title: WT3 (CONTROL)

description:
WThTERT replicate three
SAMPLE 3

source_name: WT3 (CONTROL)


title: WT10C

status: Public on Mar 31 2023

type: genomic

city: Coleraine

first: Colum

middle: Patrick

last: Walsh

state: County Londonderry

address: Cromore Road

department: Life and Health Sciences

country: United Kingdom

institute: Ulster University

description:
UH+R10 replicate three
SAMPLE 8

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 and RnBeads (v1.6.1) through R (v3.3)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

growth_protocol: The wild-type (hTERT1604) lung fibroblast cell line (Ouellette et al., 2000) and derivatives were cultured in 4.5g/l glucose DMEM with 10% FBS and 2× NEAA (all Thermo-Fisher Scientific, Loughborough, UK).

extract_protocol: The genomic DNA isolated was assessed for purity and integrity prior to quantification using the Picogreen fluorescent assay.

treatment_protocol: Depletion of UHRF1 in hTERT1604 (U5/U10/UH4 lines) for this study used GIPz Lentiviral shRNAmir (Thermo-Fisher Scientific) according to the manufacturer’s instructions.

tag: gender

value: Male

tag: sample type

value: hTERT

tag: disease state

value: UHRF1 Rescue 10 hTERT


title: f2_110_42L1

type: SRA

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

department: Plant Science

country: USA

institute: South Dakota State University

library_source: transcriptomic

data_processing:
Fastq files were generated and multiplexed with bcl2fastq.
Quality of raw sequence reads were checked using FastQC.
Sequence reads were trimmed for adapters, length of 20 nucleotides, quality of 20 nucleotides using cutadapt and prinseq respectively.
Cleaned sequence reads were aligned to the Vitis vinifera 12X.V1 genome using Tophat and Gene expression levels in FPKM were quantified using Cufflinks.
Differential gene expression analysis was performed using EdgeR
Genome_build: 12X.V1
Supplementary_files_format_and_content: Tab-delimited text files

molecule: total RNA

organism: Vitis

source_name: F2 110 long day at 42 days

growth_protocol: F2 040 and F2 110 genotypes were previously described as part of a larger F2 population (Fennell et al., 2005, Acta Hort 689:533-539).  Spur-pruned grapevines were grown under long days until shoots reached 12-15 nodes and then randomized into a continued long (LD, 15 h) or short photoperiod (13 h) for 28 or 42 days (George et al. 2018, J.Prot:187:13-24)

extract_protocol:
RNA was extracted at 28 and 42 days of long day and short day photoperiod.
Single end RNAseq libraries were prepared with TruSeq Stranded RNA Sample Prep Kit.

treatment_protocol: Spur-pruned F2 040 and 110 grapevines were grown under long days until shoots reached 12-15 nodes, vines were randomized into LD (15 h) or SD (13 h) treatment, grown for an additional 28 or 42 days prior to bud harvest.

tag: genotype

tag: photoperiod

value: Long


title: C11_1237_2

type: RNA

city: Mishima

first: Toyoyuki

last: Takada

state: Shizuoka-ken

country: Japan

institute: National Institute of Genetics

description: Gene expression data from liver at 10-week-old male

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip scanner 3000 (Affymetrix).

data_processing: The data were analyzed with DFW (Chen et al. Bioinformatics, 2007).

label: biotin

organism: Mus musculus

source_name: B6-Chr11MSM_mouse liver

label_protocol: Biotinylated cRNA were prepared from 10ug total RNA by using GeneChip 3'IVT express kit (Affymetrix) according to the standard Affymetrix protocol.

extract_protocol: Livers were immersed in RNAlater (life technologies) and stored at -20C. Total RNA was extracted by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Samples were collected after a fasting period of four hours.

value: male

tag: strain

tag: tissue

value: liver

tag: age


title: f2_110_28S3

source_name: F2 110 short day at 28 days

value: Short


title: 200385-mNG-mAID_+IAA_REP2

city: Cambridge

first: Sebastian

last: Lourido

state: Massachusetts

address: 455 Main Street, Rm 555

institute: Whitehead Institute

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v.3.6
Alignment to the T. gondii genome was performed with STAR v.2.7.0a.
Differential expression analysis was done using the DESeq2 package (v. 1.12.3) in R
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: The corresponding xls file includes the following processed data, annotated as indicated in brackets:
Supplementary files format and content: i) log2(fold-change) in mRNA abundance in parasites depleted for each factor (i.e. treated with IAA) as compared to the IAA-treated parental TIR1 strain [L2FC.TargetedGeneID_IAA.v.TIR1_IAA]
Supplementary files format and content: ii) negative log-transformed p-values for differential expression analysis [nL10p.TargetedGeneID_IAA.v.TIR1_IAA]
Supplementary files format and content: iii) normalized transcript levels in each knockdown strain, expressed as log-transformed Fragments per Kilobase Mapped [L10FPKM.TargetedGeneID_IAA]

molecule: polyA RNA

organism: Toxoplasma gondii

source_name: intracellular protozoan parasite, cultured in HFFs

growth_protocol:
For routine maintenance, parasites were cultured in human foreskin fibroblasts (HFFs) grown at 37°C under 5% CO2 in standard medium, consisting of DMEM (GIBCO) supplemented with 3% heat-inactivated fetal bovine serum (IFS), 2 mM L-glutamine, and 10 μg/mL gentamicin.
Passaging was performed on a 2-3 day cycle—prior to lysis of host cell monolayers—by scraping and transfer to fresh HFFs.

extract_protocol:
Parasites were isolated from host cells by syringe-release (described above) and filtering through a Millex filter unit (5 μm pore size, Merck Millipore) to remove host cell debris. RNA was isolated using the Rneasy mini plus kit (Qiagen).
Libraries for RNA-seq were prepared using the Swift Low-Input Library Prep Kit with poly(A) enrichment following manufacturer's protocols.

treatment_protocol:
To establish infection, parasites were mechanically released from host cells by passage through a 27-gauge needle and innoculated onto confluent human foreskin fibroblasts in standard  medium.
After 4h, infected monolayers were washed twice with PBS, switched to alkaline-stress medium (RPMI 1640 supplemented with 1% IFS, 10 μg/mL gentamicin, 50 mM HEPES, and pH-adjusted to 8.1 with 10 N NaOH), and treated with either 5uM 3-indole-acetic acid (IAA) or an equivalent volume of vehicle.
Cultures were maintained under their respective treatment condition for 96h before harvest, with fresh stress medium provided on day 2.

tag: cell type

tag: condition

value: 96hr alkaline stress

tag: treatment

value: 50uM IAA


title: C12C_0993_2

source_name: B6-Chr12CMSM_mouse liver


title: 200385-mNG-mAID_Veh._REP2

value: intracellular protozoan parasite, cultured in HFFs

value: Vehicle (PBS)


title: C15_0049_2

source_name: B6-Chr15MSM_mouse liver


title: f2_110_28S2


title: C16_1037_1

source_name: B6-Chr16MSM_mouse liver


title: f2_110_28L3

source_name: F2 110 long day at 28 days


title: 311100-mNG-mAID_Veh._REP1


title: UH1

description:
UH4 replicate one
SAMPLE 4

value: UHRF1 KD hTERT


title: parental_Veh._REP2


title: C11_1225_1


title: f2_110_28L2


title: 306620-mNG-mAID_+IAA_REP1


title: f2_040_42S3

source_name: F2 040 short day at 42 days


title: C1_1085_2

source_name: B6-Chr1MSM_mouse liver


title: 306620-mNG-mAID_Veh._REP1


title: parental_+IAA_REP2

value: 5uM IAA


title: f2_110_28S1


title: C11_1225_3


title: C11_1237_1


title: f2_040_42S2


title: f2_110_28L1


title: 224630-mNG-mAID_Veh._REP1


title: 224630-mNG-mAID_+IAA_REP1


title: f2_040_42L3

source_name: F2 040 long day at 42 days


title: f2_040_42L2


title: 208020-mNG-mAID_+IAA_REP1


title: f2_040_42L1


title: f2_040_28S3

source_name: F2 040 short day at 28 days


title: 208020-mNG-mAID_Veh._REP1


title: 253790-mNG-mAID_+IAA_REP1


title: C1_1085_1


title: f2_040_28S2


title: C1_1097_2


title: B6_1770_2

source_name: B6_mouse liver


title: B6_1770_1


title: C1_1097_1


title: 200385-mNG-mAID_Veh._REP1


title: f2_040_42S1


title: f2_040_28L3

source_name: F2 040 long day at 28 days


title: B6_1734_1


title: parental_+IAA_REP1


title: parental_Veh._REP1


title: dBFD1_3

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v.3.6
Alignment to the T. gondii genome was performed with STAR v.2.7.0a.
Differential expression analysis was done using the DESeq2 package (v. 1.12.3) in R.
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: xls file includes the following information, annotated as indicated in brackets:
Supplementary files format and content: i) raw read counts for each sample [i.e. WT.ReadCount.1, where numbers indicate separte biological replicates]
Supplementary files format and content: ii) Log2(fold-change) in mRNA abundance [i.e. L2FC.dBFD1.v.WT]
Supplementary files format and content: iii) Corresponding negative log-transformed p-values for differential expression analysis [i.e. nL10p.dBFD1.v.WT]

source_name: intracellular protozoan parasite, cultured in primary mouse neurons

growth_protocol: For routine maintenance, parasites were cultured in human foreskin fibroblasts (HFFs) grown at 37°C under 5% CO2 in standard medium, consisting of DMEM (GIBCO) supplemented with 3% heat-inactivated fetal bovine serum (IFS), 2 mM L-glutamine, and 10 μg/mL gentamicin. Passaging was performed on a 2-3 day cycle by scraping the infected monolayers and transfering to fresh HFFs.

extract_protocol:
To harvest, infected neurons were dissociated by treatment with accutase enzyme for 5 mins at 37°C, then pelleted by centrifugation and flash frozen for storage at -80°C.
Total cellular RNA was isolated using the Zymo Direct-zol RNA Miniprep Kit and RNA quality was assessed using a BioAnalyzer or Fragment analyzer.
Libraries for RNA-seq were prepared using the Swift Low-Input Library Prep Kit with poly(A) enrichment following manufacturer's protocols.

treatment_protocol: Primary murine neurons were harvested from Cre reporter mice originally obtained from Jacksons Laboratories (#007906), and cultured in vitro as previously described (Chandrasekaran et al, 2022).  After 10 days, neurons were inoculated with either the parental strain (Pru-OVA-TdTomato), BFD1-, or BFD2-knockous at an MOI of ~2 and left for an additional 48 h in culture.

value: PRU

tag: replicate information

value: Biological replicate 3


title: 253790-mNG-mAID_Veh._REP1


title: dBFD2_3

value: intracellular protozoan parasite, cultured in primary mouse neurons


title: dBFD1_2

value: Biological replicate 2


title: dBFD2_2


title: E25SCC

city: Higashiku

first: Sho

last: Okuda

state: Fukuoka

address: Maidashi 3-1-1

department: Surgery and Oncology

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Genome_build: GRCh38
Supplementary_files_format_and_content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: tumor tissue

extract_protocol:
Esophagus were resected, and a part of resected tissue was made into sigle cells. RNA was extracted and barcorded using Chromium Single Cell 3' Reagent Kits v3.1 (PN- 1000121).
Same as above.
single cell RNA-sequence

value: esophagus

tag: collection method

value: biopsy


title: E23SCC


title: E24SCC


title: B6_1734_2


title: 200385-mNG-mAID_+IAA_REP1


title: dBFD1_1

value: Biological replicate 1


title: f2_040_28S1


title: parental_1

value: Pru-OVA-TdTomato


title: E22SCC

value: surgery


title: f2_040_28L2

value: Long


title: dBFD2_1


title: E21SCC


title: HA-BFD2_stress_INPUT

data_processing:
Reads were trimmed to remove adapter sequences with Cutadapt (v.3.6) and aligned to the T. gondii genome with STAR (v.2.7.0a). BFD2-bound transcripts were identified based on the following enrichment analysis pipeline:
i) From raw read counts, we calculated a read coverage score for each message, defined as the square root of the sum of squares for reads in both the IP and input control. Only transcripts with i) read coverage greater than 10 and ii) more than 5 mapped reads in both the IP and input were included in downstream analysis.
ii) Within each trimmed data set  (i.e. IP and input), raw reads for each gene were convered to Transcripts Per Million (TPM), normalizing for sequencing depth.
iii) An enrichment ratio was generated for each gene, defined as TPM in the IP divided by TPM in the input.
iv) Gaussian mixture modeling was perfomred on log2-transformed enrichment ratios, which fit two Gaussian curves to the data—an upper 'enriched' distribution which comprised only the highest enrichment ratios and a lower  'background' distribution corresponding to all other unenriched messages.
v) Posterior probabilities were generated from this model and used to calculate an odds ratio for each gene. To set a cutoff for calling BFD2-enriched transcripts, we used the log of the odds (LOD) ratio between the two Gaussian functions. LOD greater than 0 indicates a higher probability of falling within the upper distribution compared to lower background distribution; thus, LOD > 0 was used as a threshold to call individual transcripts as highly enriched.
Assembly: T. gondii ME49 (ToxoDB v.56 assembly)
Supplementary files format and content: Tabulated xls file includes raw read counts for all genes measured in both IP and input samples (Tab "RIP_ALL") and the results of each step in the analysis pipeline outlined above (Tab "RIP_TRIMMED"), performed on a reduced data set trimmed to only include only genes meeting our minimal threshold for detection.

extract_protocol:
At the time of harvest, monolayers were scraped and serially extruded through 27-and 30-gauge needles to release intracellular parasites. Parasites were then isolated from host cell debris by additional passaging through a Millex filter unit (5 μm pore size, Merck Millipore), pelleted by centrifugation, and resuspended in MAGNA-RIP lysis buffer. For an 'input' sample, 10% of the starting lysate was set aside. The remaining 90% was subjected to IP with mouse anti-HA antibodies (clone 16B12, Abcam) using the MAGNA-RIP kit (Millipore) as described in the product technical manual. Total RNA was isolated in parallel from both enriched (IP) and unenriched (input) samples by canonical phenol:chloroform extraction.
Libraries for RNA-seq were prepared using the Swift Low-Input Library Prep Kit with poly(A) enrichment following manufacturer's protocols.

treatment_protocol: Extracellular parasites were innoculated onto confluent HFFs and allowed to invade in standard medium. After 4 hr, monolayers were washed twice with PBS and switched to alkaline-stress medium (RPMI 1640 supplemented with 1% IFS, 10 μg/mL gentamicin, 50 mM HEPES, and pH-adjusted to 8.1 with 10 N NaOH) to induce differentiation, then left for an additional 72hr of culture.

value: alkaline stress

value: input (unenriched)


title: parental_3


title: E19SCC


title: f2_040_28L1


title: E20SCC


title: parental_2


title: E17SCN

source_name: normal mucosa


title: E16SCC


title: T_4_3_4

city: 北京

first: zhu

last: jie

address: 北京市海淀区学院路38号

country: China

institute: 北京大学医学部

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Matrix table with raw gene counts for every gene and every sample

source_name: Trametinib-treated MCD mice group

growth_protocol: The animals were housed in a temperature-controlled animal room (24 ± 2 ℃) with a relative humidity of 60-80%.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trametinib was dissolved in 0.5% Sodium Carboxymethylcellulose  and administered i.p. once a day for 14 days at doses of 0.1mg/kg.

tag: group

value: MCD mice group

value: Trametinib

value: liver


title: E17SCC


title: HA-BFD2_stress_IP

value: intracellular protozoan parasite, cultured in HFFs

value: IP (enriched by HA-BFD2 pull-down)


title: WT2 (CONTROL)

description:
WThTERT replicate two
SAMPLE 2

source_name: WT2 (CONTROL)

value: Male

value: hTERT

value: WT hTERT


title: T_4_3_3

address: 北京市海淀区学院路38号


title: M5_MCD

address: 北京市海淀区学院路38号

source_name: vehicle-treated MCD mice group

value: vehicle


title: E18SCN

value: esophagus


title: T_4_3_2

address: 北京市海淀区学院路38号


title: M4_MCD

address: 北京市海淀区学院路38号


title: CT3_N

address: 北京市海淀区学院路38号

source_name: vehicle-treated normal group

value: normal group


title: M3_MCD

address: 北京市海淀区学院路38号


title: E16SCN


title: E18SCC


title: CT2_N

address: 北京市海淀区学院路38号


title: Z3_shen

address: 北京市海淀区学院路38号

source_name: Perillen-treated Hyperuricemia mice group

extract_protocol:
Kidney were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Perillen was dissolved in normal saline and administered i.g. once a day for 14 days at doses of 10mg/kg.

value: Hyperuricemia mice group

value: Perillen

tag: breed

value: KunMing mice

value: kidney


title: RECTUM_BIOPSY_pat240

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

description: Human pretherapeutic rectal cancer pat240

hyb_protocol: 1.5 mg of Cy3-labeled cRNA was hybridized to an oligonucleotide-based Whole Human Genome Microarray (4x44K, Agilent Technologies) and incubated at 65˚C for 17 hours.

scan_protocol: Slides were washed and scanned using an Agilent G2565BA scanner.

data_processing: Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.

source_name: Pretherapeutic rectal cancer patient biopsy

label_protocol: 1 µg of total RNA was labeled with Cy3 using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent Technologies, Santa Clara, CA). Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

extract_protocol: Biospies from patients not cell lines were used for analyses. Biopsies were immediately stored in RNAlater (Qiagen, Hilden, Germany). Subsequently, RNA and DNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer´s instructions.  Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment prior to expression profiling analysis was performed.

tag: dataset

value: Validation

tag: Sex

value: male

tag: therapy

value: 5-FU + RT

tag: surgery type

value: Abdominoperineal excision (APE)

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: III B

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

value: IV

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)

tag: rin


title: CT1_N

address: 北京市海淀区学院路38号

tag: group

tag: treatment

tag: age

tag: strain

tag: tissue

value: liver


title: RECTUM_BIOPSY_pat243

description: Human pretherapeutic rectal cancer pat243

tag: dataset

tag: Sex

value: female

tag: therapy

tag: surgery type

value: deep anterior resection (TAbdominoperineal resection (APR))

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: III


title: RECTUM_BIOPSY_pat245

description: Human pretherapeutic rectal cancer pat245

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

value: II A


title: RECTUM_BIOPSY_pat242

description: Human pretherapeutic rectal cancer pat242

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)


title: Z2_shen

address: 北京市海淀区学院路38号

tag: group

tag: treatment

tag: age

tag: breed


title: RECTUM_BIOPSY_pat244

description: Human pretherapeutic rectal cancer pat244

tag: dataset

tag: Sex

tag: therapy

value: III A

tag: rin


title: RECTUM_BIOPSY_pat241

description: Human pretherapeutic rectal cancer pat241

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: I


title: Z1_shen

address: 北京市海淀区学院路38号

value: Hyperuricemia mice group

tag: tissue


title: Model3_shen

address: 北京市海淀区学院路38号

source_name: vehicle-treated Hyperuricemia mice group

value: vehicle


title: RECTUM_BIOPSY_pat236

description: Human pretherapeutic rectal cancer pat236

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

value: II

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat239

description: Human pretherapeutic rectal cancer pat239

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat237

description: Human pretherapeutic rectal cancer pat237

tag: dataset

tag: age


title: Model2_shen

address: 北京市海淀区学院路38号

tag: group

tag: treatment

tag: breed

value: KunMing mice

value: kidney


title: Model1_shen

address: 北京市海淀区学院路38号


title: RECTUM_BIOPSY_pat238

description: Human pretherapeutic rectal cancer pat238

value: Validation

tag: Sex

value: male

tag: therapy

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

tag: rin


title: RECTUM_BIOPSY_pat234

description: Human pretherapeutic rectal cancer pat234

value: 5-FU + RT

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat232

description: Human pretherapeutic rectal cancer pat232

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat233

description: Human pretherapeutic rectal cancer pat233

tag: dataset

tag: age

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)


title: Wt3_shen

address: 北京市海淀区学院路38号

tag: group

value: normal group

tag: treatment

tag: breed

tag: tissue


title: RECTUM_BIOPSY_pat235

description: Human pretherapeutic rectal cancer pat235

tag: Sex

tag: therapy

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: III B

tag: rin


title: RECTUM_BIOPSY_pat229

description: Human pretherapeutic rectal cancer pat229

value: 5-FU + Oxaliplatin + RT

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: Wt2_shen

address: 北京市海淀区学院路38号

tag: age


title: RECTUM_BIOPSY_pat230

description: Human pretherapeutic rectal cancer pat230

tag: dataset

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: cancer specific survival (css) in months from surgery date


title: Wt1_shen

address: 北京市海淀区学院路38号

tag: group

tag: treatment

tag: breed

tag: tissue


title: RECTUM_BIOPSY_pat231

description: Human pretherapeutic rectal cancer pat231

tag: Sex

tag: therapy

tag: surgery type

value: Abdominoperineal excision (APE)

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: III C

tag: tumor related death (1) or data censoring without event (0)


title: wt3_stWAT

address: 北京市海淀区学院路38号

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The animals were housed in a temperature-controlled animal room (23 ± 2 ℃) with a relative humidity of 60-80%.

extract_protocol:
Subcutaneous fatty tissue were removed, flash frozen on dry ice, and -80 ℃ to keep the sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chikusetsusaponin IV was dissolved in 0.5% Sodium Carboxymethylcellulose  and administered i.p. once a day for 35 days at doses of 20mg/kg.

tag: strain

value: subcutaneous fatty tissue


title: wt2_stWAT

address: 北京市海淀区学院路38号


title: wt1_stWAT

address: 北京市海淀区学院路38号


title: RECTUM_BIOPSY_pat228

description: Human pretherapeutic rectal cancer pat228

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: IV

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

tag: rin


title: ct7_stWAT

address: 北京市海淀区学院路38号

source_name: vehicle-treated HFD mice group

value: HFD mice group

tag: age


title: RECTUM_BIOPSY_pat227

description: Human pretherapeutic rectal cancer pat227

tag: dataset

value: deep anterior resection (TAbdominoperineal resection (APR))

value: III

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: cancer specific survival (css) in months from surgery date


title: ct5_stWAT

address: 北京市海淀区学院路38号

tag: group

tag: treatment

value: vehicle

tag: tissue


title: ct2_stWAT

address: 北京市海淀区学院路38号


title: C7_stWAT

address: 北京市海淀区学院路38号

source_name: Chikusetsusaponin IV-treated HFD mice group

value: Chikusetsusaponin IV


title: RECTUM_BIOPSY_pat226

description: Human pretherapeutic rectal cancer pat226

tag: Sex

tag: therapy

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: II

tag: tumor related death (1) or data censoring without event (0)


title: C3_stWAT

address: 北京市海淀区学院路38号

tag: strain


title: RECTUM_BIOPSY_pat225

description: Human pretherapeutic rectal cancer pat225

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: C1_stWAT

address: 北京市海淀区学院路38号

tag: age


title: RECTUM_BIOPSY_pat220

description: Human pretherapeutic rectal cancer pat220

tag: dataset

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: rin


title: RECTUM_BIOPSY_pat221

description: Human pretherapeutic rectal cancer pat221

tag: Sex

value: II A

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat224

description: Human pretherapeutic rectal cancer pat224

value: Validation

tag: therapy

tag: surgery type

value: I


title: RECTUM_BIOPSY_pat223

description: Human pretherapeutic rectal cancer pat223

value: female

value: 5-FU + RT

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

tag: tumor related death (1) or data censoring without event (0)


title: 311100-mNG-mAID_+IAA_REP1

source_name: intracellular protozoan parasite, cultured in HFFs

tag: strain

tag: cell type

tag: genotype

tag: condition

value: 96hr alkaline stress

tag: treatment

value: 50uM IAA


title: RECTUM_BIOPSY_pat219

description: Human pretherapeutic rectal cancer pat219

tag: age

value: male

value: Abdominoperineal resection (APR)

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: III B

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat217

description: Human pretherapeutic rectal cancer pat217

tag: dataset

tag: Sex

value: III A

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: rin


title: RECTUM_BIOPSY_pat215

description: Human pretherapeutic rectal cancer pat215

tag: therapy

value: 5-FU + Oxaliplatin + RT

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat222

description: Human pretherapeutic rectal cancer pat222

tag: age

value: deep anterior resection (TAbdominoperineal resection (APR))


title: RECTUM_BIOPSY_pat216

description: Human pretherapeutic rectal cancer pat216

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat218

description: Human pretherapeutic rectal cancer pat218

value: Abdominoperineal excision (APE)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: IV


title: RECTUM_BIOPSY_pat212

description: Human pretherapeutic rectal cancer pat212

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat210

description: Human pretherapeutic rectal cancer pat210

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat214

description: Human pretherapeutic rectal cancer pat214

value: III

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat213

description: Human pretherapeutic rectal cancer pat213

tag: dataset

value: III C


title: RECTUM_BIOPSY_pat211

description: Human pretherapeutic rectal cancer pat211

tag: Sex

value: II A


title: RECTUM_BIOPSY_pat208

description: Human pretherapeutic rectal cancer pat208

value: Validation


title: RECTUM_BIOPSY_pat205

description: Human pretherapeutic rectal cancer pat205

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat197

description: Human pretherapeutic rectal cancer pat197

value: Training

value: II

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat204

description: Human pretherapeutic rectal cancer pat204

value: 5-FU + RT

value: I

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat199

description: Human pretherapeutic rectal cancer pat199

value: Other

tag: rin


title: RECTUM_BIOPSY_pat203

description: Human pretherapeutic rectal cancer pat203

value: male

tag: therapy


title: RECTUM_BIOPSY_pat201

description: Human pretherapeutic rectal cancer pat201

tag: surgery type


title: RECTUM_BIOPSY_pat209

description: Human pretherapeutic rectal cancer pat209

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat195

description: Human pretherapeutic rectal cancer pat195

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat200

description: Human pretherapeutic rectal cancer pat200

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat192

description: Human pretherapeutic rectal cancer pat192

tag: age

value: female


title: RECTUM_BIOPSY_pat207

description: Human pretherapeutic rectal cancer pat207

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat202

description: Human pretherapeutic rectal cancer pat202

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat198

description: Human pretherapeutic rectal cancer pat198

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat196

description: Human pretherapeutic rectal cancer pat196

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

value: III B


title: RECTUM_BIOPSY_pat191

description: Human pretherapeutic rectal cancer pat191

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat188

description: Human pretherapeutic rectal cancer pat188

tag: dataset


title: RECTUM_BIOPSY_pat187

description: Human pretherapeutic rectal cancer pat187

tag: Sex


title: RECTUM_BIOPSY_pat194

description: Human pretherapeutic rectal cancer pat194

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat206

description: Human pretherapeutic rectal cancer pat206

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat193

description: Human pretherapeutic rectal cancer pat193

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat185

description: Human pretherapeutic rectal cancer pat185

value: III A

tag: rin


title: RECTUM_BIOPSY_pat186

description: Human pretherapeutic rectal cancer pat186

tag: therapy


title: RECTUM_BIOPSY_pat182

description: Human pretherapeutic rectal cancer pat182

tag: surgery type


title: RECTUM_BIOPSY_pat184

description: Human pretherapeutic rectal cancer pat184

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat183

description: Human pretherapeutic rectal cancer pat183

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat171

description: Human pretherapeutic rectal cancer pat171

value: II B

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat190

description: Human pretherapeutic rectal cancer pat190

tag: age

value: deep anterior resection (TAbdominoperineal resection (APR))


title: RECTUM_BIOPSY_pat178

description: Human pretherapeutic rectal cancer pat178

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat180

description: Human pretherapeutic rectal cancer pat180

value: Abdominoperineal excision (APE)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat189

description: Human pretherapeutic rectal cancer pat189

value: 5-FU + Oxaliplatin + RT

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat176

description: Human pretherapeutic rectal cancer pat176

value: III

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat179

description: Human pretherapeutic rectal cancer pat179

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat174

description: Human pretherapeutic rectal cancer pat174

tag: dataset


title: RECTUM_BIOPSY_pat172

description: Human pretherapeutic rectal cancer pat172

tag: Sex


title: RECTUM_BIOPSY_pat168

description: Human pretherapeutic rectal cancer pat168

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat173

description: Human pretherapeutic rectal cancer pat173

value: Abdominoperineal resection (APR)

value: III C

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat177

description: Human pretherapeutic rectal cancer pat177

value: II A

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat181

description: Human pretherapeutic rectal cancer pat181

value: Training

tag: rin


title: RECTUM_BIOPSY_pat170

description: Human pretherapeutic rectal cancer pat170

tag: therapy


title: RECTUM_BIOPSY_pat169

description: Human pretherapeutic rectal cancer pat169

tag: surgery type


title: RECTUM_BIOPSY_pat175

description: Human pretherapeutic rectal cancer pat175

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat166

description: Human pretherapeutic rectal cancer pat166

value: II

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat162

description: Human pretherapeutic rectal cancer pat162

value: IV

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat167

description: Human pretherapeutic rectal cancer pat167

tag: age

value: I


title: RECTUM_BIOPSY_pat165

description: Human pretherapeutic rectal cancer pat165

value: 5-FU + RT

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat157

description: Human pretherapeutic rectal cancer pat157

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat163

description: Human pretherapeutic rectal cancer pat163

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat161

description: Human pretherapeutic rectal cancer pat161

value: male

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat156

description: Human pretherapeutic rectal cancer pat156

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat159

description: Human pretherapeutic rectal cancer pat159

tag: dataset


title: RECTUM_BIOPSY_pat158

description: Human pretherapeutic rectal cancer pat158

tag: Sex

value: female


title: RECTUM_BIOPSY_pat164

description: Human pretherapeutic rectal cancer pat164

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat153

description: Human pretherapeutic rectal cancer pat153

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat154

description: Human pretherapeutic rectal cancer pat154

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat152

description: Human pretherapeutic rectal cancer pat152

tag: rin


title: RECTUM_BIOPSY_pat149

description: Human pretherapeutic rectal cancer pat149

tag: therapy

value: Other


title: RECTUM_BIOPSY_pat150

description: Human pretherapeutic rectal cancer pat150

tag: surgery type


title: RECTUM_BIOPSY_pat148

description: Human pretherapeutic rectal cancer pat148

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat155

description: Human pretherapeutic rectal cancer pat155

value: III B

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat147

description: Human pretherapeutic rectal cancer pat147

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat139

description: Human pretherapeutic rectal cancer pat139

tag: age


title: RECTUM_BIOPSY_pat138

description: Human pretherapeutic rectal cancer pat138

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

value: III A


title: RECTUM_BIOPSY_pat151

description: Human pretherapeutic rectal cancer pat151

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat146

description: Human pretherapeutic rectal cancer pat146

value: deep anterior resection (TAbdominoperineal resection (APR))

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat143

description: Human pretherapeutic rectal cancer pat143

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat145

description: Human pretherapeutic rectal cancer pat145

value: Abdominoperineal excision (APE)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat144

description: Human pretherapeutic rectal cancer pat144

tag: dataset

value: 5-FU + Oxaliplatin + RT


title: RECTUM_BIOPSY_pat141

description: Human pretherapeutic rectal cancer pat141

tag: Sex

value: III


title: RECTUM_BIOPSY_pat136

description: Human pretherapeutic rectal cancer pat136

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat130

description: Human pretherapeutic rectal cancer pat130

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat140

description: Human pretherapeutic rectal cancer pat140

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat131

description: Human pretherapeutic rectal cancer pat131

tag: rin


title: RECTUM_BIOPSY_pat142

description: Human pretherapeutic rectal cancer pat142

tag: therapy


title: RECTUM_BIOPSY_pat135

description: Human pretherapeutic rectal cancer pat135

tag: surgery type


title: RECTUM_BIOPSY_pat133

description: Human pretherapeutic rectal cancer pat133

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat137

description: Human pretherapeutic rectal cancer pat137

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat129

description: Human pretherapeutic rectal cancer pat129

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat134

description: Human pretherapeutic rectal cancer pat134

tag: age


title: RECTUM_BIOPSY_pat126

description: Human pretherapeutic rectal cancer pat126

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat122

description: Human pretherapeutic rectal cancer pat122

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat128

description: Human pretherapeutic rectal cancer pat128

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat125

description: Human pretherapeutic rectal cancer pat125

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat132

description: Human pretherapeutic rectal cancer pat132

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat121

description: Human pretherapeutic rectal cancer pat121

tag: dataset


title: RECTUM_BIOPSY_pat124

description: Human pretherapeutic rectal cancer pat124

tag: Sex


title: RECTUM_BIOPSY_pat127

description: Human pretherapeutic rectal cancer pat127

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat118

description: Human pretherapeutic rectal cancer pat118

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat119

description: Human pretherapeutic rectal cancer pat119

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat117

description: Human pretherapeutic rectal cancer pat117

value: II B

tag: rin


title: RECTUM_BIOPSY_pat120

description: Human pretherapeutic rectal cancer pat120

tag: therapy


title: RECTUM_BIOPSY_pat123

description: Human pretherapeutic rectal cancer pat123

tag: surgery type


title: RECTUM_BIOPSY_pat116

description: Human pretherapeutic rectal cancer pat116

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat114

description: Human pretherapeutic rectal cancer pat114

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat115

description: Human pretherapeutic rectal cancer pat115

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat111

description: Human pretherapeutic rectal cancer pat111

tag: age


title: RECTUM_BIOPSY_pat113

description: Human pretherapeutic rectal cancer pat113

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat110

description: Human pretherapeutic rectal cancer pat110

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat106

description: Human pretherapeutic rectal cancer pat106

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat109

description: Human pretherapeutic rectal cancer pat109

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat108

description: Human pretherapeutic rectal cancer pat108

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat102

description: Human pretherapeutic rectal cancer pat102

tag: dataset


title: RECTUM_BIOPSY_pat100

description: Human pretherapeutic rectal cancer pat100

tag: Sex


title: RECTUM_BIOPSY_pat107

description: Human pretherapeutic rectal cancer pat107

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat104

description: Human pretherapeutic rectal cancer pat104

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat97

description: Human pretherapeutic rectal cancer pat97

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat112

description: Human pretherapeutic rectal cancer pat112

tag: rin


title: RECTUM_BIOPSY_pat98

description: Human pretherapeutic rectal cancer pat98

tag: therapy


title: RECTUM_BIOPSY_pat103

description: Human pretherapeutic rectal cancer pat103

tag: surgery type


title: RECTUM_BIOPSY_pat95

description: Human pretherapeutic rectal cancer pat95

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat99

description: Human pretherapeutic rectal cancer pat99

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat105

description: Human pretherapeutic rectal cancer pat105

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat93

description: Human pretherapeutic rectal cancer pat93

tag: age


title: RECTUM_BIOPSY_pat96

description: Human pretherapeutic rectal cancer pat96

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat101

description: Human pretherapeutic rectal cancer pat101

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat94

description: Human pretherapeutic rectal cancer pat94

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat89

description: Human pretherapeutic rectal cancer pat89

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat91

description: Human pretherapeutic rectal cancer pat91

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat90

description: Human pretherapeutic rectal cancer pat90

tag: dataset


title: RECTUM_BIOPSY_pat87

description: Human pretherapeutic rectal cancer pat87

tag: Sex

value: III C


title: RECTUM_BIOPSY_pat160

description: Human pretherapeutic rectal cancer pat160

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat84

description: Human pretherapeutic rectal cancer pat84

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat86

description: Human pretherapeutic rectal cancer pat86

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat88

description: Human pretherapeutic rectal cancer pat88

tag: rin


title: RECTUM_BIOPSY_pat82

description: Human pretherapeutic rectal cancer pat82

tag: therapy

value: II A


title: RECTUM_BIOPSY_pat85

description: Human pretherapeutic rectal cancer pat85

value: Training

tag: surgery type


title: RECTUM_BIOPSY_pat80

description: Human pretherapeutic rectal cancer pat80

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: II


title: RECTUM_BIOPSY_pat81

description: Human pretherapeutic rectal cancer pat81

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat79

description: Human pretherapeutic rectal cancer pat79

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat73

description: Human pretherapeutic rectal cancer pat73

tag: age


title: RECTUM_BIOPSY_pat70

description: Human pretherapeutic rectal cancer pat70

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat77

description: Human pretherapeutic rectal cancer pat77

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat71

description: Human pretherapeutic rectal cancer pat71

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat76

description: Human pretherapeutic rectal cancer pat76

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat72

description: Human pretherapeutic rectal cancer pat72

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat92

description: Human pretherapeutic rectal cancer pat92

tag: dataset


title: RECTUM_BIOPSY_pat74

description: Human pretherapeutic rectal cancer pat74

tag: Sex


title: RECTUM_BIOPSY_pat75

description: Human pretherapeutic rectal cancer pat75

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat78

description: Human pretherapeutic rectal cancer pat78

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat66

description: Human pretherapeutic rectal cancer pat66

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat68

description: Human pretherapeutic rectal cancer pat68

tag: rin


title: RECTUM_BIOPSY_pat83

description: Human pretherapeutic rectal cancer pat83

tag: therapy


title: RECTUM_BIOPSY_pat67

description: Human pretherapeutic rectal cancer pat67

tag: surgery type


title: RECTUM_BIOPSY_pat64

description: Human pretherapeutic rectal cancer pat64

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat69

description: Human pretherapeutic rectal cancer pat69

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat65

description: Human pretherapeutic rectal cancer pat65

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat59

description: Human pretherapeutic rectal cancer pat59

tag: age


title: RECTUM_BIOPSY_pat62

description: Human pretherapeutic rectal cancer pat62

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat61

description: Human pretherapeutic rectal cancer pat61

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat56

description: Human pretherapeutic rectal cancer pat56

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat50

description: Human pretherapeutic rectal cancer pat50

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat57

description: Human pretherapeutic rectal cancer pat57

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat48

description: Human pretherapeutic rectal cancer pat48

tag: dataset


title: RECTUM_BIOPSY_pat53

description: Human pretherapeutic rectal cancer pat53

tag: Sex


title: RECTUM_BIOPSY_pat51

description: Human pretherapeutic rectal cancer pat51

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat63

description: Human pretherapeutic rectal cancer pat63

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat58

description: Human pretherapeutic rectal cancer pat58

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat45

description: Human pretherapeutic rectal cancer pat45

value: Abdominoperineal resection (APR)

tag: rin


title: RECTUM_BIOPSY_pat43

description: Human pretherapeutic rectal cancer pat43

tag: therapy

value: I


title: RECTUM_BIOPSY_pat44

description: Human pretherapeutic rectal cancer pat44

value: 5-FU + RT

tag: surgery type


title: RECTUM_BIOPSY_pat52

description: Human pretherapeutic rectal cancer pat52

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat49

description: Human pretherapeutic rectal cancer pat49

value: male

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat47

description: Human pretherapeutic rectal cancer pat47

value: female

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat42

description: Human pretherapeutic rectal cancer pat42

tag: age


title: RECTUM_BIOPSY_pat35

description: Human pretherapeutic rectal cancer pat35

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat40

description: Human pretherapeutic rectal cancer pat40

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat60

description: Human pretherapeutic rectal cancer pat60

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat55

description: Human pretherapeutic rectal cancer pat55

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat41

description: Human pretherapeutic rectal cancer pat41

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat46

description: Human pretherapeutic rectal cancer pat46

tag: dataset


title: RECTUM_BIOPSY_pat39

description: Human pretherapeutic rectal cancer pat39

tag: Sex


title: RECTUM_BIOPSY_pat38

description: Human pretherapeutic rectal cancer pat38

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat36

description: Human pretherapeutic rectal cancer pat36

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat54

description: Human pretherapeutic rectal cancer pat54

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat34

description: Human pretherapeutic rectal cancer pat34

tag: rin


title: RECTUM_BIOPSY_pat37

description: Human pretherapeutic rectal cancer pat37

tag: therapy


title: RECTUM_BIOPSY_pat33

description: Human pretherapeutic rectal cancer pat33

tag: surgery type


title: RECTUM_BIOPSY_pat30

description: Human pretherapeutic rectal cancer pat30

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: IV


title: RECTUM_BIOPSY_pat31

description: Human pretherapeutic rectal cancer pat31

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat32

description: Human pretherapeutic rectal cancer pat32

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat29

description: Human pretherapeutic rectal cancer pat29

tag: age


title: RECTUM_BIOPSY_pat26

description: Human pretherapeutic rectal cancer pat26

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat22

description: Human pretherapeutic rectal cancer pat22

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat25

description: Human pretherapeutic rectal cancer pat25

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat17

description: Human pretherapeutic rectal cancer pat17

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat16

description: Human pretherapeutic rectal cancer pat16

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat21

description: Human pretherapeutic rectal cancer pat21

tag: dataset


title: RECTUM_BIOPSY_pat23

description: Human pretherapeutic rectal cancer pat23

tag: Sex


title: RECTUM_BIOPSY_pat20

description: Human pretherapeutic rectal cancer pat20

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: RECTUM_BIOPSY_pat28

description: Human pretherapeutic rectal cancer pat28

tag: disease free survival (dfs) in months from surgery date


title: RECTUM_BIOPSY_pat7

description: Human pretherapeutic rectal cancer pat7

tag: local recurrence or distance metastasis event (1) or no event (0)


title: RECTUM_BIOPSY_pat4

description: Human pretherapeutic rectal cancer pat4

tag: rin


title: RECTUM_BIOPSY_pat18

description: Human pretherapeutic rectal cancer pat18

tag: therapy


title: RECTUM_BIOPSY_pat6

description: Human pretherapeutic rectal cancer pat6

tag: surgery type


title: RECTUM_BIOPSY_pat13

description: Human pretherapeutic rectal cancer pat13

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: III B


title: RECTUM_BIOPSY_pat27

description: Human pretherapeutic rectal cancer pat27

tag: cancer specific survival (css) in months from surgery date


title: RECTUM_BIOPSY_pat19

description: Human pretherapeutic rectal cancer pat19

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat24

description: Human pretherapeutic rectal cancer pat24

tag: age


title: RECTUM_BIOPSY_pat5

description: Human pretherapeutic rectal cancer pat5

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat15

description: Human pretherapeutic rectal cancer pat15

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat9

description: Human pretherapeutic rectal cancer pat9

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat11

description: Human pretherapeutic rectal cancer pat11

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

value: III A


title: RECTUM_BIOPSY_pat10

description: Human pretherapeutic rectal cancer pat10

value: deep anterior resection (TAbdominoperineal resection (APR))

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)


title: RECTUM_BIOPSY_pat8

description: Human pretherapeutic rectal cancer pat8

tag: dataset

value: Other


title: RECTUM_BIOPSY_pat12

description: Human pretherapeutic rectal cancer pat12

tag: Sex


title: RECTUM_BIOPSY_pat3

description: Human pretherapeutic rectal cancer pat3

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: N16, scRNA-Seq

city: Su Zhou

first: Shiyou

last: Wang

state: Jiang Su

address: Chong Wen street

department: Suzhou Institute of Systems Medicine

institute: Peking Union Medical College

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was mapped to rat reference genome (Rnor_6.0, genome-date 2014-07, NCBI:GCA_000001895.4) using Cell Ranger (cellranger-6.1.2) with default parameters, giving rise to gene expression matrix for downstream analysis.
Rnor_6.0, genome-date 2014-07, NCBI:GCA_000001895.4
Sparse matrix including three file (barcode, counts and features)

organism: Rattus norvegicus

source_name: Penis

extract_protocol:
The collected tissues were rinsed using 1× phosphate-buffered saline, then quick-frozen, and stored in liquid nitrogen. Nuclei of each tissue were separated by mechanical extraction. Briefly, the tissues were first thawed, infiltrated by 1× homogenization buffer (containing 30 mM CaCl2, 18 mM Mg(Ac)2, 60 mM Tris-HCl pH 7.8, 320 mM sucrose, 0.1% NP-40, 0.1 mM EDTA, and 0.2 U/µl RNase inhibitor), and cut into smaller pieces, with the single nucleus then isolated by 2 ml of Dounce homogenizer. After filtration with a 30 µm strainer, the nuclear extraction was resuspended in 1% bovine serum albumin (BSA) containing 0.2 U/µl RNase inhibitor and centrifuged at 500 × g for 10 min at 4 °C to discard cellular impurities within the supernatant. This step was repeated twice, after which the nuclei were recollected with 0.1% BSA containing 0.2 U/µl RNase inhibitor. Subsequently, 4′,6-diamidino-2-phenylindole was used to stain the nuclei and nucleus density was calculated under a fluorescence microscope for subsequent library construction.
Extracted nuclei from two rat penis were mixed and subjected to single nucleus library construction using chromium single cell 3' reagent kits (v3 Chemistry) following the manufacture’s protocol.

tag: tissue

value: Penis

tag: cell line

value: No

tag: cell type

value: Penis tissue cell

tag: genotype

value: WT

tag: treatment

value: Vacuum erection devices


title: RECTUM_BIOPSY_pat14

description: Human pretherapeutic rectal cancer pat14

value: Training

tag: therapy

value: 5-FU + Oxaliplatin + RT

tag: surgery type

tag: clinical tumor category (0,i,ii,iii,iv - according to uicc tnm classification)

value: III

tag: disease free survival (dfs) in months from surgery date

tag: local recurrence or distance metastasis event (1) or no event (0)

tag: rin


title: PAT2V2, CBD

city: Gainesville

first: Simone

last: Marini

state: FLORIDA

address: 2004 Mowry road

institute: University of Florida

description: 10X Genomics

data_processing:
CellRanger 7.0.1 to extract count matrix
Seurat 4.2 for downstream analysis
Downsteam analysis code: https://github.com/smarini/CBD_HIV_scRNAseq
Further details publicly available at: https://www.medrxiv.org/content/10.1101/2023.02.24.23285761v1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Fresh blood was collected and diluted in wash buffer (Phosphate buffered saline [137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4]; 1mM EDTA) prior to careful layering over Lymphoprep Separation Media by gravity release. Tubes were centrifuged in a swinging bucket centrifuge with brake off for 30 minutes at room temperature. The human peripheral blood mononuclear cell (PBMC) layer was collected and washed twice with wash buffer. Following a lower speed wash, cells were filtered with a 70µM cell strainer, counted and frozen down at ~15 million PBMCs per patient in CryoStor Freezing Medium.  Once all samples were ready for single cell sequencing, cryopreserved PBMCs were quickly thawed at 37°C followed by the dropwise addition of warm complete medium (10% FBS in DMEM). Following centrifugation, cells were washed once more with complete medium before being subjected to dead cell removal according to the manufacturer’s instructions. After the cells were pelleted and washed with PBS, 0.04% BSA, they were filtered through a Flowmi™ Tip Strainer, counted, and resuspend at 1200 cells per µL for viability testing and library preparation.
The 10x Chromium Controller and Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) were used to construct barcoded single-cell RNA-Seq libraries following the manufacturer’s user guide (10X Genomics). Briefly, approximately 7000 single cells at 90% or greater viability are loaded onto the Chromium Controller. Single cells are captured into Gel Bead-In Emulsions (GEM) where cell lysis and cDNA synthesis occur. All cDNAs produced from a single cell will contain a unique DNA molecular bar code. Following demulsification, mRNA-derived are recovered using SPRIselect reagent (Beckman). Library construction was performed by fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR, which Illumina sequencing barcodes were added. After Ampure Beads clean up, libraries were quantified by using Agilent TapeSation 4200 and qPCR quantification with NEB Library Quanti Kit for Illumina (NEB). Finally, Libraries were sequenced on the Illumina Novaseq 6000 aiming for 50,000 reads per cell. Single cell data analysis was performed with 10x Genomics Cell Ranger Single Cell Software Suite.     10x Single cell library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression & Genotyping Core, University of Florida (UF).         NovaSeq sequencing run was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) NextGen DNA Sequencing core, University of Florida (UF).

value: blood

tag: individual id

value: PBMC

tag: sample #

value: CBD 1

value: CBD


title: PAT5V1, baseline

description: 10X Genomics

value: baseline 1

value: baseline


title: PAT3V3, CBD

description: 10X Genomics


title: PAT5V2, CBD

description: 10X Genomics


title: N17, scRNA-Seq

description: 10x Genomics

value: Control


title: iCDA4.1_untrt biol rep 1

city: Edinburgh

first: Alisha

last: May

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt (version cutadapt-1.18-venv). Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA kit (AGATCGGAAGAGC). Reads after trimming were required to have a minimum length of 50
The reference used for mapping was the Homo sapiens (GRCh38) genome from Ensembl. The annotation used for counting was the standard GTF-format annotation for that reference (annotation version 104).
Reads were aligned to the reference genome using STAR (version 2.7.3a) specifying paired-end reads and the option --outSAMtype BAM Unsorted. All other parameters were left at default.
Genes were filtered and only genes with a count of 10 or higher in at least 2 samples were kept.  Principal component analysis and multidimensional scaling were undertaken on normalised and filtered expression data. For differential gene expression analyses,  genes were filtered to include only genes with an adjusted p-value below 0.05.
Assembly: GRCh38
Supplementary files format and content: Excel file containing normalised counts for each sample. Genes were filtered and only genes with a count of 10 or higher in at least 2 samples were kept.

growth_protocol: iPSC-derived macrophages were maintained in X-VIVO medium supplemented with 100 ng/ml M-CSF, 1% Penicillin-Streptomycin, and 2 mM GlutaMAX supplement at 37°C.

extract_protocol:
RNA was harvested using the Qiagen RNeasy Mini Kit.
TruSeq stranded mRNA-seq library prepared by Edinburgh Genomics.

treatment_protocol: iPSC-derived macrophages were either untreated or treated with 100 nM 4OH-tamoxifen.

value: iPSC-derived macrophage

value: KLF1-E325K-ERT2 construct

value: untreated


title: iCDA4.1_trt biol rep 2

value: 100 nM of 4OH-tamoxifen


title: iCDA4.1_trt biol rep 3


title: iCDA4.1_untrt biol rep 2


title: iCDA4.1_trt biol rep 1


title: iCDA4.1_untrt biol rep 3


title: iCDA4.1_trt biol rep 4


title: iCDA4.1_untrt biol rep 5


title: iCDA4.1_trt biol rep 5


title: iCDA4.1_untrt biol rep 4


title: K2_trt biol rep 2

value: KLF1-WT-ERT2 construct


title: K2_trt biol rep 4


title: PAT3V1, baseline

description: 10X Genomics


title: PAT2V1, baseline

description: 10X Genomics


title: RECTUM_BIOPSY_pat1

description: Human pretherapeutic rectal cancer pat1

tag: age

value: female

value: deep anterior resection (TAbdominoperineal resection (APR))

tag: clinical lymphnode status (0,1 - according to uicc tnm classification)

tag: clinical tumor stage (0,i,ii,iii,iv - according to uicc tnm classification)

value: IV

tag: pathological tumor category after neoadjuvant treatment and surgery (0,i,ii,iii,iv - according to uicc tnm classification)

tag: pathological lymphnode status after neoadjuvant treatment and surgery (0,1,2 - according to uicc tnm classification)

tag: pathological tumor stage after neoadjuvant treatment and surgery (0,i,ii,iii, iv - according to uicc tnm classification)

tag: cancer specific survival (css) in months from surgery date

tag: tumor related death (1) or data censoring without event (0)


title: RECTUM_BIOPSY_pat2

description: Human pretherapeutic rectal cancer pat2

tag: dataset

value: Training

tag: Sex

value: male

value: 5-FU + RT

tag: tumor regression grading (trg) after neoadjuvant treatment and surgery (0=no regression - iv=maximal regression)


title: K2_untrt biol rep 1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: K2_untrt biol rep 4


title: K2_untrt biol rep 3


title: K2_untrt biol rep 2


title: K2_trt biol rep 5


title: SFCi55_trt biol rep 5

value: WT


title: K2_untrt biol rep 5


title: SFCi55_untrt biol rep 5


title: K2_trt biol rep 1


title: SFCi55_untrt biol rep 1


title: SFCi55_untrt biol rep 2


title: SFCi55_untrt biol rep 4


title: Streptavidin_pull-down_H1KO_asynchrony_rep2

city: Beijing

first: Yu

last: Juan

address: 15 Datun Road, Chaoyang District

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph files

source_name: mouse embryonic stem cells

growth_protocol:
ChIP-seq:  mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.
ChOR-seq:  mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq:  Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChIP-seq:  H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.
ChOR-seq:  Cells were first crosslinked by formaldehyde, then sonicated in SDS containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with dyno beas conjucated with antibodies. For ChOR-seq, EdU pulse labeled DNA was biotinylated by Click Reaction, then  chromatin were  immunoprecipitated with streptavidin dyno beads( Invitrogent, M280).The ChIP-seq antibodies are as following: Anti-H3K27me3,GST, 9733S;Anti-V5,Gene-Protein Link,P01L075
ChOR-seq:  H3K27me3 were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova seq.

value: mouse embryonic stem cells

tag: strain

tag: chip antibody

value: no


title: Streptavidin_pull-down_WT_synchronization_rep2

value: Wild type


title: Streptavidin_pull-down_H1KO_synchronization_rep2


title: Streptavidin_pull-down_WT_asynchrony_rep2


title: 9019- IDC fibroblast

city: Kansas City

first: Nikki

last: Cheng

state: Kansas

address: 3901 Rainbow Blvd Mailstop 3045

institute: KUMC

description: Fibroblast RNA Seq raw counts.txt

data_processing:
Following collection, sequence data was converted from .bcl file format to fastq files using bcl2fastq software and de-multiplexed into individual sequences for further downstream analysis. The fastq files were QC checked with FastQC (Babraham Institute).
Reads were mapped against UCSC hg38 genome with STAR software (2.3.1z) and counted with HTSeq (0.5.4p3)
Count tables were imported into R 3.1 and differential gene expression analysis was performed with EdgeR (3.12)
The resulting differential gene files were annotated with Ensembl’s biomaRt hsapiens_gene_ensembl ver84.
Assembly: UCSC hg38
Supplementary files format and content: a single tab-delimited text file called "Fibroblast RNA Seq raw counts"with a matrix table of all samples that shows raw counts

source_name: invasive breast ductal carcinoma

growth_protocol: Fibroblasts were cultured in DMEM/10 % FBS containing penicillin/streptomycin at 37oC in 5% CO2.

extract_protocol:
RNA was isolated using the EZNA Total RNA kit I (Omega Biotech)
500 ng total RNA was used to generate transcriptome libraries, using the TruSeq Stranded mRNA LT Sample Preparation Kit according to manufacturer’s protocol (Illumina)

treatment_protocol: Not applicable

tag: tissue

value: invasive breast ductal carcinoma

value: primary

value: fibroblast

tag: cell subtype

value: IDC fibroblast


title: 2525-normal breast fibroblast

description: Fibroblast RNA Seq raw counts.txt

source_name: normal breast

value: normal breast

value: normal breast fibroblast


title: 8727-normal adjacent breast fibroblast

description: Fibroblast RNA Seq raw counts.txt

source_name: normal adjacent breast to IDC

value: normal adjacent breast to IDC

value: normal adjacent breast fibroblast


title: 8727- IDC fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: 9019- normal adjacent breast fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_AID_decrease_WT_T4_asynchrony_rep2

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS . Reads were normalized with fly reference as previous study
ChOR-seq: all sequencing data were mapped to the Mus musculus genome assembly (mm9) and D. melanogaster genome assembly (dm6) using bowtie2, with the default parameters. Low quality reads and PCR duplicates were removed by samtools and only uniquely mapped reads which mapping to a unique genomic location and strand were kept. Reads were normalized with fly reference as previous study. The enriched regions (peaks) were detected using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph files
Library strategy: ChOR-seq


title: 2300- IDC fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_AID_decrease_WT_T2_asynchrony_rep2


title: 2760- IDC fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_AID_decrease_WT_T1_asynchrony_rep2


title: 8661- IDC fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: SFCi55_untrt biol rep 3

value: iPSC-derived macrophage

value: untreated


title: 4009- normal breast fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_AID_increase_WT_T1_asynchrony_rep2


title: ChOR-seq_AID_increase_WT_T4_asynchrony_rep2


title: SFCi55_trt biol rep 3

value: 100 nM of 4OH-tamoxifen


title: ChOR-seq_AID_WT_T0_asynchrony_rep2


title: SFCi55_trt biol rep 1


title: SFCi55_trt biol rep 4


title: SFCi55_trt biol rep 2


title: 70213-DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt

source_name: breast ductal carcinoma in situ

value: breast ductal carcinoma in situ

value: DCIS fibroblast


title: 8870- IDC fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: 30413-DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_H1KO_T2_asynchrony_rep2


title: K2_trt biol rep 3

value: KLF1-WT-ERT2 construct


title: 21714-DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: 80H- DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_H1KO_T0_asynchrony_rep2

value: mouse embryonic stem cells


title: ChOR-seq_H1KO_T1_asynchrony_rep2


title: 1213249-DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChOR-seq_WT_T3_asynchrony_rep2


title: 102115- DCIS fibroblast

description: Fibroblast RNA Seq raw counts.txt


title: ChIP-seq_H1KO_HA_tetR_EZH2_targeting_H3K27me3_rep2


title: ChOR-seq_WT_T0_asynchrony_rep2


title: ChOR-seq_WT_T2_asynchrony_rep2


title: ChOR-seq_AID_increase_WT_T2_asynchrony_rep2


title: ChIP-seq_WT_HA_tetR_EZH2_targeting_H3K27me3_rep2


title: ChOR-seq_WT_T1_asynchrony_rep2


title: Normal control#4

city: Jinan

first: Bo

last: Han

address: huaiyin，jingwu

institute: Shandong Provincial Hospital Affiliated to Shandong First Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: human GRCh38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: Small extracellular vesicles in plasma

extract_protocol:
Before eating/drinking in the morning, peripheral blood samples (8mL) were collected using an EDTA tube through a routine venepathesis procedure.A total of 4mL of plasma was collected from each participant, and sEVs were extracted by ultracentrifugation.Total RNA from the sEVs was extracted using the miRNeasy® Mini kit (Qiagen, cat217204). RNA concentration, purity, and integrity were assessed using the RNA Nano 6000 detection kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small extracellular vesicles in plasma

tag: disease state

value: healthy


title: Normal control#3


title: ChOR-seq_H1KO_T3_asynchrony_rep2


title: Normal control#2


title: Normal control#5


title: ChIP-seq_WT_HA_tetR_EED_targeting_H3K27me3_rep2

value: Wild type


title: fulminant myocarditis patient#5

value: fulminant myocarditis


title: fulminant myocarditis patient#4


title: Normal control#1


title: fulminant myocarditis patient#2


title: fulminant myocarditis patient#3


title: fulminant myocarditis patient#1


title: MEC_FL3_Rep4

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Human Reference genome (GRCh38) or Mouse Reference Genome (GRCm38)
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Assembly: GRC38
Supplementary files format and content: Table with raw gene counts for every gene and every sample

extract_protocol:
RNA was harvested and isolated using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
3'-RNA-Seq

value: blood

value: CLL B cells

value: FL3 50nM

tag: time


title: MEC_FL3_Rep3


title: MEC_DMSO_Rep2

value: DMSO


title: MEC_DMSO_Rep3


title: MEC_DMSO_Rep1


title: MEC_FL3_Rep1


title: MEC_DMSO_Rep4


title: Dex

city: Guangzhou

first: chen

middle: wei

last: fen

address: 4F, Building 1, Standard Property Unit 3, International Biotech Island

institute: Forevergen

description: RNA-seq

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Qualified reads were obtained after removing raw reads with adapters or of low quality and then aligned to the human genome by HISAT with default parameters.
RSeQC was used to measured gene expression abundance as reads per kilobase per million mapped reads (RPKM).
Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. P-value <0.05 were assigned as differentially expressed gene.
Assembly: hg19

source_name: human deciduous tooth pulp

growth_protocol: BMSC was purchased from SALIAI, catalog number G02001. Use the matching complete medium for culture passage, and use cells within 5 passages for experiments. Dexamethasone belongs to the class of glucocorticoid drugs, which is used for the excessive glucocorticoid-induced BMSC cell damage in this project, and the specific concentration is 1μM. SHED was purchased from oral stem cell bank. Thoroughly sterilize the deciduous teeth, split the teeth in a biological safety cabinet, take out the pulp tissue, digest with 3 mg/mL collagenase type I and 4 mg/mL neutral protease at 37℃ for 40min, and add 10% FBS-containing solution. DMEM terminates the reaction, after centrifugation, discard the supernatant, add DMEM containing 20% FBS to resuspend, culture in a culture flask, subculture the cells to 80-90%, and perform limiting dilution to obtain monoclonal cells. After identification by flow cytometry, it is the P2 generation SHED or subsequent experiments.

extract_protocol:
Total RNA from the cells was isolated using the Trizol (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions, followed by a DNase I digestion for 30 minutes to remove genomic DNA
Total RNA was treated with the RiboMinus kit (Life Technologies) to remove the ribosomal RNAs. The remaining RNAs were fragmented and reverse-transcribed using random primers and reverse transcriptase. Second strand cDNA synthesis was completed using DNA polymerase I and RNase H. The Illumina series KAPA Library Preparation Kit (Kapa Biosystems) was used to perform end repair, dA-tailing, and adapter ligation. The dUTP-marked second strand was digested at 37 °C for 30 min using Uracil Specific Excision Reagent (USER) enzyme (New England Biolabs). The cDNA was enriched by PCR amplification to create the final cDNA libraries.

value: human deciduous tooth pulp

tag: group

value: dexamathasome


title: Dex_Exo

description: RNA-seq

value: dexamathasome - exosome


title: MEC_FL3_Rep2


title: Con

description: RNA-seq

value: control


title: HD 6

city: Washington

first: Jerry

last: Xiao

state: DC

address: 3900 Reservoir Rd NW, PCS Bldg, Room GR10C

department: Tumor Biology

institute: Georgetown University

description: total RNA from healthy blood

data_processing:
Base-calling was performed using salmon v0.14.
adapter were trimmed using trimmomatic
Reads were aligned to the human genome (Star Genecode v38) using STAR aligner v2.7.3a
reads were counted using feature counts in R annot.inbuilt='hg38' isPairedEnd = TRUE nthreads=23
Differential Expression was calculated using DESeq2 in R
Assembly: GRCH38.p13
Supplementary files format and content: raw and normalized gene counts (CSV) created from DESeq2

source_name: HD 6

growth_protocol: CTC samples were extracted from patient samples using a Ficoll-based gradient selection. Cells were grown in hypoxia on ultra-low attachment plates using a modified conditional-reprogramming (CR)-based medium.

extract_protocol:
RNA was extracted using Invitrogen RNAqueous Micro-RNA kit following manufacturer protocol.
Psomagen was used to construct libraries based on an ultra-low input library preparation.

tag: source

value: Healthy Donor Blood

value: Healthy Donor

value: Whole Blood


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shControl2

city: shanghai

first: jie

last: wang

address: 700 Moyu North Road

department: Department of Urology

institute: Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trim_galore default parameter,  then mapped to known_rRNA using bowtie2-2.4.2  with parameters  -p 16,then remove rRNA reads.
then mapped reads without rRNA to GRCm39.104 whole genome using hisat2-2.2.0 with parameters -q -p 16.
The whole quantitative step is completed by htseq-count-0.13.5
Then  statistical analysis of differences was performed using edgeR-3.34.0  Packages by  R version 4.1.0
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited files include count FPKM values for each Sample

growth_protocol: Sun-7R cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNeasy Mini Kit (Cat # 74106, Qiagen) was used for total RNA extraction of samples according to the standard operating procedures provided by the manufacturer.
Sequencing libraries were generated using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (NR612, Vazyme, Nanjing, China)  according to the manufacturer’s instructions.

treatment_protocol: Lentiviruses expressing human FUS were constructed and produced by the Sun-7R  cells were transduced following the manufacturer's instructions. After 72 h, puromycin was added to select the stably transduced cell lines.

value: renal cell carcinoma cell lines


title: CTC 19 FFPE

description: total RNA from FFPE tissues of primary tumor from patient 19

source_name: Patient 19

value: Patient FFPE Tissue

value: Cancer

value: FFPE


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shControl1


title: CTC 26 TC

description: total RNA from the cultured CTCs of patient 26

source_name: Patient 26

value: CTC Culture

value: Tissue Culture


title: CTC 26 WBM

description: total RNA from the whole blood of patient 26

value: Patient Peripheral Blood


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shControl3


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shFUS3


title: CTC 22 TC

description: total RNA from the cultured CTCs of patient 22

source_name: Patient 22


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shFUS1


title: sunitinib-resistant RCC cells 786-O(Sun-7R), shFUS2


title: CTC 22 WBM

description: total RNA from the whole blood of patient 22


title: CTC 21 TC

description: total RNA from the cultured CTCs of patient 21

source_name: Patient 21


title: HD 5

description: total RNA from healthy blood

source_name: HD 5


title: CTC 21 WBM

description: total RNA from the whole blood of patient 21


title: CTC 21 FFPE

description: total RNA from FFPE tissues of primary tumor from patient 21