title: scRNA-seq using PB10X - pool 5 - gene expression of Homo Sapiens: jurkat cells

city: Gent

first: Koen

last: Deserranno

address: Ottergemsesteenweg 460

department: Department of Pharmaceutics

country: Belgium

institute: Ghent University

description:
Library name: PB10X_GeneExpression_Jurkat_Pool5
The processed files given here are the result of the combined analysis of pool 1,2,3 and 5.

data_processing:
For Smart-seq3xpress, the zUMIs (v.2.9.7e ) pipeline was used. For PB10X, Cell Ranger (v7.2.0) was used. All analysis details can be found in the manuscript.
Assembly: GRCh38
Supplementary files format and content: For Smart-seq3xpress, the .rds object containing the count data for all cells with aditional .txt files with statistics.
Supplementary files format and content: For PB10X, the output count matrices as generated by Cell Ranger.

source_name: jurkat

extract_protocol:
No separate RNA-extraction. Single cells were FACS sorted directly in the lysis buffer plates.
Smart-seq3xpress and the newly developed PB10X protocol. All details can be found in the manuscript.

value: jurkat


title: LNCaP, siPDIA1, 48h, rep3

status: Public on Oct 14 2025

type: SRA

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: Library name: siPDIA1_48h_3

library_source: transcriptomic

data_processing:
Raw reads were trimmed and filtered for short sequences using cutadapt v.1.8, setting minimum-length option to 18, error-rate 0.2 and overlap 5.
Reads were mapped against the human reference genome (Gencode GRCh38) using STAR aligner (version:2.7.0f_0328) with default parameters.
Using featureCounts, reads were assigned to exonic regions and counted.
Differential expression analysis was done from filtered CPM normalised counts (CPM <1 across half of the samples) using DESeq2 (Bioconductor Release: 3.14) in R version 3.4.1.
Assembly: hg38
Supplementary files format and content: Excel file that includes normalised counts (RPKM) for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Prostate cancer

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).

extract_protocol:
Total RNA was extracted using Trizol, according to the manufacturer's instructions.
Stranded polyA libraries were prepared according to the Nugen Universal Plus mRNA-seq protocol and included 15 cycles of amplification.

treatment_protocol: LNCaP cells were transfected with siRNAs for 48h or 96h using RNAiMAX.

tag: tissue

value: Prostate cancer

tag: cell line

value: LNCaP

tag: treatment


title: SS142 20°C IP 3

city: Toronto

first: Julie

last: Claycomb

address: 661 University Ave

country: Canada

institute: University of Toronto

description:
Library name: 50_R6_20d_142IP
IP3
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv

data_processing:
Adapter sequences were removed using cutadapt (version 1.15, Martin, 2011) using the following command: -a ADAPTER -f fastq -m 16 -M 30 —discard-untrimmed.
The trimmed reads were aligned to the C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276) with STAR (version 2.6.0c, Dobin et al., 2013) using the following parameters: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1.
The reads were then counted using a custom R script against publicly available genome annotations. The WormBase version WS276 PRJNA13758 ce11 canonical geneset annotations were used (excluding miRNAs, repeats, and transposons). C. elegans miRNA annotations were obtained from miRBase (release 22.1). For repeats and transposons RepeatMasker+Dfam (ce10, October 2010, RepeatMasker open-4.0.6, Dfam 2.0) annotations were used. The UCSC Lift Genome Annotations tool was used to convert ce10 coordinates to ce11 coordinates. Briefly, the counting script used the findOverlaps function from the GenomicAlignments package (version 1.22.1) to assign reads to features. Multiple aligning reads or reads that align to more than one feature were dealt with by counting reads in a sequential manner to the different gene biotypes in the following order (AS stands for antisense): miRNA, piRNA, rRNA, snoRNA, snRNA, tRNA, ncRNA, lincRNA, repeats AS, protein coding AS, pseudogene AS, lincRNA AS, antisense RNA, rRNA AS, snoRNA AS, snRNA AS, tRNA AS, ncRNA AS, miRNA AS, piRNA AS, protein coding, pseudogene, antisense RNA AS, repeats. For reads that align to more than one feature in the same biotype group, the read count was split between the features based on the fraction of uniquely aligned reads to each of those features (unique weighing).
To determine small RNAs enriched in Argonaute IPs, reads were first normalized to library size (reads per million [RPM]). To determine whether small RNAs against a particular target were enriched in an Argonaute IP, the following calculation was made: enrichment = IP RPM + 0.01/Input RPM + 0.01. The 0.01 represents a pseudocount to eliminate the possibility of dividing by zero. A target was considered enriched if in every replicate it was at least twofold enriched in all replicates and had at least 5 RPM in each of the IP replicates. Where indicated, only reads of length 20-24 nucleotides were considered, representing 22G-RNAs.
Assembly: C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276)
Supplementary files format and content: For IP experiments, table of enrichment (IP/Input) values.
Supplementary files format and content: For mutant total sRNA data, matrix of count data.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: For the 20°C experiment, worms continuously maintained at 20°C were synchronized by bleaching adults only (excluding laid embryos) and plated on 15 cm NGM plates with 4 ml of OP50 bacteria. They were grown until they reached the young adult stage. For the 26°C experiment, parent worms (maintained at 20°C) were synchronized by chunking embryos onto 9 cm NGM plates seeded with OP50 bacteria. The plates were incubated at 20°C until the worms reached the L4 stage, then transferred to 26°C. After 24 hours, the adults were bleached (excluding laid embryos). Plates were kept at 26°C until the worms reached the young adult stage.

extract_protocol:
The worm pellet was resuspended at a 1:1.5 (v/v) ratio in EDTA buffer, which contained 10% glycerol, 10 mM EDTA, 30 mM HEPES, 100 mM potassium acetate, 2 mM DTT, and 0.1% NP-40, supplemented with protease, RNase, and phosphatase inhibitors: 2x cOmplete EDTA-free protease inhibitor cocktail (Roche), 1:100 SuperaseIN (Thermo Fisher), and 1:100 phosphatase inhibitor cocktails 2 and 3 (Sigma). The resuspended pellet was flash-frozen by adding it drop by drop into liquid nitrogen, and the frozen samples were stored at –80°C until lysate preparation.  The frozen samples were ground in a mortar with liquid nitrogen. Protein lysates were prepared by thawing the frozen powder, sonicating it at a low setting (3 minutes, 15 seconds ON/15 seconds OFF), and centrifuging it at 17,000 x g for 15 minutes, with all steps performed at 4°C. Once thawed, the samples were handled continuously at 4°C or kept on ice. To determine the total protein concentration, either a Lowry assay or a Bradford assay (BioRad) was used. For total sRNA sequencing, an aliquot containing 500 µg of protein was mixed with TRI Reagent (Sigma) and flash-frozen (further description in the RNA isolation step).  To sequence the sRNAs bound to WAGO-4, we performed an immunoprecipitation (IP) protocol. All the assayed strains expressed WAGO-4 tagged with 3xFLAG::GFP tag. For the IPs, 3-6 mg of total protein was used per reaction. To pre-clear the lysate, it was incubated with 20 µL of Binding Control magnetic beads (ChromoTek) at 4°C for an hour with rotation. The lysates were then incubated with GFP-Trap magnetic beads (ChromoTek) at 4°C for an hour with rotation to bind WAGO-4. Both the Binding Control and GFP-Trap magnetic beads were equilibrated with the IP buffer prior to adding the lysate. After binding to the GFP-Trap beads, the beads were washed once with a buffer containing 30 mM HEPES, 400 mM KCl, and 0.4% NP-40 and four washes with IP buffer. All washes were performed by rotating for 10 minutes at 4°C. For each replicate, 2-3 IP reactions were pooled in 200 μL of IP buffer. Next, 720 μL of TRI Reagent (Sigma) was added, and the samples were flash-frozen and stored at –80°C until RNA extraction.  RNA was isolated from the samples containing TRI Reagent (mixed with lysate for the total pool of sRNAs or with the GFP-Trap magnetic beads for the WAGO-4 bound sRNAs, as described above). Samples were vortexed at room temperature for 15 minutes. Then, 10% 1-bromo-3-chloropropane was added and the mixture was centrifuged at 12,000 × g for 15 minutes at 4°C. The aqueous phase was separated and mixed with phenol:chloroform:isoamyl alcohol (pH 4.5) in a 1:1 ratio, followed by centrifugation (12,000 × g for 15 minutes at 4°C). The clear aqueous phase was separated and mixed with 20 µg of glycogen, 0.3 M NaOAc (pH 5.2), and an equal volume of isopropyl alcohol. The RNA was precipitated at -20°C for at least 30 minutes. Samples were centrifuged at 16,000 × g for 30 minutes at 4°C, and the pellet was washed twice with 900 µL of 70% ice-cold ethanol (the centrifugation step between the two washes was at 16,000 × g for 10 minutes at 4°C). The pellet was air-dried at room temperature for 10 minutes and resuspended in 11 µL of nuclease-free water. The RNA concentration was measure using Nanodrop and up to 4 µg was used for the 5′ polyphosphatase reaction (Manufacturer). The reaction was incubated for 30 min at 37 °C and RNA was extracted using phenol:chloroform:isoamyl alcohol as described above. The air-dried pellet was resuspended with 6-7 µL nuclease free water and was used for the library preparation.
Small RNA libraries were created using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer's instructions. Starting material included 1 μg of total RNA or the entire yield of immunoprecipitated RNA. The resulting DNA libraries were size selected by excising the bands with the size range of ~135–150 bp on 8% PAGE gel (correspond to 16–30 bp RNAs). The DNA was eluted by rotating overnight in 500 μl of DNA Gel Elution buffer at room temperature. Subsequently, the DNA library was precipitated with 20 μg of glycogen 0.3 M sodium acetate (pH 5.2), and an equal volume of isopropyl alcohol; pellets were washed and dried as previously described. They were resuspended in 12 μl of nuclease free water and quantified using a Qubit HS DNA kit (Thermo Fisher). sRNA libraries were pooled in equal amounts and sequenced on Illumina Miniseq and Novaseq 6000.

treatment_protocol: Worms were washed three times with M9 buffer and once with Milli-Q water. The pellet was resuspended in RIPA buffer (Sigma) and flash-frozen by dropping it into liquid nitrogen.

value: whole worm

tag: strain

tag: genotype

value: glh-1(allele50[glh-1F>A]) I; glh-4(allele16[glh-4F>A]) I; glh-2(allele49[glh-2 delFG]) I; wago-4(gg620[3xflag::gfp::wago-4]) II

tag: temperature

tag: developmental stage

value: young adult

tag: batch

value: B


title: mAT-MSC VAT_5+11

city: Prague

first: Yusuf

middle: Caglar

last: Odabasi

state: Vestec

address: Prumyslova 595

department: BIOCEV

country: Czech Republic

institute: IBT

description:
Library name: 5+11 HFD_A
5_11_HFD

data_processing:
The quality of raw sequencing reads was evaluated with FastQC v0.12.1 and potential contamination was assessed using FastQ_Screen v0.15.3.
Low-quality reads and adaptors were removed with TrimmomaticSE v0.36 (2), employing the parameters ILLUMINACLIP:/storage/abaffyp/Adapters/Lexogen_quantseq2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Ribosomal and mitochondrial reads were filtered out using SortMeRNA v2.1b.
Aligned reads were converted into BAM files with STAR v2.7.10b, referencing the Mus musculus genome version GRCm38.
Final count tables were generated using the Python script htseq-count v0.11.3, with the annotation file genecode.vM8.gtf and the parameter -m union.
Assembly: Mus musculus genome version GRCm38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Mus musculus

source_name: Adipose

extract_protocol:
RNA integrity was assessed using a Fragment Analyzer system with the RNA Fragment Kit (Agilent Technologies). All samples had an RNA quality number (RQN) greater than 7.
Sequencing libraries were prepared from 30 ng of total RNA using the QuantSeq 3´ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s protocol. The libraries were quantified with the Qubit dsDNA assay kit and Qubit 2 fluorometer (Thermo Fisher Scientific), and their quality was evaluated using a Fragment Analyzer system with the NGS Fragment Kit (Agilent Technologies). Sequencing was performed on a NovaSeq X Plus Sequencing System using the NovaSeq™ X Series 25B Reagent Kit (300 Cyc) using one lane in 2 × 157 bp mode, generating an average of 120 million reads per sample. Only read1 were used for analysis.

value: Adipose

tag: Sex

value: male

value: Ctrl

value: no


title: scRNA-seq using PB10X - pool 3 - gene expression of Homo Sapiens: jurkat cells

description:
Library name: PB10X_GeneExpression_Jurkat_Pool3
The processed files given here are the result of the combined analysis of pool 1,2,3 and 5.

library_source: transcriptomic single cell


title: mAT-MSC VAT_14+17

description:
Library name: 14+17 HFD_A
14_17_HFD


title: mBMSC_25+27

description:
Library name: 25+27 HFD + Gln_B
25_27_HFD

source_name: Bone Marrow

value: Bone Marrow

value: Glutamine


title: scRNA-seq using PB10X - pool 2 - gene expression of Homo Sapiens: jurkat cells

description:
Library name: PB10X_GeneExpression_Jurkat_Pool2
The processed files given here are the result of the combined analysis of pool 1,2,3 and 5.


title: mAT-MSC VAT_1+3

description:
Library name: 1+3 HFD_A
1_3_HFD


title: scRNA-seq using PB10X - pool 1 - gene expression of Homo Sapiens: jurkat cells

description:
Library name: PB10X_GeneExpression_Jurkat_Pool1
The processed files given here are the result of the combined analysis of pool 1,2,3 and 5.


title: SS142 20°C Input 3

description:
Library name: 47_R6_20d_142in
Input3
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv
20d_142_22G_allBiotypes_count_matrix.csv


title: FFPE  Relapse Patient2

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

description: Library name: FFPE_Relapse_Patient2

library_source: genomic single cell

data_processing:
The scFFPE-ATAC was debarcoded using https://github.com/pengweixing/scFFPE/fastq_debarcoding.allow_mismatch.v3.1.py
Fastq were mapped to hg38 or mm10 using bwa mem
The mapped data were sort and filtered using samtools
The single cell data were processed using the pipeline from https://github.com/pengweixing/scFFPE/tree/main/Snakemake
Assembly: hg38 and mm10
Supplementary files format and content: fragments for downsteream data analysis

molecule: genomic DNA

source_name: lymphoma

extract_protocol:
Tagmentation and combinatorial indexing via ligation
Before tagmentation, 50,000 purified FFPE single-cell nuclei were centrifuged at 2,000 g for 5 minutes at 4°C and resuspended in 0.1% lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630). The nuclei were then centrifuged again at 2,000 g for 5–10 minutes at 4°C. The nuclei pellet was resuspended in 95 μl of 1× tagmentation buffer (10 mM Tris-HCl, pH 7.5, 5 mM MgCl₂, 10% dimethylformamide, and dH₂O), and 5 μl of barcoded FFPE-Tn5 transposase (2 mM) was added per sample. The reaction mix was gently mixed and incubated at 37°C for 30 minutes at 400 rpm. The reaction was stopped by directly adding EDTA to a final concentration of 30 mM to each sample. All samples were then pooled and centrifuged to obtain a nuclei pellet. Next, three rounds of ligation were performed using the split-and-pool technique in a 96-well plate, with each well containing a ramped specific linker and ligation barcode. Detailed DNA sequences are provided in Supplementary Table 1. In brief, the ligation process was performed as follows: the pooled nuclei were resuspended in 1 mL of 1× NEBuffer 3.1 and mixed with the ligation mix (100 μL of 10× NEBuffer 3.1, 22 μL of 50 mg/mL BSA, 500 μL of 10× T4 DNA ligase buffer, 2,278 μL of ultrapure water, and 100 μL of T4 DNA ligase). A total of 40 μL of this mix was transferred per well, containing 10 μL of the ramped Ligation1 mixture, and incubated at 37°C for 30 minutes at 400 rpm. Then, 10 μL of Blocker-Ligation1 solution (2.64 μL of 100 μM Blocker-Ligation1, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water) was added per well, and the reactions were incubated at 37°C for 20 minutes at 400 rpm. The samples were then pooled into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. The second and third ligation reactions were performed identically to the first. After the second and third ligations, blocking reactions were carried out using: 10 μL of Blocker-Ligation2 solution per well (2.64 μL of 100 μM Blocker-Ligation2, 2.50 μL of 10× T4 ligation buffer, and 4.86 μL of ultrapure water); 7.5 μL of Terminator_Ligation3 solution per well (2.64 μL of 100 μM Terminator_Ligation3, 2.50 μL of 0.5 M EDTA, and 2.36 μL of ultrapure water) for reaction termination. After gently mixing, the samples were pooled again into a 15 mL tube pre-coated with 0.5% BSA, followed by centrifugation at 1,500 g for 10 minutes at 4°C. After the third ligation, each nucleus acquired a unique combination of barcodes. Finally, the pellet was resuspended in PBS, nuclei were counted, and the sample was split into tubes containing 30,000–80,000 nuclei for reverse crosslinking.
Reverse-crosslinking, gap filling and in vitro transcription
After the third ligation, reverse cross-linking buffer (50 mM Tris-HCl, pH 8, 250 mM NaCl, 1 mM EDTA, and 1% SDS) and 0.22 mg/mL proteinase K were added to each tube, following previous publications 42, 43. The reaction mixture was incubated in a thermomixer at 1,200 rpm overnight at 65°C. The next day, a second proteinase K digestion was performed at 37°C for 2 hours at 850 rpm to ensure complete protein digestion. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit, following the manufacturer’s instructions. For gap filling, an equal volume of NEBNext High-Fidelity 2X PCR Master Mix was added to the eluted DNA, and the reaction mixture was incubated at 72°C for 8 minutes in a thermal cycler. The sample was then purified using the Qiagen MinElute PCR Purification Kit, following the manufacturer’s instructions. Further DNA purification was carried out using the 1X SPRI beads method to remove fragments shorter than 150 bp. Finally, the DNA was eluted in nuclease-free water. For in vitro transcription (IVT), a T7 RNA synthesis kit (New England Biolabs) was used. The following reagents were mixed:
- 12.4 μL of template DNA
- 2.5 μL of 10X T7 buffer
- 1 μL of DTT
- 2 μL each of ATP, CTP, UTP, and GTP
- 1 μL of T7 mix
- μL of RNase inhibitor (Thermo Fisher Scientific)
The IVT mixture was incubated at 37°C overnight (16 hours), followed by DNase treatment and RNA purification using the ZYMO RNA Purification Kit (RNA Clean & Concentrator-5), according to the manufacturer’s instructions. Finally, RNA was eluted in 20 μL of nuclease-free water. The RNA concentration was measured using NanoDrop, and the sample was either immediately used for DNA library preparation or stored at −80°C for future use.
Single cell FFPE-ATAC DNA library preparation
Single-stranded cDNAs are prepared from 0.5–1 μg of purified IVT transcripts using the FirstStrand_cDNA oligo (DNA oligo sequences are provided in Supplementary Table 1). The reaction mixture (11.25 μL), containing 500ng-1 μg of RNA, 1 μL of 100 μM random octamer primer stock, and 0.25 μL of RNase Inhibitor (20 U/μL), is heated at 70°C for 3 minutes, then immediately cooled on ice. Next, the master mix is added, which consists of:
- 4 μL of 5× First-Strand Buffer
- 2 μL of dNTP Mix
- 2 μL of 100 mM DTT
- 0.25 μL of RNase Inhibitor (20 U/μL)
- 0.5 μL SMART MMLV RT
The reaction is gently mixed and incubated at 42°C for 60 minutes and then at 70°C for 15 minutes. Next, 2.2 μL of 10× RNase H buffer and 0.2 μL of RNase H (5 U/μL) are added to each reaction and incubated at 37°C for 20 minutes. The RNAClean XP beads (1.8X) are used to purify the cDNA reaction mixture, and the cDNA is eluted in Qiagen Elution Buffer. A sequencing library mix is prepared using purified cDNA, NEBNext high-fidelity 2× PCR master mix, and a unique forward (i5) and reverse (i7) primer combination (DNA oligo sequences are provided in Supplementary Table 1). PCR amplification is run with the following cycling program:
- 98°C for 30 seconds
- 12 cycles of:
- 98°C for 20 seconds
- 63°C for 20 seconds
- 72°C for 1 minute
The sample is purified using the Qiagen MinElute PCR Purification Kit and run on a 6% PAGE gel. The gel region corresponding to 250–800 bp is cut, and the gel is made into fine pieces, which are incubated overnight at 55°C in crush-soak buffer (500 mM NaCl, 1 mM EDTA, 0.5% SDS) at 1,200 rpm. The DNA is purified from the gel using Costar spin-X centrifuge tubes and the Zymo ChIP DNA Clean & Concentrator Kit, following the manufacturer's instructions. A high-sensitivity DNA bioanalyzer chip is used to check the DNA size distribution and quantify the DNA concentration of the DNA library. Finally, deep sequencing is performed with NovaSeq  6000 on the mouse and human scFFPE-ATAC samples for single-cell analysis.

value: lymphoma


title: scRNA-seq using Smart-seq3xpress of Homo Sapiens: jurkat cells

description: Library name: SmartSeq3xpress_Jurkat


title: mBMSC_13+15

description:
Library name: 13+15 HFD + Gln_B
13_15_HFD


title: mBMSC_10+12

description:
Library name: 10+12 HFD + Gln_B
10_12_HFD


title: SS142 20°C Input 2

description:
Library name: 46_R5_20d_142in
Input2
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv
20d_142_22G_allBiotypes_count_matrix.csv


title: mBMSC_18+20

description:
Library name: 18+20 HFD + Gln_B
18_20_HFD


title: FFPE  Primary Patient2

description: Library name: FFPE_Primary_Patient2


title: FFPE  Relapse Patient1

description: Library name: FFPE_Relapse_Patient1


title: mBMSC_4+6

description:
Library name: 4+6 HFD + Gln_B
4_6_HFD


title: SS142 20°C Input 1

description:
Library name: 45_R4_20d_142in
Input1
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv
20d_142_22G_allBiotypes_count_matrix.csv


title: mBMSC_23+28

description:
Library name: 23+28 HFD_B
23_28_HFD


title: YY1325 20°C IP 3

description:
Library name: 44_R4_20d_123IP
IP3
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv

value: wago-4(gg620[3xflag::gfp::wago-4]) II


title: FFPE  Primary Patient1

description: Library name: FFPE_Primary_Patient1


title: FFPE  Human Lung tumor core

description: Library name: FFPE  Human_Lung_tumor_core

source_name: Lung

value: Lung


title: SS142 20°C IP 2

description:
Library name: 49_R5_20d_142IP
IP2
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv


title: FFPE  Human Lung  invasive edge

description: Library name: FFPE_Human_Lung_invasive_edge


title: mBMSC_5+11

description:
Library name: 5+11 HFD_B
5_11_HFD


title: YY1325 20°C IP 1

description:
Library name: 21_R2_20d_123IP
IP1
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv


title: SS142 20°C IP 1

description:
Library name: 48_R4_20d_142IP
IP1
20d_142_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv


title: mBMSC_14+17

description:
Library name: 14+17 HFD_B
14_17_HFD


title: FFPE_Human Lymph Node 1to4

description: Library name: FFPE_Human_Lymph_Node_patients_1to4

source_name: Lymphnode

value: Lymphnode


title: Blastema_head_5dpa_ST_C_well

status: Public on Oct 13 2025

city: kaifeng

first: Hao

last: Wang

state: Hainan

address: Jinming

country: China

institute: Henan University

description:
Library name: ST_5dpa_C_well
Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate gene expression matrix. The matrices were loaded into Seurat for future analyses.
Assembly: DJ_genome_v1
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_iducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: tissue_positions.csv: list of spital barcodes and the coordinates specifying spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Library strategy: Spatial Transcriptomics

organism: Dugesia japonica

source_name: Head blastema

extract_protocol:
ST-seq: Fresh frozen animals at 5 dpa of head were embedded in OCT, slices of 8 μm thickness were obtained by cryosectioning from anterior to posterior. Slices were selected at intervals of two and placed onto the slide array surfaces. The slices were fixed, and H&E stained.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gen expression Slides & Reagent kit according to manufacturer's construction.

value: Head blastema

value: WT


title: mBMSC_1+3

description:
Library name: 1+3 HFD_B
1_3_HFD


title: Blastema_head_5dpa_ST_B_well

description:
Library name: ST_5dpa_B_well
Fresh frozen Spatial transcriptome sequencing


title: Whole pancreatic islets, male, PDX1 P33T/P33T, rep 1

city: Neuherberg

first: Gerhard

last: Przemeck

address: Ingolstaedter Landstr..1

country: Germany

institute: Helmholtz Munich

description: Library name: P33T_M1

data_processing:
Read trimming (fastp software v0.23.1), Parameters Used: --qualified_quality_phred 5 \ --unqualified_percent_limit 50 \ --n_base_limit 15 \ --overlap_len_require 30 \ --overlap_diff_limit 1 \ --overlap_diff_percent_limit 10 \ --length_required 150 \ --length_limit 150 \ --trim_poly_g \ --thread 1
Reference genome GRCm39/mm39 (mus musculus), alignment with Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Normalization with DESeq2 v1.20.0
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5
Supplementary files format and content: tab-delimited file with linear normalized counts

source_name: pancreatric islets, whole

growth_protocol: All mice were treated in compliance with the institutional guidelines approved by the animal welfare and use committee of the government of Upper Bavaria. They were housed in standard cages in a specific pathogen-free facility, maintained on a 12-hour light/dark cycle, and given unrestricted access to food and water.

extract_protocol:
RNeasy Mini kit (Qiagen, Hilden, Germany)
Novogene NGS  RNA Library Prep Set (PT042)

treatment_protocol: No treatment

value: pancreatric islets, whole

tag: age

value: 14 weeks

value: PDX1 P33T/P33T


title: Whole pancreatic islets, male, PDX1 P33T/P33T, rep 5

description: Library name: P33T_M6


title: Whole pancreatic islets, male, PDX1 P33T/P33T, rep 4

description: Library name: P33T_M5


title: Whole pancreatic islets, male, PDX1 P33T/P33T, rep 3

description: Library name: P33T_M4


title: Whole pancreatic islets, male, PDX1 P33T/P33T, rep 2

description: Library name: P33T_M2


title: YY1325 20°C Input 3

description:
Library name: 43_R4_20d_123in
Input3
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv

value: whole worm

value: young adult


title: Blastema_head_5dpa_ST_D_well

description:
Library name: ST_5dpa_D_well
Fresh frozen Spatial transcriptome sequencing


title: Whole pancreatic islets, male, wildtype, rep 5

description: Library name: WT_M5

value: wildtype


title: Whole pancreatic islets, male, wildtype, rep 4

description: Library name: WT_M4

value: male


title: YY1325 20°C IP 2

description:
Library name: 33_R3_20d_123IP
IP2
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv

value: B


title: Whole pancreatic islets, male, wildtype, rep 6

description: Library name: WT_M6


title: Whole pancreatic islets, male, wildtype, rep 2

description: Library name: WT_M2


title: Whole pancreatic islets, male, wildtype, rep 3

description: Library name: WT_M3


title: Whole pancreatic islets, male, wildtype, rep 1

description: Library name: WT_M1


title: WT_Gly1

city: Qingdao 266237

first: Kexuan

last: Ma

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description:
Library name: sample15
WTGly1

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

organism: Penicillium oxalicum

source_name: Penicillium oxalicum

growth_protocol: The germination of Penicillium oxalicum were inoculated in modifeid vogel's culture medium with 2% glucose as carbon resource for 24 h at 30℃ as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s medium with 2% glucose, 2% glycerol or 1% bran + 1% microcrystalline cellulose as carbon resources for 18h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 50bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Penicillium oxalicum

value: 114-2(wild type)

value: Modified Mendal’s medium with 2% glycerol as carbon resource


title: WT_G3

description:
Library name: sample14
WTG3

value: Modified Mendal’s medium with 2% glucose as carbon resource


title: WT_G2

description:
Library name: sample13
WTG2


title: WT_Gly2

description:
Library name: sample16
WTGly2


title: WT_G1

description:
Library name: sample12
WTG1


title: WT_CW1

description:
Library name: sample10
WTCW1

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: WT_CW3

description:
Library name: sample11
WTCW3


title: Con7-AG3

description:
Library name: sample6
Con7-AG3

value: con7 destruction strain


title: Con7-AG1

description:
Library name: sample4
Con7-AG1


title: ApfEIN3-IP-set1

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

library_source: genomic

data_processing:
*library strategy: DAP-seq
Trimmomatic software were used to remove adapter and low quality reads.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak.
Reads distributions (from bigwig) across gene are presented as an average plot (average of reads signals across all genes). The deeptools tool is used for this analysis.
Assembly: Alternanthera philoxeroides
Supplementary files format and content: bigwig, narrowpeak

organism: Alternanthera philoxeroides

source_name: shoot

growth_protocol: Alternanthera philoxeroides grown for 4 weeks under normal conditions.

extract_protocol:
ApfEIN3 was fused with Halo-TF and expressed using a TNT SP6 Coupled Wheat Germ Extract System (Promega).
For DNA library construction, genomic DNA was extracted using plant tissue by Hi-Pure Plant Genomic DNA Kit and quantified by Qubit Fluorometer and examined by agarose gel electrophoresis.

value: shoot

value: wild type


title: Blastema_head_5dpa_ST_A_well

description:
Library name: ST_5dpa_A_well
Fresh frozen Spatial transcriptome sequencing

value: Head blastema

value: WT


title: Con7-AG2

description:
Library name: sample5
Con7-AG2


title: Con7-ACW3

description:
Library name: sample3
Con7-ACW3


title: Con7-ACW2

description:
Library name: sample2
Con7-ACW2


title: Bulk RNA seq, heart, LPS day 1, rep3

city: St. Louis

first: Douglas

last: Mann

state: MO

address: 660 S Euclid Ave

country: USA

institute: Washington University in St. Louis

description: Library name: heart_LPS_day1_rep3

data_processing:
Basecalls and demultiplexing were performed with Illumina's bcl2fastq2 software. RNA sequencing reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software. All gene counts were then imported into the R/Bioconductor package EdgeR, and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and those not expressed at more than one count per million in at least n – 1 samples (where n is the smallest group size) were excluded from further analysis. The TMM size factors and matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples, and the count matrix was transformed to moderated log2 counts-per-million with Limma's voomWithQualityWeights.
Assembly: mm10
Supplementary files format and content: read counts per sample: .quant.genes.sf

source_name: Heart

extract_protocol:
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Germantown, MD) according to the manufacturer's instructions. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies).
Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. mRNA was fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

treatment_protocol: Female 10-wk old wild-type (C57BL/6J) mice were treated with lipopolysaccharide (LPS; 2.5 mg/kg) or isoproterenol (ISO; 300 mg/kg). Mice were then euthanized at baseline (no treatment) and at 1 and 7 days later (n=3-4/group) with hearts collected for bulk RNA sequencing.

value: Heart

value: Various

value: Wild-type

value: LPS

tag: timepoint

value: LPS day 1


title: Bulk RNA seq, heart, LPS day 1, rep4

description: Library name: heart_LPS_day1_rep4


title: Bulk RNA seq, heart, LPS day 7, rep4

description: Library name: heart_LPS_day7_rep4

value: LPS day 7


title: Bulk RNA seq, heart, LPS day 7, rep1

description: Library name: heart_LPS_day7_rep1


title: Bulk RNA seq, heart, LPS day 7, rep2

description: Library name: heart_LPS_day7_rep2


title: Bulk RNA seq, heart, LPS day 1, rep2

description: Library name: heart_LPS_day1_rep2


title: Bulk RNA seq, heart, LPS day 1, rep1

description: Library name: heart_LPS_day1_rep1


title: Bulk RNA seq, heart, LPS baseline, rep4

description: Library name: heart_LPS_baseline_rep4

value: LPS baseline


title: Bulk RNA seq, heart, ISO day 7, rep4

description: Library name: heart_ISO_day7_rep4

value: ISO

value: ISO day 7


title: Bulk RNA seq, heart, ISO day 7, rep3

description: Library name: heart_ISO_day7_rep3


title: Bulk RNA seq, heart, LPS day 7, rep3

description: Library name: heart_LPS_day7_rep3


title: Bulk RNA seq, heart, LPS baseline, rep3

description: Library name: heart_LPS_baseline_rep3


title: Bulk RNA seq, heart, ISO day 7, rep1

description: Library name: heart_ISO_day7_rep1


title: Bulk RNA seq, heart, ISO day 1, rep2

description: Library name: heart_ISO_day1_rep2

value: ISO day 1


title: Bulk RNA seq, heart, LPS baseline, rep1

description: Library name: heart_LPS_baseline_rep1


title: Bulk RNA seq, heart, ISO day 1, rep1

description: Library name: heart_ISO_day1_rep1


title: Bulk RNA seq, heart, ISO baseline, rep3

description: Library name: heart_ISO_baseline_rep3

value: ISO baseline


title: Bulk RNA seq, heart, ISO day 7, rep2

description: Library name: heart_ISO_day7_rep2


title: Bulk RNA seq, heart, ISO baseline, rep4

description: Library name: heart_ISO_baseline_rep4


title: Bulk RNA seq, heart, ISO baseline, rep1

description: Library name: heart_ISO_baseline_rep1


title: Bulk RNA seq, heart, ISO baseline, rep2

description: Library name: heart_ISO_baseline_rep2


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 7

city: Geelong

first: Laurence

middle: James

last: Croft

state: Victoria

address: 75 Pigdons Road

department: School of Medicine

institute: Deakin University

description: Library name: 831-Fra1

data_processing:
Sequence reads were quality filtered using fastp and mapped to the Mus musculus genome (GRCm38.99) using two pass mapping in STAR
Reads counts were aggregated to gene counts using STAR in built quantification.
Read counts were converted to log2CPMs, quantile-normalised and precision weighted with the limma voom function
Log2CPM values were then converted to log2RPKM (reads per kilo exonic bases per million mapped reads) values
Gene set enrichment analysis was performed using GSEA v4.1.0 software from the Broad institute. The data was analysed against the MSigDB “HALLMARK” gene set signatures and a fetal intestine signature
Assembly: Mus musculus genome (GRCm38.99)

source_name: intestinal epithelial tissue

growth_protocol: Mice with the following genotypes were generated: (1) BrafV637E/+;Vil-CreERT2/+ (denoted Brafmut), (2) BrafV637E/+;Vil-CreERT2/+;Fosl1lox/lox (denoted Fra1), (3) Tet-o-Fosl1;Vil-CreERT2/+ (denoted Fra1Tg)

extract_protocol:
RNA was isolated from intestinal epithelial cells and tumours using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen) and its concentration and quality assessed using the TapeStation D1K TapeScreen assay (Agilent).
cDNA libraries were prepared using the TruSeq RNA Sample Prep Kit (v2) (Illumina Inc, San Diego, USA) or the stranded RNA library preparation kit with rRNA depletion (Illumina) and sequenced on a NovaSeq 6000 sequencer (100 paired end single reads).

treatment_protocol: 6-week-old mice were treated with 5 mg of tamoxifen diluted in sunflower seed oil from by oral gavage for 2 consecutive days. Control (Brafmut) mice were given the same dose regimen of sunflower oil (S. oil) solution. To induce the tetracycline-switchable Fosl1 transgene (Tet-o-Fosl1), mice were fed chow containing doxycycline at a concentration of 2000 mg/kg starting 1 week after tamoxifen treatment.

value: intestinal epithelial tissue

value: 5 mg of tamoxifen diluted in sunflower seed oil by oral gavage for 2 consecutive days


title: Con7-ACW1

description:
Library name: sample1
Con7-ACW1

value: Penicillium oxalicum

value: con7 destruction strain

value: Modified Mendal’s medium with 1percent bran + 1percent microcrystalline cellulose as carbon resource


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 6

description: Library name: 830-Fra1


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 5

description: Library name: 674-Fra1


title: Bulk RNA seq, heart, LPS baseline, rep2

description: Library name: heart_LPS_baseline_rep2


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 4

description: Library name: 541-Braf

source_name: intestinal epithelial tissue adenoma

value: intestinal epithelial tissue adenoma


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 3

description: Library name: 474-Fra1


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 2

description: Library name: 378-Fra1


title: control normal tissue 9

description: Library name: 1285-S-oil

value: sunflower seed oil by oral gavage for 2 consecutive days


title: control normal tissue 8

description: Library name: 1266-S-oil


title: adenoma from BrafV637E mutant mouse

description: Library name: 303-Braf


title: control normal tissue 7

description: Library name: 1213-S-oil


title: adenoma from BrafV637E mutant mouse 7

description: Library name: 1082-Braf


title: Bulk RNA seq, heart, ISO day 1, rep3

description: Library name: heart_ISO_day1_rep3

value: Heart

value: Various


title: control normal tissue 4

description: Library name: 1056-S-oil


title: control normal tissue 6

description: Library name: 1085-S-oil


title: adenoma from BrafV637E:Fosl1-/- mutant mouse 1

description: Library name: 377-Fra1


title: adenoma from BrafV637E mutant mouse 5

description: Library name: 1054-Braf


title: adenoma from FTg-ON transgene mutant mouse 3

description: Library name: 606Fra1Tg

value: FTg-ON

value: fed chow containing doxycycline at a concentration of 2000 mg/kg


title: adenoma from FTg-ON transgene mutant mouse 1

description: Library name: 593Fra1Tg


title: control normal tissue 5

description: Library name: 1066-S-oil


title: adenoma from BrafV637E mutant mouse 3

description: Library name: 343Brafmut


title: adenoma from BrafV637E mutant mouse 2

description: Library name: 335Brafmut


title: mouse pancreatic ductal cells, Pten KO, Day21, No13

city: Kawaracho

first: Kei

last: Iimori

state: Kyoto

department: Gastroenterology

country: Japan

institute: Kyoto University Graduate School of Medicine

description:
Library name: HPd21duct13
Column name in estimated_counts:HPd21duct13

data_processing:
Adaptors and low-quality bases were trimmed from the reads using Trimmomatic (version 0.39) with default parameters.
Reads were mapped to the Mus musculus reference genome build mm10 using STAR (version 2.7.3a) and counted using RNA-seq by Expectation-Maximization (version 1.3.1).
Assembly: mm10
Supplementary files format and content: RSEM v1.3.1 expected_count (EM algorithm, lengthScaledTPM = FALSE)

source_name: pancreatic ductal cell

growth_protocol: Mice were maintained under specific pathogen-free conditions. At six weeks of age, oral tamoxifen was administered to induce Cre-mediated recombination for the conditional knockout of Pten and/or Brg1.

extract_protocol:
The pancreases from three HP and three HPB mice were harvested 3 weeks after tamoxifen administration. Each pancreatic sample was digested and pancreatic ductal cells were isolated with cell-specific Dolichos biflorus agglutinin lectin labelling, followed by magnetic bead separation. Total RNA from isolated pancreatic ductal cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany)
RNA libralies for RNA-seq were prepared with SMARTer Ultra Low Input RNA Kit following manufacture's protocols.

value: pancreatic ductal cell

value: Pten KO

value: No


title: control normal tissue 3

description: Library name: 205S-oil


title: Telogen HFSC_H2AK119ub Cut&Run-2

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Avenue

department: Department of Genetics

institute: Albert Einstein College of Medicine

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) and aligned to the mouse reference genome (mm10) using Bowtie2 (v.2.2.5). Deduplicated reads were removed using samtools (v.1.14). Peaks were identified using a sliding window method to determine genomic regions with >1.5 mapping read enrichment over IgG control and adjusted p < 0.05. The BAM file for each replicate was converted to a TDF file for Integrative Genomics Viewer (IGV) software.
Assembly: mm10
Supplementary files format and content: TDF, tag density file
Library strategy: Cut&Run

source_name: skin

extract_protocol:
120,000 FACS-enriched quiescent HFSCs were isolated from the back skin of P55 C57BL/6 wildtype mice. Cut&Run was conducted using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, 14-1048) following a previously described protocol optimized for FACS-isolated epidermal keratinocytes.
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) and NEBNext Multiplex Oligos (NEB, E6609L) for Illumina following the manufacturer’s instructions. PCR-amplified libraries were purified using 1 X ratio of Agencourt AMPure-XP Beads (Beckman) and eluted in 15μl TE buffer.

value: skin

value: Hair follicle stem cells

tag: cut&run antibody

value: H2AK119ub (Cell Signalling,8240S)


title: Telogen HFSC_H2AK119ub Cut&Run-1


title: IgG

value: IgG (Epicypher, 13-0042)


title: PRC1-null HFSC H2AK119ub Cut&Run-2

description: Library name: KO_H2A2

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) and aligned to the mouse reference genome (mm10) using Bowtie2 (v.2.2.5). Deduplicated reads were removed using samtools (v.1.14). Peaks were identified using a sliding window method to determine genomic regions with >1.5 mapping read enrichment over IgG control and adjusted p < 0.05. The BAM file for each replicate was converted to a TDF file for Integrative Genomics Viewer (IGV) software.
Assembly: mm10
Supplementary files format and content: TDF, tag density file
Library strategy: CUT&Run


title: control normal tissue 2

description: Library name: 181S-oil

value: intestinal epithelial tissue


title: control normal tissue 1

description: Library name: 171S-oil


title: adenoma from BrafV637E mutant mouse 1

description: Library name: 177Brafmut


title: adenoma from BrafV637E mutant mouse 6

description: Library name: 1043-Braf


title: mouse pancreatic ductal cells, Pten KO, Day21, No12

description:
Library name: HPd21duct12
Column name in estimated_counts:HPd21duct12


title: P75 PRC1 i2KO-3

data_processing:
Paired-end RNA-seq reads were aligned to the mouse reference genome (mm39) using STAR aligner (v2.7.9a). Gene expression levels (from the Ensembl annotation v105, both coding and noncoding) were quantified using the RSEM software (v1.3.3) to estimate counts and TPMs (transcript per million). Differential expression analysis was performed for protein-coding genes using DESeq2 (v1.38.2) after excluding genes with TPM < 1 in all samples.
Assembly: mm39
Supplementary files format and content: csv text file for expression counts and TPMs

extract_protocol:
A total of 50,000 FACS-purified cells were collected directly into the RLT Plus buffer (QIAGEN, 1053393), and RNA was purified from these sorted cells with the RNeasy Plus Micro Kit (QIAGEN, 74034) and DNase1 treatment (QIAGEN, 79254) according to the manufacturer’s instructions.
For RNA-seq library preparation, sample quality was measured using an Agilent Bioanalyzer. Only samples with RNA integrity numbers of >8 were used for library preparation. For generating RNA-seq libraries, 50 ng of total RNA was subjected to polyadenylate selection using Universal Plus mRNA-Seq with NuQuant (TECAN, 0520-A01). Following elution, mRNA was subjected to fragmentation at 94°C for 8 min. First strand, second-strand cDNA synthesis, end repair, adapter ligation, and amplification were carried out by following the manufacturer’s instructions. Libraries were sequenced on the Illumina Hiseq Platform.

treatment_protocol: Mice were topically treated daily  with 1% RU-486 for 10 consecutive days.

value: K15-CrePR1:Ring1a-/-, Ring1bflox/flox


title: mouse pancreatic ductal cells, Pten and Brg1 KO, Day21, No10

description:
Library name: HPBd21duct10
Column name in estimated_counts:HPBd21duct10

value: Pten and Brg1 KO


title: adenoma from BrafV637E mutant mouse 4

description: Library name: 1041-Braf


title: mouse pancreatic ductal cells, Pten KO, Day21, No11

description:
Library name: HPd21duct11
Column name in estimated_counts:HPd21duct11


title: adenoma from FTg-ON transgene mutant mouse 2

description: Library name: 603Fra1Tg


title: P75 Control-1

value: Ring1a-/-, Ring1bflox/flox


title: P75 PRC1 i2KO-1


title: mouse pancreatic ductal cells, Pten and Brg1 KO, Day21, No6

description:
Library name: HPBd21duct6
Column name in estimated_counts:HPBd21duct6


title: P70 PRC1 i2KO-3

data_processing:
Paired-end RNA-seq reads were aligned to the mouse reference genome (mm39) using STAR aligner (v2.7.9a). Gene expression levels (from the Ensembl annotation v105, both coding and noncoding) were quantified using the RSEM software (v1.3.3) to estimate counts and TPMs (transcript per million). Differential expression analysis was performed for protein-coding genes using DESeq2 (v1.38.2) after excluding genes with TPM < 1 in all samples.
Assembly: mm39
Supplementary files format and content: tab delimited text file for expression counts and TPMs


title: 12week Hetero Heart 3

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

institute: Hyogo Medical University

description: Library name: Sample_Ir11010

data_processing:
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Cutadapt v.1.8. The trimmed reads were quantified in mapping-based mode using Salmon v.1.2.1 , based on the Mus musculus GRCm39 reference transcripts available via ENSEMBL (Release 110). After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using TCC , a comparison of gene expression between each genotype group samples was performed. The exact test was used to generate q values and log2 fold changes. Genes with a q value < 0.05 were called as differentially expressed genes. Differentially expressed genes were then analyzed using GeneSpring 14.9.1 (Agilent) to group the large sets of upregulated and downregulated genes by gene ontology (GO) terms. In addition, pathway analysis through Wikipathways was also performed using GeneSpring. Splicing analysis with Percentage Spliced In (PSI) was performed as described previously .
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include PSI values for each Sample

extract_protocol:
total RNAs from mouse hearts at the ages of 12 weeks were extracted using the RNeasy Plus Universal Mini Kit (Qiagen). Nine representative libraries were prepared for the three groups (Wild-type n=3, Heterozygote type n=3 and Homozygote type n=3) by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). The sequencing libraries were clustered on a flow cell. After clustering, the flow cell was loaded on the Illumina NovaSeq instrument 6000 (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Heterozygote


title: 12week Wild Heart 3

description: Library name: Sample_Ir11011

value: Wildtype


title: mouse pancreatic ductal cells, Pten and Brg1 KO, Day21, No9

description:
Library name: HPBd21duct9
Column name in estimated_counts:HPBd21duct9


title: 12week Wild Heart 2

description: Library name: Sample_Ir11009

value: Heart


title: PRC1-null HFSC H2AK119ub Cut&Run-1

description: Library name: KO_H2A1


title: P70 PRC1 i2KO-2


title: P70 PRC1 i2KO-1


title: 12week Hetero Heart 2

description: Library name: Sample_Ir10990


title: P70 Control-3


title: 12week Homo Heart 2

description: Library name: Sample_Ir10992

value: Homoozygote


title: 12week Homo Heart 3

description: Library name: Sample_Ir10993


title: 12week Hetero Heart 1

description: Library name: Sample_Ir10989


title: OE3

city: Shenzhen

first: Zhihua

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
Novogene used Illumina platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT2
Assembly: NCBI, Mus_musculus , GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tissue

growth_protocol: All animals were housed in a constant environment (room temperature, 24 ± 3 °C; room humidity,55 ± 5%) with a standard 12-h light/12-h dark cycle. Mice were fed with normal chow and with free access to water.

extract_protocol:
RNA of NRVMs extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Novogene.

treatment_protocol: A total of thirty 14-month-old male WT mice were randomly divided into two groups as the following: (1) mice injected with AAV9-shRNA-Fabp4 by tail vein and sWAT in situ injection with a dose of 4×10^11viral genomes, n=15; (2) mice injected with AAV9-shRNA-Neg with the same way and same amount, n=15. The above animals were kept until 20-month-old after AAV injection for sundry experiments. A group of 8-week-old WT mice were regarded as young control group (n=15).

value: liver tissue

value: old


title: 12week Homo Heart 1

description: Library name: Sample_Ir10988


title: P75 PRC1 i2KO-2


title: OE1


title: OC5


title: 12week Wild Heart 1

description: Library name: Sample_Ir10986


title: OC2


title: Y5

value: Young


title: OC1


title: Lymph node metastasis BMPC mouse 5

city: Baltimore

first: Michael

last: Rubenstein

address: 733 N Broadway

institute: Johns Hopkins University School of Medicine

description:
Library name: BMPC Metastasis 1
Column name in NormalizedCounts.csv: BMPC_Met1

data_processing:
Illumina’s CASAVA (version 1.8.4) was used to convert BCL files to FASTQ files. RSEM (version 1.3.0) was used to align reads to the mm10 reference genome and calculate transcript expression levels. Gene counts from RSEM for each sample were used to generate a count matrix for normalization and analysis using the R package DESeq2 (version 1.30.0).
Assembly: mm10
Supplementary files format and content: csv file including normalized counts for each sample

source_name: Lymph node metastasis

extract_protocol:
RNA was purified from the intervening sections using the AllPrep DNA/RNA Kit (Qiagen) per the manufacturer’s recommended protocol. Tissue was homogenized in Buffer RLT (from AllPrep kit) using gentleMACS M tubes (Miltenyi Biotec) and dissociated using program RNA_02, and subsequently passaged through a Qiashredder column (Qiagen). Ribosomal RNA depletion was performed using the Ribo-Zero Mouse rRNA Removal kit using total RNA (500 ng) as input (Illumina).
RNA-seq libraries were prepared using TruSeq Stranded Total RNA Library Kit (Illumina), and paired-end sequenced in 2 x 150-bp format on the NovaSeq6000 S4 platform (Illumina).

value: Lymph node metastasis

value: BMPC

value: 20 weeks


title: Primary prostate tumor BMPC mouse 5

description:
Library name: BMPC Primary 2
Column name in NormalizedCounts.csv: BMPC_Pri2

source_name: Primary tumor

value: Primary tumor


title: Y1


title: Lymph node metastasis BMPC mouse 6

description:
Library name: BMPC Metastasis 2
Column name in NormalizedCounts.csv: BMPC_Met2

value: 18 weeks


title: Anterior prostate BMPC mouse 3

description:
Library name: BMPC PIN 3
Column name in NormalizedCounts.csv: BMPC12wPIN3

source_name: Anterior prostate

value: Anterior prostate

value: 12 weeks


title: Anterior prostate BMPC mouse 2

description:
Library name: BMPC PIN 2
Column name in NormalizedCounts.csv: BMPC12wPIN2


title: P70 Control-2

value: skin

value: Hair follicle stem cells


title: daf10_PA14_2

city: Tianjin

first: Ming

last: Lei

address: Weijin Road, Heping District, Tianjin

institute: Tianjin University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence,then mapped to the C. elegans genome sequence using Hisat2 v2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of three biological replicates per condition was performed using the DESeq R package (1.18.0).
Assembly: WBcel2
Supplementary files format and content: tab-delimited text files include FPKM values for all Samples.

source_name: entire worm

growth_protocol: Synchronized L1 worms were placed onto NGM plates seeded with OP50 and grown at 20°C till L4 stage.

extract_protocol:
Worms were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01-01). Total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-10)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: L4 stage worms were collected and washed with M9 solution before being transferred to modified NGM plates containing OP50 or PA14 for 24 h at 25°C.

value: entire worm

value: PA14 infection


title: P75 Control-3

value: Ring1a-/-, Ring1bflox/flox


title: OE6


title: Primary prostate tumor BMPC mouse 4

description:
Library name: BMPC Primary 1
Column name in NormalizedCounts.csv: BMPC_Pri1

value: 25 weeks


title: daf10_PA14_3


title: daf10_PA14_1


title: daf10_OP50_3

value: OP50 feed


title: che3_PA14_3


title: daf10_OP50_1


title: Lymph node metastasis BMPC mouse 7

description:
Library name: BMPC Metastasis 3
Column name in NormalizedCounts.csv: BMPC_Met3

value: 26 weeks


title: Anterior prostate Hoxb1313-Cre|PtenFl/Fl mouse 1

description:
Library name: PTEN-Null Pin 1
Column name in NormalizedCounts.csv: PTEN1


title: Anterior prostate Hoxb1313-Cre|PtenFl/Fl mouse 2

description:
Library name: PTEN-Null Pin 2
Column name in NormalizedCounts.csv: PTEN2

value: 27 weeks


title: Anterior prostate Hoxb1313-Cre|PtenFl/Fl mouse 3

description:
Library name: PTEN-Null Pin 3
Column name in NormalizedCounts.csv: PTEN3


title: daf10_OP50_2


title: che3_PA14_2


title: che3_PA14_1


title: Y4

value: liver tissue

value: Young


title: che3_OP50_3


title: Primary prostate tumor BMPC mouse 6

description:
Library name: BMPC Primary 3
Column name in NormalizedCounts.csv: BMPC_Pri3

value: BMPC


title: Ventral prostate Hoxb13-MYC mouse 2

description:
Library name: MYC PIN 2
Column name in NormalizedCounts.csv: MYC2

source_name: Ventral prostate

value: Ventral prostate

value: 15 weeks


title: Ventral prostate Hoxb13-MYC mouse 1

description:
Library name: MYC PIN 1
Column name in NormalizedCounts.csv: MYC1

value: 10 weeks


title: Ventral prostate Hoxb13-MYC mouse 3

description:
Library name: MYC PIN 3
Column name in NormalizedCounts.csv: MYC3

value: 13 weeks


title: che3_OP50_2


title: Ventral prostate FVB mouse 3

description:
Library name: FVB Ventral 3
Column name in NormalizedCounts.csv: FVB3A

value: FVB/Ncrl

value: 12 weeks


title: che3_OP50_1


title: Ventral prostate FVB mouse 1

description:
Library name: FVB Ventral 1
Column name in NormalizedCounts.csv: FVB1V


title: WT_PA14_3

value: wild-type (N2)


title: Anterior prostate BMPC mouse 1

description:
Library name: BMPC PIN 1
Column name in NormalizedCounts.csv: BMPC12wPIN1

value: Anterior prostate


title: Anterior prostate FVB mouse 2

description:
Library name: FVB Anterior 2
Column name in NormalizedCounts.csv: FVB2A


title: WT_PA14_2

value: entire worm

value: PA14 infection


title: WT_PA14_1


title: Anterior prostate FVB mouse 1

description:
Library name: FVB Anterior 1
Column name in NormalizedCounts.csv: FVB1A


title: WT_OP50_2


title: Day30Pool_rep2_ATAC

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,ATAC assay
W9_ATAC

data_processing:
BCL files from sequence samples were demultiplexed using cellranger-atac-2.0.0 for the ATAC data,using bcl2fastq for HTO and ADT data and cellranger-arc for RNA data
The alignment and quantification of reads was done using cellranger_arc_2.0.2 for RNA+ATAC data,Barcounter v1.0.0 was used to quantify the reads for HTO and ADT data.
Analysis was performed in R (v4.2) using ArchR (v1.0.2), Seurat (v5.1.0) and Signac (v1.13). HTO and ADT reads were first quantified in Barcounter (v1.0.0) and combined with gene expression reads derived from cellranger to create Seurat objects
Cells with less than 500 RNA features, less than 2000 ATAC counts, less than 1500 ATAC features, a nucleosome signal greater than 5, a Transcription Site Enrichment (TSS) enrichment score greater than 4 and more than 30% mitochondrial reads and outliers with high numbers of HTO reads were excluded from downstream analysis. HTOs were normalized using the Seurat CLR method and manually demultiplexed in using the multimode package (v1.5) by inspecting the distribution of each HTO signal against all others profiled.
ATAC peaks were then called in ArchR using all cells that had passed quality control in Seurat and Signac. Briefly, additional QC was first performed by executing AddDoubletScores() then removing doublets with a filter ratio of 0.5 and filtering additional cells with a TSS Enrichment Score less than 10. Clustering based on ATAC fragments was performed in ArchR using the function addIterativeLSI() with the default parameters except for use of 25,000 variable features and a resolution of 2 with 2 iterations and then executing the addClusters() function with a resolution of 3.4.
Assembly: mm10
Supplementary files format and content: Cellranger arc output files: W8_arc_barcodes.tsv.gz,W8_arc_features.tsv.gz,W8_arc_matrix.mtx.gz, W9_arc_barcodes.tsv.gz,W9_arc_features.tsv.gz,W9_arc_matrix.mtx.gz
Supplementary files format and content: Barcounter output files: W8_ADT_Tag_Counts.csv,W8_HTO_Tag_Counts.csv,W9_ADT_Tag_Counts.csv,W9_HTO_Tag_Counts.csv

source_name: Pooled tissue cells

growth_protocol: LCMV Arm and C13 were grown in BHK cells (American Type Culture Collection (ATCC), CL-10) and titrated by performing plaque assays on Vero cells (ATCC, CCL-81)

extract_protocol:
live CD8β+CD44hiCD45.1+Vα2+ P14 cells from each sample (pooled organs from 20 Arm-infected mice or 20 C13 infected mice) were sorted into separate FBS-coated FACS tubes (Corning) containing 50%RPMI/FBS
samples were stained with individual TotalSeq-A Hashtag Oligo (HTO) antibodies and a custom pool of TotalSeq-A Antibody Derived Tag (ADT) antibodies (Biolegend; see Supplementary Table X). Samples were washed with Cell Staining Buffer (850G, 7 mins, 4°C) before resuspending cells in 2%BSA/DPBS and pooling cells. Cells were resuspended in custom TEA-seq Wash Buffer (20mM Tris-HCl, 150mM NaCl, 2mM MgCl2 and 1% BSA in H2O) containing RNase Inhibitor (1U/mL, Roche) and 0.01% Digitonin (Thermofisher) and incubated for 5 minutes on ice to permeabilize cell and nuclear membranes. Cells were topped with TEA-seq Wash Buffer and spun for 7 mins at 850G at 4°C before washing with TEA-seq Tagmentation Buffer (20mM Tris-HCl, 150mM NaCl, 2mM MgCl2 in H2O).
30,000 cells per reaction were removed and subjected to transposition and GEM generation as described in the 10x Chromium Single Cell Multiome ATAC + Gene Expression Kit across a total of two wells. Library preparation was performed as described47, with the following customizations. Indexing of ADT and HTO libraries was performed using Biolegend-recommended Illumina D70x (i7 long; HTO) or RNA PCR Index (RPIx short; ADT) adapter sequences (IDT), with three additional rounds of amplification performed on purified HTO/ADT libraries using P5/P7 primers specific for generic Illumina adapter sequences (IDT) prior to sequencing

treatment_protocol: Recipient mice were infected intraperitonealy (i.p.) with LCMV Arm (2 x 105 PFU) or i.v. with LCMV C13 (4 x 106 PFU) diluted in 1% FBS/RPMI.

value: Pooled tissue cells

tag: library type

value: DNA

value: p14 Cells

value: mixed sample (LCMV Arm + LCMV Cl13 infection)


title: Day30Pool_rep2_ADT

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,ADT assay
W9_ADT

library_source: other

molecule: protein

value: ADT

tag: adt


title: Day30Pool_rep2_HTO

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,HTO assay
W9_HTO

value: HTO

tag: hto


title: siCHRNA5 and siTP53 1

city: Ankara

first: Özlen

last: Konu

country: Turkey

institute: Bilkent University

description:
Library name: Sample 7
Column name in raw_counts.csv:  siCHRNA5_siTP53_a

data_processing:
Raw FASTQ files were uploaded to the Seven Bridges Cancer Genomics Cloud (CGC; https://www.cancergenomicscloud.org/) for analysis. Quality control was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (hg19 assembly) using the STAR aligner with default parameters. (Dobin et al., 2013). Gene-level quantification was performed using HTSeq-count, with Ensembl Gene IDs and genomic coordinates. (Anders, Pyl, & Huber, 2015).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNAeasy kit (Qiagen, Germany) 1 ug of total RNA was used for the construction of sequencing libraries.
PolyA-enriched mRNA libraries were prepared by BMLabosis, Ankara, Turkiye

treatment_protocol: Cells were treated with 20nm siRNA or siControl with Transfection reagent (HiPerfect) for 72h.

value: si-CHRNA5 + si-TP53


title: WT_OP50_1

value: OP50 feed


title: siCHRNA5 and siTP53 2

description:
Library name: Sample 8
Column name in raw_counts.csv:  siCHRNA5_siTP53_b


title: WT_OP50_3


title: Day30Pool_rep1_HTO

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,HTO assay
W8_HTO


title: Day30Pool_rep2_GEX

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,GEX assay
W9_mRNA

value: mRNA


title: Day30Pool_rep1_ATAC

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,ATAC assay
W8_ATAC


title: Day30Pool_rep1_ADT

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,ADT assay
W8_ADT


title: siCHRNA5 2

description:
Library name: Sample 4
Column name in raw_counts.csv:  siCHRNA5_b


title: siTP53 2

description:
Library name: Sample 6
Column name in raw_counts.csv:  siTP53_b


title: Day30Pool_rep1_GEX

description:
Day30 post infected cells pooled from multiple organs,naïve,arm and cl13 infection,GEX assay
W8_mRNA


title: Ventral prostate FVB mouse 2

description:
Library name: FVB Ventral 2
Column name in NormalizedCounts.csv: FVB2V

value: Ventral prostate


title: Anterior prostate FVB mouse 3

description:
Library name: FVB Anterior 3
Column name in NormalizedCounts.csv: FVB3A


title: siControl 2

description:
Library name: Sample 2
Column name in raw_counts.csv:  siControl_b

value: siControl


title: PKNO-2

city: shanghai

first: wenxin

last: feng

address: 1954 Huashan Road, Shanghai

institute: shanghai jiaotong university

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCm38
Supplementary files format and content: TXT file contain counts for each sample

source_name: pancreas

extract_protocol:
The total RNA was extracted with Trizol (Invitrogen) under the manufacturer’s guiding.
The cDNA libraries were constructed for each pooled RNA sample using the NEBNext® UltraTM Directional RNA library Prep Kit for Illumina according to the manufacturer’s instructions.

value: pancreas


title: PK-2


title: HLC treated with DHT and insulin, bio rep 3

city: Suita

first: Yosuke

last: Yoneyama

state: Osaka

address: 2-2 Yamadaoka

department: Graduate School of Medicine

institute: The University of Osaka

description:
Library name: DHT_Insulin_3
2-31-DHTins-n1

data_processing:
Sequencing was performed on NovaSeq6000 (2x150 bp configuration; 6Gb/sample).
Clean data were generated from the raw data by using Cutadapt.
Trimmed sequence reads were mapped to GRCh38 by using  HISAT2.
Count matrix and FPKM were generated with HTSeq.
Assembly: GRCh38
Supplementary files format and content: tab-separated value file includes raw counts for each sample.

source_name: Human iPSC-derived hepatocyte-like cell

extract_protocol:
RNA was harvested using FastGene RNA Basic Kit (NIPPON Genetics).
Library construction was performed with polyA sellection for Illumina.

value: Human iPSC-derived hepatocyte-like cell

value: TM6SF2 E167K homozygous


title: PK-1


title: HLC treated with DHT and insulin, bio rep 2

description:
Library name: DHT_Insulin_2
2-30-DHTins-n2


title: PKNO-1


title: HLC treated with DHT and insulin, bio rep 1

description:
Library name: DHT_Insulin_1
2-30-DHTins-n1


title: E100CGE-LGE

city: San Francisco

first: Alex

middle: A

last: Pollen

state: CA

address: 35 Medical Center Way

department: Neurology

institute: UCSF

description:
Library name: E100CGE-LGE
10X Genomics (V3) 3 capture single cell RNA seq

data_processing:
fastq files
Kallisto gene expression quantification
Cellbender ambient RNA removal
Assembly: rheMac10
Supplementary files format and content: H5AD

organism: Macaca mulatta

source_name: brain

extract_protocol:
Papain dissociated whole cells
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: E100septumANDnucleusAccumbens

description:
Library name: E100septumANDnucleusAccumbens
10X Genomics (V3) 3 capture single cell RNA seq


title: E80putamenANDclaustrumANDbasalGanglia

description:
Library name: E80putamenANDclaustrumANDbasalGanglia
10X Genomics (V3) 3 capture single cell RNA seq


title: siCHRNA5 1

description:
Library name: Sample 3
Column name in raw_counts.csv:  siCHRNA5_a


title: HLC treated with DHT, bio rep 3

description:
Library name: DHT_3
2-31-DHT-n2


title: E100hypothalamusANDPoA

description:
Library name: E100hypothalamusANDPoA
10X Genomics (V3) 3 capture single cell RNA seq


title: E100lateralANDanteriorANDvermis

description:
Library name: E100lateralANDanteriorANDvermis
10X Genomics (V3) 3 capture single cell RNA seq


title: HLC treated with insulin, bio rep 1

description:
Library name: Insulin_1
2-30-Ins-n2


title: Con7-AGly3

description:
Library name: sample9
Con7-AGly3

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 50-nt long tags.
Then low quality tags, one copy tags and tags which are not 50-nt long were removed to generate clean tags.
Reference 50-nt tag databases were created from predicted Penicillium oxalicum transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Assembly: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000.1
Supplementary files format and content: Matrix table with FPKM for every gene and every sample

source_name: Penicillium oxalicum

value: Penicillium oxalicum

value: con7 destruction strain

value: Modified Mendal’s medium with 2% glycerol as carbon resource


title: E80lateralANDanteriorANDvermis

description:
Library name: E80lateralANDanteriorANDvermis
10X Genomics (V3) 3 capture single cell RNA seq


title: Control HLC, bio rep 2

description:
Library name: Control_2
2-31-CT-n1


title: siTP53 1

description:
Library name: Sample 5
Column name in raw_counts.csv:  siTP53_a


title: Control HLC, bio rep 1

description:
Library name: Control_1
2-30-CT-n2


title: HLC treated with DHT, bio rep 2

description:
Library name: DHT_2
2-31-DHT-n1


title: E100caudateANDextBGANDintBGANDputanum

description:
Library name: E100caudateANDextBGANDintBGANDputanum
10X Genomics (V3) 3 capture single cell RNA seq


title: E80dorsalThalamusANDventralThalamus

description:
Library name: E80dorsalThalamusANDventralThalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: HLC treated with DHT, bio rep 1

description:
Library name: DHT_1
2-30-DHT-n1


title: Mac2_V1

description:
Library name: Mac2_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: HLC treated with insulin, bio rep 3

description:
Library name: Insulin_3
2-31-Ins-n2


title: E100thalamus

description:
Library name: E100thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: CSS48_scr_2

city: Paris

first: Antonin

last: Morillon

state: Paris

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
Library name: CSS48_scr_2
total ribo-depleted RNA

data_processing:
Reads were mapped on human genome version GRCh38 with tophat version 2.1.1, with the following parameters : -g 1 -N 3 --read-edit-dist 3 -r 155 --mate-std-dev 80 –no-coverage-search --library-type fr-firststrand.
Only unique mapped reads were kept for further analysis.
New transcripts were discovered using scallop 0.10.5.
Read counting was performed using featureCounts version 1.6.0 on a combined annotation of gencode.v32 and new transcripts from scallop, with the following parameters : -F "GTF" -p -s 2 -O.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene

source_name: LNCaP

growth_protocol: LNCaP cells were cultured at 37°C in a humid 5% CO2 atmosphere in either the RPMI 1640+GlutaMAX medium (Life Technologies) supplemented with 10% fetal bovine serum and 2 nM DHT (AD-cells, or +DHT) or the phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum for 15 days, 1 month, 3 months, 6 months

extract_protocol:
Total RNA extraction was performed directly from cell cultures with miRNeasy kit according to the manufacture’ instructions including the DNase treatment step (Qiagen).
Trueseq stranded Total RNA-seq protocol with Ribo-zero depletion of rRNA from 500 ng of the total RNA extract sample

value: LNCaP

value: epithelial prostate cancer cells

value: ATCC CRL-1740

value: hormon depleted media (phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum) + siPOOL scr

tag: time


title: Control HLC, bio rep 3

description:
Library name: Control_3
2-31-CT-n2


title: CSS48_scr_3

description:
Library name: CSS48_scr_3
total ribo-depleted RNA


title: E80CGE-LGE

description:
Library name: E80CGE-LGE
10X Genomics (V3) 3 capture single cell RNA seq

tag: tissue


title: siControl 1

description:
Library name: Sample 1
Column name in raw_counts.csv:  siControl_a

tag: cell line


title: CSS48_scr_1

description:
Library name: CSS48_scr_1
total ribo-depleted RNA

tag: treatment


title: Mac2_thalamus

description:
Library name: Mac2_thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: E80choroidANDE100choroid

description:
Library name: E80choroidANDE100choroid
10X Genomics (V3) 3 capture single cell RNA seq


title: Mac2_temporal

description:
Library name: Mac2_temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: Mac2_somatosensory

description:
Library name: Mac2_somatosensory
10X Genomics (V3) 3 capture single cell RNA seq


title: HLC treated with insulin, bio rep 2

description:
Library name: Insulin_2
2-31-Ins-n1


title: CSS48_siP11_2

description:
Library name: CSS48_siP11_2
total ribo-depleted RNA

value: hormon depleted media (phenol red-free RPMI 1664+GlutaMAX medium supplemented with 10% dextran charcoal-stripped fetal bovine serum) + siPOOL PROCA11


title: Mac2_PFC

description:
Library name: Mac2_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: CSS48_siP11_1

description:
Library name: CSS48_siP11_1
total ribo-depleted RNA


title: CSS48_siP11_3

description:
Library name: CSS48_siP11_3
total ribo-depleted RNA


title: MCF7_WT_Nut_rep3

city: Rehovot

first: Efrat

last: Shema

state: Israel

address: 234 Hertzel

department: Department of Immunology & Regenerative Biology

country: Israel

institute: Weizmann Institute of Science

description: Library name: MCF7_wt_nut_3

data_processing:
Reads were trimmed using cutadapt and mapped to the hg38 genome using STAR v2.4.2a (default parameters). The pipeline quantifies the genes annotated in Gencode (that have been expanded with 1000 bases toward the 5’ edge and 100 bases toward the 3’ bases). Counting was done using htseq-count (union mode). Further analysis was done only for genes having a minimum of 5 reads in at least one sample. Normalization of the counts and differential expression analysis was performed using DESeq2 with the parameters: betaPrior = True, cooksCutoff = FALSE, independentFiltering = FALSE. Differentially expressed genes were defined using FC > 1.5 and raw p-value < 0.05 as a significance cutoff.
Assembly: hg38
Supplementary files format and content: Deseq2 - differential analysis output

source_name: Breast

growth_protocol: MCF7 cells were cultured in DMEM supplemented with 10% FBS, 1% P/S and 1% sodium pyruvate solution. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel).
RNA-seq libraries were prepared from 30 ng of input RNA from each sample and were barcoded during reverse transcription and pooled. Following Agencourt AMPure XP beads cleanup (Beckman Coulter), the pooled samples underwent second-strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Sequencing was done with a Nextseq 75 cycles high output kit (Illumina).

treatment_protocol: 5uM Tamoxifen for 48h or 5uM Nutlin for 24h

value: Breast

value: p53 WT

value: Nutlin


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, untreated, rep3

city: Leicester

first: John

last: Schwabe

state: Leicestershire

address: Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

description:
Library name: Sample 18
Column name in Normalised_counts.xlsx: DNTuntreated_3

data_processing:
Sequecing files were aligned using HISAT2 (v12.3.0) using standard options to human genome build GRCh38 release 111.
Samtools (v1.17) was used to create sorted, indexed BAM files.
LiBiNorm (v2.5)(options: -z -r pos -I gene_name -s reverse) with the GRCh38 release 111 gene transfer fomat file was used to create count files.
DESeq2 (v1.44.0) was used to create normalised counts files and determine significant gene changes.
Assembly: GRCh38 release 111
Supplementary files format and content: Xcel matrix with normalised counts for each condition and replicate both pre- and post-filtering for low counts

source_name: HCT 116

growth_protocol: HCT 116 cells were maintained in DMEM (high glocuse) supplememnted with 10% foetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using a Promega Maxwell RXC by the University of Leicester Genomics facility
Library construction was performed by Novogene using mRNA library preparation (polyA enrichment

treatment_protocol: Cells were seeded and allowed to settle for 24h prior to treatment with either DMSO (control) or 100nM dTAGv1. Treatments were timed so that harvesting of all time points was carried out simultaneously. Exeriments were repeated in triplicate.

value: HCT 116

value: Colon Carcinoma

value: untreated


title: Mac2_parietal

description:
Library name: Mac2_parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: Mac2_motor

description:
Library name: Mac2_motor
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_WT_Nut_rep2

description: Library name: MCF7_wt_nut_2


title: MCF7_WT_NT_rep2

description: Library name: MCF7_wt_2

value: No treatment


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, untreated, rep2

description:
Library name: Sample 17
Column name in Normalised_counts.xlsx: DNTuntreated_2


title: Mac2_MGE

description:
Library name: Mac2_MGE
10X Genomics (V3) 3 capture single cell RNA seq


title: MCF7_WT_NT_rep3

description: Library name: MCF7_wt_3


title: MCF7_WT_NT_rep1

description: Library name: MCF7_wt_1


title: MCF7_WT_Nut_rep1

description: Library name: MCF7_wt_nut_1


title: Mac2_hypothalamus

description:
Library name: Mac2_hypothalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, untreated, rep1

description:
Library name: Sample 16
Column name in Normalised_counts.xlsx: DNTuntreated_1


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, DMSO, rep3

description:
Library name: Sample 15
Column name in Normalised_counts.xlsx: DNTcontrol_3

value: Control

value: DMSO


title: CutRun_MCF7_WT_H3K4me3

description: Library name: WT_H3K4me3

data_processing:
Paired-end reads (~17M average reads per sample) were preprocessed with cutadapt to remove adapters and low-quality bases (parameters: --times 2 -q 30 -m 20), following evaluation with FastQC. Reads were mapped to human genome (hg38, UCSC) using Bowtie version 2.5.1(--local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700). Nucleosome fragments of length >120bp were selected from the remaining unique reads using awk. Alignments were filtered to keep properly aligned and paired reads (-F 4 -f 0x2 -q 39) and were normalized based on spike-in scaling factors, which were calculated by E. coli “carry-over” DNA from the pAG-Mnase. Bigwig files were constructed from BAM alignments using deepTools2 suite, by ‘bamCoverage’ command, in 10bp bins.
Assembly: hg38
Supplementary files format and content: bw - coverage files by bamCoverage (deeptools)
Library strategy: CUT&Run

extract_protocol:
200,000 cells were harvested per reaction. Permeabilized cells, bound to Concanavalin A-coated beads, were mixed with H3K4me3 antibody (CST #9751) at a dilution of 1:50, and incubated overnight at 4°C while rotating. pAG-MNase enzyme (generated in the Department of Life Sciences Core Facilities, WIS, using Addgene plasmid 123461) was added to each sample for 1 hour at 4°C. Targeted digestion was conducted for 15 minutes at 0°C under low salt conditions. DNA purification was done using Nucleospin gel and PCR clean-up kit (Machery-Nagel, 740609).
Libraries were quantified by Qubit (ThermoFisher Scientific) and proper fragment range (200-400bp) was verified by TapeStation (Agilent). Sequencing was done on a Next-Seq 550 instrument (Illumina) using a Nextseq 150 cycles mid output kit, allocating 10M reads per sample (paired end sequencing).


title: Mac2_hippocampus

description:
Library name: Mac2_hippocampus
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: Old uPAR 2

city: Cold Spring Harbor

first: Vyom

last: Shah

state: New York

address: 1 bungtown road

department: Beyaz Lab

institute: Cold Spring Harbor Laboratory

description: Library name: O_uPAR_2

data_processing:
FASTQ files were generated using Illumina’s bcl-convert software (v2.20.0.422) with default settings. For demultiplexing, the mismatch parameter was set to 1.
Data were aligned to the human genome (Genome Fasta: GRCm39, Annotation GTF: Gencode vM29) using STAR (v2.7.8a), converted to BAM files and merged with SAMtools (v1.11) and read counts were generated using FeatureCounts (Subread package v2.02) and RSEM (v1.3.3).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw data for each sample

source_name: Intestinal Organoids

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for construction of sequencing libraries.
Libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche, Cat# KK8581), following the manufacturer’s standard protocol with 120 ng of total RNA per sample. mRNA was captured using oligo(dT) magnetic beads, fragmented (6 minutes at 85°C, aiming for 300–400 bp), and reverse transcribed into cDNA. After end repair, A-tailing, and adapter ligation, libraries were PCR-amplified (13 cycles), then purified and QCed using TapeStation and Qubit before pooling and sequencing. Libraries were sequenced on an Illumina NextSeq 2000 using a P3 flowcell with paired-end 150 bp reads (PE150), using NextSeq2000 Control Software was v1.5.0 ( release Nov 15, 2022).

treatment_protocol: Young (3 months) and old (18 months) mice were treated with 0.5x10^6 untransduced T cells (UT) or uPAR CAR T cells (m.uPAR-m.28z). Mice were harvested 8 weeks after infusion and organoids were generated from their intestinal crypts. 5 days after generation, organoids were harvested and subjected to bulk RNA sequencing.

value: Intestinal Organoids

value: WT

value: m.uPAR-m.28z CAR T cells


title: Mac2_CGE

description:
Library name: Mac2_CGE
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, DMSO, rep1

description:
Library name: Sample 13
Column name in Normalised_counts.xlsx: DNTcontrol_1


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, DMSO, rep2

description:
Library name: Sample 14
Column name in Normalised_counts.xlsx: DNTcontrol_2


title: Old uPAR 1

description: Library name: O_uPAR_1


title: Young uPAR 2

description: Library name: Y_uPAR_2


title: Old UT 1

description: Library name: O_UT_1

value: Untransduced T cells


title: E90-2019_V1

description:
Library name: E90-2019_V1
10X Genomics (V3) 3 capture single cell RNA seq


title: E90-2019_Thalamus

description:
Library name: E90-2019_Thalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 48h dTAGv1, rep2

description:
Library name: Sample 11
Column name in Normalised_counts.xlsx: DNT48hv1_2

value: DNTTIP1 knockdown


title: E90-2019_Temporal

description:
Library name: E90-2019_Temporal
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 48h dTAGv1, rep3

description:
Library name: Sample 12
Column name in Normalised_counts.xlsx: DNT48hv1_3


title: Young uPAR 1

description: Library name: Y_uPAR_1


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 48h dTAGv1, rep1

description:
Library name: Sample 10
Column name in Normalised_counts.xlsx: DNT48hv1_1


title: Ethanol etracts of JGT (Medium Dose) rep3

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

description: Library name: JGE03_M_3

data_processing:
Read count and transcripts per million (TPM) were calculated as gene expression abundance using the RSEM software (v1.3.3) and gene annotation RN6 Gene Transfer Format (GTF) file from UCSC browser
Assembly: RN6
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Rattus norvegicus

extract_protocol:
One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI Tech, China) according to manufacturer’s instruction.
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

value: neuronal cell

tag: treatment dose


title: Young UT 1

description: Library name: Y_UT_1

tag: genotype


title: Young UT 2

description: Library name: Y_UT_2


title: E90-2019_Somatosensory

description:
Library name: E90-2019_Somatosensory
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 24h dTAGv1, rep3

description:
Library name: Sample 9
Column name in Normalised_counts.xlsx: DNT24hv1_3


title: CutRun_MCF7_KO_H3K4me3

description: Library name: KO_H3K4me3

value: p53 KO


title: Ethanol etracts of JGT (Low Dose) rep2

description: Library name: JGE03_L_2

value: Ethanol etracts of JGT (Low Dose) rep2


title: Ethanol etracts of JGT (High Dose) rep3

description: Library name: JGE03_H_3

value: Ethanol etracts of JGT (High Dose) rep3


title: Ethanol etracts of JGT (Medium Dose) rep2

description: Library name: JGE03_M_2


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 24h dTAGv1, rep2

description:
Library name: Sample 8
Column name in Normalised_counts.xlsx: DNT24hv1_2


title: E90-2019_putamen_AND_Septum

description:
Library name: E90-2019_putamen_AND_Septum
10X Genomics (V3) 3 capture single cell RNA seq


title: E90-2019_PFC

description:
Library name: E90-2019_PFC
10X Genomics (V3) 3 capture single cell RNA seq


title: Ethanol etracts of JGT (High Dose) rep2

description: Library name: JGE03_H_2

value: Ethanol etracts of JGT (High Dose) rep2


title: Old UT 2

description: Library name: O_UT_2


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 24h dTAGv1, rep1

description:
Library name: Sample 7
Column name in Normalised_counts.xlsx: DNT24hv1_1

value: HCT 116


title: E90-2019_Parietal

description:
Library name: E90-2019_Parietal
10X Genomics (V3) 3 capture single cell RNA seq


title: Ethanol etracts of JGT (Medium Dose) rep1

description: Library name: JGE03_M_1


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 12h dTAGv1, rep3

description:
Library name: Sample 6
Column name in Normalised_counts.xlsx: DNT12hv1_3

value: Colon Carcinoma


title: Ethanol etracts of JGT (High Dose) rep1

description: Library name: JGE03_H_1

value: Ethanol etracts of JGT (High Dose) rep1


title: Water etracts of JGT (Low Dose) rep3

description: Library name: JGW03_L_3

value: Water etracts of JGT (Low Dose) rep3


title: Water etracts of JGT (Medium Dose) rep3

description: Library name: JGW03_M_3

value: Water etracts of JGT (Medium Dose) rep3


title: Ethanol etracts of JGT (Low Dose) rep3

description: Library name: JGE03_L_3

value: Ethanol etracts of JGT (Low Dose) rep3


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 12h dTAGv1, rep2

description:
Library name: Sample 5
Column name in Normalised_counts.xlsx: DNT12hv1_2


title: E90-2019_Motor_2

description:
Library name: E90-2019_Motor_2
10X Genomics (V3) 3 capture single cell RNA seq

value: brain


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 12h dTAGv1, rep1

description:
Library name: Sample 4
Column name in Normalised_counts.xlsx: DNT12hv1_1


title: Water etracts of JGT (Medium Dose) rep2

description: Library name: JGW03_M_2

value: Water etracts of JGT (Medium Dose) rep2


title: Water etracts of JGT (High Dose) rep1

description: Library name: JGW03_H_1

value: Water etracts of JGT (High Dose) rep1


title: Water etracts of JGT (Low Dose) rep1

description: Library name: JGW03_L_1

value: Water etracts of JGT (Low Dose) rep1


title: Water etracts of JGT (High Dose) rep3

description: Library name: JGW03_H_3

value: Water etracts of JGT (High Dose) rep3


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h dTAGv1, rep3

description:
Library name: Sample 3
Column name in Normalised_counts.xlsx: DNT6hv1_3

value: DNTTIP1 knockdown


title: E90-2019_Motor_1

description:
Library name: E90-2019_Motor_1
10X Genomics (V3) 3 capture single cell RNA seq


title: Water etracts of JGT (Medium Dose) rep1

description: Library name: JGW03_M_1

value: neuronal cell

value: Water etracts of JGT (Medium Dose) rep1


title: Water etracts of JGT (High Dose) rep2

description: Library name: JGW03_H_2

value: Water etracts of JGT (High Dose) rep2


title: Ethanol etracts of JGT (Low Dose) rep1

description: Library name: JGE03_L_1

value: Ethanol etracts of JGT (Low Dose) rep1


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h dTAGv1, rep1

description:
Library name: Sample 1
Column name in Normalised_counts.xlsx: DNT6hv1_1


title: E90-2019_Hypothalamus

description:
Library name: E90-2019_Hypothalamus
10X Genomics (V3) 3 capture single cell RNA seq


title: vehicle rep3

description: Library name: Veh_3

value: vehicle rep3

value: untreated sample


title: E90-2019_MGE_AND_CGE_AND_LGE

description:
Library name: E90-2019_MGE_AND_CGE_AND_LGE
10X Genomics (V3) 3 capture single cell RNA seq


title: HCT 116 FLAG/FKBPF36V-DNTTIP1, 6h dTAGv1, rep2

description:
Library name: Sample 2
Column name in Normalised_counts.xlsx: DNT6hv1_2

value: HCT 116

value: Colon Carcinoma


title: E90-2019_Multi-seq

description:
Library name: E90-2019_Multi-seq
10X Genomics (V3) 3 capture single cell RNA seq


title: vehicle rep1

description: Library name: Veh_1

value: vehicle rep1


title: vehicle rep2

description: Library name: Veh_2

value: vehicle rep2


title: GPX4M-eGFP clone#6 unsorted

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

description: Library name: B05

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment analysis
Assembly: hg38
Supplementary files format and content: Table of normalized read counts of extracted sgRNAs
Library strategy: CRISPR Screen

growth_protocol: Cell lines were obtained from ATCC. HCT116 cells (male) were cultured in DMEM media (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Sigma-Aldrich) and 1X Penicillin-Streptomycin (Gibco)

extract_protocol:
Genomic DNA was isolated from unsorted cells using the MasterPure Complete DNA Purification kit (Lucigen). Genomic DNA from sorted cells was isolated by phenol-chlorofom extraction.
CRISPR screen custom DNA library. Sequencing libraries were generated using two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). In the first round of PCR, 5µg of genomic DNA from unsorted cells was used in each of 24 100 µl reactions, and all recovered genomic DNA from sorted cells was split into two 100 µl reactions. Following 18 cycles of PCR1 amplification, 5 µl from the pooled reaction product was used in the second round of PCR (10 cycles), using primers containing barcodes and Illumina sequencing adaptors.

treatment_protocol: Transduced cells were selected with 1 µg/mL puromycin (Thermo Fisher Scientific)

value: colon cancer cell line

value: GPX4M-eGFP Clone#6

value: Unsorted


title: GPX4-eGFP clone#10 unsorted

description: Library name: B04

value: GPX4-eGFP Clone#10