title: KI_m52

description:
KI, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Kidney

value: Kidney


title: KI_m50

status: Public on Jan 26 2024

type: SRA

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

country: USA

institute: University of Chicago

library_source: transcriptomic

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: 1_counts_LPS_timecourse.txt: counts matrix from experiment1
Supplementary files format and content: 2_counts_CLP_timecourse.txt: counts matrix from experiment2
Supplementary files format and content: 3_counts_Cytokine_combo.txt: counts matrix from experiment3
Supplementary files format and content: 4_counts_Cytokine_combo2.txt: counts matrix from experiment4
Supplementary files format and content: 5_counts_LPS_Plasma.txt: counts matrix from experiment7
Supplementary files format and content: 6_counts_LPS_KO.txt: counts matrix from experiment9
Supplementary files format and content: 7_counts_LPS_KO2.txt: counts matrix from experiment10
Supplementary files format and content: 8_counts_CLP_timecourse2.txt: counts matrix from experiment11
Supplementary files format and content: 9_counts_CLP_CytoBlock.txt: counts matrix from experiment12
Supplementary files format and content: 10_counts_CLP_CytoBlock2.txt: counts matrix from experiment13
Supplementary files format and content: 11_counts_CLP_antiTNF.txt: counts matrix from experiment14

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293). Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

tag: tissue

tag: genotype

value: Wild type

tag: treatment


title: KI_m51


title: 426F

city: Freising

first: Frank

last: Johannes

state: Bavaria

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

country: Germany

institute: Technical University of Munich

data_processing:
The clean sRNA data was analysed using Shortstack (Johnson et al., 2016) with default parameters
With “—locifile” we specified intervals (loci) to be analyzed.
As intervals we used 3 set of  200bp regions, based our DNA methylation analysis. One for CG context, one for CHG context and one for CHH context.
As an output in Shortstack there is a "Result: file for each line that has the total number of primary alignments (raw reads) in each locus.
The raw reads for each sample was binded in one total count_table and it is provided here as the processed data file..
Supplementary files format and content: Raw reads counts for each sample using CG regions
Supplementary files format and content: Raw reads counts for each sample using CHG regions
Supplementary files format and content: Raw reads counts for each sample using CHH regions

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Aerial rosette

growth_protocol: The 169 epiRILs were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark ) conditions.

extract_protocol:
Total RNA was extracted from each sample using the miRNeasy kit from Qiagen.
At least 1 μg of total RNA was submitted to the Beijing Genome Institute where they were prepared for Small RNA libraries.

treatment_protocol: Aerial rosette tissue 27 days after sowing (DAS) was harvested.

value: Aerial rosette

tag: line

value: epiHybrid

tag: time

value: Harvested at 27 days after sowing (DAS)


title: KI_m49


title: KI_m48


title: 424R

value: epiRil


title: 419R


title: 424F


title: 467F


title: LI_m45

description:
LI, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Liver

value: Liver


title: 393F


title: 419F


title: KI_m46

description:
KI, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: KI_m47


title: 389R


title: KI_m45


title: KI_m43


title: iLN_m52

description:
iLN, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Inguinal lymph node

value: Inguinal lymph node


title: 379R


title: iLN_m50


title: 368R


title: iLN_m49


title: 368F


title: 393R


title: iLN_m47

description:
iLN, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: iLN_m46


title: 334R


title: iLN_m48


title: 340F


title: iLN_m45


title: 334F


title: 389F


title: 330R


title: iLN_m44


title: KI_m44


title: HE_m52

description:
HE, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Heart

value: Heart


title: iLN_m43


title: 310R


title: HE_m51


title: 310F


title: 275R


title: HE_m50


title: HE_m49


title: iLN_m51


title: 275F


title: HE_m48


title: 379F


title: 340R


title: 266R


title: HE_m47

description:
HE, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: 241R


title: 241F


title: HE_m46


title: 219R


title: HE_m45


title: 266F


title: HE_m43


title: 330F


title: 211R


title: 219F


title: CO_m52

description:
CO, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Colon

value: Colon


title: CO_m50


title: HE_m44


title: CO_m51


title: 211F


title: CO_m49


title: 176R


title: CO_m48


title: CO_m47

description:
CO, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: 158R


title: 158F


title: 176F


title: 128R


title: CO_m46


title: 125R


title: CO_m45


title: CO_m44


title: 125F


title: 102R


title: 102F


title: BM_m52

description:
BM, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Bone marrow

value: Bone marrow


title: BM_m51


title: BM_m50


title: 79F


title: BM_m48


title: BM_m49


title: 79R


title: CO_m43


title: BM_m47

description:
BM, CLP_mild, d0,5
experiment2
2_counts_CLP_timecourse.txt


title: 54R


title: 50R


title: BM_m45


title: BM_m46


title: 50F


title: BM_m44


title: BM_m43


title: mouse_LCM_SG_3

city: Philadelphia

first: Jordan

last: Harris

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Transcriptomic analysis was performed in the R statistical computing environment version 4.2 and RStudio version 2022.02.1 using a pipeline adopted from an open-source toolkit for RNA sequencing analysis (Berry et al. 2021).
Kallisto was used for pseudoaligning reads to a cDNA reference genome and reads were annotated using the Ensembl species-specific database
Data was filtered based on genes with less than 1 count per million in the number of samples equal to n of the smallest group
Normalization of the data was performed by using the Trimmed Mean of M-values (TMM) method in the EdgeR package
Post-filtration, post-normalization, data was then variance stabilized via the Limma package, using the VOOM function
Differential gene expression (DGE) testing was performed using the Limma package and multiple testing correction via the Benjamini-Hochberg method
Gene ontology analysis was performed by using the gprofiler2 R package as well as the web tool for obtaining summarized lists of all terms
Gene set enrichment analysis was performed using the msigdbr, clusterprofiler, and enrichplot R packages using the Reactome and KEGG databases
Assembly: Mouse: GRCm39cDNA; Human: GRCh38cDNA
Supplementary files format and content: tab-delimited text files include raw count data for each Sample

source_name: skin

extract_protocol:
LCM was performed using the LMD 7000 system (Leica Microsystems Inc., Chicago, IL). FFPE human or mouse skin was processed onto a polyethylene naphthalate (PEN) slide designed for LCM processing (Leica Catalog #11505158). To acquire enough material for RNA sequencing of SGs, we isolated at least 1,000 SGs or 1,000,000 mm2 of tissue
RNA was extracted from isolated SGs from mouse and human using a Qiagen All Prep DNA/RNA FFPE Kit (Qiagen Catalog #80234).
Libraries were prepared using an Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina Catalog # 20040529) with IDT for Illumina RNA UD Indexes, Set A (Illumina Catalog # 20040553).

value: skin

tag: cell type

value: sebocyte

value: WT

value: laser capture microdissection


title: 41F


title: 128F


title: mouse_LCM_SG_2


title: mouse_LCM_SG_1


title: 12R


title: msCol16

description:
inter.snps.ann.vcf
inter.indels.ann.vcf

library_source: genomic

data_processing:
Clean raw reads obtained from BGI were quality-trimmed using Trimmomatic (Bolger et al., 2014)
Sequences were mapped to the reference genome using Bowtie2 (Langmead et al., 2012)
Duplicate reads were marked and sorted using Picard and Variant calling was performed with GATK (Van der Auwera & O’Connor, 2020)
SNPs & INDELs were extracted using GATK and processed separately. Low quality sites (QUAL > 40) were removed and filtered for homozygotes.
SNPs and INDELs were annotated using snpEff (Cingolani et al., 2012). We treated the two msCol siblings (msCol12 and msCol16) separately and using Bedtools (Quinlan et al., 2010) intersect we found the reported overlap
Supplementary files format and content: The processed VCF file contain the intersect of the the two siblings (one for the snps and one for the indels)
Supplementary files format and content: VCF format is tab-separated text file
Library strategy: WGS

molecule: genomic DNA

growth_protocol: All plants were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark ) conditions.

extract_protocol:
Genomic DNA was extracted from each sample using the DNAeasy plant mini kit from Qiagen
At least 1 μg of DNA were submitted to the Beijing Genome Institute where they were prepared for WGS libraries.

value: msCol


title: 12F


title: 9R

data_processing:
fastq files were analyzed using the Methylstar pipeline (Shahryary et al.2020).
Supplementary files format and content: METHimpute (Taudt et al., 2018)
Supplementary files format and content: Methylation status calls and levels for all cytosines in the genome

extract_protocol:
Aerial rosette tissue 27 days after sowing (DAS) was harvested.
Genomic DNA was extracted from each sample using the DNAeasy plant mini kit from Qiagen
At least 1 μg of DNA were submitted to the Beijing Genome Institute where they were prepared for WGBS libraries.

treatment_protocol: All plants were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark ) conditions.

value: ddm1-derived epigenetic recombinant inbred line (epiRIL)


title: 54F


title: msCol12

description:
inter.snps.ann.vcf
inter.indels.ann.vcf


title: 568R

data_processing:
The clean FASTQ data obtained from BGI were processed.
Low quality sequences were removed using Trim Galore .
The reads were aligned to the reference A. thaliana (TAIR10) genome using Tophat2.
Aligned reads were counted using featureCounts.
The resulting raw count table was used downstream and it is provided here as the processed data file.
Supplementary files format and content: Raw reads counts for each sample

extract_protocol:
Total RNA was extracted from each sample using the miRNeasy kit from Qiagen.
At least 1 μg of total RNA was submitted to the Beijing Genome Institute where they were prepared for RNAseq libraries.


title: 574R


title: 41R


title: msCol12


title: msCol16


title: 96R


title: 579F


title: 81R


title: 97R


title: 93R


title: 579R


title: 539R


title: 574F


title: 568F


title: 99R


title: 539F


title: LU_m43

description:
LU, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Lung

value: Lung


title: 503R


title: 89R


title: 62R


title: 519R


title: 80R


title: LI_m52

description:
Li, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

value: Wild type


title: 79R

value: Aerial rosette


title: 503F

value: epiHybrid


title: LU_m50

description:
LU, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: 467R

value: Harvested at 27 days after sowing (DAS)


title: 574R


title: 467F


title: 579R


title: 63R


title: 462R

value: epiRil


title: 462F


title: 454R


title: 573R


title: 59R


title: 469R


title: 539R


title: 469F


title: 578R


title: 538R


title: 531R


title: 56R


title: 424R


title: 519F


title: 424F


title: 568R


title: 454F


title: 426F


title: 518R


title: 419R


title: 393R


title: 52R


title: 54R


title: 519R


title: 50R


title: 389R


title: 513R


title: 393F


title: 426R


title: 419F


title: 389F


title: 4R


title: 503R


title: 379R


title: 497R


title: 379F


title: 368R


title: 368F


title: 494R


title: 340R


title: 479R


title: 469R


title: 334R


title: 334F


title: 467R


title: 340F


title: 466R


title: 48R


title: 462R


title: 463R


title: 310F


title: 461R


title: 504R


title: 330F


title: 457R


title: 275R


title: 454R


title: 432R


title: 266R


title: 44R


title: 275F


title: 219R


title: 447R


title: 426R


title: 266F


title: 424R


title: 455R


title: 442R


title: 413R


title: 241R


title: 176F


title: 176R


title: 211F


title: 310R


title: 241F


title: 158F


title: 330R


title: 410R


title: 430R


title: 219F


title: 211R


title: 102R


title: 41R


title: 393R


title: 419R


title: 412R


title: 125F


title: 423R


title: 128R


title: 158R


title: 402R


title: 40R


title: 54F


title: 390R


title: 125R


title: 388R


title: 401R


title: 50R


title: 384R


title: 394R


title: 128F


title: 41R


title: 102F


title: 391R


title: 79R


title: 79F


title: 37R


title: 50F


title: 54R


title: 383R


title: 389R


title: 12R


title: 382R


title: 368R


title: 41F


title: 380R


title: 12F


title: 379R


title: 373R


title: 367R


title: 354R


title: 353R


title: 350R


title: 362R


title: 35R


title: 340R


title: 352R


title: 348R


title: 344R


title: 339R


title: 337R


title: PPy/I+SW/EE, biological rep1

type: RNA

city: Mexico city

first: Angelica

last: Coyoy-Salgado

address: Av. Cuauhtémoc 330, Mexico City, Mexico

country: Mexico

institute: CONACyT-Instituto Mexicano del Seguro Social

description: Gene expression data from spinal cord with a moderate injury at thoracic level 9 after a month of giving plasma PPy/I implants treatment and rehabilitation therapies

hyb_protocol: Target cDNA was prepared according to the Whole-Transcrpt Sense Target Labeling Protocol (P/N 703174, Thermo Fisher Scientific). The labeled cDNA product was hybridized to the GeneChip rat Clariom S microarray (Affymetrix). The samples were washed with low-strongency and high-stringency buffers and were stained with streptavidin-phycoerythrin using the GeneChip Fluidics Station 450 with the FS450_0002 protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The data were were analyzed and quantile normalized using the Transcriptomic Analysis Console (TAC) Software 4.0.1. (Thermo Fisher Scientific).

label: Biotin

organism: Rattus norvegicus

source_name: spinal cord tissue after one month of traumatic injury with treatment

label_protocol: Biotin using the GeneChip Fluidics Station 450 with the FS450_0002 protocol.

growth_protocol: The animals were individually housed under standard conditions (12-h light/dark cycles, 22°C). After spinal cord injury, animals received antibiotic (bezathine penicillin) and an analgesic (paracetamol;5ml/l of water) during 5 days and the general health of each animal in the study was verified daily.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The animals included in the study were sacrificed 1 month after spinal cord injury. The spinal cord was extracted, including the epicentre of the lesion plus 0.5 cm in the rostral direction and 0.5 cm in the caudal direction, the tissue was collected fresh at 4°C and immediately stored at -70°C in the Trizol solution (Invitrogen) until RNA extraction.

tag: strain

value: Long-evans

tag: gender

value: female

value: spinal cord


title: 330R


title: 329R


title: LTME, biological rep3

description: Gene expression data from spinal cord with a moderate injury at thoracic level 9 after one month

source_name: spinal cord tissue after one month of traumatic injury without any treatment


title: LTME, biological rep1


title: 327R


title: PPy/I,biological rep1

description: Gene expression data from spinal cord with a moderate injury at thoracic level 9 after a month of administrated the treatment with plasma PPy/I implants


title: PPy/I+SW/EE, biological rep2


title: LTME, biological rep2


title: PPy/I,biological rep2


title: PPy/I,biological rep3


title: 30R


title: 310R


title: 31R


title: 328R


title: 309R


title: 318R


title: 334R


title: 305R


title: 319R


title: 302R


title: 313R


title: 2R


title: 295R


title: 28R


title: 300R


title: 286R


title: 275R


title: 273R


title: 26R


title: PPy/I+SW/EE, biological rep3


title: organoids_3-month-old-PTN_rep3

type: genomic

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

description: Mutant organoid sample

hyb_protocol: Standard Illumina Protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Raw data were proceeded with CHAMP R package following the recommeded pipeline

label: Cy5 and Cy3

organism: Homo sapiens

source_name: PTN organoid

label_protocol: Standard Illumina Protocol

extract_protocol: The genomic DNA was extracted with DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s protocol

value: male

tag: age


title: organoids_3-month-old-PTN_rep4

description: Mutant organoid sample


title: organoids_3-month-old-PTCC_rep2

description: Mutant organoid sample

source_name: PTCC organoid

value: PTCC:PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-


title: organoids_3-month-old-PTCC_rep3

description: Mutant organoid sample


title: 266R


title: 262R


title: 250R


title: organoids_3-month-old-PT_rep1

description: Mutant organoid sample

source_name: PT organoid


title: organoids_3-month-old-PT_rep3

description: Mutant organoid sample


title: 245R


title: organoids_3-month-old-PTCC_rep4

description: Mutant organoid sample


title: organoids_3-month-old-PTN_rep1

description: Mutant organoid sample


title: organoids_3-month-old-PT_rep2

description: Mutant organoid sample


title: organoids_3-month-old-WT_rep3

description: Control organoid sample

source_name: WT organoid


title: 24R


title: organoids_2-month-old-PTN_rep3

description: Mutant organoid sample


title: organoids_3-month-old-PTN_rep2

description: Mutant organoid sample


title: 241R


title: organoids_3-month-old-PT_rep4

description: Mutant organoid sample


title: 239R


title: organoids_2-month-old-PT_rep1

description: Mutant organoid sample


title: organoids_2-month-old-PT_rep3

description: Mutant organoid sample


title: organoids_3-month-old-WT_rep2

description: Control organoid sample


title: organoids_3-month-old-PTCC_rep1

description: Mutant organoid sample


title: 225R


title: organoids_2-month-old-PTCC_rep3

description: Mutant organoid sample


title: organoids_2-month-old-PTN_rep1

description: Mutant organoid sample


title: organoids_3-month-old-WT_rep1

description: Control organoid sample


title: 229R


title: organoids_2-month-old-PT_rep2

description: Mutant organoid sample


title: organoids_2-month-old-PTN_rep2

description: Mutant organoid sample


title: 223R


title: 220R


title: Pool#301/#413/#416_VDJ

first: Zibo

last: Meng

address: Im Neuenheimer Feld 280

description:
10x Genomics
Pool_GEX_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Hierarchical data format files(h5)

source_name: Pancreatic cancer tissue from #301/#413/#416

extract_protocol:
Tumors were dissociated into single-cell suspensions using the human tumor dissociation kit (Miltenyi Biotec) following the manufacturer's instructions. After filtering through a 70µm strainer, the cell suspension was collected. Generation of xenografts, tumor cell lines, and tumor-infiltrating lymphocyte (TIL) lines were performed as described previously (12, 13). As preparation for single-cell sequencing, cell suspensions were labeled with a dead cell marker (DCM-Aqua, 1:40 dilution, Thermo Fisher) and the following fluorescent-labeled antibodies: CD3-BV711 (clone: OKT3, 1:40 dilution, BioLegend), CD45-BV421 (clone: HI30), CD4-APC-Fire (1:40 dilution, clone SK3, BioLegend), CD8-PerCP Cy5.5 (clone: RPA-T8), PD-1-PE (1:8 dilution, clone: EH12.2H7, BioLegend). Cells were harvested and washed twice with cold phosphate-buffered saline (PBS) before a 10-minute incubation with Aqua Dead cell marker at 4°C. Cells, once stained with Aqua, were washed twice using a flow cytometry (FACS) staining buffer and subsequently underwent extracellular staining. Antibodies were mixed and diluted in FACS buffer as specified, and cells were incubated for 25 minutes at 4°C. After washing twice using FACS buffer, the DCM-CD45+CD3+ T cell population was sorted immediately using BD FACS Aria Fusion Cell Sorter
Library was performed according to the manufacturer’s instructions ( Single Cell 5’ Library Kit  protocol, 10x Genomics).

tag: cell line

value: Tumor-infiltrating T cells from from #301/#413/#416


title: organoids_2-month-old-PTCC_rep1

description: Mutant organoid sample


title: organoids_1-month-old-PTN_rep3

description: Mutant organoid sample


title: 21R


title: organoids_2-month-old-PTCC_rep2

description: Mutant organoid sample


title: 234R


title: Pool#301/#413/#416_HASH

value: Pancreatic cancer tissue from #301/#413/#416


title: 432_VDJ

description:
10x Genomics
432_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #432

value: Pancreatic cancer tissue from #432

value: Tumor-infiltrating T cells from from #432

value: T cells from #432


title: 219R

value: ddm1-derived epigenetic recombinant inbred line (epiRIL)


title: Pool#301/#413/#416_GEX


title: organoids_1-month-old-PTN_rep2

description: Mutant organoid sample


title: 216R


title: 215R


title: 432_HASH


title: 432_GEX


title: 213R


title: 418_VDJ

description:
10x Genomics
418_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #418

value: Pancreatic cancer tissue from #418

value: Tumor-infiltrating T cells from from #418

value: T cells from #418


title: 214R

source_name: Aerial rosette

value: Aerial rosette


title: 309_GEX

description:
10x Genomics
309_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #309

value: Pancreatic cancer tissue from #309

value: Tumor-infiltrating T cells from from #309

value: T cells from #309


title: 208R

value: Harvested at 27 days after sowing (DAS)


title: 282_VDJ

description:
10x Genomics
282_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #282

value: Pancreatic cancer tissue from #282

value: Tumor-infiltrating T cells from from #282

value: T cells from #282


title: organoids_2-month-old-WT_rep1

description: Control organoid sample

value: male


title: 418_GEX


title: 282_GEX


title: 262_VDJ

description:
10x Genomics
262_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #262

value: Pancreatic cancer tissue from #262

value: Tumor-infiltrating T cells from from #262

value: T cells from #262


title: organoids_2-month-old-WT_rep3

description: Control organoid sample


title: organoids_1-month-old-PTN_rep1

description: Mutant organoid sample


title: 203R


title: 204R


title: 231R


title: 262_GEX


title: 249_VDJ

description:
10x Genomics
249_GEX_filtered_feature_bc_matrix.h5

source_name: Pancreatic cancer tissue from #249

value: Pancreatic cancer tissue from #249

value: Tumor-infiltrating T cells from from #249

value: T cells from #249


title: 200R

value: ddm1-derived epigenetic recombinant inbred line (epiRIL)


title: 18R


title: 19R


title: CLL cells, CXCR4high, replicate 2

city: Chengdu

first: xinran

last: xue

address: No. 37, Guoxue Xiang, Wuhou District, Chengdu

department: Department of Laboratory Medicine

country: China

institute: West China Hospital, Sichuan University

data_processing:
Fastp software was used to process the raw reads in fastq format, and clean reads were obtained by removing low-quality reads for subsequent data analysis.
Reference genome comparison was performed using HISAT2 software.
The read counts of each gene were obtained by HTSeq-count, and gene expression (FPKM) was calculated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes read counts for each Sample

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from the CLL cells using TRIzol reagent, RNA purity and quantification were characterized using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples that passed quality control were used for subsequent library construction.
Ribosomal RNA was removed using the Ribo-off rRNA Depletion Kit (Vazyme, Nanjing, China), and the transcriptome library was constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the instructions.

value: Peripheral blood

value: CD19+CD5+CLL cells


title: 249_GEX


title: CLL cells, CXCR4high, replicate 1


title: 211R

value: Aerial rosette


title: CLL cells, CXCR4low, replicate 2


title: CLL cells, CXCR4low, replicate 1


title: 207R


title: organoids_2-month-old-WT_rep2

description: Control organoid sample


title: AGS cells, Vector

city: Shijiazhuang

first: Lingxue

last: Shi

address: No.89 Donggang Road

institute: The First Hospital of Hebei Medical University

data_processing:
NGS(Next Generation Sequencing, high-throughput sequencing II) technology uses high-throughput sequencing instrument (such as Illumina NovaSeq6000) to sequence cDNA.
After base recognition and error filtering, the original sequencing fragment which can be used for analysis is finally obtained.
The spliced mapping algorithm of Hisat2 is applied to Genome mapping of pretreated reads
Transforming reads into FPKM to standardize gene expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raws counts for each sample

source_name: gastric cancer cells

growth_protocol: Cells were cultured and maintained in DMEM supplemented with 10% FBS and 1% antibiotics according to the ATCC protocols. Cells were maintained at a 37°C incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer.
According to the experimental instructions, the purified Total RNA was subjected to the steps of mRNA separation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, terminal repair, 3' terminal A addition, linker connection, enrichment, etc., to complete the construction of sequencing sample library.

value: gastric cancer cells

value: AGS

value: adenocarcinoma

value: Vector


title: AGS cells, TMEM65 overexpressed

value: TMEM65 overexpressed


title: 188R

value: Harvested at 27 days after sowing (DAS)


title: 157R


title: 160R


title: 168R


title: 161R


title: 16R


title: 171R


title: 185R


title: 158R


title: 153R


title: 17R


title: 176R


title: 189R


title: 184R


title: 152R


title: AML_12_rep2 (ADT)

city: Cincinnati

first: Xuan

last: Zhang

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's hospital

description:
AML_13_ADT
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
AML-13_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
CellRanger version 6.1.2 was applied to the combined scRNA-Seq, HTO and ADT FASTQ files, alinged to both the hg38 and hg19 genomes. Example: cellranger count --id=$INPUTFILE --libraries=library.csv --transcriptome=/database/cellranger/$SPECIESDATABASE --feature-ref=$ADT-feature.csv --localmem 132 --chemistry SC3Pv3HT (for HT experiment)
SoupX ambient RNA removal was perfomred using an estimated contamination fraction of 15% on all samples.
Cells HTO associations destinguishing both donor and ADT concentration were de-multiplexed using the HTO processing module of AltAnalyze. Cell barcodes with > 30% of normalized reads assigned to multiple HTOs were annotated as doublets, with confident singlet assigned to cells with >40% of normalized reads assigned to a single HTO. Cells were further filtered based on the 7 mouse/rat isotype control antibodies counts (custom code), and nFeature_RNA>500 & nCount_RNA >1000 & percent.mt<25. This QC step filtered 393,748 cells to 315,792 high-quality single cells in the initial titration dataset and 90,889 to 72,198 cells in the final titrated CITE-Seq dataset.
Ambient corrected transcriptome counts and associated ADTs counts were supplied as input to the software TotalVI to obtain normalized and denoised ADT counts. To derive clusters from the initial titration CITE-Seq datasets, the software Azimuth or cellHarmony was used to transfer labels from counts per ten thousand (CPTT) normalized expression centroids computed in author provided labels from three prior published reference bone marrow atlases. Projected labels and unsupervised clusters were integrated in the software scTriangulate, using either RNA data alone or RNA+ADTs.
Assembly: hg38
Supplementary files format and content: CellRanger filtered HDF5 sparse count matrix
Library strategy: CITE-seq

molecule: protein

source_name: Bone marrow

extract_protocol:
Cells were isolated from bone marrow of AML patients. Frozen cells were thawed. Total nucleated cells were live and dead sorted on Sony MA900.
The CITE-Seq library construction protocol followed the Biolegend 10X 3' V3.1 single index ADT protocol and 10X 3' V3.1 dual index protocol, with additional modifications.

value: Bone marrow

tag: mutation

tag: Sex

value: Total nucleated cell

tag: library type

value: ADT

tag: adt


title: AML_14 (GEX)

description:
AML_14_GEX
titrated_AML_annotation.txt (Cell annotation file)
10X 3' V3.1 dual indexed GEX
AML-14_filtered_feature_bc_matrix.h5

value: CKIT D816V

value: Male

value: 21 yrs

value: 10x Chromium 3' V3.1 GEX


title: AML_14 (ADT)

description:
AML_14_ADT
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
AML-14_filtered_feature_bc_matrix.h5


title: organoids_1-month-old-PTCC_rep3

description: Mutant organoid sample

value: male

value: PTCC:PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-


title: AML_12_rep2 (GEX)

description:
AML_13_GEX
titrated_AML_annotation.txt (Cell annotation file)
10X 3' V3.1 dual indexed GEX
AML-13_filtered_feature_bc_matrix.h5


title: AML_7 (ADT)

description:
AML_7_2_ADT
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
AML-7_2_filtered_feature_bc_matrix.h5

value: CBL M400R, SRSF2 P95H, TET2 Q916X and S1290X

value: Female

value: 80 yrs


title: 150R

value: Aerial rosette

value: ddm1-derived epigenetic recombinant inbred line (epiRIL)


title: 139R


title: 136R


title: AML_12_rep1 (ADT)

description:
AML_12_2_ADT
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
AML-12_2_filtered_feature_bc_matrix.h5


title: 146R


title: AML_12_rep1 (GEX)

description:
AML_12_2_GEX
titrated_AML_annotation.txt (Cell annotation file)
10X 3' V3.1 dual indexed GEX
AML-12_2_filtered_feature_bc_matrix.h5


title: AML_7 (GEX)

description:
AML_7_2_GEX
titrated_AML_annotation.txt (Cell annotation file)
10X 3' V3.1 dual indexed GEX
AML-7_2_filtered_feature_bc_matrix.h5


title: WRNKO_D21_2

city: Hong Kong

first: Wai- Yee

last: Chan

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
The clean reads were stored in FASTAQ format.
FPKM method was used in calculated expression level, and the calculated gene expression can be directly used for comparing the difference of gene expression among sample.
Supplementary files format and content: excel files include FPKM values for each Sample

source_name: bone marrow

extract_protocol:
RNA was harvested using TRIzol™ Reagent (Invitrogen) following the manufacturer’s instructions.
The library was establised by Novogene company (Tianjin, China).

value: bone marrow

value: hMSCs

value: mesenchymal stem cells

value: WRN KO

value: adipogenic differentiation


title: 141R

value: Harvested at 27 days after sowing (DAS)


title: WRNKO_D21_3


title: 13R


title: 131R


title: WRNKO_D21_1


title: WRNKO_D5_3


title: organoids_1-month-old-PTCC_rep2

description: Mutant organoid sample


title: organoids_1-month-old-PT_rep1

description: Mutant organoid sample


title: WRNKO_D5_2


title: 128R


title: WRNKO_D5_1


title: 12R


title: 125R


title: WRNKO_D1_3


title: WRNKO_D1_2


title: 210R


title: WRNKO_D1_1


title: WT_D21_2

value: WT


title: WT_D21_1


title: 106R


title: WT_D21_3


title: 10R


title: 103R


title: 118R


title: WT_D5_3


title: WT_D5_2


title: 102R


title: 126R


title: 120R


title: msCol16

data_processing:
fastq files were analyzed using the Methylstar pipeline (Shahryary et al.2020).
Assembly: METHimpute (Taudt et al., 2018)
Supplementary files format and content: Methylation status calls and levels for all cytosines in the genome

extract_protocol:
Genomic DNA was extracted from each sample using the DNAeasy plant mini kit from Qiagen
At least 1 μg of DNA were submitted to the Beijing Genome Institute where they were prepared for WGBS libraries.

value: msCol


title: msCol12


title: organoids_1-month-old-WT_rep2

description: Control organoid sample


title: WT_D5_1


title: 107R


title: WT_D1_3


title: 9F

value: epiHybrid


title: 99F


title: 97F


title: organoids_1-month-old-PT_rep3

description: Mutant organoid sample


title: 96F


title: C6_PTN_rep2

data_processing:
Raw reads were aligned to GRCh38 with STAR (2.4.1) using default parameters
The aligned reads were quantified by the feature Counts in Rsubread package
TPM were then calculated and used for following PCA analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: Organoid

extract_protocol:
The RNA were extracted with Qiagen RNeasy kit (Cat#74004). The RNA was extracted and purified according to the manufacturers' protocols
Using SMARTER mRNA-Seq Library Prep Kit according to manufacturer's protocols

value: Organoid

value: C6 iPSC

value: Human induced pluripotent stem cells

value: PTN


title: C6_PTN_rep3


title: WT_D1_2


title: C6_PTCC_rep3

value: PTCC


title: WT_D1_1


title: 89F


title: 104R


title: C6_PTN_rep1


title: 80F


title: C6_PTCC_rep2


title: C6_PT_rep3

value: PT


title: 81F

value: Aerial rosette


title: 93F


title: C6_PTCC_rep1


title: 79F


title: C6_PT_rep1


title: C6_WT_rep3


title: C6_PT_rep2


title: 63F


title: 62F


title: GFP_PTN_rep1

value: GFP iPSC


title: 59F


title: GFP_PT_rep3


title: C6_WT_rep2


title: C6_WT_rep1


title: GFP_PT_rep2


title: 578F


title: GFP_PTN_rep3


title: 538F


title: GFP_PTN_rep2


title: organoids_1-month-old-WT_rep3

description: Control organoid sample

value: male


title: 573F


title: 574F


title: 539F


title: GFP_PTCC_rep2


title: 54F


title: organoids_1-month-old-PTCC_rep1

description: Mutant organoid sample

value: PTCC:PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-


title: GFP_PTCC_rep3


title: 579F


title: organoids_1-month-old-PT_rep2

description: Mutant organoid sample


title: 56F


title: GFP_PT_rep1


title: GFP_PTCC_rep1


title: GFP_WT_rep3


title: 531F


title: organoids_1-month-old-WT_rep1

description: Control organoid sample


title: 52F


title: 513F


title: BM32 and BF32 TNC (HTO) rep2

description:
TNC_34_antibody_features.csv
single indexed HTO
TNC-3-4-2_filtered_feature_bc_matrix.h5

data_processing:
CellRanger version 6.1.2 was applied to the combined scRNA-Seq, HTO and ADT FASTQ files, alinged to both the hg38 and hg19 genomes. Example: cellranger count --id=$INPUTFILE --libraries=library.csv --transcriptome=/database/cellranger/$SPECIESDATABASE --feature-ref=$ADT-feature.csv --localmem 132 --chemistry SC3Pv3HT (for HT experiment)
SoupX ambient RNA removal was perfomred using an estimated contamination fraction of 15% on all samples.
Cells HTO associations destinguishing both donor and ADT concentration were de-multiplexed using the HTO processing module of AltAnalyze. Cell barcodes with > 30% of normalized reads assigned to multiple HTOs were annotated as doublets, with confident singlet assigned to cells with >40% of normalized reads assigned to a single HTO. Cells were further filtered based on the 7 mouse/rat isotype control antibodies counts (custom code), and nFeature_RNA>500 & nCount_RNA >1000 & percent.mt<25. This QC step filtered 393,748 cells to 315,792 high-quality single cells in the initial titration dataset and 90,889 to 72,198 cells in the final titrated CITE-Seq dataset.
Ambient corrected transcriptome counts and associated ADTs counts were supplied as input to the software TotalVI to obtain normalized and denoised ADT counts. To derive clusters from the initial titration CITE-Seq datasets, the software Azimuth or cellHarmony was used to transfer labels from counts per ten thousand (CPTT) normalized expression centroids computed in author provided labels from three prior published reference bone marrow atlases. Projected labels and unsupervised clusters were integrated in the software scTriangulate, using either RNA data alone or RNA+ADTs.
Assembly: hg38
Supplementary files format and content: CellRanger filtered HDF5 sparse count matrix
Supplementary files format and content: ADT/HTO feature files
Supplementary files format and content: CD34_1_antibody_features.csv
Supplementary files format and content: CD34_2_antibody_features.csv
Supplementary files format and content: CD34_3_antibody_features.csv
Supplementary files format and content: CD34_4_antibody_features.csv
Supplementary files format and content: CD271_1_antibody_features.csv
Supplementary files format and content: CD271_2_antibody_features.csv
Supplementary files format and content: CD271_3_antibody_features.csv
Supplementary files format and content: CD271_4_antibody_features.csv
Supplementary files format and content: TNC_12_antibody_features.csv
Supplementary files format and content: TNC_34_antibody_features.csv
Supplementary files format and content: titrated_mix_human.csv
Supplementary files format and content: Cell annotation files
Supplementary files format and content: Level3R-Titrated-Titration-Annotation.txt
Supplementary files format and content: Level3M-titrated-cell-annotation.txt
Library strategy: CITE-Seq

extract_protocol:
Cells were isolated from fresh bone marrow. Total nucleated cells were live and dead sorted on Sony MA900. ficoled and enriched for CD34+ cells with double column setup on AutoMACS.
The CITE-Seq library construction protocol followed the Biolegend 10X 3' V3.1 single index ADT protocol and 10X 3' V3.1 dual index protocol, with additional modifications.

value: Bone marrow

tag: self reported_ethnicity

value: Black

value: Male and Female

value: 32 yrs

value: Total nucleated cells

value: HTO


title: 503F

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: 497F


title: WF32 CD34+CD271+ (HTO)

description:
CD271_2_antibody_features.csv
single indexed HTO
CD271-2_filtered_feature_bc_matrix.h5

value: White

value: Female


title: WM22 CD34+CD271+ (HTO)

description:
CD271_1_antibody_features.csv
single indexed HTO
CD271-1_filtered_feature_bc_matrix.h5

value: Male

value: 22 yrs


title: 494F


title: 4F


title: WM22 and WF32 TNC (HTO) rep1

description:
TNC_12_antibody_features.csv
single indexed HTO
TNC-1-2-1_filtered_feature_bc_matrix.h5

value: 22 and 32 yrs


title: WM22 and WF32 TNC (HTO) rep2

description:
TNC_12_antibody_features.csv
single indexed HTO
TNC-1-2-2_filtered_feature_bc_matrix.h5


title: 479F

value: Aerial rosette


title: 467F


title: WF32 CD34+ (HTO)

description:
CD34_2_antibody_features.csv
single indexed HTO
CD34-2_filtered_feature_bc_matrix.h5


title: WM22 CD34+ (HTO)

description:
CD34_1_antibody_features.csv
single indexed HTO
CD34-1_filtered_feature_bc_matrix.h5


title: 48F


title: 463F


title: 519F


title: 469F


title: 466F


title: WM34 TNC (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WM34-TNC_filtered_feature_bc_matrix.h5

value: 34 yrs

value: ADT


title: GFP_WT_rep1

value: Organoid

value: GFP iPSC

value: Human induced pluripotent stem cells

value: WT


title: WM34 CD34+CD271+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WM34-CD271_filtered_feature_bc_matrix.h5

value: Bone marrow


title: 462F


title: 518F


title: 50F


title: WM34 CD34+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WM34-CD34_filtered_feature_bc_matrix.h5


title: 461F


title: BM32 and BF32 TNC (HTO) rep1

description:
TNC_34_antibody_features.csv
single indexed HTO
TNC-3-4-1_filtered_feature_bc_matrix.h5

value: Black

value: Male and Female

value: 32 yrs

value: Total nucleated cells


title: 504F

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: 457F


title: 455F


title: 454F


title: BM27 TNC (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BM27-TNC_filtered_feature_bc_matrix.h5

value: Male

value: 27 yrs


title: BM27 CD34+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BM27-CD34_filtered_feature_bc_matrix.h5


title: WF26 TNC (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WF26-TNC_filtered_feature_bc_matrix.h5

value: White

value: Female

value: 26 yrs


title: BF21 TNC (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BF21-TNC_filtered_feature_bc_matrix.h5

value: 21 yrs

value: ADT


title: 447F

value: Aerial rosette


title: WF26 CD34+CD271+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WF26-CD271_filtered_feature_bc_matrix.h5


title: BF21 CD34+CD271+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BF21-CD271_filtered_feature_bc_matrix.h5


title: BF21 CD34+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BF21-CD34_filtered_feature_bc_matrix.h5


title: 426F


title: WF26 CD34+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
WF26-CD34_filtered_feature_bc_matrix.h5


title: 424F


title: BM32 and BF32 TNC (ADT) rep1

description:
TNC_34_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
TNC-3-4-1_filtered_feature_bc_matrix.h5


title: WM22 and WF32 TNC (ADT) rep2

description:
TNC_12_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
TNC-1-2-2_filtered_feature_bc_matrix.h5

value: 22 and 32 yrs


title: 41F


title: WM22 and WF32 TNC (ADT) rep1

description:
TNC_12_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
TNC-1-2-1_filtered_feature_bc_matrix.h5


title: 419F


title: BM27 CD34+CD271+ (ADT)

description:
titrated_mix_human.csv
TotalSeq-A single indexed ADT, 132-antibodies
BM27-CD271_filtered_feature_bc_matrix.h5


title: WF32 CD34+CD271+ (ADT)

description:
CD271_2_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD271-2_filtered_feature_bc_matrix.h5


title: 412F


title: 44F


title: 432F


title: 413F


title: 430F


title: 442F


title: WM22 CD34+CD271+ (ADT)

description:
CD271_1_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD271-1_filtered_feature_bc_matrix.h5

value: 22 yrs


title: 40F


title: 402F


title: WM22 CD34+ (ADT)

description:
CD34_1_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD34-1_filtered_feature_bc_matrix.h5

value: Bone marrow


title: 393F


title: 423F


title: WM34 TNC (GEX)

description:
10X 3' V3.1 dual indexed GEX
WM34-TNC_filtered_feature_bc_matrix.h5

value: 34 yrs

value: mRNA


title: 410F


title: 391F


title: 390F


title: WM34 CD34+CD271+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
WM34-CD271_filtered_feature_bc_matrix.h5


title: WF32 CD34+ (ADT)

description:
CD34_2_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
CD34-2_filtered_feature_bc_matrix.h5

value: 32 yrs


title: 401F


title: BM32 and BF32 TNC (ADT) rep2

description:
TNC_34_antibody_features.csv
TotalSeq-A single indexed ADT, 266-antibodie
TNC-3-4-2_filtered_feature_bc_matrix.h5

value: Black

value: Male and Female

value: Total nucleated cells


title: 389F

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: 388F


title: WM34 CD34+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
WM34-CD34_filtered_feature_bc_matrix.h5

value: White

value: Male


title: 384F


title: 383F


title: 380F


title: 382F


title: 394F


title: BM27 TNC (GEX)

description:
10X 3' V3.1 dual indexed GEX
BM27-TNC_filtered_feature_bc_matrix.h5

value: 27 yrs


title: BM27 CD34+CD271+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
BM27-CD271_filtered_feature_bc_matrix.h5


title: RPEcells_MYCon_shCtrl_qChIPseqSMC_exp2

city: London

first: Chiara

last: Perrod

state: England

address: Gower St

department: LMCB

country: United Kingdom

institute: UCL

data_processing:
demultiplexing, aligning, create bam, create bigwig
quantification by spike in, see Active Motif protocol
quantification of the signal by deeptools
bigwigs. Fastq were aligned by bowtie2, sam used to create bam by samtools, bam used to create bigwig by bam coverage
Assembly: Human hg19 and Drosophila melanogaster dm6
Supplementary files format and content: bigwig

source_name: RPE

growth_protocol: DMEM/F12 medium 10% FBS - glutammin - antibiotics

extract_protocol:
quantitative ChIP as in PMID 31776511, starting from 20M cells with Diagenode Pico sonicator (15min 30sec ON?OFF)
Nugene Ovation Ultralow V2 system (TECAN)

treatment_protocol: MYC induction

value: RPE

value: retinal pigment epithelium

value: shCtrl, MYC induction


title: RPEcells_MYCoff_shCtrl_qChIPseqSMC_exp2

value: shCtrl


title: BM27 CD34+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
BM27-CD34_filtered_feature_bc_matrix.h5


title: 373F

value: Aerial rosette


title: 379F


title: WF26 TNC (GEX)

description:
10X 3' V3.1 dual indexed GEX
WF26-TNC_filtered_feature_bc_matrix.h5

value: Bone marrow

value: Female

value: 26 yrs


title: WF26 CD34+CD271+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
WF26-CD271_filtered_feature_bc_matrix.h5

value: mRNA


title: RPEcells_MYCoff_shCtrl_qChIPseqSMC_exp1


title: ImP4

city: Nanjing

first: Jingyi

last: Hu

state: Jiangsu

address: Hanzhong road No155.

institute: Affiliated Hospital of Nanjing University of Chinese Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_colon.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: colon

value: wild type

value: ImP


title: ImP3


title: 37F

value: epiHybrid


title: DSS3

value: DSS


title: DSS5


title: 368F

value: Harvested at 27 days after sowing (DAS)


title: WF26 CD34+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
WF26-CD34_filtered_feature_bc_matrix.h5

value: White


title: DSS2


title: RPEcells_MYCon_shCTCF_qChIPseqSMC_exp2

value: shCTCF, MYC induction


title: 367F


title: BF21 TNC (GEX)

description:
10X 3' V3.1 dual indexed GEX
BF21-TNC_filtered_feature_bc_matrix.h5

value: Black

value: 21 yrs

value: Total nucleated cells


title: DP4

value: DSS+ImP


title: ImP1


title: RPEcells_MYCon_shCTCF_qChIPseqSMC_exp1

value: RPE

value: retinal pigment epithelium


title: RPEcells_MYCon_shCtrl_qChIPseqSMC_exp1

value: shCtrl, MYC induction


title: RPEcells_MYCoff_shCTCF_qChIPseqSMC_exp2

value: shCTCF


title: BF21 CD34+CD271+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
BF21-CD271_filtered_feature_bc_matrix.h5

value: Bone marrow

value: Female

value: mRNA


title: DP3

value: colon

value: wild type


title: DP2


title: tumorous lesion

city: Fukuoka

first: Kana

last: Hasegawa

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: primary intraosseous carcinoma, tumorous lesion

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: female

value: primary intraosseous carcinoma

tag: tissue type

value: tumorous lesion


title: 362F

value: Aerial rosette

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: Ctrl5


title: 352F


title: BM32 and BF32 TNC (GEX) rep1

description:
10X 3' V3.1 dual indexed GEX
TNC-3-4-1_filtered_feature_bc_matrix.h5

value: Black

value: Male and Female

value: 32 yrs

value: Total nucleated cells


title: Ctrl4


title: WM22 and WF32 TNC (GEX) rep2

description:
10X 3' V3.1 dual indexed GEX
TNC-1-2-2_filtered_feature_bc_matrix.h5

value: White

value: 22 and 32 yrs


title: RNA:Ribo-zerototalRNA,PF1linerep3

first: Paul

middle: Adrian

last: Ginno

state: Baden-Württemberg

address: Im Neunheimer Feld 280

description:
RNA_rep3
PF1_RNA_counts.rds

data_processing:
PF1 whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to the mm10 reference. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics
F1 tumour whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to an N-masked mm10 reference created with SNPsplit. Reads were then haplotype labeled using snpsplit. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics. Haplotype identification was done by counting assignable reads (minimum of 2) for each mutation, and fitting a dual gaussian distribution with mixtools
Omni-ATAC: Reads were mapped with Bowtie2 and peaks called with MACS2 using the flags -f BAMPE -g mm –nomodel –nolambda –keep-dup-all –call-summits -B -q 0.01. The peak file here is from sample 1 which was used in all comparisons.
RNA-seq: Transcript abundances were quantified using Kalisto (v0.46.0) with the –bias and –rf-stranded flags and the Gencode M25 transcript release. Transcription start sites were adjusted to the isoform with the highest ATAC signal within -1000 - +500 from the promoter
Assembly: mm10
Supplementary files format and content: PF1_SisterMutations.rds: RDS file of mutations in all 14 PF1 genomes (7 pairs of sisters). Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter, timepoint (T0=penning, T1=post penning) and sample name
Supplementary files format and content: PF1_RNA_counts.rds: Tags per million (tpm) ouput from Kallisto for 3 replicates. Entrez gene ID, gene name and genomic positions are noted.
Supplementary files format and content: PF1_ATAC_Peaks.rds: ATAC peak file in RDS format from MACS2 peak calling
Supplementary files format and content: F1CastB6_mutations.rds: RDS file of mutations in all 6 F1 tumors. Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter and sample name

source_name: Blood

growth_protocol: The PF1 line (P388D1 with FastFUCCI integration) was maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For PF1 cells, DNA extraction was performed using the DNeasy kit from Qiagen© as per the manufacturer's instructions. For the F1 mouse tumours, DNA was extracted using the Qiagen© AllPrep DNA/RNA Mini Kit.
Approximately 100-500 µg of genomic DNA was fragmented and libraries prepared using the NEBNext® Ultra II kit and the Unique Dual Index primers for Illumina® as per the manufacturer’s instructions, with the exception that the enzymatic fragmentation step was carried out for 15 minutes instead of 5.

treatment_protocol: PF1 cells were treated with 5,000 microjoules/cm2 of UVC and penned as single cells directly after treatment. Negative control cell samples were taken from the proliferating population at the time of treatment.

value: Blood

value: P388D1 derived PF25

value: monocyte, macrophage

value: stable FastFUCCI expression

value: UV, 5 nanojoules/cm2


title: RPEcells_MYCoff_shCTCF_qChIPseqSMC_exp1

value: RPE

value: retinal pigment epithelium

value: shCTCF


title: 353F

value: Aerial rosette


title: RNA:Ribo-zerototalRNA,PF1linerep1

description:
RNA_rep1
PF1_RNA_counts.rds

value: P388D1 derived PF23


title: QKO tumor, Keap1 knockout sample 3

city: Houston

first: Pawel

middle: Karol

last: Mazur

state: TX

address: 1515 Holcombe Blvd.

institute: University of Texas MD Anderson Cancer Center

description:
KP3
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt

data_processing:
Create a reference index (STAR software)
Alignment and mapping (STAR software)
Combined the samples' reads into a single file (Python 3)
Differential expression analysis (DESeq2 package)
Gene set enrichment analysis (GSEA package)
Assembly: mm39
Supplementary files format and content: Raw read counts extracted from each sample on which RNA-seq was run.
Supplementary files format and content: Results from DESeq analysis.

source_name: Lung

extract_protocol:
Zymo RNA clean and Concentrator Kit
mRNA library preparation at Novogene

value: Lung

value: small cell lung cancer

value: Keap1 knockout


title: 350F

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: RNA:Ribo-zerototalRNA,PF1linerep2

description:
RNA_rep2
PF1_RNA_counts.rds

value: P388D1 derived PF24


title: WM22 and WF32 TNC (GEX) rep1

description:
10X 3' V3.1 dual indexed GEX
TNC-1-2-1_filtered_feature_bc_matrix.h5

value: Bone marrow

value: White

value: Male and Female

value: 22 and 32 yrs

value: Total nucleated cells

value: mRNA


title: QKO tumor, Keap1 knockout sample 2

description:
KP2
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt


title: ATAC:BulkATAC,PF1linerep3

description:
Omni ATAC, replicate 3
PF1_ATAC_Peaks.rds

value: Blood

value: P388D1 derived PF22

value: monocyte, macrophage

value: stable FastFUCCI expression

value: UV, 5 nanojoules/cm2


title: 35F

value: Aerial rosette


title: BM32 and BF32 TNC (GEX) rep2

description:
10X 3' V3.1 dual indexed GEX
TNC-3-4-2_filtered_feature_bc_matrix.h5

value: Black

value: 32 yrs


title: ATAC:BulkATAC,PF1linerep2

description:
Omni ATAC, replicate 2
PF1_ATAC_Peaks.rds

value: P388D1 derived PF21


title: QKO tumor, Keap1 knockout sample 1

description:
KP1
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt

value: Lung

value: small cell lung cancer

value: Keap1 knockout


title: 348F

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: 344F


title: WF32 CD34+CD271+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD271-2_filtered_feature_bc_matrix.h5

value: Bone marrow

value: White

value: Female


title: 340F


title: QKO tumor, Control sample 3

description:
QKO6
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt

value: Control


title: ATAC:BulkATAC,PF1linerep1

description:
Omni ATAC, replicate 1
PF1_ATAC_Peaks.rds

value: Blood

value: P388D1 derived PF20


title: 354F


title: 568F


title: Ctrl1

value: colon

value: wild type


title: QKO tumor, Control sample 2

description:
QKO5
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt


title: 9c-Chaetocin-1-uM

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

description: Chaetocin

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program (Martin 2011) to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
The cleaned reads of each sample were mapped to the reference sequence using the STAR read mapper (Spliced Transcripts Alignment to a Reference, v2.7.9a) (Dobin et al., 2013).
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2) (Anders et al., 2015), samtools, and scripts developed in house at UF ICBR to remove potential PCR duplicates and count uniquely mapped reads for gene expression analysis.
PCA analysis (for detecting outlier samples) and volcano plot analysis based on all identified genes in each analysis were performed with the R environment (v4.1.3).
The gene expression levels were analyzed by a DESeq2-based R pipeline to identify genes showing significant differential expression.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Excel files containing fold changes and P-values for differentially expressed genes.

source_name: pancreas

growth_protocol: Acinar cells were isolated from the pancreas of 6–8-week-old p48Cre/+; LSL-KrasG12D/+ mice. Following a 30-minute digestion with collagenase P, enzyme inactivation with FBS containing HBSS, and a series of centrifugation steps, cells were passed through a series of strainers (500, 300, 200 µm). The resulting pellet was resuspended in media to the desired density to yield 50 organoids/well with growth factor reduced Matrigel (Corning) at a 1:1 ratio (media+cells:matrigel) and seeded in 384-well tissue culture plates. After solidifying the matrigel was topped up with 40 uL of media and left for 48h to develop ADM, at which point they were treated.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer instructions.
Illumina RNA library construction and sequencing were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF).

treatment_protocol: Cells were treated with solvent control (DMSO, 0.5%), chaetocin (1 µM), FK228 (1 uM), Largazole (10 and 1 uM) and it's stable homodimer (10 and 1 uM) for 72 hours.

value: pancreas

value: primary pancreatic acini

value: acinar clusters

value: Chaetocin-1uM-72h post treatment

tag: biorep


title: WGSPF1:Negativecontrol,2ndpenning a

description:
PF1_Neg2a
PF1_SisterMutations.rds

data_processing:
PF1 whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to the mm10 reference. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics
F1 tumour whole genome-sequencing: Reads were trimmed using trim-galore and mapped with Bowtie2 to an N-masked mm10 reference created with SNPsplit. Reads were then haplotype labeled using snpsplit. Mutations were called using Manta and Strelka2, filtered with bamtools and the GATK tool CalculateSNVMetrics. Haplotype identification was done by counting assignable reads (minimum of 2) for each mutation, and fitting a dual gaussian distribution with mixtools
Omni-ATAC: Reads were mapped with Bowtie2 and peaks called with MACS2 using the flags -f BAMPE -g mm –nomodel –nolambda –keep-dup-all –call-summits -B -q 0.01. The peak file here is from sample 1 which was used in all comparisons.
RNA-seq: Transcript abundances were quantified using Kalisto (v0.46.0) with the –bias and –rf-stranded flags and the Gencode M25 transcript release. Transcription start sites were adjusted to the isoform with the highest ATAC signal within -1000 - +500 from the promoter
Assembly: mm10
Supplementary files format and content: PF1_SisterMutations.rds: RDS file of mutations in all 14 PF1 genomes (7 pairs of sisters). Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter, timepoint (T0=penning, T1=post penning) and sample name
Supplementary files format and content: PF1_RNA_counts.rds: Tags per million (tpm) ouput from Kallisto for 3 replicates. Entrez gene ID, gene name and genomic positions are noted.
Supplementary files format and content: PF1_ATAC_Peaks.rds: ATAC peak file in RDS format from MACS2 peak calling
Supplementary files format and content: F1CastB6_mutations.rds: RDS file of mutations in all 6 F1 tumors. Contains chromosome, position, reference base, alternate base, QC metrics from CalculateCNVMetrics (Info), counts for each base type, coverage, filter and sample name
Library strategy: WGS

tag: tissue

value: P388D1 derived PF4

value: monocyte, macrophage

value: stable FastFUCCI expression


title: WM22 CD34+CD271+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD271-1_filtered_feature_bc_matrix.h5

value: Male

value: 22 yrs

value: mRNA


title: 339F

value: Aerial rosette

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: WGS:LiverTumor,F1Cast/B6,mouseB3

description:
MCB6B_T3
F1CastB6_mutations.rds

organism: Mus musculus castaneus

source_name: Liver

value: Liver

value: Liver tumour

tag: genotype

value: 20 mg/kg Diethylnitosamine


title: 334F

source_name: Aerial rosette


title: 9b-Chaetocin-1-uM

description: Chaetocin

tag: treatment


title: WGS:LiverTumor,F1Cast/B6,mouseB1

description:
MCB6B_T1
F1CastB6_mutations.rds


title: 330F

tag: line


title: WGS:LiverTumor,F1Cast/B6,mouseB2

description:
MCB6B_T2
F1CastB6_mutations.rds


title: 9a-Chaetocin-1-uM

description: Chaetocin


title: WF32 CD34+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD34-2_filtered_feature_bc_matrix.h5

value: Bone marrow

value: White

value: Female

value: 32 yrs


title: WGSPF1:Negativecontrol,2ndpenning b

description:
PF1_Neg2b
PF1_SisterMutations.rds

value: Blood

value: P388D1 derived PF5


title: WGS:LiverTumor,F1Cast/B6,mouseA3

description:
MCB6A_T3
F1CastB6_mutations.rds


title: 8c-FK228-1-uM

value: pancreas

value: primary pancreatic acini

value: acinar clusters

value: FK228-1uM-72h post treatment


title: BF21 CD34+ (GEX)

description:
10X 3' V3.1 dual indexed GEX
BF21-CD34_filtered_feature_bc_matrix.h5

value: Black

value: 21 yrs

value: mRNA


title: WM22 CD34+ (GEX)

description:
10X 3' V3.1 HT dual indexed GEX
CD34-1_filtered_feature_bc_matrix.h5

value: Male

value: 22 yrs


title: 328F

value: Aerial rosette

value: epiHybrid

tag: time

value: Harvested at 27 days after sowing (DAS)


title: QKO tumor, Control sample 1

description:
QKO4
RNAseq_raw_readcounts.txt
KP_vs_QKO_all_DESeq_results.txt

value: Lung

tag: cell type

value: small cell lung cancer

value: Control


title: 329F


title: 8b-FK228-1-uM


title: WGS:LiverTumor,F1Cast/B6,mouseA2

description:
MCB6A_T2
F1CastB6_mutations.rds

value: Liver

value: Liver tumour

value: 20 mg/kg Diethylnitosamine


title: 337F


title: 327F


title: S4006-20

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Demultiplexing of sequenced reads was performed using bcl2fastq (Illumina) and adapter trimming using Skewer. Trimmed raw reads were aligned to reference genome hg19-cegat using Burrows-Wheeler-Aligner. Local realignment of reads in target areas was performed with ABRA to achieve more accurate indel calling.
Proprietary software (CeGaT GmbH, Tübingen, Germany) was used to discard duplicate reads, which originate most likely from the same PCR amplicon, and reads that were aligned with the same mapping score at more than one location in the genome. For variant calling, another proprietary software (CeGaT GmbH, Tübingen, Germany) was used. Identified variants were annotated based on publicly available data bases.
Assembly: hg19
Supplementary files format and content: The processed data for each sample is provided in the form of annotated single nucleotide variants (SNVs).
Library strategy: Whole exome sequencing

source_name: Spinal ependymoma (FFPE tissue)

extract_protocol:
DNA was isolated from FFPE tissues using the ReliaPrep™ FFPE gDNA Miniprep System (Promega). 50 ng DNA were used for library preparation.
Library preparation  was conducted using the Human Core Exome Plus Kit, Human RefSeq Panel, and Mitochondrial Panel; all Twist Bioscience.

value: Spinal ependymoma (FFPE tissue)


title: WGS:LiverTumor,F1Cast/B6,mouseA1

description:
MCB6A_T1
F1CastB6_mutations.rds


title: S4006-21


title: WGS:NormalLiver,F1Cast/B6

value: Normal liver


title: 319F


title: 7c-JH-LA-23-10-uM

description: Largazole homodimer

value: pancreas

value: primary pancreatic acini

value: acinar clusters

value: Largazole homodimer-10uM-72h post treatment


title: 31F


title: S4006-18


title: 8a-FK228-1-uM

value: FK228-1uM-72h post treatment


title: CTL IP, Dicer N1, SINV-GFP, MOI 0.02 24 hpi, rep1

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Homo sapiens and Sindbis-GFP virus

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Sequencing reads of sRNA-seq libraries were processed and analyzed with the following workflow.
Cutadapt v1.16 was first run to trim the 3' adapter (command: cutadapt -a TGGAATTCTCGGGTGCCAAGG -e 0.1 --no-indels -O 6 -m 18 --discard-untrimmed -o <sample>-cutadapt.fastq <sample>.fastq) and an additional filter was applied to only keep 18- to 32-nt long trimmed reads for further analyses.
Sample quality checks were performed before and after these preprocessing steps using FastQC v0.11.8.
Preprocessed reads were then mapped simultaneously to the human (GENCODE Human (GRCh38.p13) release 41) and SINV-GFP (private sequence derived from NC_001547.1) genomes, using Bowtie v1.3.1. (command: bowtie -q --phred33-quals -v 2 -y -a --best --strata -m 30 -x hg38coreGencodeSINVGFP <sample>-preprocessed.fastq <sample>-hg38coreGencodeSINVGFP.bwtmap).
Only alignments from the lowest mismatch stratum with at most 2 mismatches were reported for each read, provided that their number was not exceeding 30.
For each library, small RNA reads deriving solely from SINV-GFP were computationally extracted and further characterized.
Furthermore, expressed human miRNAs (miRBase v22.1), among which known mirtrons, were also identified and quantified in each library using BEDTools v2.30.0 by comparing their genomic coordinates to those of the original aligned reads and by counting only reads overlapping miRs on at least 80% of their size (command: bedtools intersect -a <sample>-hg38coreGencodeSINVGFP.bwtmap.bed -b hsa-matmir.bed -f 0.80 -wa -wb -s). Multiple mapped reads were weighted by the number of mapping sites in other miRNAs, and the final counts obtained for each miR were rounded down before further analysis.
Differential miRNA expression analysis between the two AGO-IP conditions was then performed with the DESeq2 package by using an adjusted p-value < 0.05 and an absolute log2 fold change > 1 as thresholds to define statistical significance.
Assembly: GRCh38.p13 + private sequence derived from NC_001547.1
processed data files format and content: xxx-2mmMax-onlyViral-stats.txt: tab-delimited text files with properties of reads mapping only against the SINV-GFP genome in each sample
processed data files format and content: xxx-onlyViral-22nt-anyali-anymm-POS.norm.bw: bigWig files with the normalized distribution (per 100000 only viral reads) of 22-nt long only viral reads along the positive strand of SINV-GFP genome for each sample
processed data files format and content: xxx-onlyViral-22nt-anyali-anymm-NEG.norm.bw: bigWig files with the normalized distribution (per 100000 only viral reads) of 22-nt long only viral reads along the negative strand of SINV-GFP genome for each sample
processed data files format and content: hsa-matmir_rawcounts.txt:  tab-delimited text file with our pipeline quantification of human mature miRs in each sample
processed data files format and content: hsa-matmir_deseq2_normcounts.txt:  tab-delimited text file with DESeq2 normalized human mature miR counts in each AGO IP sample

molecule: other

organism:
Homo sapiens
Sindbis virus

growth_protocol: NoDice FHA:DICER WT #4 or N1 #6 cells were plated in P150mm petri dishes at 25 000 000 cells per dish and infected the following day with SINV-GFP at an MOI of 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

extract_protocol:
Cells were collected in 1.3 mL of ice-cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 1 % NP-40, 0.5 mM DTT, 0.1 U/mL of RNase inhibitor and protease inhibitor cocktail (complete Mini, Merck, Sigma Aldrich)). Cells were lysed by putting the extract on ice for 15 min. First, human AGO proteins were immunoprecipitated from whole extract to enrich for loaded small-RNAs. AGO-IP was done following the protocol described in (Hauptmann et al., 2015). Briefly, 50 µL of magnetic Dynabeads coupled to G protein (Invitrogen, Fisher Scientific) were coupled to anti-Flag M2 antibody (F1804, Merck, Sigma Aldrich) overnight at 4°C under rotation. The day after, Flag-TNRC6B WT or mutant (with Tryptophans mutated to Alanines; called TNRC6B Ala) peptides were incubated with the coupled beads for 3 h at 4°C under rotation. Meanwhile, lysates were cleared with a centrifugation step at 10 000 g for 10 min at 4°C and 100 µL were kept as INPUT (20 µL for proteins and 80 µL for RNAs). Then, lysates were divided in two and put on the beads coupled to the peptides and incubated at 4°C for 3 h under rotation. After 4 washing steps with 300 µL of ice-cold washing buffer, beads were split: 280 µL were eluted with 1 mL of TRI Reagent solution (Invitrogen, Fisher Scientific) and RNAs were isolated according to the manufacturer’s instructions
Illumina TruSeq small RNA library preparation kit was used according to the manufacturer’s protocol (RS-200-0012, Illumina).

treatment_protocol: Cells were infected with a modified version of Sindbis virus expressing GFP (SINV-GFP) at an MOI of 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

value: Human embryonic kidney

value: NoDice FHA:DICER N1 #6

tag: viral infection_conditions


title: CTL IP, Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus

value: NoDice FHA:DICER WT #4


title: 7a-JH-LA-23-10-uM

description: Largazole homodimer


title: 313F

first: Frank

last: Johannes

address: Emil-Ramann str. 4

value: Aerial rosette

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: S4006-17


title: 6b-JH-LA-23-1-uM

description: Largazole homodimer

value: Largazole homodimer-1uM-72h post treatment


title: 6a-JH-LA-23-1-uM

description: Largazole homodimer


title: 30F


title: 310F


title: S4006-15


title: S4006-13


title: 309F


title: 5a-JH-LA-01-10-uM

description: Largazole

value: Largazole-10uM-72h post treatment


title: S4006-19


title: 5b-JH-LA-01-10-uM

description: Largazole


title: AGO IP, Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus


title: 318F


title: AGO IP, Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus


title: AGO IP, Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus


title: S4006-16


title: S4006-14


title: AGO IP, Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep2

description: Homo sapiens and Sindbis-GFP virus


title: 305F


title: S4006-12


title: S4006-11


title: non-tumor region

source_name: primary intraosseous carcinoma, non-tumor region

tag: gender

value: female

value: primary intraosseous carcinoma

value: non-tumor region


title: AGO IP, Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus


title: 4a-JH-LA-01-1-uM

description: Largazole

value: Largazole-1uM-72h post treatment


title: 4b-JH-LA-01-1-uM

description: Largazole

value: pancreas


title: S4006-10

value: Spinal ependymoma (FFPE tissue)


title: 302F


title: Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
RNA-seq data were processed and analyzed using the following workflow.
The first 5'-end base of each read, a T-overhang added during the library preparation with the Illumina Stranded mRNA protocol, was first trimmed, before using Skewer v0.2.2 in paired-end mode for average quality read filtering and adapter trimming (command: skewer -Q 25 -x CTGTCTCTTATACACATCT -y CTGTCTCTTATACACATCT -l 31 -m pe -t 2 -o <name> --quiet <name>_R1.fq <name>_R2.fq).
Sample quality checks were performed before and after these preprocessing steps using FastQC v0.11.8.
Then, human full-length protein-coding transcripts (GENCODE Human (GRCh38.p13) release 41) and SINV-GFP both genomic and subgenomic transcripts (private sequences derived from NC_001547.1) were quantified using Salmon v1.10.0 in mapping-based mode with the selective alignment algorithm and a decoy-aware transcriptome (command: salmon quant -p 6 -i index/gencode41.hg38.sinv.decoys_index --libType A --seqBias --gcBias --numBootstraps 30 -1 data/<name>_preprocessed_R1.fq.gz -2 data/<name>_preprocessed_R2.fq.gz -o salmon-quants/<name>).
Transcript-level abundance and count estimates thus obtained were next imported into R and further analyzed with the tximport and DESeq2 packages. Briefly, original transcript-level counts were summarized to gene-level estimated counts and an offset was produced from transcript-level abundance estimates to correct for changes to the average transcript length across samples. Differential expression analyses between tested conditions were then conducted at the gene-level, and statistical significance was defined with an adjusted p-value < 0.05 and an absolute log2 fold change > 1 thresholds.
Finally, gene set enrichment analysis (GSEA) studies were performed using the GSEA_4.3.2 Mac application, as made available by the Broad Institute and the University of California, San Diego (https://www.gsea-msigdb.org/gsea/index.jsp). These analyses were conducted on the DESeq2 normalized counts of each comparison dataset against the Hallmark Gene Sets (v2023.1) provided by the Molecular Signatures Database (MSigDB), and by using the Human_Ensembl_Gene_ID_MSigDB.v2023.1.Hs.chip  annotation file and all other parameters by default, except the permutation type which was set to gene_set
Assembly: GRCh38.p13 + private sequence derived from NC_001547.1
Supplementary files format and content: salmon_quants.txt: tab-delimited text file with Salmon quantification of studied transcripts in each sample
Supplementary files format and content: deseq2_normcounts.txt: tab-delimited text file with DESeq2 normalized gene counts in each sample

growth_protocol: NoDice FHA:DICER WT #4 or N1 #6 cells were plated in P100mm petri dishes at 5 000 000 cells per dish and infected the following day with SINV-GFP at an MOI of 2 for 12 h or 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

extract_protocol:
Cells were collected in Trizol reagent (Invitrogen, Thermo Fisher Scientific) and RNAs were isolated according to the manufacturer’s instructions.
ssRNA-seq (stranded RNA-seq): RNA-Seq libraries were generated according to the manufacturer’s instructions from 250 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit (Reference Guide - PN 1000000124518) and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94°C for 2 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Cells were infected with a modified version of Sindbis virus expressing GFP (SINV-GFP) at an MOI of 2 for 12 h or 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.


title: 2F


title: 3b-DMSO

description: control

value: primary pancreatic acini

value: acinar clusters

value: vehicle control (0.5%DMSO) - 72h post treatment


title: S4006-9


title: 3a-DMSO

description: control


title: S4006-7


title: Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus

value: Human embryonic kidney


title: WGSPF1:Mitoticsister2,cloneG

description:
PF1_CGS2
PF1_SisterMutations.rds

value: Blood

value: P388D1 derived PF19

value: monocyte, macrophage

value: stable FastFUCCI expression

value: UV, 5 nanojoules/cm2


title: S4006-6


title: 28F

value: Aerial rosette

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: Dicer N1, SINV-GFP MOI 2 12 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus

value: NoDice FHA:DICER N1 #6

value: MOI 2, 12 hpi


title: S4006-5


title: 7b-JH-LA-23-10-uM

description: Largazole homodimer

value: Largazole homodimer-10uM-72h post treatment


title: WGSPF1:Mitoticsister2,cloneE

description:
PF1_CES2
PF1_SisterMutations.rds

value: P388D1 derived PF17


title: Dicer N1, SINV-GFP MOI 2 12 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus


title: WGSPF1:Mitoticsister2,cloneD

description:
PF1_CDS2
PF1_SisterMutations.rds

value: P388D1 derived PF16


title: 275F


title: Dicer N1, SINV-GFP MOI 2 12 hpi, rep2

description: Homo sapiens and Sindbis-GFP virus


title: 273F


title: WGSPF1:Mitoticsister2,cloneC

description:
PF1_CCS2
PF1_SisterMutations.rds

value: P388D1 derived PF15


title: Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus

value: NoDice FHA:DICER WT #4


title: Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep2

description: Homo sapiens and Sindbis-GFP virus


title: S4006-1

value: Spinal ependymoma (FFPE tissue)


title: 26F


title: Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep2

description: Homo sapiens and Sindbis-GFP virus

value: Human embryonic kidney


title: 266F


title: S3504-10


title: 300F


title: WGSPF1:Mitoticsister2,cloneF

description:
PF1_CFS2
PF1_SisterMutations.rds

value: Blood

value: P388D1 derived PF18


title: Dicer WT, SINV-GFP MOI 2 12 hpi, rep3

description: Homo sapiens and Sindbis-GFP virus


title: Dicer WT, SINV-GFP MOI 0.02 24 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus


title: S3504-9


title: WGSPF1:Mitoticsister2,cloneA

description:
PF1_CAS2
PF1_SisterMutations.rds

value: P388D1 derived PF13

value: monocyte, macrophage


title: 286F


title: WGSPF1:Mitoticsister1,cloneG

description:
PF1_CGS1
PF1_SisterMutations.rds

value: P388D1 derived PF12

value: stable FastFUCCI expression

value: UV, 5 nanojoules/cm2


title: S4006-4


title: 24F

value: Aerial rosette

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: S3504-7


title: WGSPF1:Mitoticsister1,cloneF

description:
PF1_CFS1
PF1_SisterMutations.rds

value: P388D1 derived PF11


title: 250F


title: Dicer WT, SINV-GFP MOI 2 12 hpi, rep2

description: Homo sapiens and Sindbis-GFP virus

value: MOI 2, 12 hpi


title: S3504-8


title: WGSPF1:Mitoticsister1,cloneE

description:
PF1_CES1
PF1_SisterMutations.rds

value: P388D1 derived PF10


title: S4006-2


title: 245F


title: 295F


title: Dicer WT, SINV-GFP MOI 2 12 hpi, rep1

description: Homo sapiens and Sindbis-GFP virus


title: S3504-6


title: WGSPF1:Mitoticsister1,cloneD

description:
PF1_CDS1
PF1_SisterMutations.rds

value: P388D1 derived PF9


title: 241F


title: WGSPF1:Mitoticsister2,cloneB

description:
PF1_CBS2
PF1_SisterMutations.rds

value: P388D1 derived PF14


title: S3504-5

value: Spinal ependymoma (FFPE tissue)


title: WGSPF1:Mitoticsister1,cloneC

description:
PF1_CCS1
PF1_SisterMutations.rds

value: P388D1 derived PF8


title: 262F


title: 239F


title: S3504-4


title: 234F


title: WGSPF1:Mitoticsister1,cloneA

description:
PF1_CAS1
PF1_SisterMutations.rds

value: Blood

value: P388D1 derived PF6


title: WGSPF1:Mitoticsister1,cloneB

description:
PF1_CBS1
PF1_SisterMutations.rds

value: P388D1 derived PF7


title: S3504-3


title: 231F


title: 225F


title: WGSPF1:Negativecontrol,1stpenning b

description:
PF1_Neg1b
PF1_SisterMutations.rds

value: P388D1 derived PF2

value: monocyte, macrophage


title: S3504-2


title: S3504-1


title: 229F


title: WGSPF1:Negativecontrol,1stpenning c

description:
PF1_Neg1c
PF1_SisterMutations.rds

value: P388D1 derived PF3

value: stable FastFUCCI expression


title: RNA_S6204Nr3

data_processing:
Pre-processing was started by checking RNA sequencing read quality using FASTQC (v0.11.9) and subsequently aligned to the human reference genome assembly (GRCh38.106) using STAR aligner (v2.7.10a) in default 1-pass mode.
Mapped reads were quantified using featureCounts (v1.6.0) as part of the Subread software package. The “isPairedEnd” parameter was specified in default “unstranded” read counting mode.
Assembly: GRCh38.106
Supplementary files format and content: The count matrix is provided as non-normalized and unfiltered raw read counts.

extract_protocol:
RNA of SP-EPN was isolated from FFPE tissues using the Maxwell® RSC RNA FFPE Kit (Promega). Concentrations were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was analyzed using the RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies).
Library preparation  was conducted using the SMART-Seq Stranded Kit (Takara Bio)


title: RNA_S4142Nr9


title: 220F

value: Aerial rosette


title: cre wt_3_ipsilateral

city: Blacksburg

first: Alicia

last: Pickrell

state: VA

address: 970 Washington Street SW

department: Neuroscience

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4)
After trimming, only reads with length greater than 30bp were mapped to mm10 by STAR (v 2.7.1a).
Raw counts and normalized counts for each gene were outputted by RSEM (v1.2.28).
The raw counts were used to identify differentially expressed genes by DESeq2 (v 1.36.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each Sample

source_name: ipsilateral cortical tissue

extract_protocol:
RNA was isolated with Trizol and cleaned up with RNA mini plus kit (Qiagen)
Illumina TruSeq stranded mRNA kit

value: ipsilateral cortical tissue

value: CCI

value: 2 hr


title: Spinal Cord_injury_7days_rep3

city: Tianjin

first: Shiqing

last: Feng

address: 154 Anshan Road, Heping District, Tianjin, China, 300052

institute: Tianjin Medical University General Hospital

description: Gene expression  7days after SCI in spinal cord

hyb_protocol: Each slide was hybridized with 600 ngCy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: spinal cord, injury, 7days, rep3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 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 mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The animals in the control group underwent laminectomy alone without SCI.  In the injury group, laminectomy was carried out at the T10 vertebra level, and the contusive SCI model was established by an Impactor Model Ⅱ (New York University, US) (a 10 g node fell freely from a height of 50 mm)

value: spinal cord

value: famale


title: Spinal Cord_injury_7days_rep2

source_name: spinal cord, injury, 7days, rep2


title: WGSPF1:Negativecontrol,1stpenning a

description:
PF1_Neg1a
PF1_SisterMutations.rds

value: P388D1 derived PF1


title: 223F

city: Freising

institute: Technical University of Munich

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: RNA_S4142Nr8

value: Spinal ependymoma (FFPE tissue)


title: 21F


title: cre wt_2_ipsilateral


title: 219F


title: RNA_S4142Nr7


title: RNA_S4142Nr6


title: cre wt_1_ipsilateral


title: Spinal Cord_injury_7days_rep1

source_name: spinal cord, injury, 7days, rep1


title: 216F


title: Spinal Cord_injury_2days_rep2

description: Gene expression  2days after SCI in spinal cord

source_name: spinal cord, injury, 2days, rep2


title: RNA_S4142Nr4


title: cre wt_2_contralateral

source_name: contralateral cortical tissue

value: contralateral cortical tissue


title: Spinal Cord_injury_2days_rep3

source_name: spinal cord, injury, 2days, rep3


title: Spinal Cord_injury_2days_rep1

source_name: spinal cord, injury, 2days, rep1


title: Spinal Cord_injury_2hours_rep3

description: Gene expression  2hours after SCI in spinal cord

source_name: spinal cord, injury, 2hours, rep3


title: 215F


title: human_LCM_SG_2

city: Philadelphia

first: Jordan

last: Harris

address: 3620 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Transcriptomic analysis was performed in the R statistical computing environment version 4.2 and RStudio version 2022.02.1 using a pipeline adopted from an open-source toolkit for RNA sequencing analysis (Berry et al. 2021).
Kallisto was used for pseudoaligning reads to a cDNA reference genome and reads were annotated using the Ensembl species-specific database
Data was filtered based on genes with less than 1 count per million in the number of samples equal to n of the smallest group
Normalization of the data was performed by using the Trimmed Mean of M-values (TMM) method in the EdgeR package
Post-filtration, post-normalization, data was then variance stabilized via the Limma package, using the VOOM function
Differential gene expression (DGE) testing was performed using the Limma package and multiple testing correction via the Benjamini-Hochberg method
Gene ontology analysis was performed by using the gprofiler2 R package as well as the web tool for obtaining summarized lists of all terms
Gene set enrichment analysis was performed using the msigdbr, clusterprofiler, and enrichplot R packages using the Reactome and KEGG databases
Assembly: Mouse: GRCm39cDNA; Human: GRCh38cDNA
Supplementary files format and content: tab-delimited text files include raw count data for each Sample

source_name: skin

extract_protocol:
LCM was performed using the LMD 7000 system (Leica Microsystems Inc., Chicago, IL). FFPE human or mouse skin was processed onto a polyethylene naphthalate (PEN) slide designed for LCM processing (Leica Catalog #11505158). To acquire enough material for RNA sequencing of SGs, we isolated at least 1,000 SGs or 1,000,000 mm2 of tissue
RNA was extracted from isolated SGs from mouse and human using a Qiagen All Prep DNA/RNA FFPE Kit (Qiagen Catalog #80234).
Libraries were prepared using an Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina Catalog # 20040529) with IDT for Illumina RNA UD Indexes, Set A (Illumina Catalog # 20040553).

value: skin

value: sebocyte

value: WT

value: laser capture microdissection


title: RNA_S4142Nr25


title: Spinal Cord_injury_2hours_rep2

source_name: spinal cord, injury, 2hours, rep2


title: cre wt_1_contralateral


title: cKO_3_ipsilateral

value: CX3CR1cre-er/+ STING fl/fl


title: Spinal Cord_injury_2hours_rep1

source_name: spinal cord, injury, 2hours, rep1


title: 213F

data_processing:
fastq files were analyzed using the Methylstar pipeline (Shahryary et al.2020).
Assembly: METHimpute (Taudt et al., 2018)
Supplementary files format and content: Methylation status calls and levels for all cytosines in the genome


title: human_LCM_SG_1


title: RNA_S4142Nr24


title: Spinal Cord_Control_rep1

description: Gene expression after laminectomy without SCI

source_name: spinal cord, control, rep1


title: 214F


title: Spinal Cord_Control_rep2

source_name: spinal cord, control, rep2


title: Spinal Cord_Control_rep3

source_name: spinal cord, control, rep3


title: cKO_2_ipsilateral


title: 211F

source_name: Aerial rosette


title: cre wt_3_contralateral


title: cKO_1_ipsilateral


title: 210F