant and Cre+ embryos were screened for TdTom+ fluorescence. Mutant and Cre Control lungs were dissected and genotyped based on visual lung/cell shape phenotypes. All genotypes were later confirmed with PCR. Mutant and Cre Control lungs were pooled (3-5 per genotype) and lungs were dissociated into single cells. Samples were sorted using the BD FACSAria II (BD Biosciences) and gating was set up using single color controls. Approximately 50,000 TdTom+Dapi- Mutant and Controls were collected. Approximately 16,000 cells for each genotype were loaded into the 10x Chromium Controller (10x Genomics).
libraries were constructed using manufacturers protocol (Chromium Single Cell 3’ V3 Kit,10x Genomics)

value: Lung

value: tdTom+ Mesothelial Cells

value: Mutant


title: AAV-GN Patient 57


title: AAV-GN Patient 50


title: Cal27, JAK1 knockout gRNA, sample 2

description: Library name: JAK1_Con2

source_name: Head and Neck Cancer cell line

growth_protocol: Cells were grown in DMEM + 10% FBS with puromycin selection (2ug/ml) for the gRNA plasmid and blasticidin selection (7.5ug/ml) for the Cas9 plasmid.

value: Head and Neck Cancer


title: AAV-GN Patient 54


title: Detroit562, non-targeting control gRNA, sample 3

description: Library name: Det_NT2_3

value: Head and Neck Cancer cell line


title: AAV-GN Patient 55


title: AAV-GN Patient 47


title: E16.5_Wt1creER_Myrf_tdTom_mutant_rep2

description: Library name: E16.5_Mutant_rep2


title: Cal27, non-targeting control gRNA, sample 3

description: Library name: NT2_Con3

value: WT


title: AAV-GN Patient 51


title: E16.5_cre_control_tdTom_rep1

description: Library name: E16.5_Control_rep1

value: Control


title: E16.5_cre_control_tdTom_rep2

description: Library name: E16.5_Control_rep2


title: AAV-GN Patient 56


title: heart, E18.5, pkm1-KO, rep2

description: Library name: Sample 5


title: AAV-GN Patient 46


title: AAV-GN Patient 58


title: Cal27, JAK1 knockout gRNA, sample 3

description: Library name: JAK1_Con3


title: AAV-GN Patient 52


title: AAV-GN Patient 45


title: AAV-GN Patient 44


title: Cal27, non-targeting control gRNA, sample 2

description: Library name: NT2_Con2


title: AAV-GN Patient 49


title: E13.5_Tbx4tetOcre_MyrfE6_lung_rep4

description:
Library name: Tbx4tetOcre_MyrfE6_mutant_lung_rep4
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/M4_Myrf.bam

data_processing:
FASTQ files were aligned to the GRCm38 mouse gennome using STAR.
FeatureCounts was used for read counting and DESeq2 was used to perform differential gene expression.
Assembly: mm10
Supplementary files format and content: .txt file contains raw counts for each sample

extract_protocol:
RNA was isolated with TRIzol LS using standard procedures and purified with the RNAeasy microkit(Qiagen).
cDNA Libraries were constructed using the Illumina mRNA Stranded prep (Illumina).


title: AAV-GN Patient 48


title: Cal27, JAK1 knockout gRNA, sample 1

description: Library name: JAK1_Con1


title: E13.5_Tbx4tetOcre_MyrfE6_lung_rep1

description:
Library name: Tbx4tetOcre_MyrfE6_mutant_lung_rep1
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/M1_Myrf.bam


title: AAV-GN Patient 38


title: E13.5_Tbx4tetOcre_MyrfE6_lung_rep3

description:
Library name: Tbx4tetOcre_MyrfE6_mutant_lung_rep3
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/M3_Myrf.bam


title: E13.5_cre control_lung_rep4

description:
Library name: cre_control_lung_rep4
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/C4_Myrf.bam

value: cre control


title: E13.5_Tbx4tetOcre_MyrfE6_lung_rep2

description:
Library name: Tbx4tetOcre_MyrfE6_mutant_lung_rep2
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/M2_Myrf.bam


title: AAV-GN Patient 40


title: AAV-GN Patient 43


title: VCaP, control, replicate2

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

description: Library name: VCaP_CTCF_control_replicate2

data_processing:
Raw sequencing reads in FASTQ format were processed using a custom nextflow pipeline (https://github.com/ylab-hi/nf_hichip).
Assembly: hg38
Supplementary files format and content: .hic Hi-ChIP matrix
Library strategy: HiChIP

source_name: VCaP

extract_protocol:
Chromatin from 5 million of VCaP cells was crosslinked with 1% formaldehyde for 10 minutes, digested with the MboI restriction enzyme, end-repaired with dNTP including biotin-labeled dATP, and ligated with T4 DNA ligase. Ligated chromatin was sonicated with Qsonica Q800 (1.5 minutes total sonication time, 50% amplitude) and processed with ChIP using an CTCF antibody (Cell Signaling, #3418, 15ul per HiChIP). ChIP-enriched DNA was de-crosslinked, purified, and processed with streptavidin beads to enrich ligated DNA fragments
Sequencing libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit, and subjected to high-throughput sequencing.

treatment_protocol: For IGF1R-AS1 knockdown, one siRNA were designed targeting IGF1R-AS1 and purchased from Horizon Discovery. VCaP cells in 6 well plate were transfected with 30 pmol siRNAs using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacture instruction, and cells were harvested for analysis 72 h after transfection.

value: VCaP

value: epithelial cell


title: AAV-GN Patient 39

value: AAV-GN


title: AAV-GN Patient 42


title: AAV-GN Patient 35


title: VCaP, si025, replicate2

description: Library name: VCaP_CTCF_si025_replicate2

value: IGF1R-AS1 knockdown


title: AAV-GN Patient 41


title: AAV-GN Patient 36


title: Cal27, non-targeting control gRNA, sample 1

description: Library name: NT2_Con1


title: AAV-GN Patient 37


title: E13.5_cre control_lung_rep3

description:
Library name: cre_control_lung_rep3
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/C3_Myrf.bam


title: AAV-GN Patient 31


title: VCaP, control, replicate1

description: Library name: VCaP_CTCF_control_replicate1


title: VCaP, si025, replicate1

description: Library name: VCaP_CTCF_si025_replicate1


title: E13.5_cre control_lung_rep2

description:
Library name: cre_control_lung_rep2
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/C2_Myrf.bam


title: AAV-GN Patient 34


title: AAV-GN Patient 59


title: AAV-GN Patient 28


title: VCaP, control, replicate3

description: Library name: VCaP_control_replicate3

data_processing:
Raw sequencing reads in FASTQ format were processed using the ENCODE ATAC-seq pipeline (v2.2.1). Reads were first trimmed using Cutadapt (v1.9.1) and aligned to hg38 using Bowtie2 (v2.2.6). Mapped reads overlapping blacklisted regions or mitochondrial DNA, as well as duplicate reads, were removed using SAMtools (v1.7) and PICARD MarkDuplicates (v1.26) respectively.
Assembly: hg38
Supplementary files format and content: The bigWig files are coverage tracks.

extract_protocol:
DNA was extracted from VCaP cells using Active Motif ATAC-Seq Kit (53150).
Sequencing libraries were constructed using Active Motif ATAC-Seq Kit (53150).

treatment_protocol: For SMARCA1 knockdown, one siRNAs was designed targeting on SMARCA1, and purchased from OriGene Technologies. VCaP cells in 6 well plate were transfected with 30 pmol siRNAs using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacture instruction, and cells were harvested for RNA extraction 72 h after transfection.


title: Epithelium_IgG_500k_Rep2

description: Library name: 6GL_Epithelium_IgG_500k_Rep2

data_processing:
FastQC was used to perform quality control metrics on sequencing samples. Tru-Seq Adapters and Poly G tails were trimmed using Cutadapt (version 4.8).
Alignment to the mm10 genome was performed using Bowtie2(version 2.5.3) using the following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using Macs2(version 2.2.9.1) using the following parameters: --broad --broad-cutoff 0.1 --keep-dup all.
To generate bigwig files for IGV visualization, deepTools (version 3.5.5 ) was used. bamCoverage was used with the following parameters : --binSize 20 --smoothLength 60 -- extendReads --normalizeUsing CPM --centerReads. Peak visualization was performed using deepTools (version 3.5.5) computematrix and plotHeatmap commands.
Diffbind (version 3.6.5) was used to identify differentially enriched peaks between mesothelial and epithelial cells using default parameters (summits=500).  Data was normalized using edgeR. Motif analysis was performed using Homer in both differentially enriched peaks (bedtools v2.31.1) peaks using findMotifsGenome.pl and -size 500.
Assembly: mm10
Supplementary files format and content: bigwig, broadPeak(except for IgG control)
Library strategy: CUT&Run

extract_protocol:
For CUT&RUN, Timed Myrf Fl/Fl mating’s were set up and pregnant E16.5 females were euthanized at E16.5. Lungs were pooled and and dissociated into single cells. After dissociation, cells were resuspended at a max staining volume of 50 million cells/mL. Cells were blocked with BD FC block (1:200, BD Biosciences) for 20 minutes on ice. Cells were stained with the following antibodies: APC/Cyanine7 anti-mouse CD326 (1:500, Biolegend), APC anti-mouse Podoplanin (1:500, Biolegend), FITC anti-mouse CD31 (1:50, Biolegend), Brilliant Violet 510™ anti-mouse CD45 (1:100) for 25 minutes on ice. Two washes with DPBS+ 0.2% FBS were performed, and prior to sorting samples were resuspended in DPBS + 0.2% FBS and DAPI(1:16,000). Samples were sorted using the BD FACSAria II (BD Biosciences). Mesothelial Cells were sorted as PDPN+EPCAM-CD45-CD31-DAPI- and Epithelial Cells were sorted as PDPN+EPCAM+CD45-CD31-DAPI-. Approximately 60-100k Mesothelial cells were collected and approximately 100-500k Epithelial cells were collected. CUT&RUN was performed using the CUT&RUN Assay Kit (CST) according to manufacturer’s instructions. Live sorted 60-100k mesothelial and epithelial cells were used to profile H3K27ac and 500K epithelial cells were used to profile the IgG negative control.
DNA library prep was performed using the KAPA HyperPrep Kit (Roche) and sequenced on the NovaSeq 6000 with 150 bp Paired End Reads


title: E13.5_cre control_lung_rep1

description:
Library name: cre_control_lung_rep1
column name in Myrf_counts: /home/giluna/scratch/Myrf_E13.5/star_bams/C1_Myrf.bam


title: VCaP, siSMARCA1, SiC, replicate2

description: Library name: VCaP_siSMARCA1_C_replicate2


title: AAV-GN Patient 29

data_processing:
Raw gene expression data were analyzed using nSolver Analysis Software v4.0 (NanoString Technologies) with the Advanced Analysis Module v2.0. The software first identifies and checks standard quality controls such as imaging, binding density, and positive controls to ensure the samples were read and reported properly.
For gene expression data, raw counts were normalized to the positive controls and then log2 transformed. To reduce technical bias, background thresholding was performed using the eight negative controls included within the panel. Genes with counts below a threshold of three standard deviations above the mean background signal were excluded from subsequent analysis. Data normalization was performed on background-thresholded samples using internal positive controls and selected housekeeping genes that were identified using the geNorm algorithm. Data were normalized for hybridization and counting efficiency and kept within the range of 0.3–3 (Nanostring recommended).

extract_protocol: Kidney biopsies containing at least 4 glomeruli and sufficient tissue after clinical use were selected for subsequent mRNA extraction. This pragmatic cutoff was chosen to reflect the broad range of biopsies encountered in clinical practice. Ten-micrometer sections were cut from the formalin-fixed paraffin-embedded (FFPE) blocks and placed in 2 ml microcentrifuge tubes after discarding the first two sections (to avoid collecting RNA that would have been damaged by contact with air). Whole sections, including glomeruli and tubulo-interstitium were used. The number of sections per sample was dependent on the size of the FFPE tissue. Preliminary studies allowed us to determine that 3 to 6 sections were necessary to obtain a minimum of 100 ng of total RNA.  Extraction of total RNA from FFPE specimens was performed using the High Pure FFPE RNA Isolation Kit (Roche Molecular Diagnostics, Rotkreuz, Switzerland) according to the manufacturer’s instructions. Extraction of RNA was either performed immediately after FFPE sectioning or sections were frozen at -20°C until the extraction was performed.  RNA purity and quantification were assessed by spectrophotometry (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA): RNA with a 260/280 ratio of 1.7–2.0 as well as a 260/230 ratio in the range of 1.8–2.3 were considered to be of acceptable quality for downstream assays). RNA quality analysis (fragmentation analysis) was performed to assess the integrity of RNA by measuring the proportion of RNA fragments greater than 200 base pairs (DV200) (TapeStation; Agilent, Santa Clara, CA). The resulting data were used to calculate the corrected RNA input for each NanoString hybridization reaction following the manufacturer’s instructions. Only samples with DV200 > 30% were considered for subsequent analyses. RNA was stored at −80 °C prior to NanoString assays. RNA was diluted in nuclease free water at a concentration of 20 ng/μL immediately before the assay, and 100 ng (5 µL) of total RNA per sample were used for quantification.


title: AAV-GN Patient 32


title: AAV-GN Patient 33


title: Epithelium_H3K27ac_200k_Rep2

description: Library name: 4GL_Epithelium_H3K27ac_200k_Rep2


title: AAV-GN Patient 26


title: VCaP, siSMARCA1, SiC, replicate1

description: Library name: VCaP_siSMARCA1_C_replicate1


title: Mesothelium_H3K27ac_100k_Rep2

description: Library name: 2GL_Mesothelium_H3K27ac_100k_Rep2


title: VCaP, control, replicate2

description: Library name: VCaP_control_replicate2


title: AAV-GN Patient 27


title: AAV-GN Patient 23


title: AAV-GN Patient 30


title: AAV-GN Patient 22


title: Epithelium_H3K27ac_100k_Rep1

description: Library name: 3GL_Epithelium_H3K27ac_100k_Rep1


title: AAV-GN Patient 25


title: VCaP, control, replicate1

description: Library name: VCaP_control_replicate1


title: Epithelium_IgG_500k_Rep1

description: Library name: 5GL_Epithelium_IgG_500k_Rep1


title: AAV-GN Patient 18


title: AAV-GN Patient 24


title: VCaP, siSMARCA1, SiC, replicate3

description: Library name: VCaP_siSMARCA1_C_replicate3


title: 3066_PBMC

city: New Haven

first: Shelli

last: Farhadian

state: CT

address: 135 College St, PO BOX 208022

institute: Yale School of Medicine

description:
Library name: 3066_PBMC
final_processed_tpm_values_pbmc.txt

data_processing:
Reads were trimmed for quality and length using trimmomatic.
Trimmed reads were mapped to hg38 genome using HiSAT2
Per-gene count matrices were geneated using StringTie
Gene count matrices and associated metadata were analyzed using DESeq2 in R, and plotted using appropriate software.
Assembly: hg38
Supplementary files format and content: TPM matrix. Tab separate values file with TPM values for each gene in each sample.

source_name: PBMC

extract_protocol:
DNA/RNA was extracted from thawed CSF cells using the AllPrep DNA/RNA Micro Kit (CAT No 80284). DNA/RNA was extracted from thawed PBMC using the AllPrep DNA/RNA/miRNA Universal Kit (CAT No: 80224)
Paired end library preparation

value: PBMC


title: AAV-GN Patient 20


title: AAV-GN Patient 17


title: AAV-GN Patient 16


title: Mus CD8+ T cell, KO, 48h , rep1

description: Library name: Sample13

data_processing:
software we used are bowtie2,silva and Hisat2
Assembly: GRCm38
Supplementary files format and content: xlsx files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for the construction of sequencing libraries.
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system. RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library. After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing.

value: lymph node

value: KO


title: AAV-GN Patient 14

value: kidney


title: 3070_PBMC

description:
Library name: 3070_PBMC
final_processed_tpm_values_pbmc.txt


title: 3059_PBMC

description:
Library name: 3059_PBMC
final_processed_tpm_values_pbmc.txt


title: Mesothelium_H3K27ac_25k_Rep1

description: Library name: 1GL_Mesothelium_H3K27ac_25k_Rep1


title: Mus CD8+ T cell, WT, 48h , rep2

description: Library name: Sample12


title: Mus CD8+ T cell, WT, 48h , rep1

description: Library name: Sample11


title: Mus CD8+ T cell, KO, 48h , rep2

description: Library name: Sample14


title: AAV-GN Patient 13


title: AAV-GN Patient 19


title: AAV-GN Patient 9


title: AAV-GN Patient 15


title: AAV-GN Patient 10


title: AAV-GN Patient 11


title: 3065_PBMC

description:
Library name: 3065_PBMC
final_processed_tpm_values_pbmc.txt


title: Mus CD8+ T cell, WT, 24h , rep2

description: Library name: Sample8


title: AAV-GN Patient 12


title: AAV-GN Patient 21


title: 3051_PBMC

description:
Library name: 3051_PBMC
final_processed_tpm_values_pbmc.txt


title: Mus CD8+ T cell, KO, 24h , rep2

description: Library name: Sample10


title: 3067_PBMC

description:
Library name: 3067_PBMC
final_processed_tpm_values_pbmc.txt


title: Mus CD8+ T cell, KO, 24h , rep1

description: Library name: Sample9


title: 3046_V2_PBMC

description:
Library name: 3046V2_PBMC
final_processed_tpm_values_pbmc.txt


title: AAV-GN Patient 8


title: 3039_PBMC

description:
Library name: 3039_PBMC
final_processed_tpm_values_pbmc.txt


title: Mus CD8+ T cell, KO, 12h , rep1

description: Library name: Sample5


title: AAV-GN Patient 6


title: AAV-GN Patient 1

description:
duplicate AAV1 for batch calibration
AAV1


title: 2080_PBMC

description:
Library name: 2080_PBMC
final_processed_tpm_values_pbmc.txt

value: NP-Long COVID


title: AAV-GN Patient 4


title: AAV-GN Patient 2 (duplicate)

description:
duplicate AAV2 for batch calibration
AAV2_dup


title: Mus CD8+ T cell, WT, 24h , rep1

description: Library name: Sample7


title: Mus CD8+ T cell, WT, 12h , rep2

description: Library name: Sample4


title: 2081_PBMC

description:
Library name: 2081_PBMC
final_processed_tpm_values_pbmc.txt


title: 3034_PBMC

description:
Library name: 3034_PBMC
final_processed_tpm_values_pbmc.txt


title: 2075_PBMC

description:
Library name: 2075_PBMC
final_processed_tpm_values_pbmc.txt


title: 2063_PBMC

description:
Library name: 2063_PBMC
final_processed_tpm_values_pbmc.txt


title: Mus CD8+ T cell, KO, 0h

description: Library name: Sample2


title: RNA-seq of H_D34 from HEPE irradiation, replicate 3

city: hangzhou

first: xinyuan

last: feng

state: zhejiang

address: xihu street yuhangtang road 866

institute: zhejiang university

description: Library name: H_D34_Rep3

data_processing:
Sequence reads were trimmed for adaptor sequence or low quality sequence using fastp benchwork  (parameter- Quality limit: 0.05).
Trimmed sequence were mapped to reference sequence using Bowtie 2 (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performend using RSEM software.
Assembly: Genome of Streptomyces lividans 1326 (SAMN48554414) was used as reference sequence for read alignment.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includeTPM values for each Sample

organism: Streptomyces lividans

source_name: bacterial cell

growth_protocol: The cryo-preserved cultures of S.lividans 1326 were plated on SFM agar (2% soybean, 2%mannitol, 2% agar, pH 7.0). From the agar plate, a single colony was picked and inoculated into YEME medium (0.3% yeast extract, 0.3% malt extract, 0.5% peptone, 1% glucose, 10.7% sucrose, pH 7.0) and incubated at 30℃ for 1-2days.

extract_protocol:
Total RNA was extracted from the tissue using Trizol reagent
RNA-seq transcriptome library was prepared following the NEBNext® Ultra II™ Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The spore suspension was used for mutagenesis experiments.

value: bacterial cell

value: Mutant 2

value: HEPE irradiation


title: RNA-seq of A_D28 from HEPE irradiation, replicate 1

description: Library name: A_D28_Rep1

value: Mutant 3


title: Mus CD8+ T cell, WT, 0h

description: Library name: Sample1


title: Mus CD8+ T cell, WT, 12h , rep1

description: Library name: Sample3


title: AAV-GN Patient 3


title: AAV-GN Patient 1 (duplicate)

description:
duplicate AAV1 for batch calibration
AAV1_dup


title: RNA-seq of H_D34 from HEPE irradiation, replicate 1

description: Library name: H_D34_Rep1


title: AAV-GN Patient 7


title: AAV-GN Patient 2

description:
duplicate AAV2 for batch calibration
AAV2


title: RNA - Pancreas - 28 days post-cerulein injection #1

city: Padua

first: Marco

last: Fantuz

state: Veneto

address: Via Orus, 2

country: Italy

institute: Veneto Institute of Molecular Medicine

description:
Library name: 2302_28days_1_RNA
pooled file from 6 sequencing runs

data_processing:
The sequencing data was aligned to the mouse genome (mm10/GRCm38) using cellrangerarc (10x Genomic - v2.0.0) and afterwards aggregated. The 10x format matrix files are provided as processed data. To reduce the noise caused by ambient RNA, the R package SoupX2 v1.5.259 was used with the manually set gene sets following here: (Cpa1, Cpa2, Clps, Reg1, Ctrb1, Prss2); (Bicc1, Cftr, Sox5); (Ins1, Ins2, Iapp); (Wt1, Lama2); (Pecam1, Ptprb); (Dock2, Ptprc). The obtained bam files and the correspective indexes are provided as processed data files.
The data was filtered for quality control, subjected to unsupervised clustering, integrated and analyzed using the R packages Seurat v4.1.028 and Signac v1.6.060. During quality control all nuclei with less than 100 genes and 1000 molecules and more than 30,000 molecules in the RNA assay, 160000 molecules in the ATAC assay and more than 5 % mitochondrial genes were removed. The dimensional reduction, clustering and integration was done on both assays independently. Afterwards, a weighted nearest neighbors (WNN) graph was calculated combining the RNA and ATAC modalities.
Upon WNN integration, Principal Component analysis was run on the integrated dataset employing the RunPCA command of the Seurat pipeline, and dimensions up to PC30 were selected using the ElbowPlot method to identify the top 3000 highly variable features using the FindVariableFeatures command. Upon selection of variable features, neighbor identification and cluster selection was performed using respectively the FindNeighbors and FindClusters commands on the integrated WNN graph. Top 500 variable features  for the RNA assay were employed to obtain an heatmap of expressed genes stratified for experimental timepoints using the heatmap base R function. Cluster names were then assigned using a panel of well-described markers. The resulting Seurat object is provided as a processed supplementary data file.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz files - cell/features matrixes in 10x format
Supplementary files format and content: features.tsv.gz files - features matrixes in 10x format
Supplementary files format and content: barcode.tsv.gz.files - cell matrixes in 10x format
Supplementary files format and content: full_dataset_Seurat.rds - full processed Seurat object for the whole dataset

molecule: nuclear RNA

source_name: purified nuclei from flash-frozen powderized whole pancreas

growth_protocol: For single nucleus analysis of mouse pancreata, three groups were examined (n=3, each group): one control group (saline injected), two experimental groups (cerulein injected). All animals were littermates purchased from Jackson laboratories. Each group was housed in a dedicated cage.

extract_protocol:
Pancreata from mice were collected upon sacrifice; after collection, first, a small piece of each clamp frozen pancreas piece was pulverized by using a liquid nitrogen cooled Cellcrusher. Nuclei were isolated from tissue powder employing a protocol for isolating nuclei from RNAse-rich tissue that uses citric acid, previously described (Tosti et al., Gastroenterology, 2019). In short, one small spoon of tissue powder (5-10 mg approximately) was suspended into 1 mL of pre-cooled S25 buffer, composed by 1.5M sucrose (Sigma-Aldrich – S7903), 250mM citric acid (Sigma-Aldrich – C0759), 0.1% Hoechst 33258 (Life Technologies – H3569), inside a glass douncer tissue grinder (DWK Life Sciences - 357358). With 5 strokes of a tight pestle every 3 minutes for 10 minutes, nuclei were released into the buffer. Subsequently, the lysate was transferred through a 35 μm strainer into a 1.5 mL Eppendorf tube and centrifuged at 4°C for 5 min at 500 g. Afterwards, the supernatant was removed and the pellet was resuspended in 500 μL S25 buffer. To remove clearly visible cell debris, a density centrifugation was performed, by carefully adding 500 μL S88 buffer, composed by 1.5M sucrose and 250mM citric acid, to the bottom of the Eppendorf tube followed by centrifugation at 4°C for 10 min at 1000 g. After removal of the supernatant, the nuclei were resuspended in 250 μL S25 buffer, their integrity was checked and they were counted with a CountessTM II FL Automated Cell Counter (Thermo Fisher Scientific). The samples were spun down again at 4°C for 5 min at 500 g, filtered through a 10 μm strainer and resuspended in 100μL resuspension buffer.
The nuclei suspension was diluted to load 10000 nuclei per sample onto the 10x Genomics Chromium controller. Libraries were generated with the Multiome Kit (10x Genomics - PN231000283) following the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide and the finished libraries were sequenced on an Illumina NovaSeq6000 (S4, paired-end). The provided fastq files are provided for simplicity as concatenation of 4/6 sequencing runs, as indicated, as named according to 10X cellranger conventions.

treatment_protocol: Acute pancreatitis was induced in 6- to 7-week-old mice of the indicated genotype. Mice were injected with caerulein (50 μg/kg diluted in saline; Sigma-Aldrich) or saline on two consecutive days once every hour for 8 hours each day. The first day of injection was considered day 0.

value: wild-type, 28 days post-injection

value: 8 hourly injections/die, 2 following days - cerulein 50 mg/kg


title: AAV-GN Patient 5


title: 2057_V2_PBMC

description:
Library name: 2057V2_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA-seq of WT strain, replicate 1

description: Library name: S1326_1_Rep1

value: WT

value: control


title: RNA-seq of A_D28 from HEPE irradiation, replicate 2

description: Library name: A_D28_Rep2


title: 2054_PBMC

description:
Library name: 2054_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA-seq of H_D34 from HEPE irradiation, replicate 2

description: Library name: H_D34_Rep2


title: RNA-seq of H_D1 from HEPE irradiation, replicate 3

description: Library name: H_D1_Rep3

value: Mutant 1


title: PC-9 cells, shKRT19-1, RNA-Seq rep2

city: Zhengzhou

first: Yue

last: Du

address: No. 1, Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

department: Department of Clinical Laboratory

institute: The First Affiliated Hospital of Zhengzhou University

description: Library name: PC-9_shKRT19-1_rep2

data_processing:
The raw image data files obtained from Illumina Hiseq™ are converted into raw sequencing sequences (Sequenced Reads) through CASAVA base calling analysis.
Use Trimmomatic to perform quality trimming and obtain relatively accurate, valid data. Remove sequences containing N bases and adapter sequences from reads. Remove low-quality bases (Q value <20) from reads in the 5' to 3' direction using a sliding window method (window size of 5 bp). Remove reads shorter than 35 nt and their paired reads.
Use HISAT2 to align the sample's effective data to the reference genome and calculate the mapping information. Use RSeQC to analyse redundant sequences and insert fragment distribution based on the alignment results. Use Qualimap to analyse uniformity distribution and genome structure based on the alignment results. Use BEDTools to analyse gene coverage and the distribution of sequencing sequences on chromosomes.
We used DESeq for the analysis. To identify genes with significant differences, we set the screening criteria as follows: q-value ≤ 0.05 and log₂ fold change ≥ 1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes readcount values for each Sample.

growth_protocol: RPMI-1640, 10% fetal bovine serum, 2mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.Cells were cultured in a humidiﬁed 5% CO2 incubator at 37℃.

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human non-small cell lung cancer


title: 2048_PBMC

description:
Library name: 2048_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA - Pancreas - 7 days post-cerulein injection #3

description:
Library name: 2298_7days_3_RNA
pooled file from 6 sequencing runs

value: purified nuclei from flash-frozen powderized whole pancreas

value: wild-type, 7 days post-injection


title: 2047_PBMC

description:
Library name: 2047_PBMC
final_processed_tpm_values_pbmc.txt

value: PBMC


title: RNA-seq of WT strain, replicate 3

description: Library name: S1326_1_Rep3


title: RNA-seq of A_D28 from HEPE irradiation, replicate 3

description: Library name: A_D28_Rep3


title: Mus CD8+ T cell, KO, 12h , rep2

description: Library name: Sample6

value: lymph node


title: PC-9 cells, shScramble, RNA-Seq rep1

description: Library name: PC-9_shScramble_rep1

value: shScramble


title: RNA - Pancreas - 7 days post-cerulein injection #1

description:
Library name: 2297_7days_1_RNA
pooled file from 6 sequencing runs


title: RNA - Pancreas - 28 days post-cerulein injection #3

description:
Library name: 2304_28days_3_RNA
pooled file from 4 sequencing runs


title: RNA-seq of H_D1 from HEPE irradiation, replicate 2

description: Library name: H_D1_Rep2


title: RNA-seq of WT strain, replicate 2

description: Library name: S1326_1_Rep2


title: PC-9 cells, shKRT19-1, RNA-Seq rep3

description: Library name: PC-9_shKRT19-1_rep3


title: 2053_PBMC

description:
Library name: 2053_PBMC
final_processed_tpm_values_pbmc.txt


title: 2050_PBMC

description:
Library name: 2050_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA-seq of H_D1 from HEPE irradiation, replicate 1

description: Library name: H_D1_Rep1


title: PC-9 cells, shKRT19-1, RNA-Seq rep1

description: Library name: PC-9_shKRT19-1_rep1


title: 2052_PBMC

description:
Library name: 2052_PBMC
final_processed_tpm_values_pbmc.txt


title: PC-9 cells, shScramble, RNA-Seq rep2

description: Library name: PC-9_shScramble_rep2


title: RNA - Pancreas - CTRL #3

description:
Library name: 2292_CTRL_3_RNA
pooled file from 6 sequencing runs

value: 8 hourly injections/die, 2 following days - saline solution


title: 2028CA_PBMC

description:
Library name: 2028CA_PBMC
final_processed_tpm_values_pbmc.txt

value: NP-Long COVID


title: RNA - Pancreas - CTRL #2

description:
Library name: 2291_CTRL_2_RNA
pooled file from 6 sequencing runs


title: KT-47 pretreatment_1

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: Library name: Sample 1

data_processing:
paired-end reads of 100bp reads were processed by Juicer(v1.5, default parameters)(PMID:27467249) based on hg38 and ligation sites GATCGATC.
Three replicates were performed for each cell type and processed independently, replicates are merged after visual confirmation of reproducibility and achieved 800M/1000M read pairs respectively. Juicebox(PMID:27467250)and https://proteinpaint.stjude.org/(PMID:33434514) have been used for visualization.
Assembly: hg38
Supplementary files format and content: .hic

source_name: kidney tumor

growth_protocol: KT-47 was heterotopically engrafted into the flanks of C.B-17 scid (C.B-Igh-1b/IcrTac-Prkdcscid) mice (6–8 weeks old; Taconic Farms, Hudson, NY, USA) without cell culture intermediates.

extract_protocol:
Cell suspensions of KT47 Pretreatment and KT47R1 were isolated using EDTA 1mM, 2% FBS in PBS. Cell processing and library preparation for Hi-C was performed following the manufacturer’s protocol using Qiagen’s EpiTect Hi-C kit (cat# 59971).  DNA fragmentation was achieved using a Diagenode Biorupter Pico to a median DNA fragment size of 400-600bp.
Cell processing and library preparation for Hi-C was performed following the manufacturer’s protocol using Qiagen’s EpiTect Hi-C kit (cat# 59971).

treatment_protocol: Tumor-bearing mice were treated with actinomycin-D (0.30 mg/kg intraperitoneal q21 days x 3; Baxter Oncology, Lebanon, NJ), vincristine (1 mg/kg intraperitoneal q7 days x 8; Hospira, Lake Forest, IL), and doxorubicin (4 mg/kg IV q7 days x 8; Pfizer, New York, NY, USA). Three timepoints were selected as experimental groups during this treatment schema for further inquiry: pre-treatment (no VAD chemotherapy exposure in WTPDX model), pre-resistance (VAD chemotherapy exposure without evidence of complete chemoresistance), and resistance (VAD chemotherapy exposure with complete chemotherapy resistance documented). The resistance timepoint was separated into resistance clone 1 and resistance clone 2 (KT-47R1, KT-47R2) which were originally derived from two different mice.

value: kidney tumor

value: Wilms tumor patient-derived xenograft


title: KT-47 pretreatment_2

description: Library name: Sample 2


title: PC-9 cells, shScramble, RNA-Seq rep3

description: Library name: PC-9_shScramble_rep3


title: 2027R_PBMC

description:
Library name: 2027R_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA - Pancreas - 28 days post-cerulein injection #2

description:
Library name: 2303_28days_2_RNA
pooled file from 6 sequencing runs


title: 2023_PBMC

description:
Library name: 2023_PBMC
final_processed_tpm_values_pbmc.txt


title: RNA - Pancreas - 7 days post-cerulein injection #2

description:
Library name: 229x_7days_2_RNA
pooled file from 4 sequencing runs


title: ES-hTSC-CM-1

city: Bathesda

first: Kotb

last: Abdelmohsen

state: MD

address: 9000 Rockville Pike

institute: NIH

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
After demultiplexing, sequence data was checked for overall quality and yield. Then, raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the Human reference genome GRCh38 available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany)
RNA samples were quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). ERCC RNA Spike-In Mix kit (cat. 4456740) from ThermoFisher Scientific, was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAseq® FastSelect™−rRNA HMR kit (Qiagen, Germantown, MD, USA), which was conducted following the manufacturer’s protocol. Strand specific RNA sequencing library was prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, the enriched RNAs were fragmented for 8 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on a flowcell. After clustering, the flowcell was loaded onto the Illumina NovaSeq X instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired-End (PE) configuration.

value: Fibroblasts

value: 10 Gy IR+hTSC-CM


title: KT-47 Resistance 1_2

description: Library name: Sample 5

value: VAD


title: 2039R_PBMC

description:
Library name: 2039R_PBMC
final_processed_tpm_values_pbmc.txt


title: ES-CM3

value: 10 Gy IR+CM


title: 2030R_PBMC

description:
Library name: 2030R_PBMC
final_processed_tpm_values_pbmc.txt


title: KT-47 Resistance 1_1

description: Library name: Sample 4


title: KT-47 pretreatment_3

description: Library name: Sample 3


title: ES-hTSC-CM-2

value: WT


title: ES-hTSC-CM-3


title: ATAC - Pancreas - 28 days post-cerulein injection #1

description:
Library name: 2302_28days_1_ATAC
pooled file from 6 sequencing runs

library_source: genomic single cell

value: wild-type, 28 days post-injection

value: 8 hourly injections/die, 2 following days - cerulein 50 mg/kg


title: LX-2 cells, control D2,Day 2

city: Chongqing

first: Ailing

last: Liang

state: Chongqing

address: Yuanjiagang Campus, Chongqing Medical University, Shiyou Road, Yuzhong District, Chongqing

department: College of Traditional Chinese Medicine

institute: Chongqing Medical University

description:
Library name: Sample 2
D2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean  reads were separately aligned to reference genome with orientation mode using HISAT2 software.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

source_name: hepatic

growth_protocol: LX-2 cells were maintained in high-glucose Dulbecco's Modified Eagle Medium (DMEM) (VivaCell, China) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin solution. Cells were cultured at 37°C in a humidified atmosphere containing 5% CO₂. Subculture (passaging) of LX-2 cells was performed every two days.

extract_protocol:
Total RNA from LX-2 cells was isolated using TRIzol reagent.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions . The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: LX-2 cells were treated with P7C3(20µM) for 2 days (n = 3) and the normal group was treated without drugs for 2 days (n = 3).

value: hepatic

value: Human hepatic stellate cell line

value: No drug treatment for 2 days (n = 3)

value: Same batch


title: RNA - Pancreas - CTRL #1

description:
Library name: 2290_CTRL_1_RNA
pooled file from 6 sequencing runs

value: purified nuclei from flash-frozen powderized whole pancreas


title: ATAC - Pancreas - 28 days post-cerulein injection #3

description:
Library name: 2304_28days_3_ATAC
pooled file from 4 sequencing runs


title: 3065_CSF

description:
Library name: 3065_CSF
final_processed_tpm_values_csf.txt

source_name: Cerebrospinal Fluid

value: Cerebrospinal Fluid

value: Control


title: ATAC - Pancreas - 28 days post-cerulein injection #2

description:
Library name: 2303_28days_2_ATAC
pooled file from 6 sequencing runs


title: KT-47 Resistance 1_3

description: Library name: Sample 6


title: 2014R_PBMC

description:
Library name: 2014R_PBMC
final_processed_tpm_values_pbmc.txt

value: PBMC

value: NP-Long COVID


title: ES-CM2


title: LX-2 cells, control D1,Day 2

description:
Library name: Sample 1
D1


title: ATAC - Pancreas - 7 days post-cerulein injection #3

description:
Library name: 2298_7days_3_ATAC
pooled file from 6 sequencing runs

value: wild-type, 7 days post-injection


title: ATAC - Pancreas - 7 days post-cerulein injection #2

description:
Library name: 229x_7days_2_ATAC
pooled file from 4 sequencing runs


title: LX-2 cells,  treatment P2,Day 2

description:
Library name: Sample 5
P2

value: P7C3(20µM) treatment for 2 days


title: LX-2 cells,  treatment P3,Day 2

description:
Library name: Sample 6
P3


title: ES-CM1

value: Fibroblasts


title: 3067_CSF

description:
Library name: 3967_CSF
final_processed_tpm_values_csf.txt


title: 3051_CSF

description:
Library name: 3051_CSF
final_processed_tpm_values_csf.txt


title: LX-2 cells, control D3,Day 2

description:
Library name: Sample 3
D3


title: ATAC - Pancreas - 7 days post-cerulein injection #1

description:
Library name: 2297_7days_1_ATAC
pooled file from 6 sequencing runs


title: LX-2 cells,  treatment P1,Day 2

description:
Library name: Sample 4
P1


title: 3068_CSF

description:
Library name: 3068_CSF
final_processed_tpm_values_csf.txt


title: Hepatocellular Carcinoma patient 1

city: GuiLin

first: jingwen

last: Xiao

address: No.109, Huancheng Beier Road

institute: GuiLin Meidical University

description:
Library name: Sample 4
LC_4(norm)

data_processing:
ACGT101-miR(v4.2) was used to analyze the data of miRNA, and 3' connectors and junk sequences were removed to obtain Clean Data.
the remaining sequences were compared with mRNA, RFam and Repbase databases (without miRNA) and filtered.
Comparison and analysis of various RNA databases: the remaining sequences were compared with mRNA, RFam and Repbase databases (without miRNA) and filtered.
Reads after length filtering, RFam and other database filtering were obtained, and the precursor and genome were compared for miRNA identification.
Differential expression analysis of miRNA
Assembly: hg38
Supplementary files format and content: Excel file include the of known and predicted miRNA and Expression of all detected miRNAsin each sequencing sample.

source_name: blood

growth_protocol: Venous blood elbow of patients with hepatocellular carcinoma in fasting state was collected by using ordinary serum long tube (adding coagulant)

extract_protocol:
The total RNA extraction kit of exosomes produced by QIAGEN company in Germany was used to extract RNA.
SRNA sequencing library was prepared by truseq small RNA sample prep kits (Illumina, San Diego, USA) kit. After the preparation of the library, the constructed library was sequenced by Illumina Hiseq 2000/2500, and the sequencing length was 50bp(SE50).

treatment_protocol: Samples were  stand at 4℃ for 3-4 hours, slowly suck the upper pale yellow serum into an enzyme-free EP tube (discard hemolytic samples) with a pipette, centrifuge at 4℃ for 15 minutes at 3000× g, then suck the supernatant into a new EP tube again, mark it, and freeze it in a refrigerator at -80℃.

value: blood

value: human genome

value: serum

value: Hepatocellular Carcinoma


title: ATAC - Pancreas - CTRL #3

description:
Library name: 2292_CTRL_3_ATAC
pooled file from 6 sequencing runs

value: wild-type, 28 days post-injection

value: 8 hourly injections/die, 2 following days - saline solution


title: healthy control 3

description:
Library name: Sample 3
LC_3(norm)

value: healthy control


title: 3046_V2_CSF

description:
Library name: 3046_CSF
final_processed_tpm_values_csf.txt


title: ATAC - Pancreas - CTRL #1

description:
Library name: 2290_CTRL_1_ATAC
pooled file from 6 sequencing runs


title: 3039_CSF

description:
Library name: 3039_CSF
final_processed_tpm_values_csf.txt


title: 3059_CSF

description:
Library name: 3059_CSF
final_processed_tpm_values_csf.txt


title: B6 CD8T 3 TCR-Seq

city: Chiba

first: Ryo

last: Nasu

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba University

description: Library name: B6 CD8T 3

data_processing:
Sequencing was performed using the MiSeq platform (Illumina, USA). The acquired sequences were aligned and assembled, and the clonotypes were identified using the MiXCR software program (version 3.0.12) with default parameters.
VDJtools (version 1.2.1) was employed for data format conversion, categorization based on V/D/J segments, and computation of diversity information used to draw rarefaction curve plots for conventional CD4T and CD8T cells.
Diversity calculations for iNKT cell subsets using the Shannon index involved constructing a downsampling series from count tables generated by VDJtools, followed by computation with custom in-house scripts.
Assembly: mm10
Supplementary files format and content: Tab delimeted text files include the TCR clonotype tables in VDJtools output format
Library strategy: TCR-Seq

source_name: thymus

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
For cDNA library construction, we used the SMARTer Mouse TCR a/b Profiling Kit (Clontech, Takara Bio USA, Inc) following the manufacturer’s protocols.

value: thymus

value: CD8T cells


title: Hepatocellular Carcinoma patient 2

description:
Library name: Sample 5
LC_5(norm)


title: Knee joint, LOXL2, Knockout, Replicate4

city: Boston

first: Manish

middle: V.

last: Bais

address: W216, 700 Albany street

department: Translational Dental Medicine

institute: Boston University

description: Library name: KO_DMM_LOXL2ko_Rep4

data_processing:
In-house perl script developed by NOVOGENE bioinformatics facility.
Reference genome alignment using HISAT2.
Gene expression quantification using featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count for each samples

source_name: Knee joint

extract_protocol:
RNA was isolated using TRIzol and purified with RNeasy Mini kit (Qiagen). Around 400 nanogram of RNA was used for sequencing at NOVOGENE facility.
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.

value: Knee joint


title: Knee joint, LOXL2, Knockout, Replicate3

description: Library name: KO_DMM_LOXL2ko_Rep3


title: Hepatocellular Carcinoma patient 3

description:
Library name: Sample 6
LC_6(norm)


title: healthy control 2

description:
Library name: Sample 2
LC_2(norm)


title: healthy control 1

description:
Library name: Sample 1
LC_1(norm)


title: Knee joint, LOXL2, Knockout, Replicate2

description: Library name: KO_DMM_LOXL2ko_Rep2


title: B6 CD4T 3 TCR-Seq

description: Library name: B6 CD4T 3

value: CD4T cells


title: 2051_CSF

description:
Library name: 2051_CSF
final_processed_tpm_values_csf.txt

value: Cerebrospinal Fluid


title: B6 CD8T 1 TCR-Seq

description: Library name: B6 CD8T 1


title: B6 CD8T 4 TCR-Seq

description: Library name: B6 CD8T 4


title: 2080_CSF

description:
Library name: 2080_CSF
final_processed_tpm_values_csf.txt


title: Knee joint, LOXL2, Knockout, Replicate1

description: Library name: KO_DMM_LOXL2ko_Rep1


title: B6 CD4T 2 TCR-Seq

description: Library name: B6 CD4T 2


title: B6 iNKT17 3 TCR-Seq

description: Library name: B6 iNKT17 3

value: iNKT17 cells


title: B6 CD8T 2 TCR-Seq

description: Library name: B6 CD8T 2


title: ATAC - Pancreas - CTRL #2

description:
Library name: 2291_CTRL_2_ATAC
pooled file from 6 sequencing runs

value: purified nuclei from flash-frozen powderized whole pancreas


title: 2049_CSF

description:
Library name: 2049_CSF
final_processed_tpm_values_csf.txt

value: NP-Long COVID


title: Knee joint, LOXL2, Control, Replicate4

description: Library name: Vehicle_DMM_LOXL2wt_Rep4


title: B6 CD4T 4 TCR-Seq

description: Library name: B6 CD4T 4


title: 2075_CSF

description:
Library name: 2075_CSF
final_processed_tpm_values_csf.txt


title: 2050_CSF

description:
Library name: 2050_CSF
final_processed_tpm_values_csf.txt


title: B6 iNKT17 1 TCR-Seq

description: Library name: B6 iNKT17 1


title: B6 iNKT2 4 TCR-Seq

description: Library name: B6 iNKT2 4

value: iNKT2 cells


title: B6 CD4T 1 TCR-Seq

description: Library name: B6 CD4T 1


title: B6 iNKT2 2 TCR-Seq

description: Library name: B6 iNKT2 2


title: 2047_CSF

description:
Library name: 2047_CSF
final_processed_tpm_values_csf.txt


title: Knee joint, LOXL2, Control, Replicate2

description: Library name: Vehicle_DMM_LOXL2wt_Rep2


title: 2043_CSF

description:
Library name: 2043_CSF
final_processed_tpm_values_csf.txt


title: B6 iNKT2 3 TCR-Seq

description: Library name: B6 iNKT2 3


title: B6 iNKT2 1 TCR-Seq

description: Library name: B6 iNKT2 1


title: Knee joint, LOXL2, Control, Replicate1

description: Library name: Vehicle_DMM_LOXL2wt_Rep1


title: 2039R_CSF

description:
Library name: 2039R_CSF
final_processed_tpm_values_csf.txt


title: BALB/c CD8T 3 TCR-Seq

description: Library name: BALB/c CD8T 3

value: BALB/c