title: PBMC_scRNA-seq

city: Manchester

first: Ali

last: Al-Janabi

address: Oxford Road

institute: University of Manchester

description: Multiplexed sample. Two technical replicates: "AA1" and "AA2" sequenced on different lanes of a flow cell.

data_processing:
Initial pre-processing. The sequence files generated from the instrument were then processed using 10x Genomics custom pipeline Cell Ranger v7.0.0, which aligned the .fastq files to the transcriptome, identified the valid barcodes as cells, counted UMIs and reported a gene by cell count matrix in sparse matrix format. Sequences were mapped to the pre-built references provided by 10x Genomics based on GRCh38, GENCODE release 32 (GRCh38-2020-A).
Demultiplexing. We used donor genotype data to assign a donor to each barcode (droplet) based on natural genetic variation using Demuxlet.
Multiplet identification and exclusion. Several methods were used to identify multiplets. Firstly, the Demuxlet output annotates droplets containing barcodes allocated to more than one donor. Secondly, we used the SCDS package in R to additionally identify same-donor heterotypic doublets. Lastly, we used Seurat to perform unsupervised clustering, and visually inspected UMAP plots highlighting cells identified by Demuxlet as multiplets. Clusters predominantly consisting of multiplets were then manually excluded. For further filtering of low-quality cells or multiplets, QC thresholds were applied per participant for the distribution of mitochondrial DNA percentage and the number of features.
Cell clustering. This was undertaken using R version 4.1.3. Using the Seurat package (v4.3.0), data was split by donor, and count normalisation and variance stabilisation undertaken using sctransform v2. The data from each donor were then integrated (normalised to each other). This final assay in the Seurat object is named "SCT_pre_integration". Clustering was performed using a multi-modal PBMC reference dataset (Hao et al, 2021) and Seurat's reference mapping functionality. To additionally annotate T-helper subsets, we used SingleR to identify these cell types using a different reference PBMC dataset by Monaco et al (2019).
Sub-clustering. We further sub-clustered CD4 T cells, CD8 T cells and monocytes by performing unsupervised clustering on three Seurat objects excluding all other cell types. Sub-clusters were manually identified using canonical marker expression.
Assembly: Sequences were mapped to the pre-built references provided by 10x Genomics based on GRCh38, GENCODE release 32 (GRCh38-2020-A).
Supplementary files format and content: "seurat_object.rds" - Seurat object containing expression data following quality control, de-multiplexing, multiplet exclusion, normalization and cell cluster annotation.
Supplementary files format and content: "seurat_object_CD4.rds", "seurat_object_CD8.rds" and "seurat_object_Mono.rds" - Seurat objects including annotations for CD4 T cell, CD8 T cell and Monocyte sub-clusters.

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were isolated from whole blood within 2 hours of collection. The protocol is as follows.

1.Make up media with Dulbeccomicros phosphate-buffered saline (PBS) and 2mM EDTA.
2.Fill a Leucoseps tube with 15 mL Ficoll Paque Plus (room temperature)
3.Centrifuge at 1000 g for 30 seconds.
4.Transfer whole blood from EDTA tubes into a 50 mL Falcon tube.
5.Add equivalent volume of media to the whole blood.
6.Transfer a maximum of 30 mL of blood/media mix into each Ficoll-loaded Leucosep tube.
7.Centrifuge at 800g, 15 minutes, room temperature with deceleration set to 0.
8.Remove the majority of plasma from the Leucoseps tube using a pipette, leaving approximately a 1cm layer of plasma above the cell layer.
9.Gently swirl the Leucoseps tube to mix the remaining contents, and transfer into a new Falcon tube.
10.Top up to 40 mL with media.
11.Centrifuge at 200g at room temperature, ensuring deceleration is set back to 9.
12.When completed, set the centrifuge to 4°C.
13.Gently remove the supernatant using a pipette, resuspend cell pellet using a 100 microL pipette and add 5 mL of red blood cell lysis solution (1 part 10X RBC lysis buffer, 9 parts sterile water). Gently mix and leave at room temperature for 5 minutes.
14.If currently have multiple tubes of PBMCs, these can be combined at this point.
15.Top up to 40mL with media.
16.Centrifuge at 500g, 4°C for 10 minutes.
17.Gently discard supernatant using a pipette.
18.Discard the supernatant and resuspend the pellet using a 100 microL pipette.
19.Bring up the volume to 30-40 mL using media.
20.Count cells.
21.Centrifuge at 500g, 4°C for 10 minutes.
22.Discard supernatant using pipette.
23.Resuspend pellet in residual volume using 100 microL pipette and put cells on ice.
24.Add enough cold Recovery Cell Culture Freezing Medium (Thermo Fisher, 12648010) dropwise to store cells at desired concentration, such as 3 or 6 million cells per mL.
25.Add 1mL of cell suspension to separate cryovials.
26.Place cryovials into a Mr Frosty and transfer to a -80°C freezer.
27.After 24 hours, transfer PBMCs to a -150°C freezer.

Protocol for PBMC thawing and pooling prior to scRNA-seq
1.Prepare medium with RPMI and 10% FBS. Warm to 37°C in a water bath.
2.For each cryovial which will be thawed, label a 15 mL Falcon tube.
3.Thaw cryovial in water bath, without submerging fully, for 2-3 minutes until there is a small ice ball.
4.Wipe cap with 70% ethanol and pour gently into the 15 mL Falcon tube.
5.Add 1 mL media to each empty cryovial (to collect remaining cells), and pipette dropwise into Falcon tube.
6.Add 8mL warmed media dropwise to Falcon tube.
7.Swirl tube gently and centrifuge at 300g for 5 minutes, room temperature.
8.Discard supernatant using a pipette.
9.Resuspend with 100 microL pipette and top up to 1ml with media
10.Count cells.
11.Add 9mL media, and transfer equal number of cells (e.g. 1 million) from each donor into a new 15 mL Falcon tube.
12.Centrifuge at 300g for 5 minutes, room temperature.
13.Discard supernatant and resuspend pellet in residual volume.
14.Add enough media to achieve a concentration of 1500 cells per microL.
15.Pass through a 40 microm filter and repeat count.
16.Transfer 1 mL into a new tube and place on ice until cDNA library preparation.
Gene expression libraries were prepared from single cells using the Chromium Controller and Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics, Inc. Pleasanton, USA) according to the manufacturer's protocol (CG000315 Rev E). Briefly, nanoliter-scale Gel Beads-in-emulsion (GEMs) were generated by combining barcoded Gel Beads, a master mix containing cells, and partitioning oil onto a Chromium chip. Cells were delivered at a limiting dilution, such that the majority (90-99%) of generated GEMs contain no cell, while the remainder largely contain a single cell. The Gel Beads were then dissolved, primers released, and any co-partitioned cells lysed. Primers containing an Illumina TruSeq Read 1 sequencing primer, a 16-nucleotide 10x Barcode, a 10-nucleotide unique molecular identifier (UMI) and a 30-nucleotide poly(dT) sequence were then mixed with the cell lysate and a master mix containing reverse transcription (RT) reagents. Incubation of the GEMs then yielded barcoded cDNA from poly-adenylated mRNA. Following incubation, GEMs were broken and pooled fractions recovered. First-strand cDNA was then purified from the post GEM-RT reaction mixture using silane magnetic beads and amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were then used to optimize the cDNA amplicon size. Illumina P5 & P7 sequences, a sample index, and TruSeq Read 2 sequence were added via end repair, A-tailing, adaptor ligation, and PCR to yield final Illumina-compatible sequencing libraries.

value: Peripheral blood mononuclear cells


title: HepG2 small RNA rep1

status: Public on May 16 2025

type: SRA

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

country: USA

institute: The University of Chicago

description:
ZA1
mutation.hepG2.txt

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.6)
PCR duplicates were removed with the BBMap tool (https://sourceforge.net/projects/bbmap/).
Random barcodes at reads end were trimmed, and low-quality reads were removed using the cutadapt tool again
Then the remaining reads were aligned to the human genome (hg38) using  bowtie2 (version 2.5.1) allowing a maximum of three mismatches.
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
Cleaned reads that failed to align to the human genome were applied using Kraken2 with its standard database, which contains bacterial, archaeal, viral, and human sequences. Based on the aligned results from Kraken2, we normalized the data by calculating the reads per million (RPM). Then we performed student t-test (two tailed) to calculate the p value for the differential expression.
We identified microbial species in cfRNA samples using kraken2 (version 2.1.3)52, setting a threshold whereby the median reads of the specie must exceed 10 in at least one group (CRC or non-cancer). Following species identification, we extracted their sequences from the kraken2 reference genome. To construct a new, streamlined reference, we limited each microbial species to a maximum of ten reference genomes, minimizing redundancy Subsequently, we aligned the reads that failed to align to the human genome to this curated microbiome reference genome using bowtie2. The alignments generated by bowtie2 were applied in the calculation of the microbiome mapping ratio. Variant identification within these sequences is then achieved through the precise analysis of base composition at each genomic position, employing bam-readcount tool (https://github.com/genome/bam-readcount). The generated bam-readcount output results were parsed and analyzed to calculate the misincorporation ratio.
Assembly: hg38 (GRCh38.107)
Assembly: Kraken 2 standard database
Supplementary files format and content: abundance.host.csv|containing the abundance (raw reads), fold change, p value of various human transcirpts from cfRNA.
Supplementary files format and content: abundance.microbiome.csv|containing the RPM, fold change, p value of various microbial abundance from cfRNA.
Supplementary files format and content: mutation.microbiome.csv |containing the p value, fold change, and mutation ratio at modified sites in microbiome-dervied cfRNA.
Supplementary files format and content: mutation.host.rRNA.csv |containing the p value, fold change, and mutation ratio at human rRNA from cfRNA.
Supplementary files format and content: mutation.host.tRNA.csv |containing the p value, fold change, and mutation ratio at human tRNA from cfRNA.
Supplementary files format and content: mutation.hepG2.csv |containing mutation ratio of human tRNA from HepG2.
Library strategy: LIME-seq

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
cfRNAs were isolated from 600 μl plasma using QIAamp ccfDNA/RNA Kit (Qiagen, Cat. 55184) according to the manufacturer's protocol. In brief, 180 μl RPL buffer was added into 600 μl plasma, followed by vortexing for 5 s. After leaving at room temperature for 3 mins, 100 μl RPP buffer is added. Then close EP tube cap and immediately mix vigorously by vortexing 10 s for 2 times, which is important to disperse the solid. Incubate the EP tube on ice for 3 min. After the standard steps of washing and concentration following the manufacturer's protocol, the purified cfRNA was finally eluted in 14 µl of RNase-free water.
Plasma cell-free RNA (cfRNA) or small RNA from HepG2 (<200 nt) were fragmented to lengths of ~35-55 nucleotides using the 10X RNA Fragmentation Reagent (AM8740, Invitrogen), which was used as 15X with heating at 70 °C for 14 mins. Purify the fragmented RNA using the Oligo Clean & Concentrator kit (Zymo Research) with a final elution volume of 10 μl. The subsequent 3′-end repair involved the preparation of a mixture of fragmented RNA, 2 μl of 10× T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB), 2 μl of T4 PNK, 1 μl SUPERase•In RNase Inhibitor and a proper volume of RNase-free water. Mix the 20 μl reaction mixture very well and incubate at 37°C for 1 hour. 3’-end-repaired RNA fragments were purified by Oligo Clean & Concentrator kit and eluted in 10 μl of RNase-free water. For 3′-adapter ligation, RNA fragments were denatured with 1ul of 10 μM RNA 3′-linker (5′rApp-NNNNN AGATCGGAAGAGCGTCGTG-3SpC3) by heating at 70°C for 2 minutes and then immediately moved onto ice. Then a mixture of 2.5 μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 7.5 μl of 50% PEG8000, 1 μl SUPERase•In, and 2 μl T4 RNA ligase 2 truncated KQ (NEB) was prepared, followed by mixing well and incubating at 25°C for 2 hrs and then at 16°C for 10 hrs. The excessive adapters were removed by adding 2 μl of 5′-deadenylase (NEB) with an incubation at 30 °C for 45 mins, followed by adding 1.0 μl of RecJf (NEB) with an incubation at 37 °C for 45 mins. The 3’-ligated RNA was then purified by RNA Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water.  Reverse transcription was initiated by mixing the 3’-ligated RNA with 1 ul of 2.0 μM RT primer (5′-ACACGACGCTCTTCCGATCT-3′) and heating at 65°C for 2 minutes. Then move the samples onto ice immediately. A mixture of 2 μl of 10× AMV Reverse Transcriptase Reaction Buffer (NEB), 2 μl of 10 mM dNTPs, 1 μl RNaseOUT (Thermo Fisher Scientific), 2 μl HIV Recombinant Reverse Transcriptase (Worthington) and a proper volume of RNase-free water was prepared, to give a final volume of 20 μl for a one-hour incubation at 37°C. Upon the completion of RT, 1.0 μl volume of RNase H (NEB, M0297L) was added to the reaction mixture, followed by incubation at 37 °C for 20 min and 70 °C for 5 min. The produced cDNAs after RT were purified by Oligo Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water. A mixture of eluted cDNA and 2.0 μl of 10 μM cDNA 3′-linker (5′Phos-NNNNNAGATCGGAAGAGCACACGTCTG-3SpC3) was denatured at 75 °C for 2 min and then moved onto ice immediately. 3-μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 15 μl of 50% PEG8000, 3 μl of 10 mM ATP, and 1.0 μl of T4 RNA ligase 1 (high concentration, NEB) were added to the cDNA–adapter mixture and mixed very well. Incubate the ligation reaction mixture at 25 °C for 12 h. The libraries were amplified using universal and indexed primers from NEBNext Multiplex Oligos for Illumina (NEB). All libraries were sequenced on an Illumina NovaSeq 6000 or NovaSeqX with SE100 bp mode. The LIME-seq method enables high mutation ratio detection across multiple RNA modifications, including m1A, m3C, m1G, m22G, m3U, etc., with an enhanced read-through at these methylation sites. Such performance has been facilitated by the robust HIV RT enzyme, and it effectively uncovered methylation fraction information at methylated sites

tag: tissue

value: Blood

tag: disease state

value: WT

tag: cell line

tag: fraction

value: small RNA


title: 011-1-3

city: Yangzhou

first: Jiao

last: Hu

address: 48 Wenhui Road

country: China

institute: Yangzhou University

data_processing:
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 4200 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration.
Tophat v2.1.0 were used to map the cleaned reads to the human h38 reference genome with two mismatches. After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models. Significant differentially expressed (SDE) genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR)
Assembly: human h38 reference genome
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: 293T cells

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To screen the crucial host factors involved in Lnc#61 inhibiting the replication of H5N1 subtype AIVs, 293T cells (6-well plate, 1×107.0 cells/well, in triplicate) were transfected  with 500 ng/well of Lnc#61 or  or the pcDNA3.1 empty vector as an internal control and then infected or uninfected with CK10 virus,samples were collected and then stored at -80 ℃ for further RNA-seq.

value: 293T cells

tag: cell type

value: human embryonic kidney

tag: transfection

tag: ck10 infection

value: infected


title: 011-1-2


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt

library_source: genomic

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

molecule: genomic DNA

organism: Mus musculus

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) Sox2 mCherry+/eGFP+ were cultured in Serum+Lif+2i condition. Briefly, cells were cultured on gelatin-coated (0.1%) culture plates in Glasgow minimum essential medium (Sigma-Aldrich, G5154) supplemented with 15% fetal bovine serum (Thermo Fisher Scientific, 10270-106), 1% L-glutamine (Thermo Fisher Scientific, 25030024), 1% sodium pyruvate (Thermo Fisher Scientific, 11360-70), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140-50), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063), 100 µM ß-mercaptoethanol, 10 x 4 U leukemia inhibitory factor (LIF; esg1107, Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress) in 5% CO2 at 37°C. Cells were passaged every 2 days.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.

treatment_protocol: SB hopping was induced by transfecting 2.5 to 5 million cells with the bicistronic plasmid (pME07) encoding SB transposase SB100x and the human nerve growth factor receptor (LNGFR), using Lipofectamine 2000 (Invitrogen, 11668019) and 5 µg of plasmid per million cells. After 30 hours, transfected cells were enriched using MACS MS columns (130-042-201, Miltenyi Biotec) and LNGFR MicroBeads (130-091-330, Miltenyi Biotec) according to the manufacturer’s protocol. One week after transfection, 0.2 million SB-transposase-transfected cells were set apart as an unsorted pool and the remaining cells were FACS sorted into pools (of up to 1000 cells) based on reporter expression. Clones were obtained by sorting single cells from previously obtained pools, or sorted directly from the full pool of SB-transposase-transfected cells.

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

value: Sox2::mCherry deleted

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1:TACC1 r2

city: Boston

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)54. Differential expression analysis was performed using the R package DESeq2 v1.22.155. RNAseq analysis was performed using the VIPER snakemake pipeline56.
Assembly: mm10
Supplementary files format and content: CSV file with raw counts for all samples
Supplementary files format and content: DE analysis results in the paper supplemental files

molecule: polyA RNA

source_name: mouse neural stem cells from CD1 mice

growth_protocol: Mouse neural stem cells (mNSC) obtained from the subventricular zone of CD1 mice23 were cultured as neurospheres in ultra-low adherence vessels (Corning, NY, USA) in tumor stem media (TSM) (500 mL Neurobasal-A (#10888-022), 500 mL DMEM/F12 (#11330-032), 10 mL HEPES Buffer Solution 1M (#15630-080), 10 mL MEM sodium pyruvate solution 100 mM (#11360-070), 10 mL MEM Non-essential amino acid solution 10 mM (#11140-050), 10 mL GlutaMAX solution (#35050-061), 10 mL Penicillin/Streptomycin (#15140122) and 1X B-27 Supplement Minus Vitamin A (from 50X) (#12587-010) from Invitrogen (MA, USA). When indicated, TSM media was supplemented with 12 ng/mL human-EGF (#78006), 12 ng/mL human-bFGF (#78006) and 2 ug/mL heparin solution 0.2% (#07980) from Stemcell Technologies (Vancouver, Canada). Neurospheres were dissociated using Accutase (#00-4555-56, Invitrogen) every 3-4 days and reseeded as single cells suspension with a density of 80-100,000 cells/mL in ULA flasks/plates.

extract_protocol:
Bulk RNA was extracted from mNSC cells using the Qiagen RNeasy kit (74104).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: strain

value: mouse neural stem cells from CD1 mice


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool5 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2_H pool5 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1:TACC1 r3


title: 011-1-1


title: FGFR1:TACC1 r1


title: C1-1-3


title: FGFR1-ITD r2


title: FGFR1 N546K + PTPN11 E69K r3


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool2 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool2 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: C1-1-2


description:
Library name: E2716 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1_H pool1 rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: C1-1-1


title: FGFR1 N546K + PTPN11 E69K r1


description:
Library name: E2712 Sox2P-reporter -116 kb, population P3 50Kpool rep4 Rv
Sox2P-reporter -116 kb, population P3 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1 N546K + PTPN11 E69K r2


description:
Library name: E2712 Sox2P-reporter -116 kb, population P5 50Kpool rep4 Rv
Sox2P-reporter -116 kb, population P5 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


title: wei011-3

value: non-infected


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1 N546K r3


title: FGFR1 N546K r2


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: wei011-2


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: wei011-1


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep4 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: FGFR1 N546K r1


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: PTPN11 E69K alone r3


description:
Library name: E2712 Sox2P-reporter -116 kb, population P4 50Kpool rep4 Rv
Sox2P-reporter -116 kb, population P4 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


title: weiC2


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P3 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P4 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -116 kb, population P5 50Kpool rep4 Fw
Sox2P-reporter -116 kb, population P5 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: PTPN11 E69K alone r1


description:
Library name: E2712 Sox2P-reporter -116 kb, population P4 50Kpool rep4 Fw
Sox2P-reporter -116 kb, population P4 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


title: panax notoginseng derived exosome-like nanoparticles transfected group-3

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University

data_processing:
Illumina PE150/SE50  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples

source_name: Human umbilical vein endothelial cells

growth_protocol: HUVECs were purchased from the Shanghai Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), which contained 10% fetal bovine serum (Gibco) in a 5% CO2 incubator at 37 °C. When the cell density was more than 80%, washing the cells twice by sterilized PBS. Subsequently, 0.25% trypsin was added to dissociate the cell-cell contacts. After centrifugation (1000 r/min, 5min), the cells were resuspended in complete medium with 10% fetal bovine serum for further use.

extract_protocol:
Total RNA was extracted from HUVECs using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were incubated with PBS and panax notoginseng derived exosome-like nanoparticles, respectively. The cells were washed with PBS thrice to remove impurities.

tag: treatment

value: panax notoginseng derived exosome-like nanoparticles overexpressing cells

value: HUVECs


description:
Library name: E2712 Sox2P-reporter -116 kb, population P3 50Kpool rep4 Fw
Sox2P-reporter -116 kb, population P3 50Kpool rep4
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep4 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P6 50Kpool rep4
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: Vector control r3


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep3 Fw
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P2 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: panax notoginseng derived exosome-like nanoparticles transfected group-2


title: weiC3


title: Vector control r2


title: 34_195_Na

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: Adv-Cre+, wt (ATF3 wt control)

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

extract_protocol:
DRGs were enzymatically and mechanically dissociated and passed through 20% Percoll phase. Neuron enriched pellets were lysed for RNA extraction and purification using Qiagen RNeasy Micro kit.
Library was prepared using TruSeq Stranded RNA
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end

value: Adv-Cre+, wt (ATF3 wt control)

value: Naive

tag: Sex

value: Male


description:
Library name: E2712 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep3 Rv
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P5 50Kpool rep3
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt


title: panax notoginseng derived exosome-like nanoparticles transfected group-1


title: 33_195_Inj

description: Adv-Cre+, wt (ATF3 wt control)

value: Injury


title: 32_194_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: normal control-3

value: PBS treated cells


title: 31_194_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: Vector control r1


title: IL-15IRES-EGFP, replicate 3, scRNAseq

city: Vienna

first: Dietmar

last: Herndler-Brandstetter

address: Borschkegasse 8a

country: Austria

institute: Medical University of Vienna

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software version 7.1.0. using intron mode and including a custom reference genome including the IRES and GFP construct.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files
Supplementary files format and content: annotated Seurat object (RDS file)

source_name: Bone marrow

extract_protocol:
IL-15 positive bone marrow stromal cells were isolated by enzymatic digestion after dissecting femurs and tibias from IL-15IRES-EGFP mice. In detail, single cell suspensions of both bone marrow and bone samples were generated by flushing bone marrow with PBS and crushing the remaining bone using a mortar and pestle. The pelleted bone marrow and bone fractions were then digested for 30-40 minutes at 37°C in an enzymatic cocktail of Collagenase IV (1mg/mL),  DNase I (1mg/mL) and Dispase (0.5mg/mL). Filtered cell suspensions from a total of 7 individual (male and female, 8-12 week old) IL15-GFP mice were Fc-blocked, stained, and sorted on a BD FACSMelody for Aqua Zombie- CD45- Ter119- and CD31- IL15-GFP+ (MSCs) and CD31+ IL15-GFP+ (endothelial cells).
Library was performed according to the manufacturer's instructions (single cell 3' v1 protocol, 10x Genomics).

value: Bone marrow


title: PTPN11 E69K alone r2


title: weiC1

value: 293T cells

value: human embryonic kidney


title: 29_193_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Female


title: 30_193_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: normal control-2


title: IL-15IRES-EGFP, replicate 2, scRNAseq

description: 10x Genomics


title: 28_192_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: normal control-1


title: 27_192_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: IL-15IRES-EGFP, replicate 1, scRNAseq

description: 10x Genomics


title: 26_176_Na

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)

value: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: PBS treated group group-3

data_processing:
Illumina PE150/SE50 software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples

source_name: HA-HSF

growth_protocol: HA-HSF were purchased from the Shanghai Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), which contained 10% fetal bovine serum (Gibco) in a 5% CO2 incubator at 37 °C. When the cell density was more than 80%, washing the cells twice by sterilized PBS. Subsequently, 0.25% trypsin was added to dissociate the cell-cell contacts. After centrifugation (1000 r/min, 5min), the cells were resuspended in complete medium with 10% fetal bovine serum for further use.

extract_protocol:
Total RNA was extracted from DCs using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with Panax notoginseng exosome,H2O2 and PBS respectively. The cells were passaged at 1:10 with fresh growth medium 48 h after transfection, and then selected by adding selective medium in the next day.

value: Human skin fibroblast cells

value: HA-HSF


title: 25_176_Inj

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: 24_175_Na

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: RC6

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequenced libraries were evaluated with FastQC/0.11.5
Transcripts were quantified using Salmon. Salmon index for mouse was generated based on the Ensembl fasta file for GRCm38.
Differential expression analysis was performed using DESeq2 package based on the criteria of false discovery rates (FDR) < 0.05 and log2|FC| ≥ 1.
Assembly: mm10
Supplementary files format and content: txt files include pseudo read counts for each sample

source_name: Bone

extract_protocol:
For humerus RNA isolation from 10-week-old mice, RNA was extracted by tissue blender with TRIzol (Invitrogen)/Chloroform based method, and further purification was performed with PureLink RNA mini column.
RNA libraries for RNA-seq were contructed and sequenced with Novoseq6000.

value: Bone

tag: age

value: adult

value: osteoblast, osteocyte

value: female


title: PBS treated group group-2


title: 23_175_Inj

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: 22_172_Na

description: Adv-Cre+, wt (ATF3 wt control)

value: Adv-Cre+, wt (ATF3 wt control)


title: RC4


title: PBS treated group group-1


title: 21_172_Inj

description: Adv-Cre+, wt (ATF3 wt control)


title: 20_163_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Naive


title: 19_163_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Male


title: H2O2 treated group group-3

value: H2O2 treated cells


title: 18_156_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: 17_156_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Injury


title: 16_155_Na

description: Adv-Cre+, wt (ATF3 wt control)


title: RC2


title: H2O2 treated group group-1


title: 15_155_Inj

description: Adv-Cre+, wt (ATF3 wt control)


title: RC3


title: RC1


title: 12_150_Na

description: Adv-Cre-, wt (ATF3 wt control)

value: Adv-Cre-, wt (ATF3 wt control)


title: WT6

value: WT


title: Panax notoginseng exosome treated group-3

value: Panax notoginseng exosome treated cells


title: 13_152_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)

value: Female


title: Panax notoginseng exosome treated group-2


title: WT5


title: 11_150_Inj

description: Adv-Cre-, wt (ATF3 wt control)


title: 9_146_Inj

description: Adv-Cre-, wt (ATF3 wt control)


title: RC5


title: Panax notoginseng exosome treated group-1


title: WT4


title: 10_146_Na

description: Adv-Cre-, wt (ATF3 wt control)


title: H2O2 treated group group-2


title: 8_141_Na

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)

value: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: 7_141_Inj

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: EMX1 on- and off-targets

city: Cambridge

first: Gary

last: Ge

state: Massachusetts

address: 100 Cambridgepark Dr #101

department: QBio

institute: Vor Biopharma Inc

description: Library name: EMX1

library_source: other

data_processing:
Sequence reads are trimmed using Trim-galore, and pair-end reads were merged using flash2.
The merged reads were analyzed in Cas9 mode using SANTON package (https://github.com/VOR-Quantitative-Biology/SANTON)
Assembly: hg38
Supplementary files format and content: tab-delemited text file including a list of template IDs and annotation of their proto-side off-target sequence
Supplementary files format and content: tab-delemited text file including a list of template IDs and annotation of their pam-side off-target sequence

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Chemically synthesized
The synthetic oligonucleotide-based sequencing library was amplified and converted into double-stranded DNA. The PCR reaction was purified using Ampure beads, followed by in vitro cleavage with SpCas9 and Proteinase K treatment. The resulting product was purified with Ampure beads and subjected to end extension and adaptor ligation. The adaptor-ligated product was size-selected for fragments between 100-200 bp using the BluePippin platform. After size selection, the product was purified, amplified, and appropriately diluted. The diluted product was then used for standard barcoding PCR. The final product was sequenced on a MiSeq system following Illumina's standard protocol.

value: synthetic construct


title: 6_139_Na

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: Multiome, NONHAND sample4, GEX

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

description:
Library name: Sample4_GEX
paired multiomic snRNA and snATAC

data_processing:
Libraries were sequenced on a NovaSeq X Plus instrument, and reads were subsequently processed using 10x Genomics Cell Ranger ARC (v 2.0.2) analytical pipeline and human GRCh38 (2020-A) reference. Dataset aggregation was performed using the cellranger-arc aggr function, normalizing for the total number of confidently mapped reads across libraries. The data were then processed through Seurat and Signac (R tools) and python.
Assembly: GRCh38 (2020-A)
Supplementary files format and content: fastqs

molecule: nuclear RNA

source_name: Brain, prefrontal cortex

extract_protocol:
Flash-frozen human brain tissue samples were homogenized, and lysed and permeabilized with Nonidet P40 Substitute, Digitonin, and Tween-20. The isolated nuclei were purified, centrifuged, and resuspended in Diluted Nuclei Buffer. The nuclei were then loaded into the Chromium X (10x Genomics, Pleasanton, CA) to encapsulate single nuclei into droplet emulsions following the manufacturer’s recommendations. 5000 nuclei were targeted to be captured per sample.
Single nuclei gene expression libraries and single nuclei ATAC libraries were constructed from nuclei isolated from flash-frozen human brain tissue samples on the 10x Genomics Chromium System using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle.

value: Brain, prefrontal cortex


title: 5_139_Inj

description: Adv-Cre-, ATF3-fl_het (ATF3 wt control)


title: WT3

value: Bone


title: 4_131_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: Multiome, NONHAND sample3, GEX

description:
Library name: Sample3_GEX
paired multiomic snRNA and snATAC


title: 3_131_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: 14_152_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: WT1

value: adult


title: 1_130_Inj

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: 2_130_Na

description: Adv-Cre+, ATF3-fl_homo (ATF3 cKO)


title: WT2

value: osteoblast, osteocyte


title: Multiome, HAND sample1, GEX

description:
Library name: Sample1_GEX
paired multiomic snRNA and snATAC


title: Wildtype 2MO

city: Davis

first: Raneesh

last: Ramarapu

state: California

institute: UC Davis School of Veterinary Medicine

description: 10x Genomics

data_processing:
Raw fastq.gz sequencing data was processed by the UC Davis Bioinformatics Core using 10X CellRanger for alignment to the 10x Genomics mouse reference genome. Analysis was then continued using Seurat v5
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Cornea

extract_protocol:
Six corneas from 2 female and 1 male 129S6/SvEvTac mice of each age group (2, 6, and 11-month-old) were dissected and pooled in 600 µL of papain solution (CAT LK003178; Worthington Biochemical Corp., Lakewood, NJ) and incubated for 1.75 hours at 37 °C. The tube was inverted every 10-20 minutes during incubation to improve cell dissociation. The suspension was aspirated and passed through a Flowmi cell strainer (40 µM; CAT 136800040, Bel-Art, Wayne, NJ) and the strainer was rinsed with 300 µL of 1X PBS to collect additional adherent cells. The filtered suspension was centrifuged at 400 g for 10 minutes at 4 °C. The supernatant was discarded. The cell pellet was washed twice with 0.04% bovine serum albumin (BSA) in 1X PBS, centrifuging at 300 g for 5 minutes at 4 °C and the final pellet was resuspended on 40 µL of 2% BSA-PBS. Single cell suspensions for each age group were prepared in the same manner.
All single cell suspensions were immediately submitted to the UC Davis DNA Technologies and Expression Analysis Core for 10X Chromium Single Cell 3’ library preparation

value: Cornea

value: Wildtype


title: RNAseq, primary murine ERP, biological replicate 1

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

institute: Yale University

data_processing:
Bulk RNAseq (primary murine MKP/ERP): After quality control (FastQC version 0.11.5), reads generated from each sample were aligned to the mouse genome (GRCm38.p3) with STAR (version 2.5.3a,–quantMode GeneCounts), using the Gencode M15 transcript annotation as a transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR Bioconductor package, using a double threshold on the log2 fold change (absolute value >0.5) and corresponding statistical significance (P < 0.05).
Bulk RNAseq (HEL, 6133, CAOM cells): After quality control (FastQC version 0.11.9,  https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ), reads generated from each sample were deduplicated with FastUniq (version 1.1, FastUniq download | SourceForge.net) and aligned to the mouse genome (GRCm39) or the human genome (GRCh38) with STAR (version 2.7.10a, - quantMode GeneCounts), using the Gencode M31 (mouse) and 37 (human) gene annotation, respectively. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR (version 4.2.0) package in Bioconductor (https://bioconductor.org/). Differentially expressed genes were identified with the “glmQLFTest” function, using a double threshold on gene expression changes and associated statistical significance (absolute log2 fold change > 0.75, FDR < 0.05).
eCLIP and m6A eCLIP: Initial peak calling was performed with PureCLIP(Krakau, Richard, and Marsico 2017) (version 1.3.1, https://github.com/skrakau/PureCLIP). Nucleotides with a Hidden state of 3 (enriched + crosslink) were considered potential crosslink nucleotides. The regions of the initial crosslinked nucleotides were extended by 7 nucleotides upstream and downstream, resulting in 15 nucleotide long regions. Overlapping regions on the same strand were merged with the merge Bedtools function. Read coverage on each region for each replicate was quantified with Bedtools coverage. Only regions with a minimum count of 10 among all the replicates in at least 1 condition were considered as regions with sufficient signal. Additionally, for m6A eCLIP, only regions containing at least one A were considered. Read counts for each region were normalized and differential analysis was performed in the same manner as RNA-seq. To identify high-confidence CLIP regions for eCLIP, only regions enriched over both input and control conditions were considered; for m6A eCLIP, only the regions enriched over input were considered (p-value <0.05 and log2 fold enrichment >1).
TimeLapse-seq: Reads were trimmed and aligned with HISAT-3N to the human hg38 genome as described in the TimeLapse preprocessing pipeline (Schofield et al. 2018). After T-to-C mutation calling, bakR and DESeq2 were used to calculate differences in kinetic parameters and gene expression levels across RBM15 overexpression, RM overexpression, and parental control conditions(Love, Huber, and Anders 2014; Vock and Simon 2023). Library size factors were estimated using DESeq2. The cB output file of the TimeLapse preprocessing pipeline was used as a count table in bakR to model transcript-specific changes in RNA degradation and synthesis rates. bakR was run using the hybrid model with all read filtering parameters set to default.
Assembly: 6133 and CAOM experiments: GRCm39. Primary MKP/ERP experiments: GRCh38.p3. HEL cell experiments: GRCh38.
Supplementary files format and content: eCLIP and meCLIP files.bed: bed files indicating peak coverage in CLIP experiments
Supplementary files format and content: HEL_RNAseq_counts.xlsx, 6133_CAOM_METTL3i_RNAseq.xlsx, MKP_WT_1_ReadsPerGene.out.tab, MKP_WT_2_ReadsPerGene.out.tab, ERP_WT_1_ReadsPerGene.out.tab, ERP_WT_2_ReadsPerGene.out.tab: gene counts for indicated RNAseq experiments
Supplementary files format and content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).

source_name: tissue

growth_protocol: HEL cells: RPMI 1640 with 10% tetracycline-negative FBS 1% L-glutamine 1% penicillin-streptomycin, 5μg/mL blasticidin. HEL-RBM15, HEL-RM, and HEL-MKL1 cells were additionally cultured with 375μg/mL hygromycin. 6133 and CAOM cells: RPMI 1640 with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, 100ng/mL murine stem cell factor and 10ng/mL murine interleukin 3.

extract_protocol:
HEL cell RNAseq: QIAGEN RNeasy Mini Kit. 6133 and CAOM cell RNAseq: ThermoFisher SCIENTIFIC TRIzol. TL-seq: ThermoFisher SCIENTIFIC TRIzol. eCLIP-seq: Zymo Research RNA Clean & Concentrator-5 kit m6A eCLIP-seq: QIAGEN RNeasy Mini kit with DNAse treatment. ERP/MKP RNAseq: QIAGEN RNeasy Mini Kit.
eCLIP-seq: HEL cells expressing FLAG-tagged RBM15 or RM or empty vector control were UV-crosslinked twice at 2000mJ/cm2 using a Stratalinker at 254nm. Cells were sonicated for a total of 60 seconds in lysis buffer and treated with RNAse 1 (ThermoFisher SCIENTIFIC cat# AM2295) for 3 minutes at 37ºC. Protein-RNA complexes were immunoprecipitated using Dynabeads (ThermoFisher SCIENTIFIC cat# 10004D) and 12ug anti-FLAG antibody (Sigma Aldrich, cat# F1804). Libraries were prepared as described (Biancon et al., 2022). m6A eCLIP-seq: mRNA was isolated from 75ug total RNA by oligo-dT beads (ThermoFisher Dynabeads™ mRNA Purification Kit, cat#61006) and eluted in 5μL DNase-RNase free water. RNA was fragmented using 2 μL of RNA fragmentation reagent (ThermoFisher, cat# AM8740) at 75ºC for 6 minutes and RNA integrity and fragment size wasnassessed using an Agilent TapeStation. mRNA was incubated with 2μL of ribonuclease inhibitor (SuperaseIn) and 5ug anti-m6A antibody (202 011, Synaptic Systems) for 2 hours, rotating, at 4ºC. Each sample was then UV-crosslinked and immunoprecipitated using Dynabeads as for eCLIP-seq. HEL cell and 6133/CAOM RNA-seq: RNA underwent poly-A selection, reverse transcription, and library preparation using the KAPA mRNA HyperPrep kit. TimeLapse-seq: Total RNA was isolated and extracted with phenol-chloroform. Following precipitation in isopropanol supplemented with 1mM DTT and 20µg of glycogen, RNA pellets were washed twice with fresh 75% EtOH. Dried RNA pellets were resuspended in DEPC-treated water and treated with Turbo DNase to deplete genomic DNA. After purification with one equivalent volume of Agencourt RNAClean XP beads, 5µg of eluted RNA were processed for TimeLapse chemistry using meta-chloroperoxybenzoic acid as the oxidant(Schofield et al. 2018). For each sample, 10ng of TimeLapse-treated RNA input were used to prepare sequencing libraries from the Clontech SMARTer Stranded Total RNA-Seq kit (Pico Input) with ribosomal cDNA depletion. ERP/MKP RNAseq: RT with SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and library construction with Nextera XT DNA Sample Preparation kit.

treatment_protocol: Dox induction: 10ng/mL for 24hr. TL-seq: 100uM 4-thiouridine for 2 hours. METTL3 inhibitor: 1uM STM3675 for 48hr.

value: tissue

value: primary sorted murine ERP


title: Wildtype 11MO

description: 10x Genomics


title: RNAseq, primary murine ERP, biological replicate 2


title: Multiome, NONHAND sample4, ATAC

description:
Library name: Sample4_ATAC
paired multiomic snRNA and snATAC

library_source: genomic single cell


title: RNAseq, primary murine MKP, biological replicate 2

value: primary sorted murine MKP


title: RNAseq, primary murine MKP, biological replicate 1


title: CKO.IL2.24h rep3

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: flu-infected, CKO.IL2.24h rep3

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.0.11
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Assembly: mm10/GRCm38
Supplementary files format and content: Gene expression in text format, content include gene name, symbol, chromosome, length of transcripts, and raw reads

source_name: spleen

growth_protocol: CD4+ T cells were isolated from mouse spleens using a negative selection kit (#19852, Stem Cell Technologies) according to the manufacturer’s protocol.

extract_protocol:
Cells were harvested and total RNA was extracted using Direct-zol RNA MiniPrep kit (#R2052, Zymo Research) according to the kit’s protocol.
RNA-Sequencing libraries were prepared using 200 ng of total RNA using the KAPA RNA HyperPrep Kit (#KK8542, KAPABIOSYSTEMS) per the manufacturer’s protocol. Barcoded samples were mixed and sequenced on an Illumina NovaSeq system.

treatment_protocol: Purified CD4+ T cells were activated with plate-bound 2 mg/ml anti-mouse CD3 (#BE0001-1; clone 145-2C11, BioXCell) and 1 mg/ml soluble anti-mouse CD28 (#BE0015-1; clone 37.51, BioXCell) and cultured in RPMI medium (#11875093, Gibco) supplemented with 10% fetal bovine serum (FBS) (#100-106, GeminiBio), 2 mM L-glutamine (#25030-149, Gibco), 50 U/ml penicillin + 50 mg/ml streptomycin (#15070-063, Gibco), and 50 mM 2-mercaptoethanol (#21985-023, Gibco) for 72 hours in the presence of 100 IU/ml recombinant human IL-2 (#Ro 23-6019, Roche) at 37°C after which the cells were harvested and assayed.

value: spleen

value: CD4+ T cells

value: conditional Knock-out

value: influenza-infected, then treated with IL-2


title: Injury replicate 4 [Inj_24h_4]

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Reads were trimmed with software BBDUK, and aligned to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: Dissociated L4-L6 DRG

extract_protocol:
RNA was extracted and purified using RNeasy Mini kit (Qiagen)
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep (REV) according to the manufactures’ instructions (Lexogen).

value: Dissociated L4-L6 DRG

tag: condition

value: injury


title: Injury replicate 3 [Inj_24h_3]

tag: tissue


title: Injury replicate 2 [Inj_24h_2]


title: CKO.IL2.24h rep2

description: flu-infected, CKO.IL2.24h rep2


title: Multiome, NONHAND sample3, ATAC

description:
Library name: Sample3_ATAC
paired multiomic snRNA and snATAC


title: Injury replicate 1 [Inj_24h_1]


title: CKO.IL2.24h rep1

description: flu-infected, CKO.IL2.24h rep1


title: Multiome, HAND sample2, ATAC

description:
Library name: Sample2_ATAC
paired multiomic snRNA and snATAC


title: Naïve replicate 4 [Na_24h_4]

value: naïve


title: Naïve replicate 3 [Na_24h_3]


title: Multiome, HAND sample1, ATAC

description:
Library name: Sample1_ATAC
paired multiomic snRNA and snATAC


title: Multiome, HAND sample2, GEX

description:
Library name: Sample2_GEX
paired multiomic snRNA and snATAC


title: WT.IL2.24h rep3

description: flu-infected, WT.IL2.24h rep3

value: wild-type


title: Naïve replicate 2 [Na_24h_2]


title: Naïve replicate 1 [Na_24h_1]


title: Sample from skin surface scraping, rep1

description: Library name: NN-12

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.6)
PCR duplicates were removed with the BBMap tool (https://sourceforge.net/projects/bbmap/).
Random barcodes at reads end were trimmed, and low-quality reads were removed using the cutadapt tool again
Then the remaining reads were aligned to the human genome (hg38) using  bowtie2 (version 2.5.1) allowing a maximum of three mismatches.
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
Cleaned reads that failed to align to the human genome were applied using Kraken2 with its standard database, which contains bacterial, archaeal, viral, and human sequences. Based on the aligned results from Kraken2, we normalized the data by calculating the reads per million (RPM). Then we performed student t-test (two tailed) to calculate the p value for the differential expression.
We identified microbial species in cfRNA samples using kraken2 (version 2.1.3)52, setting a threshold whereby the median reads of the specie must exceed 10 in at least one group (CRC or non-cancer). Following species identification, we extracted their sequences from the kraken2 reference genome. To construct a new, streamlined reference, we limited each microbial species to a maximum of ten reference genomes, minimizing redundancy Subsequently, we aligned the reads that failed to align to the human genome to this curated microbiome reference genome using bowtie2. The alignments generated by bowtie2 were applied in the calculation of the microbiome mapping ratio. Variant identification within these sequences is then achieved through the precise analysis of base composition at each genomic position, employing bam-readcount tool (https://github.com/genome/bam-readcount). The generated bam-readcount output results were parsed and analyzed to calculate the misincorporation ratio.
Assembly: hg38 (GRCh38.107)
Assembly: Kraken 2 standard database
Supplementary files format and content: abundance.host.csv|containing the abundance (raw reads), fold change, p value of various human transcirpts from cfRNA.
Supplementary files format and content: abundance.microbiome.csv|containing the RPM, fold change, p value of various microbial abundance from cfRNA.
Supplementary files format and content: mutation.microbiome.csv |containing the p value, fold change, and mutation ratio at modified sites in microbiome-dervied cfRNA.
Supplementary files format and content: mutation.host.rRNA.csv |containing the p value, fold change, and mutation ratio at human rRNA from cfRNA.
Supplementary files format and content: mutation.host.tRNA.csv |containing the p value, fold change, and mutation ratio at human tRNA from cfRNA.
Supplementary files format and content: mutation.hepG2.csv |containing mutation ratio of human tRNA from HepG2.

source_name: skin

extract_protocol:
cfRNAs were isolated from 600 μl plasma using QIAamp ccfDNA/RNA Kit (Qiagen, Cat. 55184) according to the manufacturer's protocol. In brief, 180 μl RPL buffer was added into 600 μl plasma, followed by vortexing for 5 s. After leaving at room temperature for 3 mins, 100 μl RPP buffer is added. Then close EP tube cap and immediately mix vigorously by vortexing 10 s for 2 times, which is important to disperse the solid. Incubate the EP tube on ice for 3 min. After the standard steps of washing and concentration following the manufacturer's protocol, the purified cfRNA was finally eluted in 14 µl of RNase-free water.
Plasma cell-free RNA (cfRNA) or small RNA from HepG2 (<200 nt) were fragmented to lengths of ~35-55 nucleotides using the 10X RNA Fragmentation Reagent (AM8740, Invitrogen), which was used as 15X with heating at 70 °C for 14 mins. Purify the fragmented RNA using the Oligo Clean & Concentrator kit (Zymo Research) with a final elution volume of 10 μl. The subsequent 3′-end repair involved the preparation of a mixture of fragmented RNA, 2 μl of 10× T4 Polynucleotide Kinase Reaction Buffer (B0201S, NEB), 2 μl of T4 PNK, 1 μl SUPERase•In RNase Inhibitor and a proper volume of RNase-free water. Mix the 20 μl reaction mixture very well and incubate at 37°C for 1 hour. 3’-end-repaired RNA fragments were purified by Oligo Clean & Concentrator kit and eluted in 10 μl of RNase-free water. For 3′-adapter ligation, RNA fragments were denatured with 1ul of 10 μM RNA 3′-linker (5′rApp-NNNNN AGATCGGAAGAGCGTCGTG-3SpC3) by heating at 70°C for 2 minutes and then immediately moved onto ice. Then a mixture of 2.5 μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 7.5 μl of 50% PEG8000, 1 μl SUPERase•In, and 2 μl T4 RNA ligase 2 truncated KQ (NEB) was prepared, followed by mixing well and incubating at 25°C for 2 hrs and then at 16°C for 10 hrs. The excessive adapters were removed by adding 2 μl of 5′-deadenylase (NEB) with an incubation at 30 °C for 45 mins, followed by adding 1.0 μl of RecJf (NEB) with an incubation at 37 °C for 45 mins. The 3’-ligated RNA was then purified by RNA Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water. Reverse transcription was initiated by mixing the 3’-ligated RNA with 1 ul of 2.0 μM RT primer (5′-ACACGACGCTCTTCCGATCT-3′) and heating at 65°C for 2 minutes. Then move the samples onto ice immediately. A mixture of 2 μl of 10× AMV Reverse Transcriptase Reaction Buffer (NEB), 2 μl of 10 mM dNTPs, 1 μl RNaseOUT (Thermo Fisher Scientific), 2 μl HIV Recombinant Reverse Transcriptase (Worthington) and a proper volume of RNase-free water was prepared, to give a final volume of 20 μl for a one-hour incubation at 37°C. Upon the completion of RT, 1.0 μl volume of RNase H (NEB, M0297L) was added to the reaction mixture, followed by incubation at 37 °C for 20 min and 70 °C for 5 min. The produced cDNAs after RT were purified by Oligo Clean & Concentrator (Zymo Research) and eluted in 10 μl of RNase-free water. A mixture of eluted cDNA and 2.0 μl of 10 μM cDNA 3′-linker (5′Phos-NNNNNAGATCGGAAGAGCACACGTCTG-3SpC3) was denatured at 75 °C for 2 min and then moved onto ice immediately. 3-μl of 10× T4 RNA Ligase Reaction Buffer (NEB), 15 μl of 50% PEG8000, 3 μl of 10 mM ATP, and 1.0 μl of T4 RNA ligase 1 (high concentration, NEB) were added to the cDNA–adapter mixture and mixed very well. Incubate the ligation reaction mixture at 25 °C for 12 h. The libraries were amplified using universal and indexed primers from NEBNext Multiplex Oligos for Illumina (NEB). All libraries were sequenced on an Illumina NovaSeq 6000 or NovaSeqX with SE100 bp mode. The LIME-seq method enables high mutation ratio detection across multiple RNA modifications, including m1A, m3C, m1G, m22G, m3U, etc., with an enhanced read-through at these methylation sites. Such performance has been facilitated by the robust HIV RT enzyme, and it effectively uncovered methylation fraction information at methylated sites

value: skin

value: Non cancer individuals


title: WT.IL2.24h rep2

description: flu-infected, WT.IL2.24h rep2


title: Input Injury replicate 3 [4_3_Input_Inj]

source_name: L4-L6 DRG

value: L4-L6 DRG

value: Input Injury


title: Input Injury replicate 2 [4_2_Input_Inj]


title: Input Injury replicate 1 [4_1_Input_Inj]


title: WT.IL2.24h rep1

description: flu-infected, WT.IL2.24h rep1


title: Input Naïve replicate 2 [3_2_Input_Na]

value: Input Naïve


title: Input Naïve replicate 1 [3_1_Input_Na]


title: Input Naïve replicate 3 [3_3_Input_Na]


title: IP Injury replicate 3 [2_3_IP_Inj]

value: IP Injury

tag: antibody

value: immunoprecipitation (IP) of Ribotag ribosomal marker (HA-tagged Rpl22)


title: patient 3, NAT, demethylation

description: Library name: NP-08

source_name: normal tissue adjacent to the tumor

value: normal tissue adjacent to the tumor

value: Cancer patient


title: patient 4, tumor tissue, demethylation

description: Library name: NP-09

source_name: CRC tumor

value: CRC tumor


title: IP Injury replicate 2 [2_2_IP_Inj]


title: patient 3, tumor tissue, demethylation

description: Library name: NP-07


title: patient 2, tumor tissue, demethylation

description: Library name: NP-05


title: IP Naïve replicate 3 [1_3_IP_Na]

value: IP Naïve


title: patient 2, NAT, demethylation

description: Library name: NP-06


title: IP Naïve replicate 2 [1_2_IP_Na]


title: IP Injury replicate 1 [2_1_IP_Inj]


title: IP Naïve replicate 1 [1_1_IP_Na]


title: patient 1, NAT, demethylation

description: Library name: NP-02


title: SSRP1KO  no  crush  rep3

description: SSRP1KO  no  crush  replicate 3

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: Retina

extract_protocol:
Retinas were dissected in Ames solution, digested in papain, and dissociated into single cells. The cells were then stained with anti-CD90.2 and Calcein Blue (a live cell marker), and Calcein Blue+ RGCs were collected based on CD90.2 and/or GFP (under the Vglut2 promoter) and/or mCherry (co-expressed with sgRNAs) using FACS. RNA from FACS-sorted RGCs was extracted using the RNeasy Micro Kit (Qiagen).
RNA-seq libraries were prepared with SMART-Seq v4Ultra Low Input RNA Kit.
Libraries were sequenced using a HiSeq4000 instrument to generate 69bp pair-end reads.

treatment_protocol: Two microliters of AAV2 carrying either non-targeting control sgRNAs (NT group) or Ssrp1 targeting sgRNAs (SSRP1KO group) were injected intravitreally into LSL-Cas9-GFP; Vglut2-Cre mice. Two weeks later, the mice's optic nerves were exposed intraorbitally and crushed. RGCs were collected at 1 (1dpc group), 2 (2dpc group), 3 (3dpc group), and 4 (4dpc group) days after optic nerve crush.

value: Retina

value: SSRP1KO  no  crush


title: patient 4, NAT, demethylation

description: Library name: NP-10


title: SSRP1KO  no  crush  rep1

description: SSRP1KO  no  crush  replicate 1


title: patient 1, tumor tissue, demethylation

description: Library name: NP-01


title: DRG culture, untransfected replicate 2

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38(mm10) as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: Primary DRG culture

extract_protocol:
RNA was extracted and purified using RNeasy Mini kit (Qiagen)
Library was prepared using TruSeq Stranded RNA
RNA samples were prepared into cDNA libraries and sequencing was carried out as paired end, 2X150bp
Novaseq S4

value: Primary DRG culture

value: C57/Bl6 wt

value: Untransfected


title: SSRP1KO  4dpc  rep3

description: SSRP1KO  4dpc  replicate 3

value: SSRP1KO  4dpc


title: SSRP1KO  no  crush  rep2

description: SSRP1KO  no  crush  replicate 2


title: SSRP1KO  4dpc  rep2

description: SSRP1KO  4dpc  replicate 2


title: DRG culture, untransfected replicate 3


title: patient 4, NAT

description: Library name: NO-10


title: SSRP1KO  4dpc  rep1

description: SSRP1KO  4dpc  replicate 1


title: DRG culture, untransfected replicate 1


title: patient 4, tumor tissue

description: Library name: NO-09


title: patient 3, NAT

description: Library name: NO-08


title: SSRP1KO  2dpc  rep5

description: SSRP1KO  2dpc  replicate 5

value: SSRP1KO  2dpc


title: DRG culture, ASO mix 50nM replicate 4

value: GI-SINE ASO mix 50nM


title: DRG culture, ASO mix 50nM replicate 3


title: SSRP1KO  2dpc  rep4

description: SSRP1KO  2dpc  replicate 4


title: DRG culture, untransfected replicate 4


title: SSRP1KO  2dpc  rep3

description: SSRP1KO  2dpc  replicate 3


title: patient 3, tumor tissue

description: Library name: NO-07


title: DRG culture, ASO mix 50nM replicate 2


title: patient 2, NAT

description: Library name: NO-06


title: DRG culture, ASO mix 50nM replicate 1


title: NT  no  crush  rep3

description: NT  no  crush  replicate 3

value: NT  no  crush


title: DRG culture, ASO Control 50nM replicate 4

value: ASO Control 50nM


title: patient 1, NAT

description: Library name: NO-02


title: DRG culture, ASO Control 50nM replicate 3


title: NT  no  crush  rep1

description: NT  no  crush  replicate 1


title: patient 1, tumor tissue

description: Library name: NO-01


title: NT  no  crush  rep2

description: NT  no  crush  replicate 2


title: SSRP1KO  3dpc  rep2

description: SSRP1KO  3dpc  replicate 2

value: SSRP1KO  3dpc


title: SSRP1KO  3dpc  rep1

description: SSRP1KO  3dpc  replicate 1


title: DRG culture, ASO Control 50nM replicate 2


title: individual 2, blood stored 24 hrs

description: Library name: NG-08

source_name: plasma

value: plasma

value: Non cancer individuals


title: NT  3dpc  rep3

description: NT  3dpc  replicate 3

value: NT  3dpc


title: SSRP1KO  3dpc  rep3

description: SSRP1KO  3dpc  replicate 3


title: NT  4dpc  rep2

description: NT  4dpc  replicate 2

value: NT  4dpc


title: patient 2, tumor tissue

description: Library name: NO-05

value: CRC tumor

value: Cancer patient


title: NT  3dpc  rep2

description: NT  3dpc  replicate 2

value: Retina


title: SSRP1KO  1dpc  rep3

description: SSRP1KO  1dpc  replicate 3

value: SSRP1KO  1dpc


title: SSRP1KO  1dpc  rep2

description: SSRP1KO  1dpc  replicate 2


title: individual 1, blood stored 24 hrs

description: Library name: NG-07


title: NT  3dpc  rep1

description: NT  3dpc  replicate 1


title: DRG culture, ASO Control 50nM replicate 1

value: Primary DRG culture


title: NT  4dpc  rep3

description: NT  4dpc  replicate 3


title: individual 2, blood stored 8 hrs

description: Library name: NG-05


title: NT  2dpc  rep3

description: NT  2dpc  replicate 3

value: NT  2dpc


title: 29_8_22_Unt_4

description: Untransduced replicate 10

extract_protocol:
RNA was extracted and purified using RNeasy Micro kit (Qiagen)
Library constructed with TruSeq library prep RNA kit from Illumina

value: Untransduced

value: C57/Bl6 wt


title: SSRP1KO  1dpc  rep1

description: SSRP1KO  1dpc  replicate 1


title: NT  2dpc  rep2

description: NT  2dpc  replicate 2


title: 29_8_22_Unt_3

description: Untransduced replicate 9


title: individual 1, blood stored 8 hrs

description: Library name: NG-04


title: NT  4dpc  rep1

description: NT  4dpc  replicate 1


title: NT  2dpc  rep1

description: NT  2dpc  replicate 1


title: 29_8_22_Unt_2

description: Untransduced replicate 8


title: NT  1dpc  rep2

description: NT  1dpc  replicate 2

value: NT  1dpc


title: NT  1dpc  rep3

description: NT  1dpc  replicate 3


title: NT  1dpc  rep1

description: NT  1dpc  replicate 1


title: 29_8_22_Unt_1

description: Untransduced replicate 7


title: individual 1, blood stored within 2 hrs

description: Library name: NG-01


title: Naïve con IP  replicate 6

description: Naïve control  IP  replicate 6

source_name: L4-5 DRG

extract_protocol:
RNA was isolated as described in Nature 2020, 581: 77-82. For IP fractions, chicken-anti-GFP antibody (Aves cat#GFP1020) conjugated to magnetic beads was used for pulldown.
SMART-Seq v4 RNA Ultra low input + Nextera XT
Preparation included 75bp paired-end reads and sequencing run was carried out over 1 lanes

treatment_protocol: Sciatic nerve crush at times indicated before cell extraction.  Mice are BAC-TRAP BR145-GFP mouse line

value: L4-5 DRG

value: IP

tag: timepoint

value: control


title: Naïve con IP  replicate 7

description: Naïve control  IP  replicate 7


title: 29_8_22_GFP_4

description: GFP replicate 10

value: GFP


title: Naïve con IP  replicate 5

description: Naïve control  IP  replicate 5


title: Cancer patient 7 (Pancretic cancer cohort)

description: Library name: NI-04

value: plasma


title: Naïve con IP  replicate 4

description: Naïve control  IP  replicate 4


title: 29_8_22_GFP_3

description: GFP replicate 9


title: Naïve con IP  replicate 1

description: Naïve control  IP  replicate 1


title: 29_8_22_GFP_2

description: GFP replicate 8


title: Naïve con IP  replicate 2

description: Naïve control  IP  replicate 2


title: Naïve con IP  replicate 3

description: Naïve control  IP  replicate 3


title: Cancer patient 6 (Pancretic cancer cohort)

description: Library name: NK-03


title: Naïve con Input  replicate 7

description: Naïve control Input  replicate 7

value: Input


title: Cancer patient 5 (Pancretic cancer cohort)

description: Library name: NK-02


title: 29_8_22_GFP_1

description: GFP replicate 7


title: Naïve con Input  replicate 5

description: Naïve control Input  replicate 5


title: Naïve con Input  replicate 6

description: Naïve control Input  replicate 6


title: Cancer patient 4 (Pancretic cancer cohort)

description: Library name: NJ-08


title: individual 2, blood stored within 2 hrs

description: Library name: NG-02

value: Non cancer individuals


title: 29_8_22_DN_AP1_4

description: DN replicate 10


title: Naïve con Input  replicate 4

description: Naïve control Input  replicate 4


title: Cancer patient 3 (Pancretic cancer cohort)

description: Library name: NJ-07


title: 29_8_22_DN_AP1_3

description: DN replicate 9


title: Naïve con Input  replicate 2

description: Naïve control Input  replicate 2


title: Cancer patient 2 (Pancretic cancer cohort)

description: Library name: NJ-06


title: Naïve con Input  replicate 1

description: Naïve control Input  replicate 1


title: 29_8_22_DN_AP1_2

description: DN replicate 8


title: CA0090_Z2, RNA-seq

first: Kei

last: Mizuno

state: MASSACHUSETTS

address: 450 Brookline Avenue

institute: Dana-Farber Cancer institute

description: Library name: Sample103

data_processing:
The raw sequencing data were processed using the STAR aligner for mapping to the human reference genome (GRCh37).
RSEM was used for quantification of gene expression.
Assembly: GRCh37
Supplementary files format and content: txt file

source_name: Brain

extract_protocol:
RNA-seq was performed according to the manufacturer’s protocol.
Library preparation for RNA-seq samples was performed according to the manufacturer’s protocol

value: Brain

value: advanced prostate cancer


title: 7 Days IP replicate 3

description: 7 Days IP replicate 3

value: 7 days


title: 7 Days IP replicate 2

description: 7 Days IP replicate 2


title: Non cancer control 8 (Pancretic cancer cohort)

description: Library name: NK-06

value: Non cancer control


title: 29_8_22_DN_AP1_1

description: DN replicate 7


title: 7 Days IP replicate 1

description: 7 Days IP replicate 1


title: 7 Days Input replicate 4

description: 7 Days Input replicate 4


title: Untreated_B_7DIV

description: Untransduced replicate 5


title: 7 Days Input replicate 3

description: 7 Days Input replicate 3


title: 7 Days Input replicate 2

description: 7 Days Input replicate 2


title: 7 Days Input replicate 1

description: 7 Days Input replicate 1


title: Non cancer control 6 (Pancretic cancer cohort)

description: Library name: NK-04


title: Non cancer control 7 (Pancretic cancer cohort)

description: Library name: NK-05


title: Untreated_A_7DIV

description: Untransduced replicate 4


title: Non cancer control 5 (Pancretic cancer cohort)

description: Library name: NJ-04


title: Naïve con Input  replicate 3

description: Naïve control Input  replicate 3


title: 72 HRS IP replicate 6

description: 72 HRS IP replicate 6

value: 72 hrs


title: 72 HRS IP replicate 5

description: 72 HRS IP replicate 5


title: Unt_C

description: Untransduced replicate 3

value: Primary DRG culture


title: Non cancer control 4 (Pancretic cancer cohort)

description: Library name: NJ-03


title: 72 HRS IP replicate 4

description: 72 HRS IP replicate 4


title: Non cancer control 3 (Pancretic cancer cohort)

description: Library name: NJ-02


title: Unt_B

description: Untransduced replicate 2


title: 72 HRS IP replicate 2

description: 72 HRS IP replicate 2


title: 7 Days IP replicate 4

description: 7 Days IP replicate 4


title: Cancer patient 1 (Pancretic cancer cohort)

description: Library name: NJ-05

value: Cancer patient


title: Unt_A

description: Untransduced replicate 1

value: Untransduced


title: 72 HRS IP replicate 1

description: 72 HRS IP replicate 1


title: Non cancer control 2 (Pancretic cancer cohort)

description: Library name: NJ-01


title: Untreated_C_7DIV

description: Untransduced replicate 6

value: C57/Bl6 wt


title: 72 HRS Input replicate 6

description: 72 HRS Input replicate 6


title: 72 HRS Input replicate 7

description: 72 HRS Input replicate 7


title: 72 HRS Input replicate 5

description: 72 HRS Input replicate 5


title: Non cancer control 1 (Pancretic cancer cohort)

description: Library name: NI-01


title: Non cancer control 8 (Validation cohort 2)

description: Library name: CV-04


title: phps_GFP_B_7DIV

description: GFP replicate 5


title: 72 HRS Input replicate 4

description: 72 HRS Input replicate 4


title: phps_GFP_A_7DIV

description: GFP replicate 4


title: 72 HRS Input replicate 3

description: 72 HRS Input replicate 3


title: 72 HRS Input replicate 2

description: 72 HRS Input replicate 2


title: 72 HRS Input replicate 1

description: 72 HRS Input replicate 1


title: phps_DN_C_7DIV

description: DN replicate 6


title: Non cancer control 7 (Validation cohort 2)

description: Library name: CV-13


title: 48 HRS IP replicate 6

description: 48 HRS IP replicate 6

value: 48 hrs


title: phps_DN_B_7DIV

description: DN replicate 5


title: 48 HRS IP replicate 5

description: 48 HRS IP replicate 5

value: L4-5 DRG


title: 72 HRS IP replicate 3

description: 72 HRS IP replicate 3

value: IP


title: 48 HRS IP replicate 4

description: 48 HRS IP replicate 4


title: phps_DN_A_7DIV

description: DN replicate 4


title: 48 HRS IP replicate 2

description: 48 HRS IP replicate 2


title: Non cancer control 5 (Validation cohort 2)

description: Library name: CX-03


title: GFP_C

description: GFP replicate 3


title: 48 HRS IP replicate 3

description: 48 HRS IP replicate 3


title: 72 HRS IP replicate 7

description: 72 HRS IP replicate 7


title: 48 HRS IP replicate 1

description: 48 HRS IP replicate 1


title: 48 HRS Input replicate 6

description: 48 HRS Input replicate 6


title: Non cancer control 4 (Validation cohort 2)

description: Library name: CX-05


title: phps_GFP_C_7DIV

description: GFP 7DIV replicate 6


title: Non cancer control 3 (Validation cohort 2)

description: Library name: CX-13


title: GFP_B

description: GFP replicate 2


title: Non cancer control 2 (Validation cohort 2)

description: Library name: CX-14


title: GFP_A

description: GFP replicate 1


title: Non cancer control 1 (Validation cohort 2)

description: Library name: CX-15


title: 48 HRS Input replicate 2

description: 48 HRS Input replicate 2


title: 48 HRS Input replicate 3

description: 48 HRS Input replicate 3


title: 48 HRS Input replicate 1

description: 48 HRS Input replicate 1


title: DN_C

description: DN replicate 3


title: Non cancer control 6 (Validation cohort 2)

description: Library name: CX-01


title: 24 HRS IP replicate 3

description: 24 HRS IP replicate 3

value: 24 hrs


title: 24 HRS IP replicate 4

description: 24 HRS IP replicate 4


title: Cancer patient 7 (Validation cohort 2)

description: Library name: CV-07


title: Cancer patient 6 (Validation cohort 2)

description: Library name: CV-19


title: 24 HRS IP replicate 1

description: 24 HRS IP replicate 1


title: Cancer patient 5 (Validation cohort 2)

description: Library name: CV-20


title: 24 HRS IP replicate 2

description: 24 HRS IP replicate 2


title: 24 HRS Input replicate 2

description: 24 HRS Input replicate 2


title: DN_B

description: DN replicate 2


title: 24 HRS Input replicate 1

description: 24 HRS Input replicate 1


title: Cancer patient 4 (Validation cohort 2)

description: Library name: CX-07


title: 24 HRS Input replicate 5

description: 24 HRS Input replicate 5


title: 24 HRS Input replicate 4

description: 24 HRS Input replicate 4


title: Cancer patient 3 (Validation cohort 2)

description: Library name: CX-08


title: Camk2a-Vps13D KO, replicate 2, scRNAseq

city: Unionville

first: Haibo

last: Liu

state: CT

address: 164 Plantation St

department: MCCB

institute: UMass Chan

description: 10x Genomics

data_processing:
Reads 1 were trimmed to only keep the first 28 bases consisting of the 10x Genomic Cell barcodes and UMI using the seqtk trimfq command.
The primary assembly of the mouse reference genome sequence (GRCm39 Release 111) and the corresponding GTF were downloaded from Ensembl. The GTF file was filtered to remove non-polyadenylated genes as suggested by 10x Genomics CellRanger (v7.2.0) (https://www.10xgenomics.com/support/software/cell-ranger/latest) tutorial using cellranger mkgtf.
The genome index was built using the cellranger mkref command. Single cell gene expression quantification was performed using the cellranger count command.
Assembly: Ensembl GRCm39 Release 111
Supplementary files format and content: The processed data submitted are from the outs/filtered_feature_bc_matrix directory generated by the cellranger count command. The *_barcodes.tsv.gz file contains cell barcode information for each cell; *_feature.tsv.gz file contains feature identifiers in the format of Ensembl GeneID:Gene Symbol; *_matrix.mtx.gz contains the gene-by-cell count sparse matrix in the matrix market format. All files are compressed in the .gzip format.

source_name: Hippocampus

extract_protocol:
Mice were transcardial perfused, dissected out brain and placed in chilled 1xHBSS on ice. Then minced the brain with sterile scapel and disassociated with Papain Dissociation System (Worthington, #LK003150) according to the manufacturer’s instructions.
Library was performed accoding to the manufacturer’s instructions(Chromium Next GEM Single Cell 3' Reagent Kits v3.1(Dual Index)).

value: Hippocampus

tag: cell line

value: neurons, glias, vascular cells, and other cells in the brain

value: Camk2a-Vps14D KO


title: 48 HRS Input replicate 4

description: 48 HRS Input replicate 4

value: Input


title: 1 HRS IP replicate 5

description: 1 HRS IP replicate 5

value: 1 hrs


title: Camk2a-Vps13D KO, replicate 3, scRNAseq

description: 10x Genomics

tag: cell type

value: Camk2a-Vps15D KO


title: 48 HRS Input replicate 5

description: 48 HRS Input replicate 5


title: 1 HRS IP replicate 4

description: 1 HRS IP replicate 4


title: Camk2a-Vps13D KO, replicate 1, scRNAseq

description: 10x Genomics

value: Camk2a-Vps13D KO


title: Cancer patient 2 (Validation cohort 2)

description: Library name: CX-18

value: plasma


title: 1 HRS IP replicate 2

description: 1 HRS IP replicate 2


title: Cancer patient 1 (Validation cohort 2)

description: Library name: CV-03


title: Wilt type, replicate 3, scRNAseq

description: 10x Genomics

value: Wilt type


title: 1 HRS IP replicate 1

description: 1 HRS IP replicate 1


title: Wilt type, replicate 2, scRNAseq

description: 10x Genomics


title: DN_A

description: DN replicate 1

value: Primary DRG culture


title: Non cancer control 8 (Validation cohort 1)

description: Library name: NL-04

value: Non cancer control


title: 1 HRS Input replicate 4

description: 1 HRS Input replicate 4


title: 24 HRS Input replicate 3

description: 24 HRS Input replicate 3


title: Wilt type, replicate 1, scRNAseq

description: 10x Genomics, this WT1 is an outlier


title: Non cancer control 7 (Validation cohort 1)

description: Library name: NL-03


title: 1 HRS Input replicate 3

description: 1 HRS Input replicate 3


title: 1 HRS Input replicate 1

description: 1 HRS Input replicate 1


title: Stenotrophomonas maltophilia, rep2, demethylation

description: Library name: NQ-10

organism: Stenotrophomonas maltophilia

source_name: Stenotrophomonas maltophilia

value: Stenotrophomonas maltophilia

value: WT


title: 12 HRS IP replicate 6

description: 12 HRS IP replicate 6

value: 12 hrs


title: 12 HRS IP replicate 4

description: 12 HRS IP replicate 4

value: L4-5 DRG


title: Non cancer control 6 (Validation cohort 1)

description: Library name: NL-02


title: Non cancer control 5 (Validation cohort 1)

description: Library name: NL-01


title: 12 HRS IP replicate 3

description: 12 HRS IP replicate 3

value: IP


title: 12 HRS IP replicate 5

description: 12 HRS IP replicate 5


title: Stenotrophomonas maltophilia, rep2

description: Library name: NQ-04


title: 12 HRS IP replicate 2

description: 12 HRS IP replicate 2


title: Non cancer control 4 (Validation cohort 1)

description: Library name: NK-09


title: Stenotrophomonas maltophilia, rep1

description: Library name: NQ-03


title: 12 HRS IP replicate 1

description: 12 HRS IP replicate 1


title: 1 HRS IP replicate 3

description: 1 HRS IP replicate 3


title: Non cancer control 3 (Validation cohort 1)

description: Library name: NK-08


title: 1 HRS Input replicate 5

description: 1 HRS Input replicate 5


title: 12 HRS Input replicate 6

description: 12 HRS Input replicate 6


title: 12 HRS Input replicate 4

description: 12 HRS Input replicate 4


title: 12 HRS Input replicate 5

description: 12 HRS Input replicate 5


title: 12 HRS Input replicate 3

description: 12 HRS Input replicate 3


title: Non cancer control 2 (Validation cohort 1)

description: Library name: NK-07


title: scRNA-seq of KPC orthotopic tumor treated with 10 mg/Kg EIPA

city: La Jolla

first: Cosimo

last: Commisso

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: KPC_EIPA_scRNAseq

data_processing:
Raw sequencing data from scRNA-seq samples were processed using cellranger multi from 10X Genomics Cellranger v8.0.0 using mouse mm10 reference genome (refdata-gex-mm10-2020-A) and mouse transcriptome probe set v1.0 (mm10-2020-A). Cellranger outputs for the samples were aggregated and normalized for sequencing depth using cellranger aggr with parameter “--normalize=mapped”. Cell barcodes with suffix "-1" and "-2" are from DMSO and EIPA treated samples respectively.
Assembly: mm10
Supplementary files format and content: Tab-delimited aggregated cell barcodes, features, and counts matrix (cell barcodes with "-1" = DMSO, "-2" = EIPA)

source_name: Pancreatic tumor

extract_protocol:
Fixed, single cell suspension was prepared from flash frozen KPC orthotopic tumors treated with DMSO or 10 mg/kg EIPA (4 tumors pooled for each sample) using the Chromium Next GEM Single Cell Fixed RNA Preparation kit (10x Genomics) according to the user guide (CG000553, Rev B). Cell dissociation was performed using the gentleMACS Octo Dissociator (Miltenyi).
Libraries were constructed using the single-plex Chromium Fixed RNA Profiling kit (CG000477, Rev C). Probes were incubated for 20 hours at 42 oC and 12 cycles were performed for the indexing PCR. Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences).

value: Pancreatic tumor

value: 10 mg/Kg EIPA


title: scRNA-seq of KPC orthotopic tumor treated with DMSO

description: Library name: KPC_DMSO_scRNAseq

value: DMSO


title: Non cancer control 1 (Validation cohort 1)

description: Library name: NJ-13


title: 1 HRS Input replicate 2

description: 1 HRS Input replicate 2


title: 12 HRS Input replicate 1

description: 12 HRS Input replicate 1


title: Murine CAFs treated with 4 mM glutamine + DMSO, Rep5

description: Library name: 4Qveh05

data_processing:
Bulk RNA-seq samples were processed using nf-core rnaseq pipeline v3.14.090 using parameters “--aligner star_rsem” to perform read trimming, quality control, alignment, gene quantification and normalization. We used mouse mm10 genome sequence and gene annotations provided by 10X Genomics (refdata-gex-mm10-2020-A) with the nf-core pipeline. Differential expression and gene set enrichment analysis (GSEA) were performed using nf-core differential abundance pipeline v1.5.0 with parameters ‘--filtering_min_abundance 4 --filtering_min_proportion 0.50 --differential_min_fold_change 1.5 --gsea_run true --gsea_permute "gene_set" --gsea_nperm 1000’ and mouse gene sets v2023.2.Mm from MSigDB.
Assembly: mm10
Supplementary files format and content: Tab-delimited Transcripts Per Million (TPM)

source_name: Immortalized primary CAFs

extract_protocol:
Total RNA was extracted using a PureLink RNA Mini Kit (Invitrogen).
PolyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001) with xGEN Stubby adaptors (IDT, Cat# 336338420) and xGEN 10nt UDIs (IDT, Cat# 336338436). Libraries were sequenced (2x75bp) with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat# 860-00015).

treatment_protocol: Murine CAFs were treated with or without 25 mM EIPA in 0.2 mM glutamine, or treated with or without 25 pg/mL IL-1a in 4 mM glutamine, for 32 hours. DMSO was used as the vehicle for EIPA and added to each treatment to maintain consistency across all conditions.

value: Immortalized primary CAFs

value: 4 mM glutamine + DMSO


title: Cancer patient 29 (Validation cohort 1)

description: Library name: NL-14

value: Cancer patient


title: 12 HRS Input replicate 2

description: 12 HRS Input replicate 2

value: Input


title: Stenotrophomonas maltophilia, rep1, demethylation

description: Library name: NQ-09


title: Cancer patient 28 (Validation cohort 1)

description: Library name: NK-15


title: Murine CAFs treated with 4 mM glutamine + DMSO, Rep3

description: Library name: 4Qveh03


title: Injury replicate 2

description: Injury replicate 2

value: Dissociated L4-L6 DRG

value: injury


title: Injury replicate 3

description: Injury replicate 3


title: Naïve replicate 4

description: Naïve replicate 4

value: naïve


title: Injury replicate 1

description: Injury replicate 1


title: Murine CAFs treated with 4 mM glutamine + DMSO, Rep4

description: Library name: 4Qveh04


title: Injury replicate 4

description: Injury replicate 4


title: Murine CAFs treated with 4 mM glutamine + DMSO, Rep2

description: Library name: 4Qveh02


title: Murine CAFs treated with 4 mM glutamine + DMSO, Rep1

description: Library name: 4Qveh01


title: Naïve replicate 3

description: Naïve replicate 3


title: Cancer patient 26 (Validation cohort 1)

description: Library name: NJ-11

value: plasma


title: Naïve replicate 2

description: Naïve replicate 2


title: Cancer patient 27 (Validation cohort 1)

description: Library name: NK-14


title: Naïve replicate 1

description: Naïve replicate 1


title: Cancer patient 25 (Validation cohort 1)

description: Library name: NI-08


title: PC 72h Na replicate 4

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18

extract_protocol:
RNA was extracted and purified using RNeasy Mini kit (Qiagen)
Library constructed with TruSeq library prep RNA kit from Illumina

value: pcDRG  L46  Na  3d


title: Murine CAFs treated with 4 mM glutamine + DMSO + 25 pg/mL IL1a, Rep5

description: Library name: 4Qil1a05

value: 4 mM glutamine + DMSO + 25 pg/mL IL1a


title: Murine CAFs treated with 4 mM glutamine + DMSO + 25 pg/mL IL1a, Rep4

description: Library name: 4Qil1a04


title: Cancer patient 23 (Validation cohort 1)

description: Library name: NK-13


title: PC 72h Na replicate 1

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: PC 72h Na replicate 2

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: PC 72h Inj replicate 4

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18

value: pcDRG  L46  Inj  3d


title: Murine CAFs treated with 4 mM glutamine + DMSO + 25 pg/mL IL1a, Rep3

description: Library name: 4Qil1a03


title: PC 72h Inj replicate 3

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: Cancer patient 22 (Validation cohort 1)

description: Library name: NK-12


title: PC 72h Inj replicate 2

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: Murine CAFs treated with 4 mM glutamine + DMSO + 25 pg/mL IL1a, Rep2

description: Library name: 4Qil1a02


title: PC 24h Na  replicate 4

description: DRG L4-6 Injury 24h Percoll(IK)-17/12/18

value: pcDRG  L46  Na  24h


title: Murine CAFs treated with 4 mM glutamine + DMSO + 25 pg/mL IL1a, Rep1

description: Library name: 4Qil1a01


title: Cancer patient 20 (Validation cohort 1)

description: Library name: NI-06


title: PC 72h Inj replicate 1

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: PC 24h Na  replicate 2


title: Cancer patient 21 (Validation cohort 1)

description: Library name: NJ-09


title: PC 24h Na  replicate 3


title: Murine CAFs treated with 0.2 mM glutamine + DMSO, Rep5

description: Library name: 02Qveh05

value: 0.2 mM glutamine + DMSO


title: PC 24h Na  replicate 1


title: PC 24h Inj replicate 3

value: pcDRG  L46  Inj  24h


title: Cancer patient 19 (Validation cohort 1)

description: Library name: NL-12


title: PC 24h Inj replicate 4


title: Cancer patient 24 (Validation cohort 1)

description: Library name: NL-16


title: Murine CAFs treated with 0.2 mM glutamine + DMSO, Rep4

description: Library name: 02Qveh04


title: PC 72h Na replicate 3

description: DRG L4-6 Injury 3d Percoll(IK)-17/12/18


title: PC 24h Inj replicate 2


title: Murine CAFs treated with 0.2 mM glutamine + DMSO, Rep3

description: Library name: 02Qveh03


title: Cancer patient 17 (Validation cohort 1)

description: Library name: NL-10


title: PC 24h Inj replicate 1