title: Primary stromal cells, undifferentiated, donor P37

description:
Library name: 9296
P37


title: CUMC_E142

status: Public on Mar 02 2026

type: SRA

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

library_source: transcriptomic

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

molecule: total RNA

organism: Homo sapiens

source_name: PDAC

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2

tag: compartment

value: Epithelium

tag: group

value: Primary


title: Subject_034_second dose

type: protein

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

country: United Kingdom

institute: The University of Manchester

description: Individual participant of trial NCT00962691

hyb_protocol: Slides were blocked with 200 µL of SuperG Blocking Buffer (Grace Biolabs, US) per well and incubated for one hour at room temperature (RT). Washes were done three times with 300μL TBS‐T (0.05% Tween‐20) and once in TBS for 10 min, slides were incubated in the dark for 1hr at 20°C with 100μL of Goat Anti-Human IgG Fc (DyLight 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK), using a working dilution of 1:5000 in blocking agent. The arrays were incubated for IgA detection with 100 μL of Goat Anti-Human IgA alpha chain (DyLight 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK), using a working dilution of 1:5000 in blocking agent. Slides were rinsed in de-ionised water and dried by centrifugation at 200 x g for 2 min.

scan_protocol: Slides were scanned in an InnoScan 710 (Innopsys, France) with the photomultiplier tube set to 100% for 635 nm. Image analysis and data quantification were carried out using Mapix v9.1.0 - Microarray image acquisition and analysis software (Innopsys, France).

data_processing: Microarray spot intensities were quantified using Mapix v9.1.0 Microarray Image Analysis software (Innopsys, France), which utilises automatic background subtraction for each spot. The spot intensities for each protein were recorded in quintuplicate; arithmetic means were determined, and spot intensities for buffer-only controls were subtracted

molecule: protein

source_name: MenOccy Trial

label_protocol: Secondary antibody was purchased from Abcam: Goat anti-human IgG Fc (DyLight® 650) preadsorbed secondary antibody (ab98622, Abcam, UK)

extract_protocol: Human sera collected from an open-label phase II study NCT00962624

tag: tissue

value: Blood

value: Serum


title: Subject_035_Pre-immune

description: Individual participant of trial NCT00962693

label: Goat anti-human IgG Fc (DyLight® 650) preadsorbed secondary antibody


title: caRNA MeRIP-seq IP Col-0 rep3

city: Chicago

first: Long

last: Zhao

state: Il

address: 929 E 57th Street

department: Department of Chemistry

country: USA

institute: University of Chicago

description: Library name: CHe-LJ-38s-P01

library_source: other

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: MeRIP-Seq

molecule: other

organism: Arabidopsis thaliana

source_name: Whole seedling

extract_protocol:
For caRNA MeRIP-seq, caRNA was isolated and non-ribosome RNA was further enriched using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL of 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 0.5-1 μg non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer’s instructions. For nascent RNA-seq in mESCs, cells were incubated in media containing 1 mM EU with different time points and lysed with TRIzol (Invitrogen) for total RNA extraction. An equal amount of RNA extracted from EU-labeled Drosophila cells was added to each sample as a spike-in for further normalization. Nascent RNA was captured using the Click-iT™ Nascent RNA Capture Kit (Invitrogen) according to the manufacturer’s instructions. For CLIP-seq in mESCs, cells were UV crosslinked at 400 mJ/cm² (254 nm) once and nuclei were isolated following the cell fractionation protocol. For ATAC-seq, CUT&Tag, CUT&RUN in mESCs, nuclei were isolated by incubation with complete nuclei isolation buffer (Active Motif) according to the manufacturer’s instructions. For ATAC-seq, CUT&Tag, CUT&RUN in Arabidopsis, nuclei were extracted from 10-day-old seedlings after germination.
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer’s protocol. ATAC-seq was performed by using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s instructions. CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer’s instructions. CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer’s instructions.

treatment_protocol: All wild-type (WT) and transgenic Arabidopsis lines used in this study were in the Arabidopsis thaliana Columbia (Col-0) background. Seeds were surface sterilized in 10% sodium hypochlorite solution for 10 minutes, washed five times with sterile water, and grown on Murashige and Skoog (MS) medium (PhytoTech Labs) supplemented with 1.5% sucrose and 0.8% agar (pH 5.8). Seedlings were grown under controlled conditions in either a growth chamber or a growth room at 21 °C with a 16-hour light/8-hour dark photoperiod.                                                                                E14TG2a mES cells (ATCC) were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 1% EmbryoMax nucleosides (Sigma), 1% GlutaMAX supplement (Gibco), 1% MEM non-essential amino acids solution (Gibco), 1% Penicillin-Streptomycin (Gibco), 0.1 mM 2-Mercaptoethanol (Gibco), 1000 U/ml LIF (Sigma), 1 µM PD0325901 (Stemcell) and 3 µM CHIR99021 (Stemcell) at 37 °C in a humidified atmosphere with 5% CO2.

value: Whole seedling

tag: ecotype

tag: genotype

value: WT


title: caRNA MeRIP-seq input ALKBH5 del-cIDR mutant rep3

description: Library name: CHe-LJ-38s-N05

value: OE ALKBH5 del-cIDR H204A


title: caRNA MeRIP-seq IP ALKBH5 FL rep3

description: Library name: CHe-LJ-38s-P02

value: OE ALKBH5 FL


title: Primary stromal cells, undifferentiated, donor P55

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description:
Library name: 9173
P55

library_source: transcriptomic single cell

data_processing:
Raw base calls of 10x libraries were demultiplexed into fastq files and then aligned and quantified at the exon and intron level using zUMI (Parekh S, et al., Gigascience 7:giy059) and STAR (Dobin A, et al., Bioinformatics 29:15-21) with genome GRCh38. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411) to yield a gene count matrix for 136,014 cells. The seurat object ("SeuratObject") of the article can be found at OSF (https://osf.io/s8nfb/) and as processed data in this series.
Bulk RNA-seq reads were aligned to GRCh378(hg38) genome using STAR (Dobin A, et al., Bioinformatics 29:15-21) and default settings. Bam files were used to quantify tag distribution at gene bodies using featureCounts from the Subread package (Liao Y,  et al. 2014. Bioinformatics 30: 923) . Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing treatment conditions (siITGA11 vs. siCTR, ITGA11high vs ITGA11low) and including donor information in the model.
Assembly: GRCh38
Supplementary files format and content: 8524.dgecounts.rds, 8525.dgecounts.rds, 8890.dgecounts.rds, 8983.dgecounts.rds, 8984.dgecounts.rds, 8985.dgecounts.rds, 9171.dgecounts.rds, 9172.dgecounts.rds, 9173.dgecounts.rds, 9174.dgecounts.rds, 9294.dgecounts.rds, 9295.dgecounts.rds, 9296.dgecounts.rds, A174.dgecounts.rds, A175.dgecounts.rds, A176.dgecounts.rds, A177.dgecounts.rds, A178.dgecounts.rds, A323.dgecounts.rds, A324.dgecounts.rds, s1.dgecounts.rds, s2.dgecounts.rds, s3.dgecounts.rds, s4.dgecounts.rds, s6.dgecounts.rds, s8.dgecounts.rds, tab delimited files to retrieve zUMI derrived raw gene count matrices of the individual 10x scRNA-seq libraries.
Supplementary files format and content: SeuratObject.qs, serialized and compressed seurat object using R package "qs"
Supplementary files format and content: Bulk_Counts.txt, tab delimited file with featureCounts derrived raw gene counts from bulk RNA-seq as well as DESeq derived rlog values, normalized counts, fold changes and adjusted p-values for the comparisons from bulk RNA-seq

molecule: polyA RNA

source_name: cultured primary stromal cells from iliac crest aspirate

growth_protocol: Cells were seeded in tissue culture flasks and expanded in culture medium consisting of minimum essential medium (MEM, 32561-094, Invitrogen) supplemented with 10% fetal bovine serum (FBS, 16000044, Life Technologies) and 1% penicillin/streptomycin (P/S, 15140-130, Invitrogen). They were incubated at 37 °C with 5% CO2 and 95% humidity. The culture medium was changed three times a week, and the cells were either passaged or set out for differentiation when reaching 80-90% confluency.

extract_protocol:
For 10x scRNA-seq, cells have been trypsinized and spun down at 200 g and washed twice in culture media. Cells were separated using a 40 µm mesh, washed 3 times in PBS with 0.04% non-acetylated BSA, and cell numbers were adjusted to 0.7 million cells per ml followed by a final transfer through a 40 µm mesh.
Bulk RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
scRNA-seq: Libraries were prepared according to manufactures instructions (10x Genomics).
Bulk RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol:
For 10x scRNA-seq libraries, cells were trypsinised at 90 % confluency.
For bulk-RNA-seq on siRNA transfected primary, reverse transfection was done 3 days prior to differentiation, using a final concentration of 30 nM siRNA, 0.15% lipofectamin 2000 and 140,000 cells per ml using alphaMEM without additives. For a single 12-well, 1.5 µl of 20 µM siRNA stock was mixed with 150 µl alphaMEM, 1.5 µl lipofectamin 200 was mixed with 150 µl alphaMEM, and both mixtures were united after 5 minutes incubation. After additional 20 minutes incubation, 140,000 cells in 0.7 ml were added and 1 ml of cell-transfection-mix was plated to a 12-well, yielding 40,000 cells per squar-cm.
For bulk-RNA-seq on sorted primary cells, cells at passge 2 or 3  with unconjugated primary ITGA11 antibody (0519-100/ITGA11-203E3, Nanotools) followed by secondary FITC-conjugated anti-mouse immunoglobulin (F0261, Dako Denmark A/S) and sorted on a BD FACSAria III  to capture the lowest 30% and highest and 30% of ITGA11 expresison. Cells were plated at a density of either 50.000 or 5.000 cells per square-cm and harvested in Trizol three or 7 days after, respectively.

tag: cell type

tag: treatment


title: Primary stromal cells, undifferentiated, donor P38

description:
Library name: 9171
P38

value: cultured primary stromal cells from iliac crest aspirate


title: Primary stromal cells, undifferentiated, donor P49

description:
Library name: 9172
P49


title: Subject_034_third dose

description: Individual participant of trial NCT00962692


title: CUMC_E138


title: CUMC_E141


title: CUMC_E139


title: Primary stromal cells, undifferentiated, donor P40

description:
Library name: 8984
P40


title: caRNA MeRIP-seq input ALKBH5 del-cIDR rep3

description: Library name: CHe-LJ-38s-N04

value: OE ALKBH5 del-cIDR


title: Subject_034_Pre-immune

description: Individual participant of trial NCT00962690


title: Subject_031_third dose

description: Individual participant of trial NCT00962689


title: Subject_031_second dose

description: Individual participant of trial NCT00962688


title: Primary stromal cells, undifferentiated, donor P35

description:
Library name: 8983
P35


title: CUMC_E137


title: Subject_031_Pre-immune

description: Individual participant of trial NCT00962687


title: caRNA MeRIP-seq input ALKBH5 FL mutant rep3

description: Library name: CHe-LJ-38s-N03

value: OE ALKBH5 FL H204A


title: Primary stromal cells, undifferentiated, donor P65

description:
Library name: 8890
P65


title: caRNA MeRIP-seq input ALKBH5 FL rep3

description: Library name: CHe-LJ-38s-N02


title: CUMC_E136


title: caRNA MeRIP-seq input Col-0 rep3

description: Library name: CHe-LJ-38s-N01


title: Primary stromal cells, undifferentiated, donor P48

description:
Library name: 8985
P48


title: CUMC_E140


title: Subject_030_second dose

description: Individual participant of trial NCT00962685


title: ATAC ALKBH5 del-cIDR rep3 Arabidopsis

description: Library name: CHe-LJ-38s-A14

library_source: genomic

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39

molecule: genomic DNA


title: Primary stromal cells, undifferentiated, donor P1

description:
Library name: 8525
P1


title: Primary stromal cells, undifferentiated, donor P10

description:
Library name: 8524
P10


title: CUMC_E134


title: ATAC ALKBH5 FL rep3 Arabidopsis

description: Library name: CHe-LJ-38s-A13


title: CUMC_E135


title: ATAC Col-0 rep3 Arabidopsis

description: Library name: CHe-LJ-38s-A12


title: CUMC_E132


title: Subject_029_third dose

description: Individual participant of trial NCT00962683


title: CUMC_E133


title: Subject_029_second dose

description: Individual participant of trial NCT00962682


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_N1060E with targeting crRNA, replicate 2)

city: Hong Kong

first: Joe

last: Lam

address: 21 Sassoon road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description:
Library name: biol rep2 Psp-N1060E
Cleavage site analysis of different PspCas13b mutants

data_processing:
bowtie2 (--score-min C,0,-1 --norc -k 1)
Assembly: ref03_EGFP_CKB.fa
Supplementary files format and content: Excel files of cleavage frequency for each cleavage position of each sample

growth_protocol: HEK293E cells were maintained in DMEM supplemented with 10% FBS in humified atmosphere with 5% CO2 at 37˚C

extract_protocol:
RNA was extracted by RNA mini-prep (Zymo) according to manufacturer's instruction
To map the cleavage sites of various Cas13 mutants on target RNA, we carried out an in vivo adaptor ligation method. After reverse transcription, a total of 2 rounds of PCR were done to amplify the libraries with an in vivo adaptor-specific forward primer coupled with a target-gene-specific reverse primer.

treatment_protocol: HEK29E cells were transfected with the required plasmids. 2 days after transfection, cells were collecte.

tag: cell line

value: human embryonic kidney cell

tag: batch

value: biological replicate 2


title: Subject_030_Pre-immune

description: Individual participant of trial NCT00962684


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_N1060A with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-N1060A
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq input ALKBH5 FL mutant rep2

description:
Library name: SAMPLES20
column: caMeINmut5W_2
Expr_norm.tsv

data_processing:
*library strategy: MeRIP-Seq
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the Arabidopsis thaliana genome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
For comparison analysis, union peaks across samples were generated using bedtools, and reads under these peaks were counted using featureCounts95 for both IP and input samples. Raw counts were normalized to Counts Per Million (CPM). IP enrichment was calculated as CPMIP/CPMInput. A scaling factor (SF) was computed based on CPMIP m6A control RNA/CPMinput m6A control RNA. The final m6A quantification for each sample was calculated using IP enrichment/SF.
Assembly: TAIR10
Supplementary files format and content: m6A_norm.tsv
Supplementary files format and content: Expr_norm.tsv

growth_protocol: All wild-type (WT) and transgenic Arabidopsis lines used in this study were in the Arabidopsis thaliana Columbia (Col-0) background. Seeds were surface sterilized in 10% sodium hypochlorite solution for 10 minutes, washed five times with sterile water, and grown on Murashige and Skoog (MS) medium (PhytoTech Labs) supplemented with 1.5% sucrose and 0.8% agar (pH 5.8). Seedlings were grown under controlled conditions in either a growth chamber or a growth room at 21 °C with a 16-hour light/8-hour dark photoperiod.

extract_protocol:
caRNA was extracted from 10-day-old seedlings after germination
For Arabidopsis, 1 µl of 1:100 diluted m6A and non-m6A spike-in controls from the same kit was added as a spike-in to 200 ng of non-ribosomal RNA isolated from the chromatin-associated fraction. RNA was fragmented using RNA Fragmentation Reagents (Invitrogen) by incubating at 70 °C for 6 minutes, followed by purification with the Oligo Clean & Concentrator Kit (Zymo Research). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer’s instructions. RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturers protocol.

tag: strain

tag: sample type

value: MeRIP-seq input


title: CUMC_E131


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1057N with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-D1057N
Cleavage site analysis of different PspCas13b mutants


title: Subject_029_Pre-immune

description: Individual participant of trial NCT00962681


title: caRNA MeRIP-seq input ALKBH5 FL mutant rep1

description:
Library name: SAMPLES19
column: caMeINmut5W_1
Expr_norm.tsv


title: CUMC_E130


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1057A with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-D1057A
Cleavage site analysis of different PspCas13b mutants


title: Subject_026_third dose

description: Individual participant of trial NCT00962680


title: caRNA MeRIP-seq input ALKBH5 del-cIDR mutant rep2

description:
Library name: SAMPLES18
column: caMeINmut5L2_2
Expr_norm.tsv


title: Subject_026_second dose

description: Individual participant of trial NCT00962679


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1027A with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-D1027A
Cleavage site analysis of different PspCas13b mutants


title: Subject_026_Pre-immune

description: Individual participant of trial NCT00962678


title: CUMC_E129


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_T136A with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-T136A
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq input Col-0 rep2

description:
Library name: SAMPLES16
column: caMeINcol0_2
Expr_norm.tsv


title: Subject_024_third dose

description: Individual participant of trial NCT00962677


title: CUMC_E127


title: CUMC_E128


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D129N with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-D129N
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq input Col-0 rep1

description:
Library name: SAMPLES15
column: caMeINcol0_1
Expr_norm.tsv


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D129H with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-D129H
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq input ALKBH5 del-cIDR mutant rep1

description:
Library name: SAMPLES17
column: caMeINmut5L2_1
Expr_norm.tsv


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_WT with targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-WT
Cleavage site analysis of different PspCas13b mutants


title: CUMC_E125


title: CUMC_E126


title: caRNA MeRIP-seq input ALKBH5 FL rep2

description:
Library name: SAMPLES14
column: caMeIN5W_2
Expr_norm.tsv


title: Subject_024_second dose

description: Individual participant of trial NCT00962676


title: Subject_023_third dose

description: Individual participant of trial NCT00962674


title: Subject_030_third dose

description: Individual participant of trial NCT00962686


title: Subject_024_Pre-immune

description: Individual participant of trial NCT00962675


title: CUMC_E122


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_N1060E with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-N1060E
Cleavage site analysis of different PspCas13b mutants

value: biological replicate 1


title: caRNA MeRIP-seq input ALKBH5 FL rep1

description:
Library name: SAMPLES13
column: caMeIN5W_1
Expr_norm.tsv


title: Subject_023_second dose

description: Individual participant of trial NCT00962673


title: Subject_023_Pre-immune

description: Individual participant of trial NCT00962672


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1057N with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-D1057N
Cleavage site analysis of different PspCas13b mutants


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_N1060A with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-N1060A
Cleavage site analysis of different PspCas13b mutants


title: CUMC_E120


title: Subject_022_second dose

description: Individual participant of trial NCT00962670


title: CUMC_E124


title: caRNA MeRIP-seq IP ALKBH5 FL mutant rep2

description:
Library name: SAMPLES10
column: caMeIPmut5W_2
m6A_norm.tsv

value: MeRIP-seq IP


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_WT with non-targeting crRNA, replicate 2)

description:
Library name: biol rep2 Psp-NT
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR mutant rep1

description:
Library name: SAMPLES7
column: caMeIPmut5L2_1
m6A_norm.tsv


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1057A with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-D1057A
Cleavage site analysis of different PspCas13b mutants


title: CUMC_E123


title: CUMC_E121


title: Subject_022_third dose

description: Individual participant of trial NCT00962671


title: caRNA MeRIP-seq IP Col-0 rep2

description:
Library name: SAMPLES6
column: caMeIPcol0_2
m6A_norm.tsv


title: caRNA MeRIP-seq input ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES11
column: caMeIN5L18_1
Expr_norm.tsv


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D1027A with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-D1027A
Cleavage site analysis of different PspCas13b mutants


title: CUMC_E118


title: CUMC_E119


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR mutant rep2

description:
Library name: SAMPLES8
column: caMeIPmut5L2_2
m6A_norm.tsv


title: Subject_021_third dose

description: Individual participant of trial NCT00962668


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D129N with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-D129N
Cleavage site analysis of different PspCas13b mutants


title: Subject_021_second dose

description: Individual participant of trial NCT00962667


title: caRNA MeRIP-seq IP ALKBH5 FL mutant rep1

description:
Library name: SAMPLES9
column: caMeIPmut5W_1
m6A_norm.tsv


title: Subject_021_Pre-immune

description: Individual participant of trial NCT00962666


title: Subject_022_Pre-immune

description: Individual participant of trial NCT00962669


title: caRNA MeRIP-seq IP Col-0 rep1

description:
Library name: SAMPLES5
column: caMeIPcol0_1
m6A_norm.tsv


title: caRNA MeRIP-seq IP ALKBH5 FL rep2

description:
Library name: SAMPLES4
column: caMeIP5W_2
m6A_norm.tsv


title: CUMC_E117


title: Subject_020_third dose

description: Individual participant of trial NCT00962665


title: CUMC_E116


title: CUMC_E115


title: CUMC_E113


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_T136A with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-T136A
Cleavage site analysis of different PspCas13b mutants


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_WT with non-targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-NT
Cleavage site analysis of different PspCas13b mutants


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting HTT-EGFP, cr6,  replicate 2)

description: Library name: biol rep2 Psp.T136A-cr6-HTT

data_processing:
bowtie2 (--score-min C,0,-1 --norc -k 1)
Assembly: ref01_halfEGFP.fa, ref02_ROSA_HTT.fa, ref03_EGFP_CKB.fa
Supplementary files format and content: Excel files of cleavage frequency for each cleavage position of each sample

extract_protocol:
RNA was extracted by RNA mini-prep (Zymo) according to manufacturer's instruction
To map the 5’ end of Cas13 cleavage sites on target RNA, we carried out 5’ RACE and an in vivo adaptor ligation method. For 5’ RACE, a template-switching oligo (TSO) was included during reverse transcription by following a previous protocol (EMBO Rep 2025, 26:1891). For the in vivo adaptor ligation library, the TSO is not required. A total of 2 rounds of PCR were performed to amplify the libraries using either a TSO-specific forward primer or an in vivo adaptor-specific forward primer, coupled with a target-gene-specific reverse primer.


title: CUMC_E114


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES1
column: caMeIP5L18_1
m6A_norm.tsv


title: CUT&tag H3K4me3 Col-0 rep2

description:
Library name: SAMPLES24
Bigwig files for merged bam
tagK4me3col0.bw

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

extract_protocol:
Nuclei were extracted from 10-day-old seedlings after germination
ATAC-seq was performed using the ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions. CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer's instructions.  CUT&RUNwas performed using the ChIC/CUT&RUN Assay Kit (Active Motif) following manufacturer's instructions.


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_WT with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-WT
Cleavage site analysis of different PspCas13b mutants


title: Subject_020_second dose

description: Individual participant of trial NCT00962664


title: caRNA MeRIP-seq IP ALKBH5 FL rep1

description:
Library name: SAMPLES3
column: caMeIP5W_1
m6A_norm.tsv


title: Subject_020_Pre-immune

description: Individual participant of trial NCT00962663


title: Different PspCas13b mutant cleavage site profiles (PspCas13b_D129H with targeting crRNA, replicate 1)

description:
Library name: biol rep1 Psp-D129H
Cleavage site analysis of different PspCas13b mutants


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES2
column: caMeIP5L18_2
m6A_norm.tsv


title: Subject_019_third dose

description: Individual participant of trial NCT00962662


title: Cleavage site profiles (PspCas13b with crRNA targeting HTT-EGFP, cr7,  replicate 2)

description: Library name: biol rep2 Psp-cr7-HTT


title: Subject_019_second dose

description: Individual participant of trial NCT00962661


title: Cleavage site profiles (PspCas13b with crRNA targeting HTT-EGFP, cr6,  replicate 2)

description: Library name: biol rep2 Psp-cr6-HTT


title: CUMC_E111


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting HTT-EGFP, cr7,  replicate 1)

description: Library name: biol rep1 Psp.T136A-cr7-HTT


title: CUMC_E112


title: Subject_017_third dose

description: Individual participant of trial NCT00962659


title: Subject_019_Pre-immune

description: Individual participant of trial NCT00962660


title: CUT&tag H3K4me3 ALKBH5 FL rep2

description:
Library name: SAMPLES22
Bigwig files for merged bam
tagK4me3-5w.bw


title: CUT&tag H3K4me3 ALKBH5 FL rep1

description:
Library name: SAMPLES21
Bigwig files for merged bam
tagK4me3-5w.bw


title: CUMC_E110


title: CUMC_E109


title: caRNA MeRIP-seq input ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES12
column: caMeIN5L18_2
Expr_norm.tsv


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting HTT-EGFP, cr6,  replicate 1)

description: Library name: biol rep1 Psp.T136A-cr6-HTT


title: CUMC_E107


title: Subject_017_second dose

description: Individual participant of trial NCT00962658


title: CUMC_E106


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting HTT-EGFP, cr7,  replicate 2)

description: Library name: biol rep2 Psp.T136A-cr7-HTT


title: Subject_015_third dose

description: Individual participant of trial NCT00962656


title: CUMC_E105


title: CUT&tag H3K27ac Col-0 rep1

description:
Library name: SAMPLES17
Bigwig files for merged bam
tagK27ACcol0.bw


title: Cleavage site profiles (PspCas13b with crRNA targeting mCherry-linker-EGFP, replicate 2)

description: Library name: biol rep2 Psp-ROSA


title: CUT&tag H3K4me3 Col-0 rep1

description:
Library name: SAMPLES23
Bigwig files for merged bam
tagK4me3col0.bw


title: Subject_012_third dose

description: Individual participant of trial NCT00962653


title: Cleavage site profiles (PspCas13b with crRNA targeting HTT-EGFP, cr7,  replicate 1)

description: Library name: biol rep1 Psp-cr7-HTT


title: CUT&tag H3K4me3 ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES19
Bigwig files for merged bam
tagK4me3-5L18.bw


title: CUT&tag H3K27ac ALKBH5 FL rep2

description:
Library name: SAMPLES16
Bigwig files for merged bam
tagK27AC5w.bw


title: CUMC_E103


title: Cleavage site profiles (PspCas13b with crRNA targeting HTT-EGFP, cr6,  replicate 1)

description: Library name: biol rep1 Psp-cr6-HTT


title: CUT&tag H3K27ac Col-0 rep2

description:
Library name: SAMPLES18
Bigwig files for merged bam
tagK27ACcol0.bw


title: CUT&tag H3K27ac ALKBH5 FL rep1

description:
Library name: SAMPLES15
Bigwig files for merged bam
tagK27AC5w.bw


title: Subject_017_Pre-immune

description: Individual participant of trial NCT00962657


title: Cleavage site profiles (Cas13bt1 with crRNA targeting mCherry-linker-EGFP, replicate 2)

description: Library name: biol rep2 bt1-ROSA


title: Subject_015_second dose

description: Individual participant of trial NCT00962655


title: CUMC_E104


title: CUT&tag H3K4me3 ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES20
Bigwig files for merged bam
tagK4me3-5L18.bw


title: CUMC_E102


title: CUMC_E108


title: Cleavage site profiles (Cas13bt1 with crRNA targeting mCherry-linker-EGFP, replicate 1)

description: Library name: biol rep1 bt1-ROSA


title: Subject_015_Pre-immune

description: Individual participant of trial NCT00962654


title: CUT&tag H3K27ac ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES14
Bigwig files for merged bam
tagK27AC5L18.bw


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting CKB, replicate 2)

description: Library name: biol rep2 Psp.T136A-CKB


title: Cleavage site profiles (SthCsm with crRNA targeting CKB, replicate 2)

description: Library name: biol rep2 Csm-CKB


title: Subject_012_Pre-immune

description: Individual participant of trial NCT00962651


title: CUT&tag H3K27ac ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES13
Bigwig files for merged bam
tagK27AC5L18.bw


title: CUMC_E100


title: Subject_012_second dose

description: Individual participant of trial NCT00962652


title: Cleavage site profiles (PspCas13b with crRNA targeting CKB, replicate 2)

description: Library name: biol rep2 Psp-CKB


title: Subject_009_second dose

description: Individual participant of trial NCT00962649


title: CUT&RUN Flag Col-0 rep2

description:
Library name: SAMPLES12
Bigwig files for merged bam
RunFlagcol0.bw

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10
Supplementary files format and content: bigwig
Library strategy: CUT&Run


title: Cleavage site profiles (PspCas13b with crRNA targeting mCherry-linker-EGFP, replicate 1)

description: Library name: biol rep1 Psp-ROSA


title: CUMC_E101


title: CUT&RUN Flag ALKBH5 FL rep2

description:
Library name: SAMPLES10
Bigwig files for merged bam
RunFlag5W.bw


title: Cleavage site profiles (SthCsm with crRNA targeting CKB, replicate 1)

description: Library name: biol rep1 Csm-CKB


title: CUMC_E97


title: CUT&RUN Flag ALKBH5 FL rep1

description:
Library name: SAMPLES9
Bigwig files for merged bam
RunFlag5W.bw


title: Cleavage site profiles (PspCas13b.T136A with crRNA targeting CKB, replicate 1)

description: Library name: biol rep1 Psp.T136A-CKB


title: CUMC_E96


title: CUMC_E98


title: Cleavage site profiles (PspCas13b with crRNA targeting CKB, replicate 1)

description: Library name: biol rep1 Psp-CKB


title: Subject_009_third dose

description: Individual participant of trial NCT00962650


title: Subject_008_third dose

description: Individual participant of trial NCT00962647


title: Subject_009_Pre-immune

description: Individual participant of trial NCT00962648


title: Subject_008_Pre-immune

description: Individual participant of trial NCT00962645


title: CUT&RUN Flag ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES8
Bigwig files for merged bam
RunFlag5L18.bw


title: CUMC_E95


title: Cleavage site profiles (In vivo adaptor ligation of PspCas13b with crRNA targeting EGFP, replicate 2)

description: Library name: biol rep2 ligation-Psp-EGFP7


title: Cleavage site profiles (5' RACE of PspCas13b with crRNA targeting EGFP, replicate 2)

description: Library name: biol rep2 5RACE-Psp-EGFP7


title: ATAC Col-0 rep2

description:
Library name: SAMPLES6
Bigwig files for merged bam
ataccol0.bw

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10
Supplementary files format and content: bigwig


title: CUT&RUN Flag ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES7
Bigwig files for merged bam
RunFlag5L18.bw


title: CUT&RUN Flag Col-0 rep1

description:
Library name: SAMPLES11
Bigwig files for merged bam
RunFlagcol0.bw


title: CUMC_E94


title: ATAC Col-0 rep1

description:
Library name: SAMPLES5
Bigwig files for merged bam
ataccol0.bw


title: Cleavage site profiles (5' RACE of PspCas13b with crRNA targeting EGFP, replicate 1)

description: Library name: biol rep1 5RACE-Psp-EGFP7


title: Subject_008_second dose

description: Individual participant of trial NCT00962646


title: CUMC_E99


title: CUMC_E91


title: CUMC_E92


title: Cleavage site profiles (Csm:EGFP2, replicate 2)

description: Library name: biol rep2 CsmEGFP2


title: Subject_007_third dose

description: Individual participant of trial NCT00962644


title: ATAC ALKBH5 FL rep2

description:
Library name: SAMPLES4
Bigwig files for merged bam
atac5w.bw


title: Subject_007_second dose

description: Individual participant of trial NCT00962643


title: Subject_007_Pre-immune

description: Individual participant of trial NCT00962642


title: ATAC ALKBH5 FL rep1

description:
Library name: SAMPLES3
Bigwig files for merged bam
atac5w.bw


title: Cleavage site profiles (Csm:EGFP2, replicate 1)

description: Library name: biol rep1 CsmEGFP2


title: ATAC ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES2
Bigwig files for merged bam
atac5L18.bw


title: Subject_006_third dose

description: Individual participant of trial NCT00962641


title: CUMC_E90


title: CUMC_E93


title: Cleavage site profiles (halfEGFP, replicate 2)

description: Library name: biol rep2 CtEGFP


title: Cleavage site profiles (In vivo adaptor ligation of PspCas13b with crRNA targeting EGFP, replicate 1)

description: Library name: biol rep1 ligation-Psp-EGFP7


title: Subject_006_Pre-immune

description: Individual participant of trial NCT00962639


title: Subject_006_second dose

description: Individual participant of trial NCT00962640


title: CUMC_E88


title: Δafu-182 grown at 42˚C, biol rep 3

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

description: Library name: Del_42_3

data_processing:
Reads were quality controlled with fastp
Trimmed reads were aligned with STAR v2.7.11a to the A1163 genome
Alignments were transformed to BAM file and processed with featureCounts (subread package v 2.0.6) to obtain per gene read counts
DESeq analysis of the treatment to produced the normalized read counts
Assembly: Aspergillus_fumigatus_A1163 VEuPathDB release 68 // GCA_000150145.1
Supplementary files format and content: tab delimited file with read counts per experiment by gene
Supplementary files format and content: tab delimited FPM normalized

organism: Aspergillus fumigatus

growth_protocol: Fungal strains were grown at 25˚C, 37˚C, or 42˚C for 72 hours  in glucose minimal medium.

extract_protocol:
AGPC method, followed by silica membrane based column purification, DNAse treatment and magnetic beads purification
Illumina’s TruSeq-stranded-mRNA sample preparation protocol

value: pyrG-;delta afu-182::pyrG

tag: replicate


title: CUMC_E89

value: Epithelium


title: Cleavage site profiles (halfEGFP, replicate 1)

description: Library name: biol rep1 CtEGFP


title: Subject_005_second dose

description: Individual participant of trial NCT00962637


title: SW480-Bsg-3

city: Innsbruck

first: Markus

last: Hartl

state: Tyrol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

description:
Library name: sample 9
endogenous BASP1

data_processing:
Demultiplexing and trimming of Illumina adapter residuals
Total demultiplexed reads: 728'539'558 Total demultiplexed bases: 100'370'275'768 Mean read length: 138 bp Q20 %: 97 Q30 %: 93 Mean Q: 36 Masked: 613273
Detailed results: Summary_File_Reads.xlsx
Assembly: Differential gene expression analysis using GRCh37 (Ensembl) reference (Homo sapiens)
Supplementary files format and content: processed data filtered (fastq.gz format)
Supplementary files format and content: processed data RNA mapped (txt format)

source_name: adenocarcinoma

growth_protocol: The large intestine hypotriploid cell line SW480 from Dukes C colorectal cancer (CCL-228) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW480 was cultivated using the original Leibovitz L-15 medium with no additional CO2 supplemented with 10% (v/v) FBS in a water-saturated atmosphere. The cell lines SW480-B and SW480-gRNA-B-all (Bsg) are derivatives of SW480.

extract_protocol:
Total RNA was isolated using the Monarch total RNA miniprep kit (New England Biolabs cat. no.T2010S)
Illumina stranded TruSeq RNA library incl. poly(A) enrichment for sequencing on Illumina NovaSeq, 2*150 bases

treatment_protocol: To generate SW480-B, SW480 cells were nucleofected with the pcDNA3-BASP1 construct using the cell line nucleofector kit V (Lonza, Basel, Switzerland) and the program L-24. To construct pcDNA3-BASP1, the PCR-amplified coding sequence of human BASP1 was inserted into pcDNA3 (Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA) containing a cytomegalovirus (CMV) promoter. Transfected cells were selected with geneticin (G418) (1 mg/ml), and surviving cells subjected to single cell cloning in 96-well plates using appropriate dilutions. Constitutive BASP1-expressing cell clones were first verified by immunoblot analysis and then expanded into cell lines. The CRISPR (clustered regularly interspaced short palindromic repeats)-based techniques was used for transcriptional BASP1 activation. For oligodeoxynucleotide design encoding small guide (sg) RNAs (SI, Table 1), the programs e-crisp (e crispr.org) and chopchop (chopchop.cbu.uib.no) were used. Initially, four different sgRNAs were designed to reactivate the BASP1 gene. Corresponding double-stranded oligodeoxynucleotides were inserted into the lenti sgRNA(MS2)-puro plasmid using the two BsmBI restriction enzyme sites. lenti sgRNA(MS2)_puro optimized backbone was a gift from Feng Zhang (Addgene plasmid # 73797; http://n2t.net/addgene:73797; RRID:Addgene_73797). SW480-derived lines with reactivated endogenous BASP1 (SW480-gRNA-B1, -B3, -B-all) were generated by three lentiviral transduction steps, each after viral stock preparation. For this, 10 µg of the relevant lentiviral vector and each 5 µg of pMD2.G and psPAX2 were transfected into sub-confluent HEK293T cells grown on a 100-mm dish using the transfection reagent TransIT-LT1 (mirus/Merck, Darmstadt, Germany). pMD2.G and psPAX2 were gifts from Didier Trono (Addgene plasmid # 12259; http://n2t.net/addgene:12259; RRID:Addgene_12259, and Addgene plasmid # 12260; http://n2t.net/addgene:12260; RRID:Addgene_12260, respectively). After 48 h, lentivirus was harvested, filtrated using a polyvinylidene fluoride (PVDF) filter with 0.45 µM pore size, and subjected to ultracentrifugation at 16,500 × g for 2.5 h at 4 °C. For viral transduction, polybrene (hexadimethrine bromide, H9268, Sigma-Aldrich, St. Louis, MO, USA) was added to the filtered lentiviral medium (8 µg/ml). Transduction of SW480 cells was performed via spinoculation at 700 × g for 45 min at 22 °C. After 48 h, cells were selected with respective antibiotics. SW480 cells were first transduced with virus derived from lenti MS2-P65-HSF1-Hygro. lenti MS2-P65-HSF1_Hygro was a gift from Feng Zhang (Addgene plasmid # 61426; http://n2t.net/addgene:61426; RRID:Addgene_61426). After hygromycin B selection (600 µg/ml), the resulting cell line termed SW480-MS2 was transduced with virus derived from dCas9-VP64-GFP. dCAS9-VP64_GFP was a gift from Feng Zhang (Addgene plasmid # 61422; http://n2t.net/addgene:61422; RRID:Addgene_61422). Cells were analyzed for GFP expression via flow cytometry, and single cell cloning was then performed on GFP-positive cells resulting in the cell line SW480-MS2-dCas9. These cells were subsequently transduced with virus derived from lenti sgRNA(MS2)-puro derivatives, encoding the BASP1 promoter-specific sgRNAs. lenti sgRNA(MS2)_puro optimized backbone was a gift from Feng Zhang (Addgene plasmid # 73797; http://n2t.net/addgene:73797; RRID:Addgene_73797). Thereby viruses containing individual or pooled sgRNA plasmids were applied. Transduced cells were selected with puromycin (1 µg/ml), characterized by immunoblot analysis to test for BASP1 expression, and then expanded into the final cell lines.

value: adenocarcinoma

value: colorectal cancer

value: CRISPRa BASP1

value: BASP1 activation


title: Subject_005_third dose

description: Individual participant of trial NCT00962638

value: Blood

value: Serum


title: Subject_005_Pre-immune

description: Individual participant of trial NCT00962636


title: Δafu-182 grown at 42˚C, biol rep 2

description: Library name: Del_42_2


title: Δafu-182 grown at 42˚C, biol rep 1

description: Library name: Del_42_1


title: CUMC_E86

value: Primary


title: ATAC ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES1
Bigwig files for merged bam
atac5L18.bw

value: Whole seedling


title: CUMC_E85


title: Δafu-182 grown at 37˚C, biol rep 2

description: Library name: Del_37_2


title: Subject_004_third dose

description: Individual participant of trial NCT00962635


title: CUMC_E82


title: Subject_004_second dose

description: Individual participant of trial NCT00962634


title: SW480-Bsg-1

description:
Library name: sample 7
endogenous BASP1


title: Subject_003_second dose

description: Individual participant of trial NCT00962631


title: CUMC_E87


title: Δafu-182 grown at 37˚C, biol rep 1

description: Library name: Del_37_1


title: CUMC_E83


title: SW480-B-2

description:
Library name: sample 5
exogenous BASP1

value: ectopic BASP1


title: Δafu-182 grown at 25˚C, biol rep 3

description: Library name: Del_25_3


title: CUMC_E84


title: Subject_003_third dose

description: Individual participant of trial NCT00962632


title: SW480-Bsg-2

description:
Library name: sample 8
endogenous BASP1


title: SW480-2

description:
Library name: sample 2
wild type

value: WT


title: Subject_004_Pre-immune

description: Individual participant of trial NCT00962633


title: SW480-B-1

description:
Library name: sample 4
exogenous BASP1


title: Δafu-182 grown at 37˚C, biol rep 3

description: Library name: Del_37_3


title: Δafu-182 grown at 25˚C, biol rep 1

description: Library name: Del_25_1


title: SW480-1

description:
Library name: sample 1
wild type


title: SW480-B-3

description:
Library name: sample 6
exogenous BASP1


title: Δafu-182 grown at 25˚C, biol rep 2

description: Library name: Del_25_2


title: SW480-3

description:
Library name: sample 3
wild type


title: Subject_002_third dose

description: Individual participant of trial NCT00962629


title: CUMC_E79


title: CUMC_E80


title: WT CEA10 grown at 42˚C, biol rep 2

description: Library name: WT_42_2


title: Subject_002_second dose

description: Individual participant of trial NCT00962628


title: Subject_003_Pre-immune

description: Individual participant of trial NCT00962630


title: HepaRG cells, BX795 & siADAR, replicate 1

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

description: Library name: BX795_siADAR_1

data_processing:
Alignment utilized the nf-core (v24.10.5) RNA-Seq (v3.18.0) pipeline (doi: 10.5281/zenodo.1400710). STAR alignment was modified with ENCODE settings: (outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000)
Transcript counts were generated using the default pipeline approach of STAR alignments followed by Salmon quantification. Gene count matrices were generated in R using tximport(files, type = "salmon", tx2gene = tx2gene) of the resulting transcript counts
Assembly: The GENCODE v48 primary comprehensive annotation and GRCH38.p14 primary assembly were used.
Supplementary files format and content: comma-delimited gene counts file for all samples with gene-level quantifications

source_name: HepaRG

growth_protocol: HepaRG® cells were purchased from Biopredic International (Saint Grégoire, France) and cultured and differentiated according to the manufacturer’s protocols. Undifferentiated cells were maintained in HepaRG growth media: William’s E Media (A1217601, Gibco™, ThermoFisher), HepaRG Growth media supplement (ADD711C, Biopredic International), 1x GlutaMAX™ (Gibco™, ThermoFisher), 1x P/S (Gibco™, ThermoFisher). Cell differentiation and maintenance occurred in the same media, but the HepaRG differentiation supplement (ADD721C, Biopredic International) was substituted for the growth supplement. Undifferentiated cells were seeded into 12-well plates, expanded, and differentiated.

extract_protocol:
Total RNA was extracted using TRI Reagent® (Zymo Research, CA, USA) and purified using the Direct-zol RNA Miniprep kit (Zymo Research, CA, USA
For library preparation, ribosomal RNAs were removed by Illumina epidemiology rRNA Removal Kits, and the RNA-seq library was processed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. The library was barcoded, enriched, and purified using Agencourt AMPure beads (Beckman Coulter, catalog # A63881). The size and mass of the library were assessed using the Agilent TapeStation with a DNA5000 Screen Tape. Quantitative PCR was used to validate the library's functionality using the NEBNext Library Quantification kit for Illumina (NEB, E7630S). The libraries were pooled at equal molar concentrations and sequenced on an Illumina NovaSeq 6000 at the University of Florida ICBR NextGen Sequencing Core (RRID: SCR_019152). The pooled library was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2 x 150 cycles) with 1% PhiX spike-in control.

treatment_protocol: Differentiated HepaRG cells were transfected using Lipofectamine™ RNAiMAX (ThermoFisher) following the manufacturer’s protocol with 20 nM Silencer™ Select siRNAs (ThermoFisher): ADAR (siRNA ID#: s1007), ADARB1 (siRNA ID#: s1010), or the Silencer™ Select negative control #1. Twenty-four hours after transfection, the media was replaced with HepaRG differentiation media. Forty-eight hours post-transfection, the media was changed to a serum-free induction media composed of William’s E Media (A1217601), 1x GlutaMAX™, 1x P/S, 1x ITS (41400045), 15 mM HEPES (Gibco™, ThermoFisher). Treatment with IFNα (1000 U/mL) and BX795 (1 µM) coincided with siRNA transfection. More specifically, both compounds were included in the media on the day of transfection and maintained throughout media changes

value: HepaRG

value: Hepatic carcinoma

value: BX795 & ADAR knockdown

value: siADAR, 1 uM BX795

value: batch 2


title: CUMC_E81


title: WT CEA10 grown at 42˚C, biol rep 3

description: Library name: WT_42_3


title: CUMC_E78


title: CUMC_E75


title: HepaRG cells, BX795 & siADAR, replicate 2

description: Library name: BX795_siADAR_2


title: HepaRG cells, BX795, replicate 1

description: Library name: BX795_1

value: BX795 treated

value: 1 uM BX795


title: WT CEA10 grown at 37˚C, biol rep 2

description: Library name: WT_37_2


title: CUMC_E77

value: Epithelium


title: Subject_001_second dose

description: Individual participant of trial NCT00962625


title: Subject_002_Pre-immune

description: Individual participant of trial NCT00962627


title: HepaRG cells, BX795, replicate 3

description: Library name: BX795_3


title: CUMC_E74


title: WT CEA10 grown at 42˚C, biol rep 1

description: Library name: WT_42_1


title: Subject_001_third dose

description: Individual participant of trial NCT00962626


title: WT CEA10 grown at 37˚C, biol rep 3

description: Library name: WT_37_3


title: D80 human-chimp-orang-macaque interspecies pools, CHIR0.8, replicate 3, ATAC

city: San Francisco

first: Alex

last: Pollen

address: 651 4th Street

institute: UCSF

description: Library name: D80_M_0-8_CNTRL-3_ATAC

library_source: genomic single cell

data_processing:
Demultiplexing of species and cell line identity was done using cellbouncer (https://github.com/nkschaefer/cellbouncer)
snRNA-seq and snATAC-seq library FASTQs were pre-processed using cellranger-arc version 2.0.2 (10x Genomics) and aligned to either an ancestral genome or to individual species genomes hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque)
For snRNA-seq data: cell doublets were deteced and removed based on species and individual demultiplexing. During the processign of the GEX data, cells with more than 15% mitochondrial reads or more then 10% ribosomal reads were removed. Cells were also filtered based on the number of genes (< 1,000 or > 7,500 for D40-100, and <500 or > 7,500 for D16) and reads (< 1,000) and any gene detected in less than 10 cells was removed. Counts in cells were then normalized by read depth (CPM normalization), log transformed and then scaled to unit variance and zero mean, with a max value of 10.
To obtain clusters with merged species identities, we applied Batch Integration of batch-balanced k-nearest neighbors (BBKNN) to the developmental data sets. Because rotenone exposure reduced cell type marker gene expression and made it more difficult to delineate homologous cell types across species, we used a slightly different approach to integrate and cluster the rotenone data set. we performed reciprocal PCA (rPCA)-based integration to integrate data from each sequencing library for each species and rotenone time point using Seurat default rPCA parameters.We classified cells as DA neurons if they belonged to subclusters with marker expression of established DA markers, including TH, NR4A2, EN1 and LMX1A.
For snATAC-seq data: Signac v1.13.9003152 was used to quantify counts for each species for the original peak set called for each species (after merging across cell types), CrossPeak consensus peaks, and CrossPeak species-only peaks in each species’ own genome coordinates. Cells that passed snRNA-seq quality filters and had cell type identities assigned based on snRNA-seq were included, and further filtered (quality metrics calculated based on each species’ original peak set) to retain cells with TSSenrichment (as calculated with Signac function TSSEnrichment()) > 2 and counts > 1000.
Fragment count matrix for scATAC-seq was generated using PycisTopic from the fragments files output by cellranger using consensus peak set defined in each species.
MULTIseq library FASTQs were processed using py-multi-seq (https://github.com/mtvector/py-multi-seq)
Assembly: Individual species' genomes:hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). Ancestral genome: our reference data were aligned and annotated in a prior study (Mao et al. 2021, PMID: 33953399).The authors aligned many human and nonhuman primate genomes using Progressive Cactus (Armstrong et al. 2020, PMID: 33177663) and annotated them using the Comparative Annotation Toolkit (CAT) (Fiddes et al. 2018, PMID: 29884752) with the human Gencode annotation v33 (Frankish et al. 2021, PMID: 33270111) as the source for homology-based annotations. The genome assembly versions that we used from this alignment were hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). As part of its alignment strategy, Progressive Cactus imputes the genome of the most recent common ancestor of each group of genomes it aligns, and we chose to use the Homo/Pan most recent common ancestor (MRCA) for snRNA-seq alignment to mitigate reference bias toward either the human or chimpanzee lineage.
Supplementary files format and content: GEX_pre-QC.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs all cells before quality control and filtering.
Supplementary files format and content: GEX_processed-clustered.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs cells that passed quality control and filtering and that were used for clustering.
Supplementary files format and content: GEX_ancestral_sce.rds files are SingleCellExperiment objects with RNA counts after alignments to the ancestral genome
Supplementary files format and content: D80-rotenone-exp_GEX.h5ad contains GEX data from the rotenone experiment, before subsetting DA lineage cells
Supplementary files format and content: D80-rotenone-exp_GEX_DA_subset.h5ad contains GEX data from the rotenone expeiement, after subsetting the DA lineage cells that were used for the analysis in Figure 7
Supplementary files format and content: D40-100_ATAC_human_specific_sce.rds and D40-100_ATAC_chimp_specific_sce.rds files are SingleCellExperiment objects with human-specific or chimp-specific ATAC peaks counts
Supplementary files format and content: D40-100_ATAC_consensus_sce.rds is a SingleCellExperiment object with consensus ATAC peaks counts for  human, chimp, and rhesus
Supplementary files format and content: D40-100_ATAC_seurat.rds is a Seurat object with consensus ATAC peaks - data integrated across species including the UMAP calculated
Supplementary files format and content: cistopic_obj.pk files are fragment count matrices for scATAC-seq
Supplementary files format and content: multiseq_calls.csv list the MULTIseq call assignment after demultiplexing with py-multi-seq
Supplementary files format and content: MULTIseq_counts.txt are MULTIseq count tables after demultiplexing with py-multi-seq

organism:
Macaca mulatta
Pan troglodytes
Pongo abelii
Homo sapiens

extract_protocol:
D16 ventral midbrain progenitors were dissociated for 10 min in Accutase, counted and distributed into Eppendorf tubes at 1-2 million cells per tube. The cells were centrifuged at 400 x g for 5 min and all liquid was removed before the tubes were dipped into an isopentane bath on dry ice for flash freezing To isolate the nuclei from D16 progenitors, the 10x Genomics demonstrated protocol 'Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000365 - Rev B) was used with a few modifications. The cells were incubated for 4 min on ice in 0.1x lysis buffer and washed in wash buffer containing 2% BSA.  After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM. D40, 80 and 100 organoids were cut into smaller pieces under a dissection microscope using scalpels (halves or quarters depending on time point). For the D40 time point, 20 organoids were placed in each tube and for D80-100, 10-15 organoids were used. The tubes were centrifuged at 100x g for 2 min to remove all the liquid and then dipped into an isopentane bath on dry ice for flash freezing. To isolate nuclei from organoids, the 10x demonstrated protocol Nuclei Isolation from Embryonic Mouse Brain for 'Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000366 - Rev C) was used and the organoid pieces were incubated for 5 + 5 min on ice in 0.1x lysis buffer and then washed in wash buffer containing 2% BSA. For the D80 and D100 organoid samples, two additional x washes were added to the procedure to remove as much debris as possible. After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM.
Library was constructed according to manufacturer's instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev C). To prepare the MULTIseq library, 10 μl of the product from ‘Pre-Amplification SPRI Cleanup’ (Step 4.3 in above protocol) portion of the 10x was used and libraries were constructed as described in McGinnis et al. 2019 [PMID: 31209384]

value: PSC-derived midbrain organoids


title: HepaRG cells, BX795, replicate 2

description: Library name: BX795_2


title: Subject_001_Pre-immune

description: Individual participant of trial NCT00962624


title: D80 human-chimp-orang-macaque interspecies pools, CHIR0.8, replicate 3, GEX

description: Library name: D80_M_0-8_CNTRL-3_GEX


title: CUMC_E71


title: HepaRG cells, siNC Control for BX795&IFNa treatments, replicate 3

description: Library name: Con_IFNa_3

value: Control for BX795/IFNa treatments

value: siNC


title: CUMC_E76


title: CUMC_E70


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 3, GEX

description: Library name: D80_outgroup-exp_3_GEX


title: HepaRG cells, IFNa, replicate 2

description: Library name: IFNa_2

value: IFNa treated

value: 1000 U/mL IFNa


title: D80 human-chimp-orang-macaque interspecies pools, CHIR0.8, replicate 2, ATAC

description: Library name: D80_M_0-8_CNTRL-2_ATAC


title: FB,GLU,rep12

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Library name: 1032

data_processing:
Library construction, sequencing on the DNB-sequencing platform, and read clean-up were performed at Beijing Genomics Institute (BGI, Hong Kong, China). Quality check of the clean reads was performed using FASTQC , reads were aligned to the Drosophila melanogaster genome (BDGP6.46) using STAR2.7, and counts were quantified using HTSeq.
Assembly: BDGP6.46
Supplementary files format and content: Raw counts from HTseq, in txt file

organism: Drosophila melanogaster

source_name: Abdominal carcasses

extract_protocol:
Twenty-eight days after eclosion, adult female flies from GLU-HGLU and GLUGAL-HGLU groups were anesthetized under CO2 and dissected in cold, RNase-free PBS under a stereomicroscope, and the abdominal carcasses were isolated (the dorsal body wall tissue with removal of internal organs like digestive tract and ovary, etc., retaining primarily metabolic organs including fat body and oenocyte) and were snap frozen in liquid nitrogen. Each group had 12 biological replicates (pools of 10 abdominal carcasses per replicate). Total RNA was extracted from pooled abdomens using Invitrogen Trizol reagent (Thermo Fisher Scientific, Schwerte, Germany), according to the manufacturer’s instructions. RNA integrity was verified on the Agilent 2100 Tapestation (Agilent Technologies Inc, Santa Clara, CA, USA); all samples had a RNA integrity number above 7.
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: Abdominal carcasses

value: Female

value: GLU-HGLU


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 2, ATAC

description: Library name: D80_outgroup-exp_2_ATAC


title: CUMC_E69

value: Primary


title: CUMC_E73


title: HepaRG cells, siNC Control for BX795&IFNa treatments, replicate 1

description: Library name: Con_IFNa_1

value: HepaRG


title: D80 human-chimp-orang-macaque interspecies pools, CHIR0.8, replicate 2, GEX

description: Library name: D80_M_0-8_CNTRL-2_GEX


title: WT CEA10 grown at 25˚C, biol rep 2

description: Library name: WT_25_2

value: WT


title: WT CEA10 grown at 37˚C, biol rep 1

description: Library name: WT_37_1


title: FB,GLU,rep11

description: Library name: 1031


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 2, GEX

description: Library name: D80_outgroup-exp_2_GEX


title: HepaRG cells, siNC Control for BX795&IFNa treatments, replicate 2

description: Library name: Con_IFNa_2

value: Hepatic carcinoma


title: WT CEA10 grown at 25˚C, biol rep 3

description: Library name: WT_25_3


title: CUMC_E72


title: FB,GLUGAL,rep12

description: Library name: 1027

value: GLUGAL-HGLU


title: HepaRG cells, IFNa, replicate 1

description: Library name: IFNa_1

value: batch 2


title: CUMC_E67


title: WT CEA10 grown at 25˚C, biol rep 1

description: Library name: WT_25_1


title: HepaRG cells, siADARB1, replicate 2

description: Library name: siADARB1_2

value: ADARB1 knockdown

value: batch 1


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 3, ATAC

description: Library name: D80_outgroup-exp_3_ATAC


title: HepaRG cells, siADARB1, replicate 3

description: Library name: siADARB1_3


title: FB,GLUGAL,rep11

description: Library name: 1024


title: CUMC_E68

value: Epithelium


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 1, ATAC

description: Library name: D80_outgroup-exp_1_ATAC

value: PSC-derived midbrain organoids


title: HepaRG cells, siADARB1, replicate 1

description: Library name: siADARB1_1


title: CUMC_E9


title: FB,GLU,rep10

description: Library name: 1023


title: D80 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 1, GEX

description: Library name: D80_outgroup-exp_1_GEX


title: HepaRG cells, siADAR, replicate 2

description: Library name: siADAR_2

value: ADAR knockdown

value: siADAR


title: D40 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 2, ATAC

description: Library name: D40_outgroup-exp_2_ATAC


title: D40 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 2, GEX

description: Library name: D40_outgroup-exp_2_GEX


title: CUMC_E7


title: HepaRG cells, siADAR, replicate 3

description: Library name: siADAR_3


title: CUMC_E66


title: FB,GLUGAL,rep10

description: Library name: 1022


title: HepaRG cells, siADAR, replicate 1

description: Library name: siADAR_1


title: CUMC_E8


title: D40 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 1, GEX

description: Library name: D40_outgroup-exp_1_GEX


title: D40 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, replicate 1, ATAC

description: Library name: D40_outgroup-exp_1_ATAC


title: CUMC_E65


title: HepaRG cells, siNC Control, replicate 3

description: Library name: siNC_3

value: Control

value: siNC


title: FB,GLU,rep8

description: Library name: 1020

value: Abdominal carcasses


title: FB,GLUGAL,rep9

description: Library name: 1018

value: Female


title: FB,GLU,rep9

description: Library name: 1021

value: GLU-HGLU


title: HepaRG cells, siNC Control, replicate 2

description: Library name: siNC_2


title: D16 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8,  ATAC

description: Library name: D16_outgroup-exp_ATAC

value: PSC-derived midbrain progenitors


title: HepaRG cells, siNC Control, replicate 1

description: Library name: siNC_1

value: HepaRG


title: IMR-90 SV40-T cells expressing H2B E76R

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description: Library name: IMR90_H2B_E76R

data_processing:
Raw sequencing data were processed using Cell Ranger (v8.0.0) for demultiplexing, alignment to GRCh38 and generation of gene-barcode matrices. Further filtering and analysis were performed using Scanpy (v1.9.8).
Assembly: GRCh38
Supplementary files format and content: Scanpy ANN data objects.

growth_protocol: IMR-90 SV40-T cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin/streptomycin at 37°C in 5% CO₂ and 5% O₂.

extract_protocol:
Single-cell suspensions were prepared and loaded onto the Chromium controller for partitioning and barcoding.
Libraries were prepared using the Chromium Single Cell 3’ v3.1 kit (10x Genomics) following the manufacturer’s protocol.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: fibroblast

value: SV40-T, H2B E76R


title: CUMC_E63

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

value: Primary


title: D16 orang-macaque single individuals, human-chimp intraspecies pools, CHIR0.8, GEX

description: Library name: D16_outgroup-exp_GEX


title: CUMC_E64


title: FB,GLUGAL,rep8

description: Library name: 1017

value: GLUGAL-HGLU


title: FB,GLUGAL,rep7

description: Library name: 1016


title: FB,GLUGAL,rep6

description: Library name: 1015


title: CUMC_E62


title: D80 ROT-72H human-chimp-orang-macaque interspecies pools, CHIR0.8, ATAC

description: Library name: D80_M_0-8_72H_ATAC

value: 500 nM Rotenone, 72 hours


title: IMR-90 SV40-T cells expressing H2B E76K

description: Library name: IMR90_H2B_E76K

value: SV40-T, H2B E76K


title: D80 ROT-72H human-chimp-orang-macaque interspecies pools, CHIR0.8, GEX

description: Library name: D80_M_0-8_72H_GEX


title: FB,GLUGAL,rep5

description: Library name: 1014


title: CUMC_E60

value: Epithelium


title: IMR-90 SV40-T cells expressing H2B WT

description: Library name: IMR90_H2B_WT

value: SV40-T, H2B WT


title: D80 ROT-72H human-chimp-orang-macaque interspecies pools, CHIR0.6, ATAC

description: Library name: D80_M_0-6_72H_ATAC

value: PSC-derived midbrain organoids


title: CUMC_E61


title: CUMC_E6


title: FB,GLUGAL,rep4

description: Library name: 1013


title: IMR-90 SV40-T cells, SLAM, E76R, rep 3

description: Library name: IMR90_SV40T_SLAM_E76R_rep3

data_processing:
Reads were trimmed for low-quality bases (Q<20) using Trimmomatic and aligned to the GRCh38 reference genome. T>C conversions were quantified using the SLAM-DUNK pipeline, which includes filtering, mapping, mutation calling and quantification. Differential expression analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing normalized T>C conversion counts per transcript per sample.

source_name: IMR-90 SV40-T

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq V2 FWD Library Generation Module (Lexogen) with Lexogen UDI 12 nt Set A1 and amplified using the Library Amplification Module.

treatment_protocol: 100 µM 4sU for 6 h

value: IMR-90 SV40-T

value: Fibroblast

value: H2B E76R

value: 100 µM 4sU for 6 h


title: FB,GLUGAL,rep2

description: Library name: 1011

value: Abdominal carcasses

value: Female


title: D80 ROT-24H human-chimp-orang-macaque interspecies pools, CHIR0.8, ATAC

description: Library name: D80_M_0-8_24H_ATAC

value: 500 nM Rotenone, 24 hours


title: D80 ROT-72H human-chimp-orang-macaque interspecies pools, CHIR0.6, GEX

description: Library name: D80_M_0-6_72H_GEX


title: CUMC_E59


title: FB,GLU,rep6

description: Library name: 108

value: GLU-HGLU


title: D80 ROT-24H human-chimp-orang-macaque interspecies pools, CHIR0.6, GEX

description: Library name: D80_M_0-6_24H_GEX


title: D80 ROT-24H human-chimp-orang-macaque interspecies pools, CHIR0.8, GEX

description: Library name: D80_M_0-8_24H_GEX


title: IMR-90 SV40-T cells, SLAM, E76R, rep 1

description: Library name: IMR90_SV40T_SLAM_E76R_rep1


title: IMR-90 SV40-T cells, SLAM, E76K, rep 1

description: Library name: IMR90_SV40T_SLAM_E76K_rep1

value: H2B E76K


title: CUMC_E58


title: CUMC_E57


title: IMR-90 SV40-T cells, SLAM, E76K, rep 2

description: Library name: IMR90_SV40T_SLAM_E76K_rep2


title: FB,GLUGAL,rep1

description: Library name: 1010


title: IMR-90 SV40-T cells, SLAM, E76R, rep 2

description: Library name: IMR90_SV40T_SLAM_E76R_rep2


title: D80 ROT-24H human-chimp-orang-macaque interspecies pools, CHIR0.6, ATAC

description: Library name: D80_M_0-6_24H_ATAC


title: CUMC_E55


title: FB,GLU,rep5

description: Library name: 107


title: CUMC_E56


title: IMR-90 SV40-T cells, SLAM, E76K, rep 3

description: Library name: IMR90_SV40T_SLAM_E76K_rep3


title: D80 CNTRL human-chimp-orang-macaque interspecies pools, CHIR0.8, ATAC

description: Library name: D80_M_0-8_CNTRL_ATAC


title: FB,GLU,rep7

description: Library name: 109


title: D80 CNTRL human-chimp-orang-macaque interspecies pools, CHIR0.8, GEX

description: Library name: D80_M_0-8_CNTRL_GEX


title: IMR-90 SV40-T cells, SLAM, WT, rep 3

description: Library name: IMR90_SV40T_SLAM_WT_rep3

value: H2B WT


title: FB,GLU,rep4

description: Library name: 106


title: FB,GLUGAL,rep3

description: Library name: 1012


title: CUMC_E54

value: Primary


title: CUMC_E53


title: IMR-90 SV40-T cells, SLAM, WT, rep 2

description: Library name: IMR90_SV40T_SLAM_WT_rep2


title: FB,GLU,rep3

description: Library name: 105


title: IMR-90 SV40-T cells, SLAM, WT, rep 1

description: Library name: IMR90_SV40T_SLAM_WT_rep1


title: D80 CNTRL human-chimp-orang-macaque interspecies pools, CHIR0.6, ATAC

description: Library name: D80_M_0-6_CNTRL_ATAC


title: CUMC_E52


title: FB,GLU,rep2

description: Library name: 104


title: D80 CNTRL human-chimp-orang-macaque interspecies pools, CHIR0.6, GEX

description: Library name: D80_M_0-6_CNTRL_GEX


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.5, ATAC

description: Library name: D100_M_0-5_ATAC


title: IMR-90 SV40-T cells, SLAM, Empty, rep 3

description: Library name: IMR90_SV40T_SLAM_Empty_rep3

value: Empty


title: FB,GLU,rep1

description: Library name: 103


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.5, GEX

description: Library name: D100_M_0-5_GEX


title: IMR-90 SV40-T cells, SLAM, Empty, rep 2

description: Library name: IMR90_SV40T_SLAM_Empty_rep2


title: e23

city: Nanjing

first: Xuetian

last: Qian

state: Jiangsu

address: No. 68 Changle Road, Nanjing, China

country: China

institute: Nanjing First Hospital Affiliated to Nanjing Medical University

data_processing:
First, reads with low quality, contaminated joints and high levels of unknown base N were filtered out. The filtered data were called clean reads. Clean reads were then matched to the reference genome, followed by new transcript prediction, SNP & InDel, and differential splicing gene testing. After the new transcript is obtained, the new transcript with protein coding potential is added to the reference gene sequence to form a complete reference sequence, and then the gene expression level is calculated. Finally, according to the requirements of multiple samples, the differentially expressed genes among different samples were detected, and in-depth cluster analysis and functional enrichment analysis were performed on the differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes FPKM values for each sample

organism: Mus musculus

source_name: 908 cell lines isolated from tumor tissues of p48cre+; KrasG12D/+; Tsc1fl/+ PDAC mice

growth_protocol: 908 murine PDAC cells were cultured with DMEM (319-005-CL, Wisent) supplemented with 10% fetal bovine serum (FBS) (04-001-1A, Biological Industries) at 37ºC, 5% CO2.

extract_protocol:
RNA was harvested using Takara TRIzol according to manufacturer's instruction. Then total RNA was treated by either mRNA enrichment or rRNA removal.
The obtained RNA was segmented by interrupting buffer, and then reverse-transcribed by random N6 primers, and then synthesized cDNA double strand to form double-stranded DNA. The end of the synthetic double-stranded DNA is patched and phosphorylated at the 5 'end, forming A sticky end with a protruding "A" at the 3' end, and then connected to a bubbling splice with a protruding "T" at the 3' end. The linked products were amplified by PCR using specific primers. The PCR products are thermologically denatured into single strand, and then the single strand DNA is cycled with a bridge primer to obtain a single strand circular DNA library.

value: murine PDAC cells

value: Aldh1a5 low overexpression

value: transfected with mouse Aldh1a3 cDNA ORF clone and monoclonal selected thereby


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.8, ATAC

description: Library name: D100_M_0-8_ATAC


title: CUMC_E50

value: Epithelium


title: CUMC_E5


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_E76K_TGFβ1_rep2

data_processing:
Sequencing reads were quality-checked with FastQC and trimmed using Trim Galore!. Clean reads were aligned to GRCh38 using Bowtie2, sorted and indexed with SAMtools and deduplicated using Picard Tools. Peaks were called with MACS2, quantified using featureCounts and analyzed for differential accessibility with DESeq2.
Assembly: hg38
Supplementary files format and content: Peak annotation files obtained from MACS2 are provided in GFF format. Normalized count matrices obtained from DESeq2 are included as tab-delimited text.

extract_protocol:
A total of 1 × 10⁵ cells were washed with PBS, resuspended in ATAC-seq lysis buffer and incubated with Tagmentation master mix at 37°C for 30 min in a thermomixer at 1,000 rpm.
Libraries were prepared using the Active Motif ATAC-seq Kit (53150), indexed with i5 and i7 primers, and size-selected using AMPure XP beads (Beckman Coulter, A63881) at a 0.5–1.3× ratio.

treatment_protocol: 2 ng/ml TGFβ1 for 24 h

value: 2 ng/ml TGFβ1 for 24 h


title: e22

value: 908 cell lines isolated from tumor tissues of p48cre+; KrasG12D/+; Tsc1fl/+ PDAC mice

value: Aldh1a4 low overexpression


title: ATAC-Seq, IMR-90 SV40-T cells, WT, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_WT_TGFβ1_rep2

value: IMR-90 SV40-T

value: Fibroblast


title: CUMC_E49

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2


title: e21

value: Aldh1a3 low overexpression


title: CUMC_E51


title: IMR-90 SV40-T cells, SLAM, Empty, rep 1

description: Library name: IMR90_SV40T_SLAM_Empty_rep1

value: 100 µM 4sU for 6 h


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.8, GEX

description: Library name: D100_M_0-8_GEX

value: PSC-derived midbrain organoids


title: e13

value: Aldh1a3 high overexpression


title: e12


title: CUMC_E48


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.6, ATAC

description: Library name: D100_M_0-6_ATAC


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.4, ATAC

description: Library name: D100_M_0-4_ATAC


title: CUMC_E47


title: CUMC_E46


title: e11


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.4, GEX

description: Library name: D100_M_0-4_GEX


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, rep 2

description: Library name: IMR90_SV40-T_ATAC_E76K_rep2

value: H2B E76K


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, TGFβ1, rep 2

description: Library name: IMR90_SV40-T_ATAC_Empty_TGFβ1_rep2


title: c3

value: WT

value: transfected with mouse control ORF clone and selected by geneticin


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, rep 2

description: Library name: IMR90_SV40-T_ATAC_Empty_rep2

value: Empty


title: D100 human-chimp-orang-macaque interspecies pools, CHIR0.6, GEX

description: Library name: D100_M_0-6_GEX


title: CUMC_E45

value: Primary


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_E76K_TGFβ1_rep1


title: ATAC-Seq, IMR-90 SV40-T cells, WT, rep 2

description: Library name: IMR90_SV40-T_ATAC_WT_rep2

value: H2B WT


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 2, MULTISEQ

description: Library name: D40_M0-5_2_MULTISEQ


title: CUMC_E44


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 2, ATAC

description: Library name: D40_M0-5_2_ATAC


title: c2

value: murine PDAC cells


title: CUMC_E43

value: Epithelium


title: CUMC_E42


title: c1


title: ATAC-Seq, IMR-90 SV40-T cells, WT, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_WT_TGFβ1_rep1

value: 2 ng/ml TGFβ1 for 24 h


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 2, GEX

description: Library name: D40_M0-5_2_GEX


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, TGFβ1, rep 1

description: Library name: IMR90_SV40-T_ATAC_Empty_TGFβ1_rep1


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230405

city: New York

first: Aileen

last: Ugurbil

state: NY

address: 87 Bedford St, Apt 4

institute: The Rockefeller University

description:
Library name: 230405_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

data_processing:
EasySci-RNA and EasySci-ATAC data were processed using custom pipelines as described previously (1). For RNA, cell barcodes and UMIs were extracted, adapters trimmed with Trim Galore, and reads aligned to the human genome with STAR; PCR duplicates were removed based on UMI and genomic coordinates to generate single-cell expression matrices. For ATAC, N5/N7 and cell barcodes were extracted, reads trimmed and aligned with STAR, and duplicates removed with Picard to produce fragment BED files. Single-cell RNA data were analyzed in Scanpy (v1.11.0) with Scrublet (v0.2.3) for doublet detection, normalization, scaling, PCA, and UMAP visualization. Single-cell ATAC data were analyzed in SnapATAC2 (v2.8); cells with ≥1,000 fragments and TSS enrichment ≥3 were retained, peaks were called with macs3 (q < 1e−3), blacklist regions removed, and UMAPs generated from spectral embeddings of the most variable peaks.
Assembly: hg38
Supplementary files format and content: h5ad file include an anndata object containing a peak x count matrix with cell meta data
Supplementary files format and content: h5ad file include an anndata object containing a gene x count matrix with cell meta data

source_name: cultured cell line

growth_protocol: All cell lines were maintained at 37 °C with 5% CO₂, and cultured in cell-line specific media.

extract_protocol:
Cells were trypsinized (2 mL, 37 °C, 1–5 min), quenched with 8 mL growth medium (10% FBS + 1% Pen-Strep), dissociated by pipetting, and counted using a hemocytometer. Cells were pelleted at 300 × g for 5 min (4 °C), washed once with 10 mL cold PBS, and transferred to 1.5 mL tubes. Pellets were washed again with 1 mL PBS and lysed in 1 mL ice-cold cell lysis buffer for 5 min on ice. Nuclei were pelleted at 500 × g for 5 min, resuspended in 500 µL nuclei isolation buffer, filtered through a 20 µm filter, and pelleted again. Final nuclei were resuspended in 500 µL NIB for counting or 500 µL Sort Buffer with 0.25 mg/mL DAPI for sorting, then used immediately or snap-frozen at –80 °C.
ATAC libraries were prepared following the EasySci-ATAC protocol, adapted from TrackerSci-ATAC. Nuclei isolated from cultured cell lines were tagmented with indexed Tn5 transposase for 30 min at 37 °C, quenched, pooled, and ligated with plate-specific barcodes. After cleanup and indexed PCR amplification, libraries were purified, quality-checked, and sequenced on an Illumina NextSeq 1000 (paired-end ~60 bp; dual 10 bp index reads). RNA libraries were generated using the EasySci-RNA protocol. Nuclei from cultured cell lines were distributed across 96-well plates (≤20,000 nuclei per well) in Nuclear Suspension Buffer. Reverse transcription was performed with mixed short-dT and random primers using a temperature-ramped program. Post-RT nuclei were pooled, washed, and ligated with well-specific DNA barcodes. Second-strand synthesis and AMPure cleanup were followed by Tn5 tagmentation, indexing PCR, and purification. Final libraries were quantified and sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).

value: cultured cell line

value: DB, SK-HEP-01, SK-N-AS, LNCAP-EGFP-c_2-F876L, HL-60, GA-10_Clone_4, MOLT-4

value: lymphoid, liver, neuroblastoma, prostate, blood


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230426

description:
Library name: 230426_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: lung, melanoma


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230323

description:
Library name: 230323_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: SK-LC-17, LNCAP-EGFP, PC9-Brm3, LNAR, SH-SY5Y, U2-OS, SK-BR-03, PC9-TGL

value: lung, prostate, neuroblastoma, bone, breast


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 1, MULTISEQ

description: Library name: D40_M0-5_1_MULTISEQ

value: PSC-derived midbrain organoids


title: ATAC-Seq, IMR-90 SV40-T cells, E76K, rep 1

description: Library name: IMR90_SV40-T_ATAC_E76K_rep1

value: IMR-90 SV40-T

value: Fibroblast


title: CUMC_E41


title: CUMC_E4


title: ATAC-Seq, IMR-90 SV40-T cells, WT, rep 1

description: Library name: IMR90_SV40-T_ATAC_WT_rep1


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 1, ATAC

description: Library name: D40_M0-5_1_ATAC


title: ATAC-Seq, IMR-90 SV40-T cells, Empty, rep 1

description: Library name: IMR90_SV40-T_ATAC_Empty_rep1


title: CUMC_E39


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230202

description:
Library name: 230202_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: YUHIMO, MeWo, Sk-Mel-24, WM4235, YUSEEP

value: melanoma


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 3, MULTISEQ

description: Library name: D40_M_3_MULTISEQ


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.5, replicate 1, GEX

description: Library name: D40_M0-5_1_GEX


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 3, ATAC

description: Library name: D40_M_3_ATAC


title: CUMC_E40


title: IMR-90 SV40-T cells, D68N/E76K, rep 2

description: Library name: IMR90_SV40T_D68N/E76K_rep2

data_processing:
Reads were trimmed using Trimmomatic. Alignment was performed using HISAT2 to human genome hg38. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample from DESeq2.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
NEBNext Ultra II DNA Library Prep Kit (E7645) with NEBNext Multiplex Oligos (E6609)

value: fibroblast

value: H2B D68N/E76K


title: CUMC_E38

value: Primary


title: IMR-90 SV40-T cells, D68N/E76K, rep 3

description: Library name: IMR90_SV40T_D68N/E76K_rep3


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230123

description:
Library name: 230123_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: lung, melanoma, breast, pancreas, uvea


title: CUMC_E37

value: Epithelium


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230309

description:
Library name: 230309_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: kidney, colon, ovary, bone, uterus


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8,  replicate 3, GEX

description: Library name: D40_M_3_GEX


title: CUMC_E35


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 2, MULTISEQ

description: Library name: D40_M_2_MULTISEQ


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 2, ATAC

description: Library name: D40_M_2_ATAC


title: CUMC_E36


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8,  replicate 2, GEX

description: Library name: D40_M_2_GEX


title: CUMC_E34


title: IMR-90 SV40-T cells, D68N/E76K, rep 1

description: Library name: IMR90_SV40T_D68N/E76K_rep1


title: IMR-90 SV40-T cells, E76R, rep 2

description: Library name: IMR90_SV40T_E76R_rep2

value: H2B E76R


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230317_2

description:
Library name: 20230317_CellLine6
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: cultured cell line

value: DB, LNCAP-EGFP-c.2-F876L, MOLT-4, SH-SY5Y, PC9-BrM3, SK-HEP-01, SK-BR-03, SK-N-AS, GA-10-Clone-4, PC9-TGL, LNAR, U2-OS

value: lymphoid, prostate, blood, neuroblastoma, lung, liver, breast, bone


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230616

description:
Library name: 20230616_Cell_Line_Redos
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: lung, prostate, lymphoid, breast, melanoma, blood, colon, pancreas


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230307

description:
Library name: 230307_ATAC_Cells_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: melanoma, colon, kidney, uvea, lung, bladder, bone


title: IMR-90 SV40-T cells, E76R, rep 3

description: Library name: IMR90_SV40T_E76R_rep3


title: CUMC_E33


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230317

description:
Library name: 20230317_CellLine5
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: bone, lung, melanoma, uvea, colon, kidney, bladder


title: CUMC_E32


title: IMR-90 SV40-T cells, E76K, rep 3

description: Library name: IMR90_SV40T_E76K_rep3

value: H2B E76K


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 1, MULTISEQ

description: Library name: D40_M_1_MULTISEQ

value: PSC-derived midbrain organoids


title: Easy-Sci ATAC co-proccessed human cultured cancer cell lines EXP 230109

description:
Library name: 230109_ATAC_Cells_Mets_human
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-ATAC protocol. Tn5 tagmentation with indexed adapters generated single-cell chromatin accessibility libraries, which were sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_snapatac2_w_peak_counts_frag1e3_tss3.h5ad
Pan_Cancer_ATAC_metadata.csv

value: breast, lung, melanoma


title: IMR-90 SV40-T cells, D68N, rep 3

description: Library name: IMR90_SV40T_D68N_rep3

value: H2B D68N


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8, replicate 1, ATAC

description: Library name: D40_M_1_ATAC


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230123

description:
Library name: 20230123_CellLine3
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: melanoma


title: CUMC_E3


title: IMR-90 SV40-T cells, E76R, rep 1

description: Library name: IMR90_SV40T_E76R_rep1

value: fibroblast


title: CUMC_E29

value: Primary


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.5, MULTISEQ

description: Library name: D16_M0-5_MULTISEQ

value: PSC-derived midbrain progenitors


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230117

description:
Library name: 20230117_CellLine2
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: melanoma, breast, lung, uvea, pancreas


title: IMR-90 SV40-T cells, D68N, rep 2

description: Library name: IMR90_SV40T_D68N_rep2


title: D40 human-chimp-orang-macaque interspecies pools, CHIR0.4-0.8,  replicate 1, GEX

description: Library name: D40_M_1_GEX


title: Easy-Sci RNA co-proccessed human cultured cancer cell lines EXP 20230305

description:
Library name: 20230305_CellLine4
Nuclei isolated from cultured human cancer cell lines were processed using the EasySci-RNA protocol. Reverse transcription, ligation-based barcoding, and indexed PCR amplification generated single-cell transcriptome libraries, sequenced on an Illumina NextSeq 1000 (paired-end 100 bp; dual 10 bp index reads).
pan_cancer_RNA_processed_UMAP.scanpy.h5ad
Pan_Cancer_RNA_metadata.csv

value: uterus, kidney, ovary, colon, bone, melanoma


title: D16 human-chimp-orang-macaque interspecies pools, CHIR0.5, ATAC

description: Library name: D16_M0-5_ATAC


title: IMR-90 SV40-T cells, E76K, rep 1

description: Library name: IMR90_SV40T_E76K_rep1


title: CUMC_E30

value: Epithelium