title: SPA_2

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Library name: SPA_2

data_processing:
Sequenced libraries were processed with deepTools, using STAR , for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2.
Assembly: GRCM38
Supplementary files format and content: matrix of raw gene counts per sample

source_name: LNCaP

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
For RNA sequencing of cell lines, purified RNA was sent to Admera Health who performed library preparation with polyA selection, sequencing on the Illumina HiSeq 2500 with read length configuration of 2x150bp with 60 million reads per sample, and read mapping to GRCM38

value: LNCaP

tag: plasmid


title: TA2.DN

status: Public on Nov 05 2025

type: SRA

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

country: China

institute: Nanjing Medical University

library_source: genomic

data_processing:
DNA barcoding data were analyzed using the RPBPBR pileline (https://github.com/hoefer-lab/RPBPBR)
RNA barcoding data were analyzed using the single-cell veresion (https://github.com/WXlab-NJMU/scPolylox)
CITE-seq data were analyzed using the CellRanger software (version 7.1.0)
Assembly: mm10
Supplementary files format and content: tsv, Polylox barcode count table
Supplementary files format and content: h5, single-cell gene expression matrix
Supplementary files format and content: tsv, ADT count table
Library strategy: Amplicon-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
In bulk analysis, genomic DNA was prepared from sorted cells (30,000 cells) by proteinase K treatment and heat inactivation; Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit protocol.
cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit protocol. The PolyloxExpress cassette was amplified by PCR with the Polylox-specific primers.

tag: strain

value: Tie2MCM x RosaPolyloxExpress

tag: tissue

value: Thymus

tag: cell type

value: DN

tag: induction time_point

value: Adult

tag: analysis time_point

value: 57 week


title: VEH_1

country: USA

description: Library name: VEH_1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: Vehicle


title: NKO-NPM1 WT_6

city: Chongqing

first: Xinyuan

last: Li

address: Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

description: Library name: Sample 6

data_processing:
Using the Illumina paired-end RNAseq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. 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). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: GRCh38
Supplementary files format and content: 1_genes_fpkm_expression text files include raw counts and FPKM values for each Sample

molecule: polyA RNA

source_name: HK-2 cells

extract_protocol:
Total RNA was extracted using Trizol reagent (ThermoFisher, USA) following the manufacturer’s procedure.
mRNA was purified from total RNA (2 μg) using mRNA Caprure Beads2.0 (Yeasen, CHN) with two rounds of purification. RNA fragments were reverse-transcribed to synthesize first-strand cDNA by reverse transcriptase, which were next used to synthesise second-stranded DNAs with E.coli DNA polymerase I, RNase H and dUTP Solution (Yeasen, CHN).  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 the ligated products were amplified with PCR Dual-index adapters were ligated to the fragments, followed by amplification with PCR. PCR amplification products were purified by Hieff NGS DNA Selection Beads (Yeasen, CHN) and subjuected to ssequencing on an Illumina Novaseq™ X Plus platform.

value: HK-2 cells

value: Human renal proximal tubular epithelial cell

tag: genotype

value: NKO-NPM1 WT


title: TA2.MPP

source_name: Bone marrow

value: Bone marrow

value: MPP


title: TA2.B_1

source_name: Spleen

value: Spleen

value: B


title: SPA_1

description: Library name: SPA_1


title: LNCaP_MYC_VEH_2

description: Library name: LNCaP_MYC_VEH_2

value: pCDH-puro-cMyc


title: TA2.EryP_1

value: EryP


title: NKO-NPM1 WT_4

description: Library name: Sample 4


title: TA1.B_2

value: 49 week


title: NKO-NPM1 WT_3

description: Library name: Sample 3


title: TA2.T_1

value: T


title: NKO-NPM1 K257R_NPM1

description: Library name: Sample 3

data_processing:
Library products corresponding to fragments ranging from 200 to 500 base pairs were enriched and quantified. Sequencing was performed on a Novaseq X Plus (Illumina) using the PE150 sequencing mode to generate paired-end reads.
Assembly: GRCh38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
NKO-NPM1 WT and NKO-NPM1 K257R HK-2 cells were cross-linked with 1% formaldehyde for 10 min at room temperature to stabilize DNA-protein complexes. The reaction was quenched with 0.125 M glycine for 5 min. Cells were then lysed in ice-cold lysis buffer (10 mM HEPES pH 7.5, 0.1 mM EDTA, 0.5% NP-40) supplemented with protease inhibitor cocktail. Nuclei were pelleted by centrifugation at 2,000 × g for 10 min at 4°C, and chromatin was fragmented to an average size of 100–500 bp using sonication.Fragmented chromatin was immunoprecipitated overnight at 4°C with anti-NPM1 antibody or rabbit IgG, followed by incubation with protein G-agarose beads. After washing, bound complexes were eluted and reverse-crosslinked. DNA from both input and IP samples was purified by phenol-chloroform extraction.
Sequencing libraries were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, China) and subjected to sequencing on an Illumina Novaseq™ X Plus platform.


title: VEH_2

description: Library name: VEH_2

value: LNCaP


title: LNCaP_MYC_VEH_1

description: Library name: LNCaP_MYC_VEH_1


title: NKO-NPM1 WT_1

description: Library name: Sample 1


title: LNCaP_MYC_SPA_2

description: Library name: LNCaP_MYC_SPA_2


title: NKO-NPM1 WT_5

description: Library name: Sample 5


title: TA1.B_1

value: Tie2MCM x RosaPolyloxExpress


title: TA2.proB_1

value: proB


title: NKO-NPM1 K257R_input

description: Library name: Sample 4


title: NKO-NPM1 WT_input

description: Library name: Sample 2


title: NKO-NPM1 WT_NPM1

description: Library name: Sample 1


title: LNCaP_EV_VEH_2

description: Library name: LNCaP_EV_VEH_2


title: TA1.DP_2

value: Thymus

value: DP

value: Adult


title: TA1.DP_1


title: 8902_sgELAC2_#7_woSG_RNAseq_2

city: New York

first: Robert

middle: S

last: Banh

state: NY

address: 522 First Avenue, Smilow 907

department: Radiation Oncology

institute: New York University

description:
Library name: 8902_sgELAC2_#7_woSG_RNAseq_2
mRNA

data_processing:
Ribo-seq and tRNAseq: Cutadapt: -a CTGTAGGCACCATCAAT -m 13
Assembly: hg38
Supplementary files format and content: Ribo-Seq: Ribosome protected fragments (RPFs) were analyzed as described by Darnell A.M., et al. Molecular Cell. 2018.// tRNAseq: tRNAs were analyzed as described by Evans, M.E., et al. Nucleic Acid. 2017. and with tRAX (https://trna.ucsc.edu/tRAX/).// RNAseq: STAR and DEseq2

source_name: Pancreas

growth_protocol: PATU-8902 cells were passaged in DMEM (no pyruvate) + 10% FBS + 1% Pen/Strep. 25,000,000 cells were seeded into a 15cm plate and allowed to adhere overnight.

extract_protocol:
Ribo-seq: Ribosome protected fragments (RPFs) were purified as described by Ingolia N.T., et al. Nature protocols. 2012.// tRNAseq: tRNAs were purified as described by Evans, M.E., et al. Nucleic Acid. 2017.// RNAseq: TRIzol RNA extraction protocol
Ribo-seq: Ribosome protected fragments (RPFs) libraries were prepared as described by Ingolia N.T., et al. Nature protocols. 2012.// tRNAseq: tRNA libraries were prepared as described by Evans, M.E., et al. Nucleic Acid. 2017.// RNAseq: prepared by Novogene Corp, polyA+ enrichment

treatment_protocol: Cells were washed once with PBS  and media was changed to DMEM + 10% dialyzed FBS with or without 400uM serine and 400uM glycine for 24 hours.

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma

value: -Ser/Gly

tag: batch

value: mRNA


title: 8902_sgELAC2_#7_wSG_RNAseq_2

description:
Library name: 8902_sgELAC2_#7_wSG_RNAseq_2
mRNA

value: +Ser/Gly


title: 8902_sgELAC2_#7_woSG_RNAseq_3

description:
Library name: 8902_sgELAC2_#7_woSG_RNAseq_3
mRNA


title: 8902_sgELAC2_#7_wSG_RNAseq_3

description:
Library name: 8902_sgELAC2_#7_wSG_RNAseq_3
mRNA


title: 8902_sgELAC2_#7_woSG_RNAseq_1

description:
Library name: 8902_sgELAC2_#7_woSG_RNAseq_1
mRNA


title: LNCaP_EV_VEH_1

description: Library name: LNCaP_EV_VEH_1

value: Vehicle


title: NKO-NPM1 WT_2

description: Library name: Sample 2

value: HK-2 cells

value: Human renal proximal tubular epithelial cell

value: NKO-NPM1 WT


title: 8902_sgELAC2_#7_wSG_RNAseq_1

description:
Library name: 8902_sgELAC2_#7_wSG_RNAseq_1
mRNA


title: 8902_sgLUC_woSG_RNAseq_3

description:
Library name: 8902_sgLUC_woSG_RNAseq_3
mRNA

value: sgLUC


title: LNCaP_EV_SPA_2

description: Library name: LNCaP_EV_SPA_2


title: LNCaP_EV_SPA_1

description: Library name: LNCaP_EV_SPA_1


title: 8902_sgLUC_woSG_RNAseq_2

description:
Library name: 8902_sgLUC_woSG_RNAseq_2
mRNA


title: 8902_sgLUC_wSG_RNAseq_3

description:
Library name: 8902_sgLUC_wSG_RNAseq_3
mRNA


title: 8902_sgLUC_wSG_RNAseq_2

description:
Library name: 8902_sgLUC_wSG_RNAseq_2
mRNA


title: TA1.Mono_1

value: Bone marrow

value: Mono

value: 49 week


title: DFMO_SPA_PUT_2

description: Library name: DFMO_SPA_PUT_2

value: LNCaP

value: DFMO, R1881 and PUTRESCINE


title: TA1.Mono_2

value: Tie2MCM x RosaPolyloxExpress


title: 8902_sgLUC_wSG_RNAseq_1

description:
Library name: 8902_sgLUC_wSG_RNAseq_1
mRNA


title: 8902_sgLUC_woSG_RNAseq_1

description:
Library name: 8902_sgLUC_woSG_RNAseq_1
mRNA


title: LNCaP_MYC_SPA_1

description: Library name: LNCaP_MYC_SPA_1

value: pCDH-puro-cMyc


title: 8902_sgELAC2_#9_woSG_tRNA_3

description:
Library name: 8902_sgELAC2_#9_woSG_tRNA_3
tRNA (60-100nt)

library_source: other

molecule: other

value: Pancreas

value: tRNA


title: TA1.Gr_2

value: Gr

value: Adult


title: 8902_sgELAC2_#9_woSG_tRNA_2

description:
Library name: 8902_sgELAC2_#9_woSG_tRNA_2
tRNA (60-100nt)

value: Pancreatic Ductal Adenocarcinoma

value: -Ser/Gly


title: TA1.Gr_1


title: 8902_sgELAC2_#9_woSG_tRNA_1

description:
Library name: 8902_sgELAC2_#9_woSG_tRNA_1
tRNA (60-100nt)


title: 8902_sgELAC2_#9_wSG_tRNA_3

description:
Library name: 8902_sgELAC2_#9_wSG_tRNA_3
tRNA (60-100nt)

value: +Ser/Gly


title: 8902_sgELAC2_#9_wSG_tRNA_2

description:
Library name: 8902_sgELAC2_#9_wSG_tRNA_2
tRNA (60-100nt)


title: TA1.EryP_1

value: EryP


title: 8902_sgELAC2_#9_wSG_tRNA_1

description:
Library name: 8902_sgELAC2_#9_wSG_tRNA_1
tRNA (60-100nt)


title: DFMO_PUT_2

description: Library name: DFMO_PUT_2

value: DFMO and PUTRESCINE


title: TA1.Mk

value: Mk


title: TA1.T_2

value: Spleen

value: T


title: TA1.T_1

value: 49 week


title: DFMO_SPA_2

description: Library name: DFMO_SPA_2

value: LNCaP

value: DFMO and R1881


title: DFMO_SPA_PUT_1

description: Library name: DFMO_SPA_PUT_1

value: DFMO, R1881 and PUTRESCINE


title: TA1.MkP

value: Tie2MCM x RosaPolyloxExpress

value: Bone marrow

value: MkP


title: 8902_sgELAC2_#7_wSG_tRNA_3

description:
Library name: 8902_sgELAC2_#7_wSG_tRNA_3
tRNA (60-100nt)

value: Pancreas

value: tRNA


title: TA1.EryP_2

value: Adult


title: DFMO_SPA_1

description: Library name: DFMO_SPA_1


title: DFMO_PUT_1

description: Library name: DFMO_PUT_1


title: 8902_sgELAC2_#7_woSG_tRNA_1

description:
Library name: 8902_sgELAC2_#7_woSG_tRNA_1
tRNA (60-100nt)

value: Pancreatic Ductal Adenocarcinoma

value: -Ser/Gly


title: 8902_sgELAC2_#7_wSG_tRNA_1

description:
Library name: 8902_sgELAC2_#7_wSG_tRNA_1
tRNA (60-100nt)

value: +Ser/Gly


title: 8902_sgELAC2_#7_wSG_tRNA_2

description:
Library name: 8902_sgELAC2_#7_wSG_tRNA_2
tRNA (60-100nt)


title: 8902_sgLUC_woSG_tRNA_3

description:
Library name: 8902_sgLUC_woSG_tRNA_3
tRNA (60-100nt)

value: sgLUC


title: 8902_sgLUC_woSG_tRNA_2

description:
Library name: 8902_sgLUC_woSG_tRNA_2
tRNA (60-100nt)


title: TA1.MEP

value: MEP


title: TA1.CMP_2

value: CMP


title: TA1.CMP_1


title: 8902_sgELAC2_#7_woSG_tRNA_2

description:
Library name: 8902_sgELAC2_#7_woSG_tRNA_2
tRNA (60-100nt)


title: 8902_sgLUC_wSG_tRNA_2

description:
Library name: 8902_sgLUC_wSG_tRNA_2
tRNA (60-100nt)


title: 8902_sgLUC_woSG_tRNA_1

description:
Library name: 8902_sgLUC_woSG_tRNA_1
tRNA (60-100nt)


title: HuH-7 cells, si-SLC37A3, #3

city: Tianjin

first: Ziyu

last: Meng

address: North Huairui, 6#

institute: Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology

data_processing:
NovaSeq 6000
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: HG38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
HuH-7 cells were plated in 6-well plates and transfected with si-SLC37A3 and si-NC as previously described. At 48 h after transfection, high quality total RNA was extracted from these cells by TRIzol Reagent.
RNA-seq was performed with the assistance of the Applied Protein Technology Co., Ltd. (Shanghai, China). RNA-seq libraries were performed by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (MA, United States) following the manufacturer’s instructions.

value: hepatocellular carcinoma cells

value: SLC37A3 Knockdown

value: si-SLC37A3 transfection


title: HuH-7 cells, si-SLC37A3, #2


title: 8902_sgELAC2_#9_woSG_RPF_2

description:
Library name: 8902_sgELAC2_#9_woSG_RPF_2
Ribosome Protected Fragment (RPF)

data_processing:
Ribo-seq and tRNAseq: Cutadapt: -a CTGTAGGCACCATCAAT -m 13
Assembly: hg38
Supplementary files format and content: Ribo-Seq: Ribosome protected fragments (RPFs) were analyzed as described by Darnell A.M., et al. Molecular Cell. 2018.// tRNAseq: tRNAs were analyzed as described by Evans, M.E., et al. Nucleic Acid. 2017. and with tRAX (https://trna.ucsc.edu/tRAX/).// RNAseq: STAR and DEseq2
Library strategy: Ribo-Seq

value: RPF


title: 8902_sgELAC2_#7_woSG_tRNA_3

description:
Library name: 8902_sgELAC2_#7_woSG_tRNA_3
tRNA (60-100nt)


title: 8902_sgLUC_wSG_tRNA_1

description:
Library name: 8902_sgLUC_wSG_tRNA_1
tRNA (60-100nt)


title: TA1.HSC

value: HSC

value: 49 week


title: DFMO_1

description: Library name: DFMO_1

value: LNCaP

value: DFMO


title: TE5.LK_PCR4

description:
PCR replicates
TE5.barcode.count.tsv

value: Tie2MCM x RosaPolyloxExpress

value: Bone marrow

value: LK

value: 17 week


title: 8902_sgELAC2_#9_woSG_RPF_3

description:
Library name: 8902_sgELAC2_#9_woSG_RPF_3
Ribosome Protected Fragment (RPF)

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma

value: -Ser/Gly


title: HuH-7 cells, si-NC, #2

value: NC

value: si-NC transfection


title: 8902_sgELAC2_#7_woSG_RPF_2

description:
Library name: 8902_sgELAC2_#7_woSG_RPF_2
Ribosome Protected Fragment (RPF)


title: HuH-7 cells, si-SLC37A3, #1

value: hepatocellular carcinoma cells


title: DFMO_2

description: Library name: DFMO_2


title: KO_REP4

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

data_processing:
Primary data analysis was conducted using the rnaseq pipeline from the nf-core suite (v3.7) [1].
Sequencing reads were aligned to the GRCm39 (v105) mouse reference genome using the STAR aligner (v2.7.10a) [2]. Gene quantification was conducted using Salmon (v1.5.2) [3]. The pipeline was executed with default parameters.
Downstream differential expression analysis was performed using DESeq2 (v1.36.0) [4], also with default parameters.
To correct for the deviation of the original raw p-values from the expected uniform null distribution, we used fdrtool (v1.2.17) [5] setting the stat parameter to “normal” (default). Subsequently, the Benjamini-Hochberg procedure was applied to correct the p-values for multiple tests.
GO enrichment analysis was conducted using gprofiler2 (v0.2.1) [6]. The selection criteria focused on differentially expressed genes with log2FoldChange > 0.58 and adjuested p-value < 0.05, using ordered gene query and setting the correction_method parameter to “fdr” to adjust for multiple tests.
Assembly: GRCm39
Supplementary files format and content: tab delimted file containing raw counts for each sample
Supplementary files format and content: tab delimted file containing differential expression results

source_name: lung

growth_protocol: RP and RPC cell lines were maintained in RPMI medium supplemented with 10%FCS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA isolation kit from Macherey-nagel
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina following the manufacturer's protocols.

value: lung

value: lung tumor cell line

value: RP Caspase 8 KO (RPC)


title: 8902_sgELAC2_#9_woSG_RPF_1

description:
Library name: 8902_sgELAC2_#9_woSG_RPF_1
Ribosome Protected Fragment (RPF)

value: RPF


title: HuH-7 cells, si-NC, #3


title: 8902_sgELAC2_#7_wSG_RPF_3

description:
Library name: 8902_sgELAC2_#7_wSG_RPF_3
Ribosome Protected Fragment (RPF)

value: +Ser/Gly


title: 8902_sgELAC2_#7_wSG_RPF_2

description:
Library name: 8902_sgELAC2_#7_wSG_RPF_2
Ribosome Protected Fragment (RPF)


title: 8902_sgLUC_woSG_RPF_3

description:
Library name: 8902_sgLUC_woSG_RPF_3
Ribosome Protected Fragment (RPF)

value: sgLUC


title: 8902_sgLUC_wSG_tRNA_3

description:
Library name: 8902_sgLUC_wSG_tRNA_3
tRNA (60-100nt)

value: tRNA


title: TE5.LK_PCR3

description:
PCR replicates
TE5.barcode.count.tsv

value: Tie2MCM x RosaPolyloxExpress


title: 8902_sgELAC2_#9_wSG_RPF_2

description:
Library name: 8902_sgELAC2_#9_wSG_RPF_2
Ribosome Protected Fragment (RPF)


title: 8902_sgLUC_woSG_RPF_2

description:
Library name: 8902_sgLUC_woSG_RPF_2
Ribosome Protected Fragment (RPF)


title: 8902_sgLUC_woSG_RPF_1

description:
Library name: 8902_sgLUC_woSG_RPF_1
Ribosome Protected Fragment (RPF)


title: 8902_sgELAC2_#7_woSG_RPF_3

description:
Library name: 8902_sgELAC2_#7_woSG_RPF_3
Ribosome Protected Fragment (RPF)


title: 8902_sgELAC2_#9_wSG_RPF_1

description:
Library name: 8902_sgELAC2_#9_wSG_RPF_1
Ribosome Protected Fragment (RPF)


title: TE5.LK_PCR1

description:
PCR replicates
TE5.barcode.count.tsv

value: Bone marrow


title: 8902_sgELAC2_#9_wSG_RPF_3

description:
Library name: 8902_sgELAC2_#9_wSG_RPF_3
Ribosome Protected Fragment (RPF)


title: TA1.MPP

value: MPP

value: Adult

value: 49 week


title: 8902_sgELAC2_#7_wSG_RPF_1

description:
Library name: 8902_sgELAC2_#7_wSG_RPF_1
Ribosome Protected Fragment (RPF)

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma


title: 8902_sgELAC2_#7_woSG_RPF_1

description:
Library name: 8902_sgELAC2_#7_woSG_RPF_1
Ribosome Protected Fragment (RPF)

value: -Ser/Gly


title: TE5.LK_PCR2

description:
PCR replicates
TE5.barcode.count.tsv

value: LK

value: 17 week


title: 8902_sgLUC_wSG_RPF_3

description:
Library name: 8902_sgLUC_wSG_RPF_3
Ribosome Protected Fragment (RPF)


title: KO_REP3

value: lung


title: TE5.LSK_PCR4

description:
PCR replicates
TE5.barcode.count.tsv

value: LSK


title: TE5.LSK_PCR3

description:
PCR replicates
TE5.barcode.count.tsv


title: TE5.LSK_PCR1

description:
PCR replicates
TE5.barcode.count.tsv


title: KO_REP2

value: lung tumor cell line

value: RP Caspase 8 KO (RPC)


title: IL33_rep3

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description: Library name: 14604_11_S72

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and reads in exons were counted against Gencode v27 with STAR Aligner.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1Ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer’s protocols


title: HuH-7 cells, si-NC, #1

value: hepatocellular carcinoma cells

value: NC

value: si-NC transfection


title: KO_REP1


title: TE5.LSK_PCR2

description:
PCR replicates
TE5.barcode.count.tsv

value: Tie2MCM x RosaPolyloxExpress


title: unstim_rep3

description: Library name: 14604_10_S71

value: unstim


title: WT_REP2

value: RP Caspase 8 WT (RP)


title: 8902_sgLUC_wSG_RPF_2

description:
Library name: 8902_sgLUC_wSG_RPF_2
Ribosome Protected Fragment (RPF)

value: sgLUC

value: +Ser/Gly

value: RPF


title: IL33_rep2

description: Library name: 14604_8_S69


title: WT_REP4


title: unstim_rep2

description: Library name: 14604_7_S68


title: PKS3053_IL33_rep3

description: Library name: 14604_12_S117


title: 8902_sgLUC_wSG_RPF_1

description:
Library name: 8902_sgLUC_wSG_RPF_1
Ribosome Protected Fragment (RPF)

value: Pancreas

value: Pancreatic Ductal Adenocarcinoma


title: PKS3053_IL33_rep1

description: Library name: 14604_3_S64


title: TE5.B_2

value: Spleen

value: B


title: unstim_rep1

description: Library name: 14604_1_S62


title: WT_REP3

value: lung


title: IL33_rep1

description: Library name: 14604_2_S63


title: Arabidopsis thaliana, 100µM phosphinothricin for 48h, Rep 2

city: Singapore

first: Grace

middle: Zi Hao

last: Tan

address: 1 Research Link National University of Singapore, 03-48

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M.Polymorpha v5.1, Athaliana TAIR
Supplementary files format and content: comma-separated values file includes raw read counts for each sample
Supplementary files format and content: comma-separated values file includes log-transformed read counts for each sample

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seedlings were germinated on full-strength solid MS media (pH5.8, 1% sucrose) for eight days at 22°C, under 24h light. Marchantia polymorpha gemmalings were raised in liquid half-strength B5 media (pH5.5, no sucrose) for ten days at 80rpm, at 22°C, under 24h light.

extract_protocol:
RNA was extracted using the QIAGEN Plant RNeasy kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol: Arabidopsis seedlings were transferred to liquid MS media (pH 5.7, 1% sucrose) containing the chemical of interest and grown for 48h at 80rpm, at 22°C, under 24h light. Marchantia gemmalings were washed, then transferred to liquid half-strength B5 media (pH5.5, no sucrose) containing the chemical of interest and grown for 48h at 80rpm, at 22°C, under 24h light

value: Seedlings

value: 100µM phosphinothricin treatment for 48h


title: WT_REP1

value: lung tumor cell line


title: TE5.B_1

value: 17 week


title: Arabidopsis thaliana, 100µM phosphinothricin for 48h, Rep 3


title: PKS3053_IL33_rep2

description: Library name: 14604_9_S70


title: TE5.DP_2

value: Thymus

value: DP


title: TE5.T_2

value: Tie2MCM x RosaPolyloxExpress

value: T


title: Localized PCa patient 196

city: Derio

first: Arkaitz

last: Carracedo

state: Biscay

address: Parque Científico Tecnológico de Bizkaia building 801A, POST-DOC Arkaitz, 4470

country: Spain

institute: CIC bioGUNE

description: Library name: AC95

data_processing:
Adaptor sequences specified by the Illumina TruSeq RNA kit were removed using cutadapt. Additionally, three nucleotides were trimmed from the R1 and R2 strands, respectively, as specified by the library preparation.
Reads were mapped to the reference human genome GRCh38.v94 using the Spliced Transcripts Alignment to a Reference (STAR)
Assembly: Ensmbl GRCh38.v94
Supplementary files format and content: raw_counts.txt: The raw sequencing reads were aligned to the human reference genome (GRCh38.v94) using the STAR aligner (Spliced Transcripts Alignment to a Reference). Gene-level counts were generated from the aligned reads to produce the raw count matrix.
Supplementary files format and content: counts_data_normalized_log2_counts_DESeq2.txt: For the normalized dataset, we applied the following processing steps: [1] Gene filtering: Genes with fewer than 5 raw counts in more than 70% of the samples were excluded from downstream analyses; [2] Normalization: Remaining genes were normalized using the median-of-ratios method implemented in the DESeq2 package, to account for differences in library size and sequencing depth; and [3] Transformation: The normalized counts were log2-transformed to stabilize variance across the expression range.

source_name: prostate gland biopsy

extract_protocol:
RNA from 50ng of FFPERNAsamples.RNA from these samples were not fragmented previous to 1st strand cDNAsynthesis. The 1ststrand cDNA synthesis was performed using SMARTScribe reverse Transcriptase, for 90min. at 42°C, 10min. at 70°C and pause at 4°C. Afterwards Illumina Adapters and Indexes are added, performing a preamplification PCR (60sec at 94°, 5 cycles of 15sec at 98°C, 15sec a t55°C 30sec at 68°C; and pause at 4°C). Then Ribosomal cDNA is depleted with ZapR v2 and R-Probes v2. Finally, enrichment of libraries was achieved by PCR (60sec at 94°C; 13-19 cycles of 15sec at 98°C, 15sec at 55°C, 30sec at 68°C; and pause at 4°C).
Sequencing libraries were prepared using “SMARTer Stranded TotalRNA-seq Kitv2–Pico Input Mammalian” kit (Takara Bio USA, Cat.# 634411), following “SMARTer Stranded Total RNA-seq Kitv2–Pico Input Mammalian User Manual (Rev.050619)”.

value: prostate gland biopsy

value: prostate cancer

tag: age


title: Arabidopsis thaliana, 5µM methionine sulfoxime for 48h, Rep 3

value: 5µM methionine sulfoxime treatment for 48h


title: Localized PCa patient 198

description: Library name: AC99


title: Localized PCa patient 193

description: Library name: AC91


title: TE5.DP_1


title: Localized PCa patient 192

description: Library name: AC89


title: Localized PCa patient 197

description: Library name: AC96


title: Arabidopsis thaliana, 100µM phosphinothricin for 48h, Rep 1


title: TE5.proB

value: Bone marrow

value: proB


title: TE5.Mono_2

value: Mono


title: Localized PCa patient 191

description: Library name: AC88


title: TE5.T_1

value: Spleen


title: Localized PCa patient 190

description: Library name: AC87


title: Arabidopsis thaliana, 5µM methionine sulfoxime for 48h, Rep 2


title: Arabidopsis thaliana, 5µM methionine sulfoxime for 48h, Rep 1


title: Arabidopsis thaliana, 5mM glutamine treatment for 48h, Rep 3

value: 5mM glutamine treatment for 48h


title: TE5.Mono_1


title: Localized PCa patient 187

description: Library name: AC79


title: Localized PCa patient 188

description: Library name: AC83


title: TE5.Gr_1

value: Gr


title: Localized PCa patient 184

description: Library name: AC75


title: Localized PCa patient 186

description: Library name: AC78


title: Arabidopsis thaliana, 5mM glutamine treatment for 48h, Rep 1

value: Seedlings


title: Localized PCa patient 185

description: Library name: AC76


title: Arabidopsis thaliana, 5mM glutamine treatment for 48h, Rep 2


title: Localized PCa patient 181

description: Library name: AC72


title: Localized PCa patient 195

description: Library name: AC94


title: TE5.Gr_2


title: Localized PCa patient 180

description: Library name: AC71


title: Arabidopsis thaliana, untreated control, Rep 2


title: TE5.EryP_1

value: EryP


title: Localized PCa patient 179

description: Library name: AC70


title: Localized PCa patient 178

description: Library name: AC7


title: Localized PCa patient 182

description: Library name: AC73


title: TE5.MyP_1

value: MyP


title: TE5.EryP_2

value: 17 week


title: Localized PCa patient 183

description: Library name: AC74


title: Arabidopsis thaliana, untreated control, Rep 1


title: Localized PCa patient 176

description: Library name: AC68


title: Arabidopsis thaliana, untreated control, Rep 3


title: Localized PCa patient 189

description: Library name: AC86


title: TE5.MyP_4


title: Localized PCa patient 175

description: Library name: AC67


title: Localized PCa patient 173

description: Library name: AC65


title: Localized PCa patient 174

description: Library name: AC66


title: Plasma, treatment, 31days post-stroke, biol rep 3, mRNA

city: Beijing

first: Chuheng

last: Chang

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

data_processing:
Remove adapter sequences, poly-N-containing reads, and low-quality reads from the raw data
Poly-N-containing reads: Reads containing at least 10% of unknown bases (N)
Low quality: Reads with a proportion of bases below Q30 exceeding 20%
For small RNA libraries, remove reads with a length less than 15 nt (or greater than 35 nt) after adapter removal.
Assembly: Rnor_6.0 (Rat)
Supplementary files format and content: Rat_miRNA_UMI.count.csv: Comma-separated values files include raw UMI counts for each microRNA sample.
Supplementary files format and content: Rat_mRNA_counts.csv: Comma-separated values files include read count values for each long RNA sample.
Supplementary files format and content: Rat_miRNA_sequence.txt: Text files including microRNA sequences corresponding to each microRNA.
Supplementary files format and content: Rat_newGene_sequence.txt: Text files including long RNA sequences corresponding to the unknown genes.
Supplementary files format and content: Rat_miRNA_UMI.TPM.csv: Comma-separated values files include TPM values for each microRNA sample.
Supplementary files format and content: Rat_mRNA_FPKM.csv: Comma-separated values files include FPKM values for each long RNA sample.

organism: Rattus norvegicus

source_name: Plasma

extract_protocol:
The serum EVs were isolated using size exclusion chromatography techniques as described previously by Boing et al. (doi: 10.3402/jev.v3.23430)
The isolation of EVs from brain tissue was performed using a modified protocol originally described by Vella et al. (doi: 10.1080/20013078.2017.1348885)
The total RNA was extracted and purified from EVs using the miRNeasy Advanced Kit (Qiagen, cat. No. 217204) according to the kit instructions. The RNA concentration and purity were then evaluated using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
For small RNA library preparation, 1ng-500ng RNA per sample was used as input material for libraries created with the QIAseq miRNA Library Kit (Qiagen, Frederick, MD)
For long RNA library preparation, 250pg-10ng RNA per sample was used as input material for libraries created with the SMARTer Stranded Total RNA-Seq Kit (Takara Bio USA, Inc.)

treatment_protocol: Middle cerebral occlusion, hNSCs transplantation

value: Plasma

value: Extracellular vesicles

value: WT

value: Middle cerebral occlusion, neural stem cell transplant

tag: time

value: Day 31 post-stroke

tag: library type

value: Long RNA libraries


title: Localized PCa patient 177

description: Library name: AC69

value: prostate gland biopsy

value: prostate cancer


title: TE5.MyP_3

value: Tie2MCM x RosaPolyloxExpress

value: Bone marrow


title: Plasma, treatment, 31days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 171

description: Library name: AC63


title: TE5.MyP_2


title: Localized PCa patient 172

description: Library name: AC64


title: TE5.MkMkP

value: Mk&MkP


title: Plasma, treatment, 31days post-stroke, biol rep 2, mRNA


title: Localized PCa patient 170

description: Library name: AC62


title: Plasma, treatment, 10days post-stroke, biol rep 3, mRNA

value: Day 10 post-stroke


title: Localized PCa patient 169

description: Library name: AC61


title: Localized PCa patient 168

description: Library name: AC60


title: Plasma, treatment, 10days post-stroke, biol rep 2, mRNA


title: Localized PCa patient 167

description: Library name: AC6


title: TE4.T_2

value: Spleen

value: T


title: Localized PCa patient 166

description: Library name: AC59


title: Localized PCa patient 165

description: Library name: AC58


title: Localized PCa patient 164

description: Library name: AC57


title: Plasma, treatment, 10days post-stroke, biol rep 1, mRNA


title: TE4.DP_2

value: Thymus

value: DP


title: Localized PCa patient 163

description: Library name: AC56


title: Plasma, treatment, 4days post-stroke, biol rep 2, mRNA

value: Day 4 post-stroke


title: Localized PCa patient 162

description: Library name: AC55


title: Localized PCa patient 161

description: Library name: AC54


title: TE4.DP_1

value: 17 week


title: Localized PCa patient 160

description: Library name: AC53


title: Localized PCa patient 158

description: Library name: AC51


title: TE4.B_1

value: B


title: Plasma, healthy, biol rep 3, mRNA

value: Plasma

value: Extracellular vesicles

value: WT

value: Healthy


title: Localized PCa patient 159

description: Library name: AC52

value: prostate gland biopsy


title: TE4.T_1


title: Localized PCa patient 157

description: Library name: AC50

value: prostate cancer


title: Plasma, healthy, biol rep 2, mRNA

value: Long RNA libraries


title: Plasma, treatment, 4days post-stroke, biol rep 1, mRNA

value: Middle cerebral occlusion, neural stem cell transplant


title: TE4.B_2

value: Tie2MCM x RosaPolyloxExpress


title: TE4.proB_2

value: Bone marrow

value: proB


title: Localized PCa patient 154

description: Library name: AC46


title: Localized PCa patient 156

description: Library name: AC48


title: Localized PCa patient 153

description: Library name: AC45


title: Localized PCa patient 155

description: Library name: AC47


title: Plasma, treatment, 4days post-stroke, biol rep 3, mRNA


title: Localized PCa patient 152

description: Library name: AC44


title: TE4.proB_1


title: Plasma, healthy, biol rep 1, mRNA


title: TE5.ST_MPP

value: ST&MPP


title: Localized PCa patient 149

description: Library name: AC41


title: Localized PCa patient 151

description: Library name: AC43


title: TE4.EryP_1

value: EryP


title: TE4.EryP_2


title: Localized PCa patient 150

description: Library name: AC42


title: TE4.Mo_2

value: Mo


title: Localized PCa patient 148

description: Library name: AC40


title: Plasma, control, 31days post-stroke, biol rep 2, mRNA

value: Middle cerebral occlusion

value: Day 31 post-stroke


title: Localized PCa patient 147

description: Library name: AC39


title: Plasma, control, 31days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 146

description: Library name: AC38


title: Localized PCa patient 145

description: Library name: AC37


title: Plasma, control, 10days post-stroke, biol rep 2, mRNA

value: Day 10 post-stroke


title: Localized PCa patient 144

description: Library name: AC36


title: Plasma, control, 10days post-stroke, biol rep 3, mRNA

value: Plasma


title: Localized PCa patient 143

description: Library name: AC35


title: TE4.Mo_1

value: 17 week


title: Localized PCa patient 142

description: Library name: AC34


title: Localized PCa patient 141

description: Library name: AC33


title: Plasma, control, 10days post-stroke, biol rep 1, mRNA

value: Extracellular vesicles

value: WT


title: TE4.Gr_1

value: Gr


title: TE4.Gr_2


title: Plasma, control, 4days post-stroke, biol rep 3, mRNA

value: Day 4 post-stroke


title: Localized PCa patient 139

description: Library name: AC31

value: prostate gland biopsy

value: prostate cancer


title: Localized PCa patient 140

description: Library name: AC32


title: TE4.MEP_2

value: Tie2MCM x RosaPolyloxExpress

value: MEP


title: Plasma, control, 31days post-stroke, biol rep 3, mRNA

value: Long RNA libraries


title: TE4.MEP_1

value: Bone marrow


title: Localized PCa patient 136

description: Library name: AC300


title: Plasma, control, 4days post-stroke, biol rep 2, mRNA


title: Plasma, control, 4days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 137

description: Library name: AC301


title: Localized PCa patient 134

description: Library name: AC299


title: Localized PCa patient 135

description: Library name: AC30


title: TE4.GMP_2

value: GMP


title: Localized PCa patient 132

description: Library name: AC296


title: Brain, treatment, 31days post-stroke, biol rep 2, mRNA

source_name: Brain

value: Brain

value: Middle cerebral occlusion, neural stem cell transplant


title: Brain, treatment, 31days post-stroke, biol rep 3, mRNA

value: Day 31 post-stroke


title: TE4.GMP_1


title: Localized PCa patient 130

description: Library name: AC292


title: TE4.MPP

value: MPP


title: Localized PCa patient 131

description: Library name: AC295


title: Localized PCa patient 133

description: Library name: AC297


title: TE4.CMP_2

value: CMP


title: Brain, treatment, 31days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 129

description: Library name: AC291


title: Localized PCa patient 127

description: Library name: AC29


title: Localized PCa patient 138

description: Library name: AC302


title: TE4.CMP_1

value: 17 week


title: Brain, treatment, 10days post-stroke, biol rep 3, mRNA

value: Extracellular vesicles

value: Day 10 post-stroke


title: Localized PCa patient 126

description: Library name: AC288


title: Brain, treatment, 10days post-stroke, biol rep 2, mRNA

value: WT


title: Localized PCa patient 128

description: Library name: AC290


title: Localized PCa patient 125

description: Library name: AC286


title: Localized PCa patient 124

description: Library name: AC282


title: Brain, treatment, 10days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 123

description: Library name: AC281


title: TE4.STHSC

value: STHSC


title: TE4.MkMkP

value: Mk&MkP


title: Brain, treatment, 4days post-stroke, biol rep 3, mRNA

value: Day 4 post-stroke


title: Localized PCa patient 122

description: Library name: AC280

value: prostate gland biopsy

value: prostate cancer


title: Localized PCa patient 121

description: Library name: AC28


title: TE4.LTHSC

value: Tie2MCM x RosaPolyloxExpress

value: LTHSC


title: Localized PCa patient 120

description: Library name: AC279


title: Localized PCa patient 119

description: Library name: AC278


title: TE3.B_2

value: Spleen

value: B


title: Brain, treatment, 4days post-stroke, biol rep 2, mRNA

value: Brain

value: Middle cerebral occlusion, neural stem cell transplant

value: Long RNA libraries


title: Brain, treatment, 4days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 118

description: Library name: AC276


title: TE3.B_1


title: Brain, healthy, biol rep 3, mRNA

value: Healthy


title: Localized PCa patient 115

description: Library name: AC270


title: Brain, healthy, biol rep 2, mRNA


title: Localized PCa patient 114

description: Library name: AC27


title: Localized PCa patient 112

description: Library name: AC265


title: Brain, healthy, biol rep 1, mRNA


title: Localized PCa patient 113

description: Library name: AC269


title: Localized PCa patient 111

description: Library name: AC264


title: TE3.proB_2

value: Bone marrow

value: proB

value: 17 week


title: TE3.T_1

value: T


title: Localized PCa patient 110

description: Library name: AC262


title: Localized PCa patient 108

description: Library name: AC26


title: Localized PCa patient 109

description: Library name: AC260


title: Localized PCa patient 106

description: Library name: AC254


title: TE3.DP_2

value: Thymus

value: DP


title: Brain, control, 31days post-stroke, biol rep 2, mRNA

value: Extracellular vesicles

value: WT

value: Middle cerebral occlusion

value: Day 31 post-stroke


title: Localized PCa patient 107

description: Library name: AC255

value: prostate gland biopsy

value: prostate cancer


title: Brain, control, 31days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 105

description: Library name: AC253


title: Localized PCa patient 117

description: Library name: AC273


title: Localized PCa patient 104

description: Library name: AC252


title: TE3.DP_1

value: Tie2MCM x RosaPolyloxExpress


title: Localized PCa patient 116

description: Library name: AC271


title: Localized PCa patient 103

description: Library name: AC251


title: TE3.EryP_2

value: EryP


title: Localized PCa patient 102

description: Library name: AC250


title: TE3.T_2

value: Spleen


title: Brain, control, 10days post-stroke, biol rep 2, mRNA

value: Brain

value: Day 10 post-stroke

value: Long RNA libraries


title: Localized PCa patient 100

description: Library name: AC248


title: Localized PCa patient 98

description: Library name: AC246


title: Brain, control, 10days post-stroke, biol rep 1, mRNA


title: Localized PCa patient 99

description: Library name: AC247


title: TE3.Mo_2

value: Bone marrow

value: Mo


title: Brain, control, 31days post-stroke, biol rep 3, mRNA


title: Localized PCa patient 97

description: Library name: AC245


title: TE3.proB_1

value: proB

value: 17 week


title: TE3.Mo_1


title: Localized PCa patient 96

description: Library name: AC244


title: Localized PCa patient 95

description: Library name: AC243


title: Brain, control, 4days post-stroke, biol rep 2, mRNA

value: Day 4 post-stroke


title: Brain, control, 4days post-stroke, biol rep 1, mRNA

value: Extracellular vesicles


title: Localized PCa patient 93

description: Library name: AC24


title: Brain, control, 10days post-stroke, biol rep 3, mRNA

value: WT


title: Localized PCa patient 92

description: Library name: AC239


title: TE3.Gr_2

value: Gr


title: Plasma, treatment, 31days post-stroke, biol rep 3, microRNA

value: Plasma

value: Middle cerebral occlusion, neural stem cell transplant

value: Day 31 post-stroke

value: Small RNA libraries


title: TE3.Gr_1

value: Tie2MCM x RosaPolyloxExpress


title: Localized PCa patient 101

description: Library name: AC25

value: prostate gland biopsy

value: prostate cancer


title: TE3.MEP

value: MEP


title: Localized PCa patient 90

description: Library name: AC237


title: Localized PCa patient 89

description: Library name: AC235


title: TE3.GMP_2

value: GMP


title: Localized PCa patient 88

description: Library name: AC234


title: Localized PCa patient 91

description: Library name: AC238


title: Plasma, treatment, 31days post-stroke, biol rep 2, microRNA


title: Brain, control, 4days post-stroke, biol rep 3, mRNA

value: Brain

value: Middle cerebral occlusion

value: Long RNA libraries


title: Plasma, treatment, 31days post-stroke, biol rep 1, microRNA


title: Localized PCa patient 86

description: Library name: AC231


title: TE3.GMP_1

value: Bone marrow

value: 17 week


title: Plasma, treatment, 10days post-stroke, biol rep 3, microRNA

value: Extracellular vesicles

value: Day 10 post-stroke


title: TE3.EryP_1

value: EryP


title: Localized PCa patient 85

description: Library name: AC230


title: TE3.CMP_2

value: CMP


title: Plasma, treatment, 10days post-stroke, biol rep 2, microRNA

value: Plasma

value: WT

value: Middle cerebral occlusion, neural stem cell transplant


title: Localized PCa patient 94

description: Library name: AC242


title: Localized PCa patient 84

description: Library name: AC23


title: Localized PCa patient 82

description: Library name: AC228


title: TE3.CMP_1

value: Tie2MCM x RosaPolyloxExpress


title: Plasma, treatment, 10days post-stroke, biol rep 1, microRNA

value: Small RNA libraries


title: Localized PCa patient 81

description: Library name: AC226

value: prostate gland biopsy

value: prostate cancer


title: TE3.MkMkP

value: Mk&MkP


title: Localized PCa patient 80

description: Library name: AC224


title: Plasma, treatment, 4days post-stroke, biol rep 3, microRNA

value: Day 4 post-stroke


title: Localized PCa patient 78

description: Library name: AC222


title: Localized PCa patient 79

description: Library name: AC223


title: TE3.MPP

value: MPP


title: Localized PCa patient 76

description: Library name: AC22


title: Plasma, treatment, 4days post-stroke, biol rep 2, microRNA


title: TE3.LTHSC

value: LTHSC


title: Plasma, treatment, 4days post-stroke, biol rep 1, microRNA


title: Localized PCa patient 75

description: Library name: AC218


title: Plasma, healthy, biol rep 3, microRNA

value: Healthy


title: Localized PCa patient 74

description: Library name: AC215


title: Localized PCa patient 87

description: Library name: AC232


title: Localized PCa patient 73

description: Library name: AC214


title: TE2.B_2

value: Spleen

value: B

value: 17 week


title: Localized PCa patient 71

description: Library name: AC209


title: Plasma, healthy, biol rep 2, microRNA

value: Extracellular vesicles


title: Localized PCa patient 72

description: Library name: AC213


title: Localized PCa patient 83

description: Library name: AC229


title: Localized PCa patient 70

description: Library name: AC208


title: Plasma, healthy, biol rep 1, microRNA


title: Localized PCa patient 69

description: Library name: AC207


title: Localized PCa patient 68

description: Library name: AC204


title: TE2.CD8_2

value: CD8+ T


title: TE2.CD8_1


title: Localized PCa patient 77

description: Library name: AC221


title: Localized PCa patient 66

description: Library name: AC202


title: TE3.STHSC

value: Bone marrow

value: STHSC


title: Plasma, control, 31days post-stroke, biol rep 2, microRNA

value: Plasma

value: WT

value: Middle cerebral occlusion

value: Day 31 post-stroke


title: Localized PCa patient 65

description: Library name: AC20

value: prostate gland biopsy

value: prostate cancer


title: MASH_CD5-FAPCAR

first: Scott

last: Friedman

address: 1425 Madison Ave

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

description: Library name: NASH_CD5

library_source: transcriptomic single cell

data_processing:
Gene Expression and Hashtag Libraries have been processed with 10X Cell Ranger pipeline. snRNAseq data quality control was performed with CellBender to remove ambient RNA
Assembly: Mouse mm10
Supplementary files format and content: Tab-Separated Value Files, Matrix Files

molecule: nuclear RNA

source_name: Liver

extract_protocol:
About 10-15mg of snap frozen liver tissue from four representative mice per group were pooled. Samples were prepared via an established protocol for nuclei isolation from murine MASH tissue(36). Solutions used included 2xST buffer (292 mM NaCl (Thermo Fisher Scientific, cat. no. AM9759)), 20 mM Tris-HCl pH 7.5 (Thermo Fisher Scientific, cat. no.15567027), 2 mM CaCl2 (VWR International Ltd, cat. no. 97062-820) and 42 mM MgCl2 (Sigma Aldrich, cat. no. 1028) in DNA/RNAse free water. 0.03% TST was prepared by adding 5mL of 2xST, 83uL Ribolock,83uL 2%BSA, 300uL of 1% Tween20, 4.6mL of H2O. The samples used for snRNAseq Chromium 3’ GEX were from snap frozen Chow + saline, MASH + saline, MASH + IgG-FAPCAR, and MASH + CD5-FAPCAR livers, about 3 months after euthanasia and cryopreservation. Each sample was chopped for 10 minutes over ice and passed through a strainer with 1mL TST. Samples were spun down at 500xg for 5 minutes at 4oC, supernatant was aspirated. Pellet was resuspended by pipetting 30 times with P1000 tips in 200uL of 0.4% BSA/PBS and then brought to the Genetics Core.
Library was performed according to manufacturer's instructions (single nuclei, 10x 5' Chromium - GEX)

treatment_protocol: Eight-week-old male C57BL/6J mice from Jackson Laboratory were maintained on regular chow diet, or put on the Fibrosis and Tumor (FAT) MASH model, which involves administration of a Western diet of 21.1% fat, 41% sucrose, and 1.25% cholesterol (Teklad diets, 120528) with a sugar water solution consisting of 23.1g d-fructose/L and 18.9g d-glucose/L, combined with weekly intraperitoneal injections of CCl4 at the low dose of 0.2 ml (0.32 mg)/g of body weight. Diet was maintained for 6 weeks, at which point mice received tail vein injections of saline vehicle, or lipid nanoparticles. After this injection, diets were continued for 4 more weeks. Mice were sacrificed thereafter, and portions of the left lobe of the liver were minced and snap frozen.

value: Liver

value: Hepatic cells

value: 6 weeks MASH + CD5-FAPCAR LNP + 4 more weeks MASH

value: Batch 1


title: Plasma, control, 31days post-stroke, biol rep 1, microRNA

value: Small RNA libraries


title: Localized PCa patient 64

description: Library name: AC2


title: MASH_IgG-FAPCAR

description: Library name: NASH_IgG

value: 6 weeks MASH + IgG-FAPCAR LNP + 4 more weeks MASH


title: TE2.B_1

value: Tie2MCM x RosaPolyloxExpress

value: Spleen

value: B

value: 17 week


title: TE2.CD4_1

value: CD4+ T


title: Localized PCa patient 63

description: Library name: AC198


title: TE2.Mono_2

value: Bone marrow

value: Mono


title: Chow_saline

description: Library name: chow_sal

value: 6 week chow + saline vehicle + 4 more weeks chow


title: TE2.Mono_1


title: Localized PCa patient 62

description: Library name: AC197


title: Plasma, control, 31days post-stroke, biol rep 3, microRNA

value: Plasma

value: Extracellular vesicles

value: WT

value: Middle cerebral occlusion

value: Day 31 post-stroke


title: Plasma, control, 10days post-stroke, biol rep 1, microRNA

value: Day 10 post-stroke


title: Suture+Gel, Day7-3

city: Chang Chun

first: Zhen

address: 1 xin min street

institute: The First Hospital of Jilin University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq   format were firstly processed through fastp software.
Clean data (clean reads)   were obtained by removing reads containing adapter, reads containing N base and low   quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data   were calculated. All the downstream analyses were based on the clean data with high   quality.
Index of the reference genome was built using Hisat2 (v2.0.5)  and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
We used clusterProfiler  R package (3.8.1) to test the statistical enrichment of differential expression genes in  KEGG pathways.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts and FPKM values for each sample

source_name: anastomotic tissue

extract_protocol:
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.
In order   to select cDNA fragments of preferentially 370~420 bp in length, the library fragments   were purified with AMPure XP system (Beckman Coulter, Beverly, USA).

value: anastomotic tissue

value: Suture+Gel


title: Localized PCa patient 67

description: Library name: AC203

value: prostate gland biopsy

value: prostate cancer


title: Localized PCa patient 61

description: Library name: AC193


title: TE2.EryPII_2

value: Tie2MCM x RosaPolyloxExpress

value: EryPII


title: Plasma, control, 4days post-stroke, biol rep 3, microRNA

value: Day 4 post-stroke

value: Small RNA libraries


title: Suture+Gel, Day7-2


title: TE2.EryPII_1

value: Bone marrow

value: 17 week


title: TE2.CD4_2

value: Spleen

value: CD4+ T


title: TE2.Gr_2

value: Gr


title: Plasma, control, 4days post-stroke, biol rep 2, microRNA

value: Plasma

value: Extracellular vesicles

value: WT


title: Localized PCa patient 60

description: Library name: AC192


title: Suture+Gel, Day7-1


title: Suture+FG, Day7-3

value: Suture+FG


title: Plasma, control, 10days post-stroke, biol rep 3, microRNA

value: Middle cerebral occlusion

value: Day 10 post-stroke


title: Plasma, control, 4days post-stroke, biol rep 1, microRNA


title: TE2.Gr_1


title: Plasma, control, 10days post-stroke, biol rep 2, microRNA


title: Suture+FG, Day7-2

value: anastomotic tissue


title: Brain, treatment, 31days post-stroke, biol rep 3, microRNA

value: Brain

value: Middle cerebral occlusion, neural stem cell transplant

value: Day 31 post-stroke


title: TE2.Mk

value: Tie2MCM x RosaPolyloxExpress

value: Mk


title: Localized PCa patient 57

description: Library name: AC188

value: prostate gland biopsy

value: prostate cancer


title: MASH_saline

description: Library name: NASH_sal

value: Liver

value: Hepatic cells

value: 6 weeks MASH + saline vehicle + 4 more weeks MASH

value: Batch 1


title: Brain, treatment, 31days post-stroke, biol rep 2, microRNA

value: Extracellular vesicles

value: Small RNA libraries


title: Suture+FG, Day7-1

value: WT

value: Suture+FG


title: TE2.MkP

value: Bone marrow

value: MkP

value: 17 week


title: Localized PCa patient 56

description: Library name: AC186


title: Localized PCa patient 55

description: Library name: AC183


title: TE2.HSC

value: HSC


title: Suture, Day7-3

value: anastomotic tissue

value: Suture


title: Brain, treatment, 31days post-stroke, biol rep 1, microRNA

value: Brain

value: Middle cerebral occlusion, neural stem cell transplant

value: Day 31 post-stroke


title: Suture, Day7-2


title: TE1.Mono_2

value: Tie2MCM x RosaPolyloxExpress

value: Mono

value: 16 week


title: Brain, treatment, 10days post-stroke, biol rep 3, microRNA

value: Day 10 post-stroke


title: Brain, treatment, 10days post-stroke, biol rep 2, microRNA

value: Extracellular vesicles


title: Localized PCa patient 59

description: Library name: AC191

value: prostate gland biopsy

value: prostate cancer


title: Suture, Day7-1

value: WT


title: Localized PCa patient 54

description: Library name: AC182


title: TE1.Mono_1

value: Bone marrow


title: Localized PCa patient 53

description: Library name: AC18


title: TE1.EryPII_2

value: EryPII


title: Brain, treatment, 10days post-stroke, biol rep 1, microRNA

value: Small RNA libraries


title: Localized PCa patient 58

description: Library name: AC19


title: Localized PCa patient 52

description: Library name: AC178


title: GFP-pos_500-DEHP-P12

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

data_processing:
Library sequencing was performed on an Illumina NovaSeq instrument according to the manufacturer’s instructions using a 2x150bp Paired-End (PE) configuration.
Sequence reads were trimmed to remove adapter sequences. BAM files were generated by mapping reads to the mouse reference genome (Mus musculus GRCm38, ENSEMBL) using STAR aligner v.2.5.2b.
Hit counts were calculated for unique reads within exon regions using featureCounts (Subread package v.1.5.2).
Differential expression analysis was performed using DESeq2. Differentially expressed (DE) genes were defined as genes with adjusted p-values (p-adj) < 0.05 with absolute log2 fold change > 1 (Wald test).
Assembly: GRCm38
Supplementary files format and content: raw_counts.csv contains raw counts for each sample
Supplementary files format and content: TMP_values.csv contains TPM values for each sample

source_name: fetal testis

growth_protocol: mouse fetal testes were obtained from Sox9-eGFP mice on gestational day (GD) 17

extract_protocol:
2-10 testes from fetuses in the same litter from the same treatment group were pooled for each sample. GFP-positive and GFP-negative cells were separated by FACS. Total RNA was extracted from sorted cells using hte Arcturus PicoPure Kit per manufacturer's instructions, including DNase treatment.
RNA libraries were prepared using the Illumina Nextera XT kit  for Illumina using manufacturer’s instructions (Illumina, San Diego, CA, USA).

treatment_protocol: Timed pregnant Sox9-eGFP+ mice were treated with 0 (vehicle corn oil), 20, or 500 mg/kg/d DEHP in a 6 mL/kg solution by daily oral gavage from GD 14- GD 17.

value: fetal testis

value: GFP-positive

value: 500 mg/kg/d DEHP


title: GFP-pos_500-DEHP-P14


title: Localized PCa patient 51

description: Library name: AC176


title: Brain, treatment, 4days post-stroke, biol rep 2, microRNA

value: Brain

value: Day 4 post-stroke


title: GFP-pos_500-DEHP-P11


title: Brain, treatment, 4days post-stroke, biol rep 1, microRNA

value: Middle cerebral occlusion, neural stem cell transplant


title: Localized PCa patient 50

description: Library name: AC175


title: TE1.Mk

value: Tie2MCM x RosaPolyloxExpress

value: Mk


title: TE1.EryPII_1

value: 16 week


title: TE1.MkP

value: MkP


title: Brain, healthy, biol rep 3, microRNA

value: Extracellular vesicles

value: Healthy


title: TE1.MPP

value: MPP


title: Localized PCa patient 49

description: Library name: AC174

value: prostate gland biopsy

value: prostate cancer


title: GFP-pos_500-DEHP-P9


title: Localized PCa patient 48

description: Library name: AC172


title: Brain, healthy, biol rep 2, microRNA

value: WT


title: GFP-pos_20-DEHP-P8

value: 20 mg/kg/d DEHP


title: TE1.HSC

value: Bone marrow

value: HSC


title: Brain, healthy, biol rep 1, microRNA

value: Small RNA libraries


title: Localized PCa patient 46

description: Library name: AC17


title: GFP-pos_20-DEHP-P7

value: fetal testis

value: GFP-positive


title: Localized PCa patient 47

description: Library name: AC170


title: Brain, control, 31days post-stroke, biol rep 3, microRNA

value: Brain

value: Middle cerebral occlusion

value: Day 31 post-stroke


title: Brain, control, 31days post-stroke, biol rep 2, microRNA


title: TE1.B_2

value: Tie2MCM x RosaPolyloxExpress

value: Spleen

value: B

value: 16 week


title: TE1.B_1


title: Brain, treatment, 4days post-stroke, biol rep 3, microRNA

value: Extracellular vesicles

value: Middle cerebral occlusion, neural stem cell transplant

value: Day 4 post-stroke


title: GFP-pos_20-DEHP-P5


title: GFP-pos_vehicle-P4

value: corn oil


title: GFP-pos_500-DEHP-P10

value: 500 mg/kg/d DEHP


title: Localized PCa patient 44

description: Library name: AC165

value: prostate gland biopsy

value: prostate cancer


title: Localized PCa patient 45

description: Library name: AC169


title: Localized PCa patient 43

description: Library name: AC164


title: Brain, control, 31days post-stroke, biol rep 1, microRNA

value: WT

value: Small RNA libraries


title: Brain, control, 10days post-stroke, biol rep 3, microRNA

value: Day 10 post-stroke


title: TE1.CD8_1

value: CD8+ T


title: TE1.CD8_2


title: GFP-pos_vehicle-P2

value: fetal testis

value: GFP-positive


title: TE1.CD4_2

value: Tie2MCM x RosaPolyloxExpress

value: CD4+ T


title: Localized PCa patient 42

description: Library name: AC162


title: Brain, control, 10days post-stroke, biol rep 2, microRNA

value: Brain

value: Middle cerebral occlusion


title: GFP-pos_vehicle-P1


title: TE1.CD4_1

value: Spleen

value: 16 week


title: GFP-neg_vehicle-N4

value: GFP-negative


title: Brain, control, 10days post-stroke, biol rep 1, microRNA

value: Extracellular vesicles


title: Localized PCa patient 41

description: Library name: AC160


title: TE1.Gr_2

value: Bone marrow

value: Gr


title: Localized PCa patient 40

description: Library name: AC16

value: prostate gland biopsy

value: prostate cancer


title: GFP-neg_vehicle-N3

value: corn oil


title: Brain, control, 4days post-stroke, biol rep 3, microRNA

value: WT

value: Day 4 post-stroke

value: Small RNA libraries


title: TE1.Gr_1


title: Localized PCa patient 39

description: Library name: AC159


title: GFP-neg_vehicle-N2

value: fetal testis


title: Localized PCa patient 38

description: Library name: AC157


title: I11BPOST

city: Cedarburg

first: Kevin

last: Gries

state: Wisconsin

address: W75N761 Tower Avenue Cedarburg, WI 5012

institute: Concordia University of Wisconsin

description: Library name: Sample28

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v4.0.16
Assembly: GRCh38.p10; NCBI:GCA_000001405.25
Supplementary files format and content: Matrix  (inactive -B, Active - A), xls

source_name: Skeletal Muscle

extract_protocol:
QIAGEN RNeasy with on column DNaseI treatment
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Skeletal Muscle

value: Inactive, Post-Exercise


title: Brain, control, 4days post-stroke, biol rep 2, microRNA

value: Brain


title: GFP-pos_vehicle-P3

value: GFP-positive


title: Localized PCa patient 37

description: Library name: AC156


title: Brain, control, 4days post-stroke, biol rep 1, microRNA

value: Middle cerebral occlusion


title: I11BPRE

description: Library name: Sample27

value: Inactive, Pre-Exercise


title: GFP-neg_vehicle-N1

value: GFP-negative


title: Localized PCa patient 36

description: Library name: AC155


title: D_C8_Rep4

city: Cambridge

first: Jianfeng

last: Ge

state: Cambridgeshire

address: 37, ST THOMAS'S SQUARE

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2, relative gene expression was determined using RSEM.
Assembly: hg38
Supplementary files format and content: Gene level RSEM output files.

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.

value: lung

value: immortalised human proximal tubule cell line

value: dox on


title: ID8_MAFB_Input

first: Qinke

state: 重庆

address: No. 76, Yuzhong District, Chongqing

institute: The second affiliated hospital of Chongqing Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp software(version 0.20.1). Clean data were obtained for downstream analyses by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The clean reads were mapped to the genome using bowtie2(version 2.4.2). MACS2(version 2.2.7.1) was used to call peaks.
IGV software was used to visualize called peaks from ChIP-seq samples. Called peaks were then annotated using R package ChIPseeker. And HOMER (http://homer.ucsd.edu/homer/download.html，v4.11.1) were used to find de novo and known motif.
Differential peaks analysis was performed using R package MAnorm for experimental design without replication while using R package Diffbind for experimental design with replication
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Add a final concentration of 1% formaldehyde solution for cross-linking DNA and protein. Stop the cross-linking reaction by adding a final concentration of 125 mM glycine. Extract chromatin from cross-linked cells by adding lysis buffer. Sonicate chromatin DNA to fragments ranging from 100 to 500 bp. Incubate chromatin DNA and antibody-associated beads overnight at 4°C to immunoprecipitate. Wash Dynabeads using an optimal method for eluting the immunoprecipitated protein-DNA complexes.
Generate sequencing libraries of immunoprecipitated chromatin DNA using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair under the following conditions: 20°C for 30 min, 65°C for 30 min. Add NEBNext Adaptor and Blunt/TA Ligase Master Mix to ligate the adaptor at 20°C for 15 min. Then add USER Enzyme to remove base U of the adaptor at 37°C for 5 min. After purification with beads, amplify the products with PCR under the following conditions: initial denaturation at 98°C for 10 sec; denaturation at 98°C for 10 sec, annealing at 65°C for 30 sec, and extension at 72°C for 30 sec. Select the library size and purify with AMPure XP Beads. Use Qubit for library quantification and a high-sensitivity DNA chip to test the library insert size. Sequence the libraries on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

tag: disease

value: mouse ovarian cancer

tag: chip antibody


title: I11APOST

description: Library name: Sample26

value: Active, Post-Exercise


title: ID8_MAFB_IP


title: Localized PCa patient 35

description: Library name: AC154

value: prostate gland biopsy

value: prostate cancer


title: D_C8_Rep2

value: WT


title: Localized PCa patient 34

description: Library name: AC153


title: I10BPOST

description: Library name: Sample24


title: I11APRE

description: Library name: Sample25

value: Active, Pre-Exercise


title: I10BPRE

description: Library name: Sample23


title: D_C8_Rep1


title: D_C8_Rep3


title: RP and RPC lung tumors scRNAseq, library 8

first: Fanyu

last: Liu

address: Joseph-Stelzmann Str. 26

institute: CECAD

description:
all_genes_RP1.csv
cell_metadata_RP1.csv
DGE_RP1.mtx
all_genes_RP2.csv
cell_metadata_RP2.csv
DGE_RP2.mtx
all_genes_RPC1.csv
cell_metadata_RPC1.csv
DGE_RPC1.mtx
all_genes_RPC2.csv
cell_metadata_RPC2.csv
DGE_RPC2.mtx

data_processing:
raw data were processed with the PARSE biosciences scRNAseq pipeline v1.1.1
Assembly: GRCm39.110
Supplementary files format and content: all_genes.csv, symbol to Ensemble ID conversion. mtx, sparse count matrix. cell_metada.csv, sample metadata

source_name: SCLC tumor

extract_protocol:
Isolated single nuclei was fixed using Parse Evercode Nuclei Fixation v2 kit following manufacturer's protocol and subjected to barcoding and sequencing library preparation using the Evercode WT Mega v2 kit (Parse Biosciences, ECW02050) according to the V2.1.1 user manual.
the libraries were constructed according to the manufacturer's instructions (Evercode WT Mega kit, PARSE biosciences)

value: SCLC tumor

tag: mouse

tag: gender

value: Male

value: lung primary tumor

tag: material

value: single nuclei

value: Rb1 fl/fl, Trp53 fl/fl (RP) or Rb1 fl/fl, Trp53 fl/fl, Casp8-/- (RPC)


title: D_C35_Rep4


title: Localized PCa patient 33

description: Library name: AC150


title: D_C35_Rep3


title: Localized PCa patient 32

description: Library name: AC15


title: I10PRE

description: Library name: Sample21

value: Skeletal Muscle


title: I10APOST

description: Library name: Sample22


title: D_C35_Rep2


title: RP and RPC lung tumors scRNAseq, library 4


title: RP and RPC lung tumors scRNAseq, library 6


title: Localized PCa patient 31

description: Library name: AC149


title: RP and RPC lung tumors scRNAseq, library 3


title: D_C35_Rep1


title: Localized PCa patient 29

description: Library name: AC142


title: D_C10_Rep4


title: I09BPOST

description: Library name: Sample20

value: Inactive, Post-Exercise


title: I09APRE

description: Library name: Sample18


title: Localized PCa patient 30

description: Library name: AC147


title: RP and RPC lung tumors scRNAseq, library 2


title: Localized PCa patient 28

description: Library name: AC141


title: I09APOST

description: Library name: Sample19


title: RP and RPC lung tumors scRNAseq, library 7


title: D_C10_Rep3


title: lung, WT4

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

institute: University of Cologne, Medical Faculty and University Clinic Cologne

data_processing:
Quality of the paired-end data were checked with FastQC v0.11.8 [https://www.bioinformatics.babraham.ac.uk/projects/fastqc] and mapped afterwards against mm39 (mm39, Genome Reference Consortium Mouse Build 39 (GCA_000001635.9) using bsmap v2.90 with default parameter except the maximum allowed mismatches parameter (-v 0.1). Samtools v1.4 was used to create, sort and index bam files and additionally generate mapping statistics excluding secondary alignments (-F 256). liftOver was applied on the target regions bed file (mm9) twice (mm9 to mm10 and mm10 to mm39) to reach the final genome version. IntersectBed v2.30.0 was utilized to calculate the percentage of reads that intersect with the designed target regions. Additionally, exclusively “on target” bam files were generated for the post mapping script methratio.py included in the bsmap package to calculate base-wise and context-wise (CpG, CHG, CHH) methylation values with adapted parameters (-u -p -g -x [CG|CHG|CHH]). Chromosomal positions in combination with coverage or methylation ratios were extracted to create bedGraph formated files. Defiant was applied to call differential methylated regions between the two groups. The significant DMRs (adjusted p.value < 0.05) were annotated with mm39 known genes from UCSC using ChIPseeker R package. Promoter regions were defined as +/- 3 kbp from transcription start site. Gene set overrepresentation analysis was performed with gProfiler or with STRING (string-db.org).
Assembly: GRCm39/mm39
Supplementary files format and content: text file includes the methylation values for individual CpGs
Supplementary files format and content: text file includes the annotated differentially methylated regions (DMRs) between RP and RPC tumor cell lines

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany).
3 μg genomic DNA was sheared using a BioRuptor NGS (Diagenode, Seraing, Belgium) and subjected to library preparation using the SureSelectXT Methyl-seq library preparation kit (Agilent Technologies, Waldbronn, Germany) followed by target enrichment with the SureSelectXT Mouse Methyl-seq target enrichment panel (109 Mb, #931052, Agilent Technologies). Subsequently, enriched DNA was bisulfite-converted using the EZ DNA methylation kit (Zymo Research, Freiburg, Germany) and libraries were PCRamplified according to the manufacturer’s instructions.

value: lung tumor cell line


title: lung, WT3

value: lung


title: D_C10_Rep1

value: immortalised human proximal tubule cell line


title: I07BPRE1

description: Library name: Sample16

value: Inactive, Pre-Exercise


title: Localized PCa patient 27

description: Library name: AC140


title: I07BPOST

description: Library name: Sample17


title: lung, Mut4


title: D_C10_Rep2

value: dox on


title: C8_Rep4

value: dox off


title: I06BPOST

description: Library name: Sample14


title: Localized PCa patient 24

description: Library name: AC136

value: prostate gland biopsy


title: lung, WT1


title: C8_Rep2


title: Localized PCa patient 22

description: Library name: AC133

value: prostate cancer


title: Localized PCa patient 26

description: Library name: AC14


title: I06APRE2

description: Library name: Sample11


title: C35_Rep4

value: VHL mutant


title: Localized PCa patient 21

description: Library name: AC132


title: lung, Mut1


title: I07APRE

description: Library name: Sample15

value: Active, Pre-Exercise


title: RP and RPC lung tumors scRNAseq, library 5

value: SCLC tumor


title: I05BPOST

description: Library name: Sample10


title: lung, WT2


title: I05APOST

description: Library name: Sample9

value: Active, Post-Exercise


title: C8_Rep3

value: WT


title: UPP_M53G_Prim

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples

source_name: bladder tumor

extract_protocol:
Single cell suspensions of tumors were generated using the Miltenyi Biotec Tumor Dissociation Kit and the gentleMACS Dissociator. Red blood cells were lysed using Miltenyi Biotec Red Blood Cell Lysis Solution and dead cells were removed using the Miltenyi Biotec Dead Cell Removal Kit. Single cell suspensions were subsequently loaded onto the 10X Genomics Chromium Controller to generate single-cell gel beads in emulsions (GEMs)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry) according to the manufacter's instructions

value: bladder tumor

tag: strain

value: UPP


title: I06BPRE

description: Library name: Sample13

tag: tissue

value: Skeletal Muscle


title: Localized PCa patient 23

description: Library name: AC134

tag: cell type


title: lung, Mut3


title: I06APOST1

description: Library name: Sample12


title: C8_Rep1


title: UPPA_M125C_Primary

description: 10x Genomics

value: UPPA


title: Localized PCa patient 20

description: Library name: AC131


title: lung, Mut2

value: lung tumor cell line


title: I04BPRE

description: Library name: Sample7


title: Localized PCa patient 19

description: Library name: AC130


title: C35_Rep3

value: lung


title: Localized PCa patient 17

description: Library name: AC129


title: Localized PCa patient 25

description: Library name: AC137


title: C35_Rep2

value: immortalised human proximal tubule cell line


title: Localized PCa patient 16

description: Library name: AC127


title: UPP_M40F_Prim

description: 10x Genomics


title: I04APRE

description: Library name: Sample5


title: C10_Rep3


title: Cachectic tumor mouse, Epididymal adipose tissue, Mouse #66

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

description: Library name: Cax_E66_1

data_processing:
This analysis was performed at Novogene (Cambridge, UK). Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene. FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was then calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: csv files include gene counts values for each sample

source_name: Epididymal adipose tissue

growth_protocol: 10 week-old male Balb/c mice from Charles River. All mice were maintained under specific pathogen-free conditions on a 12h light–dark cycle at 22 °C with ad libitum access to regular rodent chow diet (Kliba Nafag #3437, Promivi Kliba AG, Kaiseraugst, Switzerland) and water.

extract_protocol:
Pieces of mouse frozen tissues were homogenized in TRIzol (Life Technologies #15596018). RNA was then isolated by adding chloroform. After centrifugation at 12,000 x g for 20min, the upper phase containing RNA was collected and a volume of 0.6 absolute ethanol was added (e.g., 240 µL ethanol for 400µL of collected upper phase). RNA samples were then loaded onto an Econospin column (Econospin # 1920-250), washed three times with RPE buffer (Qiagen #1018013), dried and eluted by adding RNA/DNAse-free water. RNA samples were then sent to Novogene (Cambridge, UK) for RNA-seq.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. Further detailed methods can be found in the original paper of the study.

treatment_protocol: Animals were divided into 4 groups: mice injected with PBS, healthy controls, no tumor (PBS); mice injected with NC26 cancer cells, non-cachectic tumor controls (NC); mice injected with C26 cancer cells and killed before onset of weight loss, pre-cachectic tumor mice (Pre); mice injected with C26 cancer cells and killed once they reached a body weight loss of 5-10 %, cachectic tumor mice (Cax).

value: Epididymal adipose tissue

value: Balb/c mice, Wild type

value: C26 tumors, cachectic


title: I04BPOST

description: Library name: Sample8

value: Inactive, Post-Exercise


title: Localized PCa patient 18

description: Library name: AC13

value: prostate gland biopsy

value: prostate cancer


title: UPPA_F115E_Prim

description: 10x Genomics


title: C10_Rep1

value: VHL mutant

value: dox off


title: Localized PCa patient 15

description: Library name: AC123


title: I04APOST

description: Library name: Sample6

value: Active, Post-Exercise


title: C35_Rep1


title: Cachectic tumor mouse, Epididymal adipose tissue, Mouse #70

description: Library name: Cax_E70_1


title: I03BPOST

description: Library name: Sample4


title: C10_Rep2


title: I03BPRE

description: Library name: Sample3

value: Inactive, Pre-Exercise


title: Localized PCa patient 14

description: Library name: AC121


title: Localized PCa patient 13

description: Library name: AC120


title: Cachectic tumor mouse, Epididymal adipose tissue, Mouse #67

description: Library name: Cax_E67_1


title: I02APOST

description: Library name: Sample2


title: Localized PCa patient 12

description: Library name: AC12


title: 6hpf_Sox32delHMG_Rep1

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

description:
Embryos injected at the one-cell stage with Sox32∆HMG domain mRNA and total RNA extracted at 6 hpf, replicate #1, matrix column name Sox32delHMG1
HMG_RNA-seq_Counts_Matrix.txt

data_processing:
Quality control of raw data was performed using FastQC. Reads were mapped to danRer11 zebrafish genome and counts per gene (Ensembl version 97) generated using STAR with default settings. Differential expression was identified through adjusted P-value < 0.05 using DESeq2 (1.36.0).
Assembly: danRer11, Ensembl version 97
Supplementary files format and content: Counts matrices containing raw counts per gene produced using STAR.

organism: Danio rerio

source_name: 6 hpf gastrula

growth_protocol: Embyos were maintained in egg water at 28.5 degrees celcius.

extract_protocol:
Total RNA extraction with QIAGEN Rneasy Mini kits with optional on-column Dnase digestion.
Illumina TruSeq Stranded mRNA

treatment_protocol: Embryos were injected with mRNAs as indicated at the one-cell stage and raised until 6 hours post-fertilisation (hpf) when total RNA was extracted.

value: 6 hpf gastrula

value: AB

value: wild type

value: sox32deltaHMG mRNA injection


title: C10_Rep4


title: 6hpf_Sox32delHMG_Rep2

description:
Embryos injected at the one-cell stage with Sox32∆HMG domain mRNA and total RNA extracted at 6 hpf, replicate #2, matrix column name Sox32delHMG2
HMG_RNA-seq_Counts_Matrix.txt


title: Localized PCa patient 11

description: Library name: AC116


title: Cachectic tumor mouse, GC muscle, Mouse #67

description: Library name: Cax_GC67_1

source_name: GC muscle

value: GC muscle


title: Cachectic tumor mouse, GC muscle, Mouse #66

description: Library name: Cax_GC66_1


title: I02APRE

description: Library name: Sample1

value: Skeletal Muscle

value: Active, Pre-Exercise


title: Cachectic tumor mouse, Epididymal adipose tissue, Mouse #75

description: Library name: Cax_E75_1

value: Epididymal adipose tissue


title: Localized PCa patient 10

description: Library name: AC115


title: 6hpf_HMGSwitch_Rep2

description:
Embryos injected at the one-cell stage with Sox32-Sox17HMG domain hybrid mRNA and total RNA extracted at 6 hpf, replicate #2, matrix column name HMGSwitch1
HMG_RNA-seq_Counts_Matrix.txt

value: HMG Switch mRNA injection


title: 6hpf_HMGSwitch_Rep1

description:
Embryos injected at the one-cell stage with Sox32-Sox17HMG domain hybrid mRNA and total RNA extracted at 6 hpf, replicate #1, matrix column name HMGSwitch1
HMG_RNA-seq_Counts_Matrix.txt


title: Cachectic tumor mouse, GC muscle, Mouse #70

description: Library name: Cax_GC70_1

value: Balb/c mice, Wild type

value: C26 tumors, cachectic


title: Localized PCa patient 9

description: Library name: AC114

value: prostate gland biopsy


title: 6hpf_Sox32_Rep3

description:
Embryos injected at the one-cell stage with zebrafish sox32 mRNA and total RNA extracted at 6 hpf, replicate #3, matrix column name Sox32_3
Interspecies_RNA-seq_Counts_Matrix.txt

value: sox32 mRNA injection


title: 6hpf_Control_Rep2

description:
Control for Sox32-Sox17HMG domain hybrid transcription factor experiment, replicate #2, matrix column name Con2
HMG_RNA-seq_Counts_Matrix.txt

value: Hybrid Sox TF control


title: 24hr replicate B

first: Alok

last: Jaiswal

state: MASSACHUSETTS

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

description: 10x genomics

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq pipeline made available by CellRanger v3.1.0 software (10x Genomics)
FASTQ reads were aligned to the GRCh38 human transcriptome, to extract cell barcodes and UMI barcodes using the cellranger count function. A digital gene expression (DGE) matrix for each sample was processed further
Cells that satisfied any one of the following criteria were removed: 1) Cells with < 200 detected genes; 2) Cells having outlier number of unique molecular identifiers (UMIs) >10000; 3) percentage of mitochondrial gene expression > 10%
Assembly: GRCh38
Supplementary files format and content: timecourse.h5ad: contains gene expression raw UMI and normalized expression values. Can be read using scanpy

source_name: Skin

growth_protocol: DMEM + 10%FBS

extract_protocol:
Trypsinization and resuspension into PBS containing 0.05% BSA.
Single cell suspensions were processed using the Chromium Single Cell 3’ Gene Expression kit (v3, 10x Genomics) per manufacturer’s instructions.
Libraries were sequenced on the Illumina HiSeq X upto 100 cycles per manufacturer’s instructions.

treatment_protocol: Stimulation with TGFb and IL1b or media alone.

value: Skin

value: ATCC, CRL-4001

value: Fibroblast

tag: timepoint

tag: replicate


title: Localized PCa patient 8

description: Library name: AC112

value: prostate cancer


title: Localized PCa patient 7

description: Library name: AC110


title: Cachectic tumor mouse, Heart, Mouse #66

description: Library name: Cax_H66_1

source_name: Heart

value: Heart


title: 6hpf_Sox32_Rep2

description:
Embryos injected at the one-cell stage with zebrafish sox32 mRNA and total RNA extracted at 6 hpf, replicate #2, matrix column name Sox32_2
Interspecies_RNA-seq_Counts_Matrix.txt

value: 6 hpf gastrula

value: AB

value: wild type


title: 6hpf_Sox32_Rep1

description:
Embryos injected at the one-cell stage with zebrafish sox32 mRNA and total RNA extracted at 6 hpf, replicate #1, matrix column name Sox32_1
Interspecies_RNA-seq_Counts_Matrix.txt


title: Localized PCa patient 5

description: Library name: AC109


title: 6hpf_Control_Rep1

description:
Control for Sox32-Sox17HMG domain hybrid transcription factor experiment, replicate #1, matrix column name Con1
HMG_RNA-seq_Counts_Matrix.txt


title: 12hr replicate B

description: 10x genomics

tag: cell line


title: 6hpf_zSox17_Rep3

description:
Embryos injected at the one-cell stage with zebrafish sox17 mRNA and total RNA extracted at 6 hpf, replicate #3, matrix column name zfSox173.tab
Interspecies_RNA-seq_Counts_Matrix.txt

tag: treatment

value: sox17 mRNA injection


title: 12hr replicate A

description: 10x genomics


title: Localized PCa patient 4

description: Library name: AC104


title: Localized PCa patient 3

description: Library name: AC103


title: Localized PCa patient 6

description: Library name: AC11


title: Cachectic tumor mouse, GC muscle, Mouse #75

description: Library name: Cax_GC75_1

value: GC muscle

tag: genotype


title: 6hpf_hSOX17_Rep3

description:
Embryos injected at the one-cell stage with hSOX17 mRNA and total RNA extracted at 6 hpf, replicate #3, matrix column name hSOX173.tab
Interspecies_RNA-seq_Counts_Matrix.txt

value: hSOX17 mRNA injection


title: 0hr replicate A

description: 10x genomics


title: 24hr replicate A

description: 10x genomics


title: Cachectic tumor mouse, Inguinal adipose tissue, Mouse #70

description: Library name: Cax_I70_1

source_name: Inguinal adipose tissue

value: Inguinal adipose tissue


title: Cachectic tumor mouse, Heart, Mouse #75

description: Library name: Cax_H75_1

value: Balb/c mice, Wild type


title: 6hr replicate A

description: 10x genomics


title: 6hpf_hSOX17_Rep2

description:
Embryos injected at the one-cell stage with hSOX17 mRNA and total RNA extracted at 6 hpf, replicate #2, matrix column name hSOX172.tab
Interspecies_RNA-seq_Counts_Matrix.txt


title: Cachectic tumor mouse, Inguinal adipose tissue, Mouse #75

description: Library name: Cax_I75_1

value: C26 tumors, cachectic


title: shRNAGAPDH Normal glucose conditions Sample 1

city: Dortmund

first: Jeffrey

middle: Lesslie

last: Schloßhauer

address: Otto-Hahn-Straße 11

department: Chemical Genomics Centre

institute: Max Planck Institute of Molecular Physiology

description: Replicates for each conditions were merged and annotated (processed file)

data_processing:
The zarp pipeline was followed to process fastq files; Adapters were trimmed through Cutadapt
The reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38) using STAR
Assembly: hg38, Genome Reference Consortium GRCh38
Supplementary files format and content: Tab Separated Values file includes merged processed data of for each condition and an annotation

source_name: Molm13 cells

extract_protocol:
Total RNA was isolated from 3-5 × 106 cultured Molm13 cells using TRIzol reagent (Thermo Fisher Scientific)
For library preparation, we removed rRNA using the FastSelect-rRNA HMR Kit (QIAseq) following strand-specific cDNA library preparation with the Stranded Total RNA Lib Kit (QIAseq)

value: Molm13 cells

value: AML

value: shRNAGAPDH Normal glucose conditions


title: 6hr replicate B

description: 10x genomics

value: Skin


title: BT248_SGC707_3

city: Calgary

first: Ravinder

last: Bahia

state: Alberta

address: 3330 Hospital drive NW

department: Cell Biology and Anatomy

country: Canada

institute: University of Calgary

data_processing:
Base calls were performed using bcl2fastq for novaseq output
NCBI RefSeq mRNA transcripts were quantified using kallisto 0.42.4 with a mean insert size of 180 and a std dev of 20
Transcripts were aligned using the Rsubread package
Assembly: Differential expression was performed using DESeq2 and significantly differentially expressed genes (FDR q<0.05) were used for input into the ReactomePA package
Supplementary files format and content: CSV file

growth_protocol: BT248 cells were cultured in stem cell enriched media supplemented with EGF (20ng/ml), bFGF (20ng/ml) and heparin sulfate (2µg/ml) in humidified atmosphere with 5% CO2 at 37C and were used within 10 passages after being thawed.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen, cat# 74104) and quantified using Nanodrop.
RNA libraries were prepared using NEB ultra II directional mRNA library kit following manufacturer's protocols.

treatment_protocol: The BTSC line, BT248, was treated with IC50 dose of SGC707 and XY1 negative control for 72 hours and pellets were collected from three biological replicates

value: Brain tumour stem cell

value: 72 hours


title: shRNAGAPDH Low glucose conditions Sample 2

value: shRNAGAPDH Low glucose conditions


title: 6hpf_hSOX17_Rep1

description:
Embryos injected at the one-cell stage with hSOX17 mRNA and total RNA extracted at 6 hpf, replicate #1, matrix column name hSOX171.tab
Interspecies_RNA-seq_Counts_Matrix.txt


title: 6hpf_zSox17_Rep2

description:
Embryos injected at the one-cell stage with zebrafish sox17 mRNA and total RNA extracted at 6 hpf, replicate #2, matrix column name zfSox172.tab
Interspecies_RNA-seq_Counts_Matrix.txt


title: 6hpf_zSox17_Rep1

description:
Embryos injected at the one-cell stage with zebrafish sox17 mRNA and total RNA extracted at 6 hpf, replicate #1, matrix column name zfSox171.tab
Interspecies_RNA-seq_Counts_Matrix.txt


title: Cachectic tumor mouse, Inguinal adipose tissue, Mouse #66

description: Library name: Cax_I66_1


title: Cachectic tumor mouse, Inguinal adipose tissue, Mouse #67

description: Library name: Cax_I67_1


title: 6hpf_Interspecies_Control_Rep2

description:
Control for hSOX17 and zebrafish Sox17 and Sox32 overexpression comparison, replicate #2, matrix column name Control2.tab
Interspecies_RNA-seq_Counts_Matrix.txt

value: Control


title: shRNAGAPDH Galactose conditions Sample 2

value: shRNAGAPDH Galactose conditions


title: BT248_XY1_2


title: Localized PCa patient 2

description: Library name: AC10

value: prostate gland biopsy

value: prostate cancer


title: shRNAGAPDH Normal glucose conditions Sample 2


title: BT248_SGC707_1


title: shRNAGAPDH Galactose conditions Sample 1


title: Cachectic tumor mouse, Heart, Mouse #67

description: Library name: Cax_H67_1

value: Heart


title: Localized PCa patient 1

description: Library name: AC1


title: Cachectic tumor mouse, Heart, Mouse #70

description: Library name: Cax_H70_1


title: 0hr replicate B

description: 10x genomics

value: ATCC, CRL-4001

value: Fibroblast


title: 6hpf_Interspecies_Control_Rep3

description:
Control for hSOX17 and zebrafish Sox17 and Sox32 overexpression comparison, replicate #3, matrix column name Control3.tab
Interspecies_RNA-seq_Counts_Matrix.txt

value: 6 hpf gastrula

value: AB

value: wild type


title: Cachectic tumor mouse, Liver, Mouse #66

description: Library name: Cax_L66_1

value: Liver

value: Balb/c mice, Wild type

value: C26 tumors, cachectic


title: Cachectic tumor mouse, Liver, Mouse #67

description: Library name: Cax_L67_1


title: Marchantia polymorpha, 100µM phosphinothricin for 48h, Rep 2

first: Grace

address: 1 Research Link National University of Singapore, 03-48

institute: Temasek Life Sciences Laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M.Polymorpha v5.1, Athaliana TAIR
Supplementary files format and content: comma-separated values file includes raw read counts for each sample
Supplementary files format and content: comma-separated values file includes log-transformed read counts for each sample

organism: Marchantia polymorpha

source_name: Gemmalings

extract_protocol:
RNA was extracted using the QIAGEN Plant RNeasy kit
Directional mRNA library preparation (poly A enrichment)

value: Gemmalings

value: 100µM phosphinothricin treatment for 48h


title: Non-cachectic tumor mouse, Epididymal adipose tissue, Mouse #86

description: Library name: NC_E86_1

value: Epididymal adipose tissue

value: NC26 tumors, non-cachectic


title: shRNAGAPDH Low glucose conditions Sample 1

value: Molm13 cells

value: AML

value: shRNAGAPDH Low glucose conditions


title: BT248_SGC707_2

value: Brain tumour stem cell

value: 72 hours


title: Low glucose conditions Sample 2

value: Low glucose conditions


title: BT248_XY1_3


title: Cachectic tumor mouse, Liver, Mouse #70

description: Library name: Cax_L70_1


title: 6hpf_Interspecies_Control_Rep1

description:
Control for hSOX17 and zebrafish Sox17 and Sox32 overexpression comparison, replicate #1, matrix column name Control1.tab
Interspecies_RNA-seq_Counts_Matrix.txt

value: Control


title: Marchantia polymorpha, 100µM phosphinothricin for 48h, Rep 3


title: Non-cachectic tumor mouse, Epididymal adipose tissue, Mouse #83

description: Library name: NC_E83_1


title: Normal glucose conditions Sample 2

value: Normal glucose conditions


title: LCCC1212_562

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.1
Assembly: hg38
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples

value: bladder tumor


title: BT248_XY1_1


title: Marchantia polymorpha, 5µM methionine sulfoxime for 48h, Rep 3

value: 5µM methionine sulfoxime treatment for 48h


title: Marchantia polymorpha, 100µM phosphinothricin for 48h, Rep 1


title: Non-cachectic tumor mouse, Epididymal adipose tissue, Mouse #87

description: Library name: NC_E87_1


title: LCCC1212_550

description: 10x Genomics


title: Non-cachectic tumor mouse, Epididymal adipose tissue, Mouse #88

description: Library name: NC_E88_1


title: Non-cachectic tumor mouse, GC muscle, Mouse #83

description: Library name: NC_GC83_1

value: GC muscle


title: Cachectic tumor mouse, Liver, Mouse #75

description: Library name: Cax_L75_1

value: Liver

value: Balb/c mice, Wild type


title: LCCC1212_534

description: 10x Genomics


title: Normal glucose conditions Sample 1


title: Marchantia polymorpha, 5µM methionine sulfoxime for 48h, Rep 2

value: Gemmalings


title: Non-cachectic tumor mouse, GC muscle, Mouse #86

description: Library name: NC_GC86_1


title: Marchantia polymorpha, 5µM methionine sulfoxime for 48h, Rep 1


title: LCCC1212_543

description: 10x Genomics


title: Low glucose conditions Sample 1


title: Marchantia polymorpha, 5mM glutamine treatment for 48h, Rep 3

value: 5mM glutamine treatment for 48h


title: Normal glucose conditions Sample 2

description: norm replicates were joined (processed file)

data_processing:
The zarp pipeline was followed to process fastq files; Adapters were trimmed through Cutadapt
The reads were mapped to the human genome (hg38, Genome Reference Consortium GRCh38) using STAR
Assembly: hg38, Genome Reference Consortium GRCh38
Supplementary files format and content: Tab Separated Values file includes joined peaks of for each condition and an annotation


title: Galactose conditions Sample 1

value: Galactose conditions


title: Non-cachectic tumor mouse, GC muscle, Mouse #87

description: Library name: NC_GC87_1

value: NC26 tumors, non-cachectic


title: Non-cachectic tumor mouse, GC muscle, Mouse #88

description: Library name: NC_GC88_1


title: Normal glucose conditions Sample 1

value: Molm13 cells