title: ControlF1_6

description:
Library name: CL1008_F_3
Column name in tpm_filt_counts.csv: CL1008_F_3.bam


title: ControlF1_5

status: Public on Sep 08 2025

type: SRA

city: Nijmegen

first: Maggie MK

last: Wong

address: Wundtlaan 1

department: Language and Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

description:
Library name: CL1008_F_2
Column name in tpm_filt_counts.csv: CL1008_F_2.bam

library_source: transcriptomic

data_processing:
Image processing and basecall was performed using the Illumina Real Time Analysis Software
Reads with adapter contamination, reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%) and reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read were removed.
Fastq files were aligned to the human genome (GRCh38/hg39, Ensembl) using HISAT266 v. 2.0.5 software together with the corresponding splice junctions Ensembl GTF annotation.
At least 89% of the reads for each sample were uniquely mapped to the human genome entailing at least 36.4 million unique reads in the sample with the lowest sequencing depth for fibroblast samples.
Data pre-processing and analysis were performed using R Statistical Software v4.1.267.
Count table was created using featureCounts in Rsubread68. Transcripts that have no reads in all samples were removed.
Assembly: GRCh38/hg39, Ensembl
Supplementary files format and content: filtered raw counts: tpm_filt_counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: primary human skin fibroblasts

growth_protocol: Human dermal fibroblasts were cultured in DMEM supplemented with 20% FBS, 100 U/ml Penicillin-Streptomycin and 1% sodium pyruvate (Thermo-Fisher) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted from one to two million cells using a Qiagen Rneasy kit and performed by sequencing company Novogene.
1 μg of total RNA extracted (Qiagen) was used to generate RNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs) following the manufacturer’s protocol and index codes were added to attribute sequences to each sample. These steps are performed by sequencing company Novogene.

treatment_protocol: No treatment was performed.

tag: cell type

value: primary human skin fibroblasts

tag: genotype

value: WT

tag: age at_sampling

value: teenager

tag: batch

tag: Sex

value: F

tag: condition

value: Control


title: T962del_3

description:
Library name: T962del3
Column name in tpm_filt_counts.csv: T962del3.bam


title: T962del_2

description:
Library name: T962del2
Column name in tpm_filt_counts.csv: T962del2.bam


title: ControlF1_4

description:
Library name: CL1008_F_1
Column name in tpm_filt_counts.csv: CL1008_F_1.bam


title: L957P_2

description:
Library name: L957P_2
Column name in tpm_filt_counts.csv: L957P_2.bam

value: kid

value: M


title: L957P_3

description:
Library name: L957P_3
Column name in tpm_filt_counts.csv: L957P_3.bam


title: T962del_1

description:
Library name: T962del1
Column name in tpm_filt_counts.csv: T962del1.bam


title: L957P_1

description:
Library name: L957P_1
Column name in tpm_filt_counts.csv: L957P_1.bam


title: E858K_1_3

description:
Library name: E858K_3
Column name in tpm_filt_counts.csv: E858K_3.bam


title: E858K_1_1

description:
Library name: E858K_1
Column name in tpm_filt_counts.csv: E858K_1.bam


title: E858K_1_2

description:
Library name: E858K_2
Column name in tpm_filt_counts.csv: E858K_2.bam


title: ControlF2_2

description:
Library name: CL10_9_2
Column name in tpm_filt_counts.csv: CL10_9_2.bam

value: adult


title: ControlF1_2

description:
Library name: CL10_8_2
Column name in tpm_filt_counts.csv: CL10_8_2.bam


title: ControlF2_3

description:
Library name: CL10_9_3
Column name in tpm_filt_counts.csv: CL10_9_3.bam


title: ControlF1_1

description:
Library name: CL10_8_1
Column name in tpm_filt_counts.csv: CL10_8_1.bam


title: ControlF2_1

description:
Library name: CL10_9_1
Column name in tpm_filt_counts.csv: CL10_9_1.bam


title: ControlF1_3

description:
Library name: CL10_8_3
Column name in tpm_filt_counts.csv: CL10_8_3.bam


title: ControlM2_1

description:
Library name: C11_66_1
Column name in tpm_filt_counts.csv: C11_66_1.bam


title: ControlM2_2

description:
Library name: C11_66_2
Column name in tpm_filt_counts.csv: C11_66_2.bam


title: Pancreatic_Cancer_cfDNA_7

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

country: USA

institute: University of North Dakota

library_source: genomic

data_processing:
Raw reads were filtered based on a mean base quality score greater than 20. Adapter sequences were removed using Cutadapt, and the reads were subsequently mapped to the hg19 genome using Bowtie 1.2.2. Duplicate reads were eliminated using the MarkDuplicates tool from the Picard-tools-2.26.4 package. Paired-end reads were converted into single fragments for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each dataset, bigWig files were generated to visualize genomic coverage.
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: cfDNA

extract_protocol:
NEXTFLEX Rapid DNA-Seq Kit 2.0 (Approximately  650µL of blood plasma from cancer patients or healthy donors was used for cfDNA purification utilizing the SubXTM-Exo-DNA kit (Capital Biosciences). The purified cfDNA was then quantified using the Qubit dsDNA HS Assay kit.
Libraries were prepared using the NEXTFLEX Rapid DNA-Seq Kit 2.0 (Revvity). Half the volume of purified cfDNAs, ranging from approximately 1 ng to 10 ng, was utilized. After adapter ligation, a total of 11 PCR cycles were performed.

tag: ID

tag: cancer type

value: pancreatic cancer

value: cfDNA

tag: data ids


title: ControlM1_3

description:
Library name: C11_63_3
Column name in tpm_filt_counts.csv: C11_63_3.bam


title: Pancreatic_Cancer_cfDNA_8


title: ControlM1_1

description:
Library name: C11_63_1
Column name in tpm_filt_counts.csv: C11_63_1.bam


title: ControlM1_2

description:
Library name: C11_63_2
Column name in tpm_filt_counts.csv: C11_63_2.bam


title: Pancreatic_Cancer_cfDNA_4


title: Pancreatic_Cancer_cfDNA_3


title: Pancreatic_Cancer_cfDNA_5


title: Pancreatic_Cancer_cfDNA_2


title: Pancreatic_Cancer_cfDNA_1


title: Healthy_Donor_cfDNA_5

value: healthy donor


title: pedicel, mutant, 10DAA, rep3

city: Tsukuba

first: Fabien

last: Lombardo

address: 1-1, Tennodai 1-Chōme

country: Japan

institute: The University of Tsukuba

description: Library name: H6_1

data_processing:
Processed with the sRNAminer sofware using the One Step pipeline with default ncRNA and organelle database and default parameters.
Assembly: S. lycopersicum SL4.0
Supplementary files format and content: xls files including reads per 10 million

organism: Solanum lycopersicum

source_name: pedicel

extract_protocol:
Total RNA was extracted using a High Pure RNA Isolation kit (Roche, Basel, Switzerland) following manufacturer's instructions (single-column protocol). About 5 micrograms were used for the construction of the library by the Rhelixa company (Tokyo, Japan).
Small RNA libraries were prepared by the Rhelixa company using the  Illumina TruSeq Small RNA Library Preparation Kit.

tag: tissue

value: pedicel

tag: cell line

value: hws-1 'Micro-Tom'


title: pedicel, mutant, 10DAA, rep1

description: Library name: H4P_1


title: Healthy_Donor_cfDNA_4


title: pedicel, WT, 10DAA, rep3

description: Library name: W5_1

value: WT 'Micro-Tom'


title: pedicel, WT, 10DAA, rep2

description: Library name: W4_1


title: Healthy_Donor_cfDNA_2


title: Breast_Cancer_cfDNA_5

value: breast cancer

tag: subtype

value: luminal


title: pedicel, WT, 10DAA, rep1

description: Library name: W3_1


title: Breast_Cancer_cfDNA_4


title: Healthy_Donor_cfDNA_1


title: ControlM2_3

description:
Library name: C11_66_3
Column name in tpm_filt_counts.csv: C11_66_3.bam


title: Breast_Cancer_cfDNA_3


title: SK-N-AS, sgGal4 (NTC), CRISPRi, replicate 4

city: Solna

first: Tilen

last: Trselic

address: Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

description: Library name: P34306_1008

data_processing:
SKNAS and SKNSH CRISPRi: Samples were sequenced on NovaSeqXPlus (NovaSeqXSeries Control Software 1.2.2.48004) with a 151nt(Read1)-10nt(Index1)-10nt(Index2)-151nt(Read2) setup using '10B' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Output FastQ files are transferred securely to UPPMAX, where a number of standardised bioinformatics quality control checks are performed to ensure that data meets our guarantee of data quality and quantity before delivery. Basecalling and demultiplexing was performed using Illumina bcl2fastq (v2.20) software. Sequence data quality was assessed using FastQC (v0.11.8). Adapter trimming was performed using BBDuk (part of BBMap package v38.41). Reads were aligned to Ensembl GRCh38 reference genome using STAR (v2.6.1d). Gene counts were estimated using featureCounts (v1.5.1). SKNASH siRNA: Samples were sequenced on NovaSeqXPlus. Original image data file from high-throughput sequencing platforms  is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality. Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Assembly: Ensembl GRCh38
Supplementary files format and content: 3 tab-delimited files with raw counts for all samples - one for each knockdown, i.e. SKNSH and SKNAS CRISPRi, SKNSH siRNA

source_name: SK-N-AS

growth_protocol: Cells were grown in corresponding complete media as suggested by ATCC.

extract_protocol:
Cells were either lysed directly in RLT buffer (Qiagen) and subjected to RNA extraction using TRIzol Reagent (Invitrogen), followed by RNA cleanup with the RNeasy Mini Kit (Qiagen), using the cleanup protocol provided by the manufacturer.
SKNSH and SKNAS CRISPRi: Sequencing libraries were generated using the Illumina Stranded mRNA Prep kit. SKNSH siRNA: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: SK-N-AS

tag: treatment

value: NTC knockdown (sgRNA)


title: Pancreatic_Cancer_cfDNA_6


title: Breast_Cancer_cfDNA_2


title: Breast_Cancer_cfDNA_1


title: SK-N-AS, sgDIORA1, CRISPRi, replicate 4

description: Library name: P34306_1004

value: DIORA1 knockdown (sgRNA)


title: SK-N-AS, sgDIORA1, CRISPRi, replicate 3

description: Library name: P34306_1003


title: SK-N-AS, sgGal4 (NTC), CRISPRi, replicate 1

description: Library name: P34306_1005


title: Healthy_Donor_cfDNA_6


title: SK-N-AS, sgDIORA1, CRISPRi, replicate 2

description: Library name: P34306_1002


title: SK-N-AS, sgDIORA1, CRISPRi, replicate 1

description: Library name: P34306_1001

source_name: SK-N-SH

value: SK-N-SH


title: SK-N-AS, sgGal4 (NTC), CRISPRi, replicate 2

description: Library name: P34306_1006


title: OV81_DL78_1

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

growth_protocol: OV81.2 cells are adherent cells that grow in DMEM supplemented with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Media, PBS wash, and trypsinized cells were collected in a 15mL conical and centrifuged at 300g for 5 minutes. The supernantant was aspirated and the pellet was resuspended in a PBS wash. After a second centrifuge, the PBS was removed and the pellet was stored at -80ºC. RNA was extracted using the RNeasy Plus Kit (Qiagen #74134) according to the manufacturer’s protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

treatment_protocol: Cells were plated in triplicate in a 6-well dish and settled overnight. Media was aspirated. 10µM DL78 or equal volume of DMSO was diluted in fresh media and added to the cells for 6 hours.

value: patient-derived high grade serous cancer


title: OV81_DMSO_3

value: DMSO


title: pedicel, mutant, 10DAA, rep2

description: Library name: H5_1


title: Healthy_Donor_cfDNA_3


title: SK-N-SH, sgGal4 (NTC), CRISPRi, replicate 2

description: Library name: SH_CRISPRi_NTC_2


title: SK-N-AS, sgGal4 (NTC), CRISPRi, replicate 3

description: Library name: P34306_1007


title: OV81_DMSO_1


title: SK-N-SH, sgGal4 (NTC), CRISPRi, replicate 1

description: Library name: SH_CRISPRi_NTC_1


title: P19_IR_CONV_9Gy_3

city: Paris

first: Charles

last: Fouillade

address: 25 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
Read QC were performed using fastqc
Read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.7.6a)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Lung

growth_protocol: Lung samples were provided by Institut Mutualiste Montsouris (IMM)

extract_protocol:
Total RNA were extracted using RNAeasy Mini Kit from Qiagen. RNA quantity and quality control was assessed by capillary electrophoresis (Bioanalyzer, Agilent). All samples have a RIN > 7.
Libraries were prepared from 500 ng of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit according to manufacturer recommendation. 100 bp paired-end sequencing was performed with the Illumina NovaSeq 6000 instrument.

treatment_protocol: Lung samples were either untreated (Non-Irradiated) or irradiated in conventional  (CONV) or in FLASH modes with a dose of 9 Gy. Lung samples were then incubated for 24 hours in DMEM F-12 Glutamax medium supplemented with 1% SVF, 1% P/S, 1% L-glutamine and 1% NEAA

value: Lung


title: P19_IR_CONV_9Gy_2


title: SK-N-SH, sgDIORA1, CRISPRi, replicate 2

description: Library name: SH_CRISPRi_KD_2


title: P19_IR_CONV_9Gy_1


title: OV81_DL78_3


title: P19_IR_FLASH_9Gy_3


title: P19_IR_FLASH_9Gy_2


title: SK-N-SH, NTC siRNA, replicate 3

description: Library name: SH_siRNA_NTC_3

value: NTC knockdown (siRNA)


title: SK-N-SH, NTC siRNA, replicate 5

description: Library name: SH_siRNA_NTC_5


title: SK-N-SH, NTC siRNA, replicate 4

description: Library name: SH_siRNA_NTC_4


title: Hippocamus, 3

city: Beijing

first: Ligong

last: Chen

address: Shuangqing Road No.30

country: China

institute: tsinghua university

description: Library name: Sample3

data_processing:
Clean reads were mapped to GRCm38/mm10 using Bowtie2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the RNeasy Lipid Mini Kit (QIAGEN, 74134). RNA quality was determined by Agilent 2100.
The library was sequenced on an Illumina NovaSeq 6000 (PE150).

value: hippocampus

tag: strain

value: mixed cell types (hippocampus tissue)

value: WT


title: SK-N-SH, NTC siRNA, replicate 2

description: Library name: SH_siRNA_NTC_2


title: OV81_DL78_2


title: SK-N-SH, NTC siRNA, replicate 1

description: Library name: SH_siRNA_NTC_1


title: P19_IR_FLASH_9Gy_1


title: P19_NI_3


title: SK-N-SH, DIORA1-targetting siRNA pool, replicate 5

description: Library name: SH_siRNA_KD_5

value: DIORA1 knockdown (siRNA)


title: Hippocamus, 1

description: Library name: Sample1


title: SK-N-SH, DIORA1-targetting siRNA pool, replicate 4

description: Library name: SH_siRNA_KD_4


title: P19_NI_2


title: SK-N-SH, sgDIORA1, CRISPRi, replicate 3

description: Library name: SH_CRISPRi_KD_3


title: SK-N-SH, DIORA1-targetting siRNA pool, replicate 2

description: Library name: SH_siRNA_KD_2


title: Hippocamus, 2

description: Library name: Sample2


title: SK-N-SH, sgGal4 (NTC), CRISPRi, replicate 3

description: Library name: SH_CRISPRi_NTC_3


title: CD45.2+CD11b+ cells, TET-CD45-2B

city: Chengdu

first: Hui

last: WANG

state: Sichuan

address: No.14,3Rd Section Of Ren Min Nan Rd

department: periodontics

institute: Sichuan University

description: Library name: Sample 1

library_source: transcriptomic single cell

data_processing:
Cell Ranger 6.1.2  was used to process raw sequencing results.
Assembly: mouse mm10
Supplementary files format and content: barcodes, features, matrix files

source_name: gingiva

extract_protocol:
At 12 weeks post-transplantation, both groups of recipient mice  were subjected to LIP for 5 days.  CD45.2+CD11b+ (from 10% Tet2–/– BMT) and CD45+CD11b+ (from 10% Tet2+/+ BMT) cells from the gingiva of mice were sorted using a FACSAria™ sorter.
The cells were resuspended in 1X PBS containing 0.04% BSA (400 µg/ml) and processed with Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns (10x Genomics) at the CAG Sequencing Core of Children’s Hospital of Cell suspensions contained more than 99% viable cells as determined by microscopy. The cell numbers were adjusted to 700–1200 cells per μl and added to 10x Chromium RT mix to achieve loading target numbers of around 20000 cells. cDNA synthesis was performed per the manufacturer’s instructions, and library preparation and sequencing (Novaseq SP reagent kit; 100 cycles)Philadelphia, PA, USA. were performed using the Novaseq 6000 platform (Illumina) per the manufacturer’s instructions.

treatment_protocol: periodontitis model

value: gingiva

value: CD11b+ cells

value: 10% Tet2 BMT

value: ligature induced periodontitis


title: SK-N-SH, sgDIORA1, CRISPRi, replicate 1

description: Library name: SH_CRISPRi_KD_1


title: OV81_DMSO_2


title: SK-N-SH, DIORA1-targetting siRNA pool, replicate 1

description: Library name: SH_siRNA_KD_1


title: 5XFAD_ROI48

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description:
Library name: 2-7-24-Sample-1_48
Biological replicate 3

data_processing:
Output.fastq files from sequencing runs were converted into Digital Count Conversion (DCC) using GeoMx  NGS Pipeline software with default parameters.
Transfer the DCC files to GeoMx DSP
Run segment and biological probe QC, calculate background and filtration
normalize segments using Q3 normalization
perform data analysis for cluster, statistical analysis and pathway analysis.
Assembly: mm10
Supplementary files format and content: CSV files for list of gene, ROI , counts, areas, segment number, commment etc.
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Tissues were fixed with 10% Neutral buffered formalin and embedded into paraffin for FFPE blocks. Tissue sections (4 µm)  were incubated with the NanoString mouse Whole Transcriptome Atlas (WTA) panel probes overnight, then stained with D54D2 (CST 8243S, AF 594 secondary),   Olig2 (R&D AF2418-SP, AF647 secondary ) and the DNA stain Syto83 (Thermo S11364) as morphology markers to visualize tissue architecture. Stained slides were loaded onto the GeoMx instrument and scanned for region of interest (ROI) selection. Automatic segmentation of the ROIs based on Olig2 expression were used to define areas of interest (AOIs), allowing for the separation of Olig2-expressing cells from surounding cells. A total of 95 AOIs were exposed to 385 nm (UV) light, releasing the index oligonucleotides which were collected with a microcapillary and deposited into individual wells of a 96-well plate for subsequent processing.
Sequencing libraries were generated by PCR from the photo-released indexing oligos and AOI-specific Illumina adapter sequences, according to manufacturer's instruction.

value: brain

value: oligodendrocyte lineage (olig2)+


title: P18_IR_CONV_9Gy_3


title: P19_NI_1


title: 5XFAD_ROI47

description:
Library name: 2-7-24-Sample-1_47
Biological replicate 3


title: SK-N-SH, DIORA1-targetting siRNA pool, replicate 3

description: Library name: SH_siRNA_KD_3


title: NK_6h

city: Zurich

first: Marijne

last: Vermeer

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description:
Library name: Sample 2
10X Genomics

data_processing:
Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 5.0) (Hao et al. 2021). Potential low-quality cells with number of features below 800, above 5000 or with more than 6% mitochondrial genes were filtered out using the QC parameters of nFeature_RNA and percent.mt. Following QC, global count normalization was performed, followed by selection of variable features (n = 2000), linear transformation using ScaleData, and dimensionality reduction (PCA). Graph-based clustering and dimensionality reduction were performed using the first 30 principal components and a resolution value of 0.8. Cell type assignment and selection of NK cells were based on cluster-specific genes identified with the FindAllMarkers function (only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25).
Assembly: GRCm38.p6
Supplementary files format and content: CellRanger output and processed Seurat Objects

molecule: polyA RNA

source_name: Lung and Blood

extract_protocol:
Live NK1.1+NKp46+ cells from lungs and blood of female 9-weeks-old mice were sorted into PBS containing 2% FCS for the 10X Genomics protocol. Viability of the sorted cells was evaluated with trypan blue and was over 95% for all samples. Sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared following manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v7.0.1) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v4 workflow (Hao et al. 2021).
Initial processing was done using Cell Ranger (v7.0.1) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23). Starting from the filtered gene-cell count matrices produced by CellRranger's built-in cell calling algorithms, we proceeded with Seurat v5 workflow. Analysis, including quality control (QC), processing, graph-based clustering, visualizations, and differential gene expression analyses of the scRNA-seq data were performed in R using the Seurat pipeline (version 5.0).

treatment_protocol: Mice were intravenously inoculated with 100.000 PyMT tumor cells either 6 hours or 14 days before sacrifice.

value: Lung and Blood

value: Natural Killer Cells

value: wild-type

value: PyMT tumor iv injections, 6h prior to sacrifice


title: NK_14days

description:
Library name: Sample 3
10X Genomics

value: PyMT tumor iv injections, 14 days prior to sacrifice


title: P18_IR_CONV_9Gy_1

value: Lung


title: 5XFAD_ROI46

description:
Library name: 2-7-24-Sample-1_46
Biological replicate 3


title: NK_Naive

description:
Library name: Sample 1
10X Genomics


title: P18_IR_CONV_9Gy_2


title: 5XFAD_ROI44

description:
Library name: 2-7-24-Sample-1_44
Biological replicate 3


title: P18_IR_FLASH_9Gy_3


title: 5XFAD_ROI43

description:
Library name: 2-7-24-Sample-1_43
Biological replicate 3


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel, replicate 3

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

institute: EPFL

description: Library name: Emb_1.0mM_rep3

data_processing:
All scripts are available at https://github.com/lldelisle/allRNAseqScriptsFromWongNgPineauEtAl2025
RNA-seq preprocessing was done using a local installation of Galaxy (The Galaxy Community 2024). Adapter and bad quality bases were removed from fastq files using cutadapt version 4.4 (Martin 2011) (-q 30 -m 15 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA). Filtered reads were aligned on mm10 using STAR version 2.7.10b (Dobin et al. 2013) with the ENCODE parameters and a custom gtf (Lopez-Delisle 2021). FPKM were computed with cufflinks version 2.2.1.3 (Trapnell et al. 2010; Roberts et al. 2011) using –max-bundle-length 10000000 –multi-read-correct –library-type ”fr-firststrand” -b mm10.fa –no-effective-length-correction -M mm10 chrM.gtf. For analyses, genes from mitochondrial genes were excluded.
Pairwise differential expression analysis was computed with DESeq2 (Love, Huber, and Anders 2014) on raw counts from STAR (excluding mitochondrial genes). A gene was considered as differentially expressed when the adjusted p-value was below 0.05 and absolute log2 fold-change above 1.
Assembly: mm10
Supplementary files format and content: AllCufflinks_Simplified.txt.gz: table with all FPKM (one line per ensembl ID, one column per sample)
Supplementary files format and content: AllHTSeqCounts.txt.gz: table with all counts from STAR (one line per ensembl ID, one column per sample)
Supplementary files format and content: DESeq2_summary.txt.gz: summary of DESeq2 analysis (one line per ensembl ID, l2fc, adjusted p-values for each comparison used in the study)

source_name: Gastruloids

growth_protocol: Gastruloids were generated by manually seeding 300 cells per well in Costar Low Binding 96-well plates (Costar, Corning, 7007), in a volume of 40 μL per well. After 48 h of aggregation, spheroids were exposed to a 24 h pulse of Wnt agonist (except for no Chiron) by adding 150 μL of 3 μM CHIR 99021 (CHI in the text) in N2B27 to each well, unless stated otherwise. N2B27 media was then changed every 24 h by replacing 150 μL of media per well until 120 h.

extract_protocol:
Gastruloids in 96-well plates (control and negative control) were collected into falcon tubes. All gastruloids were then washed twice with cold PBS (Ca++/Mg++) before being snap-freezed in liquid nitrogen, and stored at -80°C until RNA extraction. RNeasy Mini kit (Qiagen) with on-column DNase digestion was used for RNA extraction following manufacturer’s instructions. RNA quality was assessed on a TapeStation TS4200, all RNA samples showed quality number (RIN) above 9.
RNAseq library preparation with Poly-A selection was performed with 550 ng of RNA using the Illumina stranded mRNA ligation and following the manufacturer’s protocol 1000000124518 v01. Libraries were quantified by qubit DNA HS and profile analysis was done on TapeStation TS4200. Libraries were sequenced on Novaseq 6000, with paired end 75 bp reads.

treatment_protocol: Embedded gastruloids were embedded in hydrogels 96 h after seeding, then left to grow until 120 h. For gastruloid embedding, 20-30 gastruloids were collected from a 96- well plate and left to sediment in a falcon tube. Meanwhile, gel components were prepared, following the proportions of the manufacturer of the 3-D Life Dextran-PEG Hydrogel FG (Cellendes, FG90-1, containing the components PEG-Link, Dextran- Maleimide and CB Buffer pH=5.5) to reach the indicated function concentrations, setting 50% of gastruloid suspension and a total volume of 120 μL per gel. For each gel, two tubes were prepared: one tube containing ultrapure water and PEG-Link, and one tube containing CB Buffer (pH=5.5) and gastruloid suspension in N2B27. Dextran-Maleimide was added to the second tube at the last moment, followed by a quick homogenization with the pipette, pooling of the two solutions, homogenization, then deposition of the gel mix into a glass-bottom dish (Cellvis, D35-10-1.5-N). Quickly, a membrane was deposited on top of the gel (Isopore filter, 5.0 μm membrane, 13mm diameter, Merck, TMTP01300), followed by an adhesive ring (Delta microscopies, slide wells D70366-12) to secure the membrane. The dish was then put in the incubator for 15 min for gel formation, after which 2mL of N2B27 was added on top, and the embedded gastruloids were kept for culture as usual.. For each replicate, about 30 gastruloids were processed per condition. At 120 h after seeding, dishes containing embedded gastruloids were treated as follow: the adhesive ring was lifted, and a solution of 1:20 Dextranase (Cellendes, D10-1) in PBS (Ca++/Mg++) was added to each dish, and left >20 min in the incubator until gastruloids were freely moving and could be collected in a falcon tube.

value: Gastruloids

tag: Stage

tag: background

tag: hydrogel concentration

tag: time of_embedding

value: Chiron 3uM


title: 5XFAD_ROI40

description:
Library name: 2-7-24-Sample-1_40
Biological replicate 3

tag: cell type

tag: genotype


title: P18_IR_FLASH_9Gy_2


title: 5XFAD_ROI39

description:
Library name: 2-7-24-Sample-1_39
Biological replicate 3


title: CD45.2+CD11b+ cells, WT-CD45-CD11B

description: Library name: Sample 9

value: 10% WT BMT


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel, replicate 2

description: Library name: Emb_1.0mM_rep2


title: 5XFAD_ROI38

description:
Library name: 2-7-24-Sample-1_38
Biological replicate 3


title: P18_IR_FLASH_9Gy_1


title: 5XFAD_ROI37

description:
Library name: 2-7-24-Sample-1_37
Biological replicate 3


title: 5XFAD_ROI45

description:
Library name: 2-7-24-Sample-1_45
Biological replicate 3


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel, replicate 1

description: Library name: Emb_1.0mM_rep1


title: 5XFAD_ROI36

description:
Library name: 2-7-24-Sample-1_36
Biological replicate 3


title: 5XFAD_ROI35

description:
Library name: 2-7-24-Sample-1_35
Biological replicate 3


title: P18_NI_3


title: RNA sequencing from gastruloids embedded at 96h in 0.8mM Dextran hydrogel, replicate 3

description: Library name: Emb_0.8mM_rep3


title: 5XFAD_ROI34

description:
Library name: 2-7-24-Sample-1_34
Biological replicate 3


title: P18_NI_1


title: RNA sequencing from gastruloids embedded at 96h in 0.8mM Dextran hydrogel, replicate 2

description: Library name: Emb_0.8mM_rep2


title: P18_NI_2


title: 5XFAD_ROI32

description:
Library name: 2-7-24-Sample-1_32
Biological replicate 2


title: 5XFAD_ROI42

description:
Library name: 2-7-24-Sample-1_42
Biological replicate 3


title: 5XFAD_ROI31

description:
Library name: 2-7-24-Sample-1_31
Biological replicate 2


title: 5XFAD_ROI41

description:
Library name: 2-7-24-Sample-1_41
Biological replicate 3


title: P17_IR_CONV_9Gy_3


title: 5XFAD_ROI30

description:
Library name: 2-7-24-Sample-1_30
Biological replicate 2


title: P17_IR_CONV_9Gy_2


title: P17_IR_CONV_9Gy_1


title: RNA sequencing from gastruloids embedded at 96h in 0.8mM Dextran hydrogel, replicate 1

description: Library name: Emb_0.8mM_rep1


title: 5XFAD_ROI29

description:
Library name: 2-7-24-Sample-1_29
Biological replicate 2


title: 5XFAD_ROI28

description:
Library name: 2-7-24-Sample-1_28
Biological replicate 2


title: RNA sequencing from gastruloids embedded at 96h in 0.7mM Dextran hydrogel, replicate 3

description: Library name: Emb_0.7mM_rep3


title: RNA sequencing from gastruloids embedded at 96h in 0.7mM Dextran hydrogel, replicate 2

description: Library name: Emb_0.7mM_rep2


title: 5XFAD_ROI26

description:
Library name: 2-7-24-Sample-1_26
Biological replicate 2


title: RNA sequencing from gastruloids embedded at 96h in 0.7mM Dextran hydrogel, replicate 1

description: Library name: Emb_0.7mM_rep1


title: 5XFAD_ROI25

description:
Library name: 2-7-24-Sample-1_25
Biological replicate 2


title: P17_IR_FLASH_9Gy_3


title: 5XFAD_ROI24

description:
Library name: 2-7-24-Sample-1_24
Biological replicate 2


title: 5XFAD_ROI22

description:
Library name: 2-7-24-Sample-1_22
Biological replicate 2


title: RNA sequencing from gastruloids grown without embedding and without Chiron pulse, replicate 3

description: Library name: noChiron_rep3


title: 5XFAD_ROI33

description:
Library name: 2-7-24-Sample-1_33
Biological replicate 3


title: 5XFAD_ROI23

description:
Library name: 2-7-24-Sample-1_23
Biological replicate 2


title: RNA sequencing from gastruloids grown without embedding and without Chiron pulse, replicate 2

description: Library name: noChiron_rep2


title: 5XFAD_ROI21

description:
Library name: 2-7-24-Sample-1_21
Biological replicate 2


title: 5XFAD_ROI20

description:
Library name: 2-7-24-Sample-1_20
Biological replicate 2


title: P17_IR_FLASH_9Gy_2


title: P17_IR_FLASH_9Gy_1


title: 5XFAD_ROI19

description:
Library name: 2-7-24-Sample-1_19
Biological replicate 2


title: 5XFAD_ROI14

description:
Library name: 2-7-24-Sample-1_14
Biological replicate 1


title: RNA sequencing from gastruloids grown without embedding and without Chiron pulse, replicate 1

description: Library name: noChiron_rep1


title: 5XFAD_ROI15

description:
Library name: 2-7-24-Sample-1_15
Biological replicate 1


title: RNA sequencing from gastruloids grown without embedding, replicate 2

description: Library name: 96wp_rep2


title: P17_NI_3


title: 5XFAD_ROI16

description:
Library name: 2-7-24-Sample-1_16
Biological replicate 1


title: P17_NI_2


title: 5XFAD_ROI27

description:
Library name: 2-7-24-Sample-1_27
Biological replicate 2


title: 5XFAD_ROI17

description:
Library name: 2-7-24-Sample-1_17
Biological replicate 2


title: 5XFAD_ROI18

description:
Library name: 2-7-24-Sample-1_18
Biological replicate 2


title: 5XFAD_ROI11

description:
Library name: 2-7-24-Sample-1_11
Biological replicate 1


title: RNA sequencing from gastruloids grown without embedding, replicate 3

description: Library name: 96wp_rep3


title: 5XFAD_ROI10

description:
Library name: 2-7-24-Sample-1_10
Biological replicate 1


title: RNA sequencing from gastruloids embedded at 96h in 1.5mM Dextran hydrogel replicate 3

description: Library name: Emb_1.5mM_at_96h_rep3

growth_protocol: Gastruloids were generated by manually seeding 300 cells per well in Costar Low Binding 96-well plates (Costar, Corning, 7007), in a volume of 40 μL per well. After 48 h of aggregation, spheroids were exposed to a 24 h pulse of Wnt agonist by adding 150 μL of 3 μM CHIR 99021 (CHI in the text) in N2B27 to each well, unless stated otherwise. N2B27 media was then changed every 24 h by replacing 150 μL of media per well until 120 h.

treatment_protocol: Gastruloids were embedded in hydrogels 72 h or 96 h after seeding, then left to grow until 120 h. For gastruloid embedding, 20-30 gastruloids were collected from a 96- well plate and left to sediment in a falcon tube. Meanwhile, gel components were prepared, following the proportions of the manufacturer of the 3-D Life Dextran-PEG Hydrogel FG (Cellendes, FG90-1, containing the components PEG-Link, Dextran- Maleimide and CB Buffer pH=5.5) to reach the indicated function concentrations, setting 50% of gastruloid suspension and a total volume of 120 μL per gel. For each gel, two tubes were prepared: one tube containing ultrapure water and PEG-Link, and one tube containing CB Buffer (pH=5.5) and gastruloid suspension in N2B27. Dextran-Maleimide was added to the second tube at the last moment, followed by a quick homogenization with the pipette, pooling of the two solutions, homogenization, then deposition of the gel mix into a glass-bottom dish (Cellvis, D35-10-1.5-N). Quickly, a membrane was deposited on top of the gel (Isopore filter, 5.0 μm membrane, 13mm diameter, Merck, TMTP01300), followed by an adhesive ring (Delta microscopies, slide wells D70366-12) to secure the membrane. The dish was then put in the incubator for 15 min for gel formation, after which 2mL of N2B27 was added on top, and the embedded gastruloids were kept for culture as usual.. For each replicate, about 30 gastruloids were processed per condition. At 120 h after seeding, dishes containing embedded gastruloids were treated as follow: the adhesive ring was lifted, and a solution of 1:20 Dextranase (Cellendes, D10-1) in PBS (Ca++/Mg++) was added to each dish, and left >20 min in the incubator until gastruloids were freely moving and could be collected in a falcon tube.


title: RNA sequencing from gastruloids embedded at 96h in 1.5mM Dextran hydrogel replicate 2

description: Library name: Emb_1.5mM_at_96h_rep2


title: 5XFAD_ROI8

description:
Library name: 2-7-24-Sample-1_8
Biological replicate 1


title: empty_electroporation_Rep2_Donor4

city: San Francisco

first: Laine

last: Goudy

state: CA

address: 400 Parnassus Ave

institute: University of California, San Francisco

description: Library name: 74b

data_processing:
Raw WGBS-seq FASTQ files were processed using the nf-methylseq:2.6.0 pipeline69 with the default parameters along with the `--three_prime_clip_R1 10` and `--three_prime_clip_r2 10`options. Differential CpG DNA methylation analysis was performed using the methylKit R package70. CpG methylation data from Bismark coverage files was imported. To search for differentially methylated tiles, the ‘tileMethylCounts’ function was used with options ‘win.size=1000’ and ‘step.size=100‘. Differentially methylated regions (DMRs) were scored by % methylation difference and q-value were calculated using the ‘calculateDiffMeth’ function with `overdispersion = "MN"` and `adjust="BH"` options using the replicates as a covariate in fitting the model. Results were visualized as Manhattan plots to display -log10-transformed p-values associated with individual methylation tiling windows. Statistically significant DMRs with FDR < 0.05 (Benjamini Hochberg) were colored based on their methylation status. To visualize the methylation status at individual loci in IGV, the base level methylation status was extracted from BedGraph files from the nf-methylseq pipeline. Then results were converted into an IGV friendly format and data were displayed as bar charts in which methylated regions were considered as methylation percentage from 50%-100% shown in range of 0.5 to 1 in red, and un-methylated regions considered as methylation percentage from 0%-50% shown in range of -1 to -0.5 in blue.
Assembly: hg38
Supplementary files format and content: Whole genome bisulfite bismark converage file

source_name: primary

growth_protocol: Human peripheral blood Leukopaks enriched for peripheral blood mononuclear cells (PBMCs) from deidentified healthy donors were purchased from STEMCELL Technologies (#200-0092). CD3+ T cells were isolated using the EasySep Human T cell isolation kit (#100-069) per manufacturer-provided instructions. After isolation, T cells were seeded at 1×106 cells ml–1 and activated with anti-CD3/CD28 Dynabeads (Life Technologies, #40203D). T cells were maintained in culture at 1×106 cells ml–1 density throughout and cultured in complete X-VIVO-15 (cX-VIVO), consisting of X-VIVO 15 (Lonza Bioscience, Visp, Switzerland #04-418Q) supplemented with 5% FCS (R&D systems, lot M19187), 5 ng μl–1 IL-7, and 5 ng μl–1 IL-15, unless otherwise indicated. CD4+CD25low Tconv were isolated from washed PBMCs using the EasySep Human CD4+CD127lowCD25+ Regulatory T Cell Isolation Kit (STEMCELL Technologies, catalog no. 18063) according to manufacturer’s protocol. Tconv were activated using Immunocult CD2/CD3/CD28 T Cell Activation reagent (STEMCELL Technologies #10990) at 12.5 μl ml–1. Tconv were maintained in culture in cX-VIVO supplemented with 300 IU ml-1 of IL2 and passaged every 2-3 days.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen), and 250 ng DNA was diluted to 2.27 ng μl–1 in 110 μl with 2 μl 0.5% lambda DNA spike-in and sheared using a Covaris E220 evolution with intensifier for 50 s to an average length of ~500 bp. Sonicated DNA was recovered using the MinElute Reaction Cleanup Kit (Qiagen), bisulfite conversion was performed using the EZ DNA methylation-Gold Kit (Zymogen), and the resulting ssDNA was quantified on the Qubit ssDNA Assay Kit (Invitrogen).
Library preparation was performed using the xGen™ Methylation-Sequencing DNA Library Preparation Kit (IDT #10009860) and xGen™ Normalase™ UDI Primers Plate 1 (IDT #10009796). The prepared libraries were quantified on a 4200 TapeStation system (Agilent) and Qubit dsDNA HS Assay Kit (Invitrogen). Libraries were sequenced using paired-end 150 bp reads on a NovaSeqX with a 10% PhiX spike-in to diversify the sample pools.

treatment_protocol: For experiments using Cas9, CRISPRi, or CRISPRoff mRNA, fresh CD3+ T cells were activated with a 1:1 bead-to-cell ratio with anti-CD3/CD28 Dynabeads (Life Technologies, #40203D). in the presence of 5 ng μl–1 IL-7 and 5 ng μl–1 IL-15 at 1×106 cells ml–1. After two days of stimulation, T cells were magnetically de-beaded, washed with PBS, and resuspended in TheraPEAK P3 buffer with supplement (Lonza #G4LP3-126000) at 0.75×106 cells in 20 μl. Cas9, CRISPRi and CRISPRoff mRNA were added to 20 μl cells at an equimolar ratio (1 μg, 1.07 μg, or 1.6 μg, respectively) with 2 μg chemically modified sgRNA (Synthego), and cells were electroporated on a Lonza 4D Nucleofector using pulse code DS137. Immediately after electroporation, 80μl pre-warmed cX-VIVO was added to each electroporation well, and cells were incubated for 30 min in a CO2 incubator at 37°C followed by distribution of each electroporation reaction into three wells of a 96-well round-bottom plate. Each well was brought to 200 μl with cX-VIVO. Cells were maintained and expanded by addition of cX-VIVO every 2 or 3 days and re-stimulated with ImmunoCult Human CD2/CD3/CD28 T Cell Activation reagent (STEMCELL Technologies #10990) every 9–10 days at 6.25 μl ml–1.

value: primary

value: Bulk T cells

value: WT

tag: batch


title: CD55_Rep2_Donor4

description: Library name: 71b


title: CD81_Rep2_Donor4

description: Library name: 70b


title: 5XFAD_ROI9

description:
Library name: 2-7-24-Sample-1_9
Biological replicate 1


title: RNA sequencing from gastruloids embedded at 96h in 1.5mM Dextran hydrogel replicate 1

description: Library name: Emb_1.5mM_at_96h_rep1


title: 5XFAD_ROI6

description:
Library name: 2-7-24-Sample-1_6
Biological replicate 1


title: 5XFAD_ROI5

description:
Library name: 2-7-24-Sample-1_5
Biological replicate 1


title: sgNEG_Rep2_Donor4

description: Library name: 66b


title: P17_NI_1


title: RNA sequencing from gastruloids grown without embedding, replicate 1

description: Library name: 96wp_rep1


title: 5XFAD_ROI13

description:
Library name: 2-7-24-Sample-1_13
Biological replicate 1


title: 5XFAD_ROI12

description:
Library name: 2-7-24-Sample-1_12
Biological replicate 1


title: empty_electroporation_Rep2_Donor3

description: Library name: 65b


title: 5XFAD_ROI1

description:
Library name: 2-7-24-Sample-1_1
Biological replicate 1


title: CD55_Rep2_Donor3

description: Library name: 62b


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel replicate 3

description: Library name: Emb_1.0mM_at_96h_rep3


title: RNA sequencing from gastruloids embedded at 72h in 1.5mM Dextran hydrogel replicate 1

description: Library name: Emb_1.5mM_at_72h_rep1


title: 5XFAD_ROI4

description:
Library name: 2-7-24-Sample-1_4
Biological replicate 1


title: 5XFAD_ROI3

description:
Library name: 2-7-24-Sample-1_3
Biological replicate 1


title: RNA sequencing from gastruloids embedded at 72h in 1.5mM Dextran hydrogel replicate 2

description: Library name: Emb_1.5mM_at_72h_rep2


title: Bl6_ROI46

description:
Library name: 2-7-24-WT-1_46
Biological replicate 3


title: Bl6_ROI45

description:
Library name: 2-7-24-WT-1_45
Biological replicate 3


title: 5XFAD_ROI7

description:
Library name: 2-7-24-Sample-1_7
Biological replicate 1


title: Bl6_ROI44

description:
Library name: 2-7-24-WT-1_44
Biological replicate 3


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel replicate 2

description: Library name: Emb_1.0mM_at_96h_rep2


title: Bl6_ROI41

description:
Library name: 2-7-24-WT-1_41
Biological replicate 3


title: RNA sequencing from gastruloids embedded at 72h in 1.5mM Dextran hydrogel replicate 3

description: Library name: Emb_1.5mM_at_72h_rep3


title: 5XFAD_ROI2

description:
Library name: 2-7-24-Sample-1_2
Biological replicate 1


title: Bl6_ROI43

description:
Library name: 2-7-24-WT-1_43
Biological replicate 3


title: Bl6_ROI42

description:
Library name: 2-7-24-WT-1_42
Biological replicate 3


title: RNA sequencing from gastruloids embedded at 96h in 1mM Dextran hydrogel replicate 1

description: Library name: Emb_1.0mM_at_96h_rep1


title: empty_electroporation_Rep1_Donor4

description: Library name: 74a


title: RNA sequencing from gastruloids embedded at 72h in 1mM Dextran hydrogel replicate 3

description: Library name: Emb_1.0mM_at_72h_rep3


title: Bl6_ROI39

description:
Library name: 2-7-24-WT-1_39
Biological replicate 3


title: CD81_Rep2_Donor3

description: Library name: 61b


title: Bl6_ROI38

description:
Library name: 2-7-24-WT-1_38
Biological replicate 3


title: CD81_Rep1_Donor4

description: Library name: 70a


title: RNA sequencing from gastruloids embedded at 72h in 1mM Dextran hydrogel replicate 2

description: Library name: Emb_1.0mM_at_72h_rep2


title: Bl6_ROI37

description:
Library name: 2-7-24-WT-1_37
Biological replicate 3


title: Bl6_ROI36

description:
Library name: 2-7-24-WT-1_36
Biological replicate 3


title: sgNEG_Rep1_Donor4

description: Library name: 66a


title: sgNEG_Rep2_Donor3

description: Library name: 57b


title: CD55_Rep1_Donor4

description: Library name: 71a


title: RNA sequencing from gastruloids embedded at 72h in 1mM Dextran hydrogel replicate 1

description: Library name: Emb_1.0mM_at_72h_rep1


title: empty_electroporation_Rep1_Donor3

description: Library name: 65a


title: Bl6_ROI33

description:
Library name: 2-7-24-WT-1_33
Biological replicate 2


title: Bl6_ROI31

description:
Library name: 2-7-24-WT-1_31
Biological replicate 2


title: Bl6_ROI32

description:
Library name: 2-7-24-WT-1_32
Biological replicate 2


title: CD55_Rep1_Donor3

description: Library name: 62a


title: Bl6_ROI40

description:
Library name: 2-7-24-WT-1_40
Biological replicate 3


title: Thymic iNKT cells, Prkd2/3-deficient, scATAC-seq

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: Prkd2/3-deficient, scATAC-seq
10x Genomics

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 28+91 base (scRNA/TCR-seq) and 50+16+49+8 base (scATAC-seq) paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
For scRNA/TCR-seq, generated reads were input into the cellranger pipeline (cellranger-8.0.1, 10x Genomics) for UMI counting for each gene-cell (barcode) combination and T cell receptor repertoire profiling.
For scATAC-seq, generated reads were input into the cellranger pipeline (cellranger-atac-1.2.0, 10x Genomics) for alignment to the mm10 genome and making cut site count of genome regions-cell (barcode) matrix.
Assembly: refdata-gex-GRCm39-2024-A, refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0, refdata-cellranger-atac-mm10-1.2.0
Supplementary files format and content: barcodes.tsv.gz : gzip compressed list of cell barcode corresponding to the matrix.mtx
Supplementary files format and content: features.tsv.gz : gzip compressed list of gene information corresponding to the matrix.mtx
Supplementary files format and content: matrix.mtx.gz : gzip compressed gene expresion matrix of gene and cell barcode in the Matrix Market file format
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the TCR clonotype information
Supplementary files format and content: filtered_peak_bc_matrix.h5: HDF5 format file including number of cut sites for genomic region and cell barcode combination
Supplementary files format and content: atac_peak_annotation.tsv: tab-delimited text file including the position and the nearby gene information of called peaks with ATAC-Seq

source_name: Thymus

extract_protocol:
Thymocytes were resuspended in 2%FBS/RPMI1640 medium and stained with anti-mouse TCRb-FITC and alpha-Galactosylceramide (a-GalCer)-loaded mouse CD1d tetramer-APC and anti-APC microbeads. Thymic iNKT cells were enriched by MACS magnetic separator (Miltenyi). Thereafter cells were passed through 0.45 um mesh, stained with propium iodide (PI) and purified for TCRβ+CD1d tetramer+PI– cells by a cell sorter (SH800S, Sony). Purified thymic iNKT cells were washed and suspended in PBS (–) containing w/v 0.04% BSA and applied to scRNA/TCR-seq analysis. For scATAC-seq analysis, nuclei were isolated from purified thymic iNKT cells according to the manufacturer's instruction (10x Genomics).
For scRNA-TCR-seq, single cell library was prepared using Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 and Chromium Single Cell V(D)J Enrichment Kit for mouse T cell (10x Genomics) following the manufacturer’s instructions. After reverse transcription, cDNA was amplified for 14 cycles, and up to 50 ng of cDNA was used for construction of gene expression and TCR libraries. For scATAC-seq, single cell library was prepared using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit (10x Genomics) following the manufacturer’s instructions.

value: Thymus

value: iNKT cells

value: Prkd2/3 deficient


title: Thymic iNKT cells, WT, scATAC-seq

description:
Library name: WT, scATAC-seq
10x Genomics

value: Wild type


title: Bl6_ROI34

description:
Library name: 2-7-24-WT-1_34
Biological replicate 2

value: brain

value: oligodendrocyte lineage (olig2)+


title: CD81_Rep1_Donor3

description: Library name: 61a


title: Bl6_ROI28

description:
Library name: 2-7-24-WT-1_28
Biological replicate 2


title: Bl6_ROI35

description:
Library name: 2-7-24-WT-1_35
Biological replicate 3


title: Bl6_ROI29

description:
Library name: 2-7-24-WT-1_29
Biological replicate 2


title: Bl6_ROI30

description:
Library name: 2-7-24-WT-1_30
Biological replicate 2


title: Bl6_ROI27

description:
Library name: 2-7-24-WT-1_27
Biological replicate 2


title: Thymic iNKT cells, Prkd2/3-deficient, scTCR-seq

description:
Library name: Prkd2/3-deficient, scTCR-seq
10x Genomics


title: sgNEG_Rep1_Donor3

description: Library name: 57a


title: Bl6_ROI25

description:
Library name: 2-7-24-WT-1_25
Biological replicate 2


title: CBO-MOK20092-WT4, WT

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: SP8_WT_4_GT24-12110_GCGCAAGC-CGGCGTGA_S94_L008
KOLF2.2J differentiated to cortical brain organoid

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study9_featureCounts.csv study9_genesCounts.csv study9_genesRawCounts.csv study9_genesTPM.csv study9_stats.csv study9_txCounts.csv study9_txRawCounts.csv study9_txTPM.csv

extract_protocol:
RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 9

tag: model system

value: Cortical brain (dorsal forebrain patterning)

tag: parental cell_line


title: Thymic iNKT cells, WT, scTCR-seq

description:
Library name: WT, scTCR-seq
10x Genomics

tag: tissue


title: Thymic iNKT cells, Prkd2/3-deficient, scRNA-seq

description:
Library name: Prkd2/3-deficient, scRNA-seq
10x Genomics


title: Bl6_ROI26

description:
Library name: 2-7-24-WT-1_26
Biological replicate 2


title: Bl6_ROI24

description:
Library name: 2-7-24-WT-1_24
Biological replicate 2


title: Bl6_ROI23

description:
Library name: 2-7-24-WT-1_23
Biological replicate 2


title: CBO-MOK20092-WT2, WT

description:
Library name: SP8_WT_2_GT24-12109_ATATGGAT-TAATACAG_S73_L008
KOLF2.2J differentiated to cortical brain organoid

tag: cell line


title: Thymic iNKT cells, WT, scRNA-seq

description:
Library name: WT, scRNA-seq
10x Genomics


title: Bl6_ROI22

description:
Library name: 2-7-24-WT-1_22
Biological replicate 2


title: CBO-MOK20092-WT1, WT

description:
Library name: SP8_WT_1_GT24-12108_CGGACAAC-AATCCGGA_S80_L008
KOLF2.2J differentiated to cortical brain organoid


title: Skeletal Muscle, Sciatic Nerve Transection, snRNA-Seq

city: Cincinnati

first: Douglas

middle: P

last: Millay

state: OH

address: 3333 Burnet Ave Cincinnati, OH 45229

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital and Medical Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control, data normalization, gene expression visualization, integration, and dimensionality reduction was performed using Seurat/5.0.1 standard workflow.
Assembly: mm10

molecule: nuclear RNA

source_name: Tibialis Anterior

extract_protocol:
Muscles were obtained from mice and then minced, homogenized, and processed through a series of steps. The nuclei were sorted using a FACS cell sorter. Further details could be found in method session in this paper.
Chromium Next GEM Single Cell 3ʹ Kit v3.1

value: Skeletal muscle

value: Unsorted

tag: gender

value: Male

tag: age

value: 5 Months


title: Bl6_ROI20

description:
Library name: 2-7-24-WT-1_20
Biological replicate 2


title: CBO-MOK20092P-G04, KO

description:
Library name: SP8_PTC_G04_GT24-12107_TAAGTGGT-GGCTTAAG_S92_L008
KOLF2.2J derived knockout cell line, SP8 PTC, differentiated to cortical brain organoid

value: Termination codon


title: Bl6_ROI18

description:
Library name: 2-7-24-WT-1_18
Biological replicate 2


title: CBO-MOK20092P-G02, KO

description:
Library name: SP8_PTC_G02_GT24-12106_CTACGACA-TTGGACTC_S82_L008
KOLF2.2J derived knockout cell line, SP8 PTC, differentiated to cortical brain organoid


title: Bl6_ROI17

description:
Library name: 2-7-24-WT-1_17
Biological replicate 1


title: Bl6_ROI19

description:
Library name: 2-7-24-WT-1_19
Biological replicate 2


title: Skeletal Muscle, Sod1 G93A, snRNA-Seq

value: 2 Months


title: Bl6_ROI16

description:
Library name: 2-7-24-WT-1_16
Biological replicate 1


title: CBO-MOK20092P-F03, KO

description:
Library name: SP8_PTC_F03_GT24-12105_TCGTAGTG-CCAAGTCT_S68_L008
KOLF2.2J derived knockout cell line, SP8 PTC, differentiated to cortical brain organoid


title: CBO-MOK20090_88-WT4, WT

description:
Library name: SOX21_POU3F1_WT_4_GT24-12104_GATTCTGC-CTCTCGTC_S90_L008
KOLF2.2J differentiated to cortical brain organoid

value: day 8


title: Bl6_ROI13

description:
Library name: 2-7-24-WT-1_13
Biological replicate 1


title: Bl6_ROI12

description:
Library name: 2-7-24-WT-1_12
Biological replicate 1


title: Bl6_ROI14

description:
Library name: 2-7-24-WT-1_14
Biological replicate 1


title: 5_FKDL210250684-1a

city: Xinxiang

first: Tianhan

last: Li

state: Henan

address: No.601, Hualan Road

institute: Xinxiang Medical University

description: BD Rhapsody

data_processing:
Set up BD rhapsody local pepline on linux operating system according to the manufacter's instruction, then load with WTA and TAG raw data and run, finally analysis the processed data (“_RSEC_MolsPerCell.csv” and “_Sample_Tag_Calls.csv”) using Segeq software.
Assembly: GRCm39
Supplementary files format and content: tab-separated values file and matrix files

source_name: aorta, lymph node and spleen

extract_protocol:
Single cell suspension from spleens and lymph nodes were firstly removed the CD5+, CD19+ and CD11b+ cells via SAV conjugated beads. Then two million live cells from spleen and lymph node were stained with mix1 (CD45.2-PE-cy7, CD11c, CD172α-FITC, MHCII- APC-eFluor780 and XCR1-APC), and all cells from aorta were stained with mix2 (CD45.2-PE-cy7, CD11b-super bright 600, CD11c-PE-cy5.5, MHCII- FITC, CD3- Alexa Fluor 700, CD19- Alexa Fluor 700, Ly6G- Alexa Fluor 700 and XCR1-APC) for 30 minutes at 4 °C. After washing with 1 mL FACS buffer two times, cells from different organs were stained with different anti-CD45 (30-F11) antibodies conjugated with barcode oligos from BD™ Ms Single Cell Sample Multiplexing Kit (BD Bioscience, Cat: 633793). Finally, cells were resuspended with Sytox blue and CD11c+ MHCII+ XCR1+ cells were sorted and subjected to the BD Rhapsody Express system.
each group was labelled with sample tag, then built the whole transcriptome analysis (WTA) and sample tag library (TAG) according to the manufacter's instructions (BD Rhapsody™ Single-Cell Analysis System Instrument User Guide (Doc ID 214062))

treatment_protocol: 7 to 8-week old ApoE−/−were fed with a high-fat diet or normal diet for 20 weeks

value: aorta, lymph node and spleen

value: immune cells

value: CD45.2+MHCII+CD11C+XCR1+ cells

value: ApoE-/- mice

tag: treatment

value: 7 to 8-week old ApoE-/- were fed with a high-fat diet or normal diet for 20 weeks


title: 6_FKDL210250685-1a

description: BD Rhapsody


title: CBO-MOK20090_88-WT3, WT

description:
Library name: SOX21_POU3F1_WT_3_GT24-12103_AGCCTCAT-TCTCTACT_S75_L008
KOLF2.2J differentiated to cortical brain organoid


title: Bl6_ROI11

description:
Library name: 2-7-24-WT-1_11
Biological replicate 1

value: brain

value: oligodendrocyte lineage (olig2)+


title: Bl6_ROI10

description:
Library name: 2-7-24-WT-1_10
Biological replicate 1


title: CBO-MOK20090_88-WT2, WT

description:
Library name: SOX21_POU3F1_WT_2_GT24-12102_CGTTAGAA-GACCTGAA_S67_L008
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable


title: Bl6_ROI9

description:
Library name: 2-7-24-WT-1_9
Biological replicate 1


title: CBO-MOK20088P-E02, KO

description:
Library name: POU3F1_PTC_E02_GT24-12101_TACCGAGG-AGTTCAGG_S71_L008
KOLF2.2J derived knockout cell line, POU3F1 PTC, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: Bl6_ROI21

description:
Library name: 2-7-24-WT-1_21
Biological replicate 2


title: NSC, cKO, 2

description: Library name: Sample5

growth_protocol: NSCs were isolated from P0 WT and cKO mouse hippocampus, dissociated into single cells, and cultured as neurospheres in DMEM-F12 medium supplemented with B27, N2, EGF, and bFGF at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Lipid Mini Kit (QIAGEN, 74134). RNA quality was determined by Agilent 2100.
Library data were assembled and analyzed by the BGISEQ institute.

value: hippocampus

value: primary

value: neural stem cell

value: cKO


title: NSC, cKO, 3

description: Library name: Sample6


title: Bl6_ROI7

description:
Library name: 2-7-24-WT-1_7
Biological replicate 1


title: NSC, cKO, 1

description: Library name: Sample4


title: Bl6_ROI8

description:
Library name: 2-7-24-WT-1_8
Biological replicate 1


title: Skeletal Muscle, Sod1 G93A Control, snRNA-Seq

value: Skeletal muscle

value: Unsorted

value: Male


title: Bl6_ROI15

description:
Library name: 2-7-24-WT-1_15
Biological replicate 1


title: Bl6_ROI6

description:
Library name: 2-7-24-WT-1_6
Biological replicate 1


title: NSC, WT, 3

description: Library name: Sample3

value: WT


title: Bl6_ROI4

description:
Library name: 2-7-24-WT-1_4
Biological replicate 1


title: NSC, WT, 2

description: Library name: Sample2


title: Bl6_ROI2

description:
Library name: 2-7-24-WT-1_2
Biological replicate 1


title: Bl6_ROI3

description:
Library name: 2-7-24-WT-1_3
Biological replicate 1


title: Bl6_ROI5

description:
Library name: 2-7-24-WT-1_5
Biological replicate 1


title: CBO-MOK20088P-A02, KO

description:
Library name: POU3F1_PTC_A02_GT24-12099_GGCATTCT-CAAGCTAG_S46_L007
KOLF2.2J derived knockout cell line, POU3F1 PTC, differentiated to cortical brain organoid

value: Termination codon

value: day 8


title: CBO-MOK20090P-D07, KO

description:
Library name: SOX21_PTC_D07_GT24-12098_TTACAGGA-GCTTGTCA_S51_L007
KOLF2.2J derived knockout cell line, SOX21 PTC, differentiated to cortical brain organoid


title: NSC, WT, 1

description: Library name: Sample1


title: CBO-MOK20090P-B10, KO

description:
Library name: SOX21_PTC_B10_GT24-12097_CCGTGAAG-ATCCACTG_S63_L007
KOLF2.2J derived knockout cell line, SOX21 PTC, differentiated to cortical brain organoid


title: CRISPRoff_FAS_SUV39H1_RC3H1_Donor4

description:
Library name: 317
normalized_counts_CO065.csv

data_processing:
RNA-seq sequencing data was aligned and counts were generated using the RNAseq pipeline of nf-core (v 3.18)69.  Raw sequencing reads were quantified using Salmon and summarized to gene-level counts using tximport. Differential gene expression analysis was conducted using the limma-voom framework, with donor variation included as a covariate in the statistical model. Gene expression was normalized using the trimmed mean of M-values (TMM) method, and low-expressed genes were filtered prior to analysis. Differentially expressed genes were identified by comparing treated samples to non-targeting controls (NTC), with significance criteria set at adjusted p-value < 0.05 (Empirical-Bayes moderated statistics with Benjamini–Hochberg correction) and absolute log2 fold change > 1. Results were visualized using volcano plots displaying log2 fold change versus -log10(adj. P-value), with genes colored based on significance thresholds or target gene.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each file

extract_protocol:
Human primary T cells were harvested 27 days post-electroporation (CD55, CD81) or 7 days post-electroporation (FAS, PTPN2, RC3H1, SUV39H1, MED12). 1×106 cells were harvested per condition, and RNA was isolated using a Quick-RNA MicroPrep Kit (Zymo #R1050). Isolated RNA was treated with TURBO DNase (Invitrogen #AM2239) and concentrated using RNA Clean and Concentrate Kit (Zymo #NC0622892).
Library preparation was carried out using 96 prep QuantSeq FWD V2 with UDI Set A1 kit and UMI Module (Lexogen #191.96). Final libraries were assessed using a 4200 TapeStation (Agilent), quantified using Qubit ds HS Assay Kit (Invitrogen), and sequenced as single-end 50 base pair reads on a HiSeq 4000 (Illumina) or NextSeq 500 (Illumina)

value: Bulk T cells

value: CRISPRoff

value: Day 7


title: CRISPRoff_FAS_SUV39H1_RC3H1_Donor3

description:
Library name: 303
normalized_counts_CO065.csv


title: CRISPRoff_NTC_multiplexing_Donor4

description:
Library name: 311
normalized_counts_CO065.csv


title: Bl6_ROI1

description:
Library name: 2-7-24-WT-1_1
Biological replicate 1

value: brain

value: oligodendrocyte lineage (olig2)+


title: CBO-MOK20090P-A07, KO

description:
Library name: SOX21_PTC_A07_GT24-12096_TCCAACGC-AAGTCCAA_S56_L007
KOLF2.2J derived knockout cell line, SOX21 PTC, differentiated to cortical brain organoid

value: iPSC


title: Cas9_AAVS1_Guide2_Donor4

description:
Library name: 296
normalized_counts_CO065.csv


title: Cas9_AAVS1_Guide1_Donor4

description:
Library name: 295
normalized_counts_CO065.csv


title: CRISPRoff_NTC_multiplexing_Donor3

description:
Library name: 297
normalized_counts_CO065.csv


title: CBO-MOK20088P-B03, KO

description:
Library name: POU3F1_PTC_B03_GT24-12100_AATGCCTC-TGGATCGA_S81_L008
KOLF2.2J derived knockout cell line, POU3F1 PTC, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: CBO-MOK20075_78_86-WT3, WT

description:
Library name: WT3_Day11_GT24-08532_ATATCTCG-ACTAAGAT_S50_L007
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: day 11


title: Cas9_RASA2_Donor4

description:
Library name: 293
normalized_counts_CO065.csv

value: primary


title: Cas9_SUV39H1_Donor4

description:
Library name: 292
normalized_counts_CO065.csv


title: Cas9_MED12_Donor4

description:
Library name: 294
normalized_counts_CO065.csv


title: CBO-MOK20086P-C12, KO

description:
Library name: HES5_PTC_C12_Day11_GT24-08530_GTTCCAAT-GCAGAATT_S68_L007
KOLF2.2J derived knockout cell line, HES5 PTC, differentiated to cortical brain organoid


title: CBO-MOK20075_78_86-WT2, WT

description:
Library name: WT2_Day11_GT24-08531_ACCTTGGC-ATGAGGCC_S56_L007
KOLF2.2J differentiated to cortical brain organoid


title: CBO-MOK20086P-C11, KO

description:
Library name: HES5_PTC_C11_Day11_GT24-08529_GCAATGCA-AACGTTCC_S60_L007
KOLF2.2J derived knockout cell line, HES5 PTC, differentiated to cortical brain organoid


title: Cas9_FAS_Donor4

description:
Library name: 289
normalized_counts_CO065.csv


title: CRISPRoff_AAVS1_Guide2_Day7_Donor4

description:
Library name: 288
normalized_counts_CO065.csv


title: GastricCancer_Ca418439_normal

type: RNA

city: Guangzhou

first: Rongpeng

state: Guangdong Province

address: No. 250 Changgang East Road, Haizhu District

department: Department of Gastrointestinal Surgery

institute: The Second Affiliated Hospital of Guangzhou Medical University

description: CircRNA expression in adjacent non-tumor gastric tissue (normal)

hyb_protocol: 1 μg of Cy3-labeled cRNA was fragmented (60 °C, 30 min), diluted with 2× hybridization buffer, and hybridized onto the Arraystar Human circRNA microarray V2 (Agilent-074301, one-color) at 65 °C for 17 h in a rotating Agilent hybridization oven. Hybridized arrays were washed and dried.

scan_protocol: Slides were scanned using the Agilent G2505C microarray scanner. Images were processed with Agilent Feature Extraction software v11.0.1.1.

data_processing: Raw intensities were extracted with Agilent Feature Extraction software. Quantile normalization and low-intensity filtering were performed using the R limma package. circRNAs flagged as Present (P) or Marginal (M) in ≥3 of 6 samples were retained. Differential expression was assessed by fold-change and t-test; volcano plots and hierarchical clustering were generated.

source_name: adjacent non-tumor gastric tissue

label_protocol: Total RNAs were digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched circRNAs were amplified and transcribed into fluorescent cRNA using the Arraystar Super RNA Labeling Kit (random priming). Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and quantified by NanoDrop ND-1000.

growth_protocol: not applicable.

extract_protocol: Total RNA was extracted using TRIzol reagent (Life Technologies, USA). RNA concentration and purity were assessed by NanoDrop ND-1000, and integrity was confirmed by agarose gel electrophoresis.

treatment_protocol: Gastric cancer tissues and matched adjacent non-tumor tissues were surgically resected and stored in liquid nitrogen until RNA extraction.

value: stomach

tag: group

value: normal

value: male


title: CRISPRoff_MED12_pool_Day7_Donor4

description:
Library name: 286
normalized_counts_CO065.csv


title: Cas9_RC3H1_Donor4

description:
Library name: 291
normalized_counts_CO065.csv


title: GastricCancer_Ca367711_normal

value: female


title: SIZ1 Overexpression, Rosette leaves, 4-week, rep 2

city: Berkeley

first: ENRICO

last: CALVANESE

address: Koshland Hall 371

department: Plant & Microbial Biology

institute: University of California, Berkeley

description: Library name: SIZ1_1_2

data_processing:
Sequencing read counts were quality-checked to remove low-quality reads. Cleaned reads were aligned to the reference genome of Arabidopsis (TAIR10) using Hisat2 (v.2.1.0, https://daehwankimlab.github.io/hisat2/). SAMtools (v.1.14, https://www.htslib.org/) was used to sort and convert SAM files to BAM files. Read counts of each gene were generated using HTseq-count with the default parameters. Differences in gene expression were analysed using the DESeq2 package.
Assembly: ncbi_arabidopsis_thaliana_gcf_000001735_4_tair10_1
Supplementary files format and content: Normalized_Counts_Supplementary.xlsx

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: Arabidopsis adult plants Col-0, siz1-2 mutant and SIZ1 overexpresison transgenic lines were grown under a 16 h light / 8 h dark–light cycle at 22 °C for 4 weeks before taking RNA sampkes

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research, 11-330) with a DNase treatment.
Library construction, quality control and RNA-seq were performed by Novogene (https://en.novogene.com/) on an Illumina NovaSeq X Plus Series (PE150)

treatment_protocol: no treatment

value: rosette leaves


title: CRISPRoff_RASA2_pool_Day7_Donor4

description:
Library name: 285
normalized_counts_CO065.csv


title: CRISPRoff_SUV39H1_Guide2_Day7_Donor4

description:
Library name: 284
normalized_counts_CO065.csv


title: GastricCancer_Ca367711_tumor

description: CircRNA expression in gastric cancer tissue (tumor)

source_name: gastric cancer tissue

value: tumor


title: CBO-MOK20078P-E12, KO

description:
Library name: SOX1_PTC_E12_Day11_GT24-08527_GGAGCGTC-GCACGGAC_S63_L007
KOLF2.2J derived knockout cell line, SOX1 PTC, differentiated to cortical brain organoid

value: Termination codon


title: SIZ1 Overexpression, Rosette leaves, 4-week, rep 1

description: Library name: SIZ1_1_1


title: CRISPRoff_RC3H1_Guide2_Day7_Donor4

description:
Library name: 283
normalized_counts_CO065.csv

value: Bulk T cells


title: CBO-MOK20086P-A11, KO

description:
Library name: HES5_PTC_A11_Day11_GT24-08528_ATGGCATG-GGTACCTT_S57_L007
KOLF2.2J derived knockout cell line, HES5 PTC, differentiated to cortical brain organoid


title: GastricCancer_Ca374744_normal


title: CBO-MOK20075_78_86-WT4, WT

description:
Library name: WT4_Day11_GT24-08533_GCGCTCTA-GTCGGAGC_S51_L007
KOLF2.2J differentiated to cortical brain organoid


title: CRISPRoff_PTPN2_Guide6_Day7_Donor4

description:
Library name: 282
normalized_counts_CO065.csv

value: CRISPRoff


title: siz1-2 Knockout, Rosette leaves, 4-week, rep 2

description: Library name: siz1_2_2


title: CRISPRoff_FAS_Guide1_Day7_Donor4

description:
Library name: 281
normalized_counts_CO065.csv

value: Day 7


title: GastricCancer_Ca418439_tumor


title: GastricCancer_Ca374744_tumor


title: CBO-MOK20078P-C10, KO

description:
Library name: SOX1_PTC_C10_Day11_GT24-08526_AAGATACT-ATGTAAGT_S49_L007
KOLF2.2J derived knockout cell line, SOX1 PTC, differentiated to cortical brain organoid


title: Cas9_AAVS1_Guide2_Donor3

description:
Library name: 280
normalized_counts_CO065.csv

value: WT


title: siz1-2 Knockout, Rosette leaves, 4-week, rep 1

description: Library name: siz1_2_1


title: CRISPRoff_AAVS1_Guide1_Day7_Donor4

description:
Library name: 287
normalized_counts_CO065.csv


title: CBO-MOK20078P-A10, KO

description:
Library name: SOX1_PTC_A10_Day11_GT24-08525_GCGCAAGC-CGGCGTGA_S66_L007
KOLF2.2J derived knockout cell line, SOX1 PTC, differentiated to cortical brain organoid


title: Cas9_MED12_Donor3

description:
Library name: 278
normalized_counts_CO065.csv


title: Cas9_AAVS1_Guide1_Donor3

description:
Library name: 279
normalized_counts_CO065.csv


title: Cas9_RASA2_Donor3

description:
Library name: 277
normalized_counts_CO065.csv


title: CBO-MOK20075P-B01, KO

description:
Library name: POU3F2_PTC_B01_Day11_GT24-08524_ATATGGAT-TAATACAG_S54_L007
KOLF2.2J derived knockout cell line, POU3F2 PTC, differentiated to cortical brain organoid


title: Wild-Type, Rosette leaves, 4-week, rep 2

description: Library name: WT_2


title: CBO-MOK20075P-A11, KO

description:
Library name: POU3F2_PTC_A11_Day11_GT24-08523_CGGACAAC-AATCCGGA_S53_L007
KOLF2.2J derived knockout cell line, POU3F2 PTC, differentiated to cortical brain organoid


title: Cas9_SUV39H1_Donor3

description:
Library name: 276
normalized_counts_CO065.csv


title: Wild-Type, Rosette leaves, 4-week, rep 1

description: Library name: WT_1


title: Cas9_RC3H1_Donor3

description:
Library name: 275
normalized_counts_CO065.csv


title: Cas9_FAS_Donor3

description:
Library name: 273
normalized_counts_CO065.csv


title: CBO-MOK20075P-A06, KO

description:
Library name: POU3F2_PTC_A06_Day11_GT24-08522_TAAGTGGT-GGCTTAAG_S62_L007
KOLF2.2J derived knockout cell line, POU3F2 PTC, differentiated to cortical brain organoid


city: Cambridge

first: C. Jake

last: Harris

address: Downing Street

department: Department of Plant Sciences

institute: University of Cambridge

description: Library name: ChIPseq_SetB_antiH3K4me3_StSDG2g4_lineCB12_rep2

data_processing:
Bowtie2 (version 2.5.0) was used to map the PE150 bp read data in fastq format to the TAIR10 genome (--no-unal), and were converted to bam format using Samtools (version 1.10). Reads were de-duplicated using the samtools fixmate and markdup commands. Tracks were generated in DeepTools (version 3.5.1) using bamCoverage (--normalizeUsing RPGC, --effectiveGenomeSize 135000000 --binSize 10) with multicopy regions blacklisted (--blackListFileName) using the regions identified in (Klasfeld et al., 2022). For analysis of reads mapping to the centromere, a modified version of the previously described pipeline (Wlodzimierz et al., 2023) was used. Briefly, PE150 bp read data in fastq format were mapped to the Col-CEN genome (Naish et al., 2021) using Bowtie2 (version 2.2.5) with (--very-sensitive -k 200 --no-unal --no-discordant) and were filtered for primary alignments using samtools view (-F 256 -q 5) prior to deduplication and track generation, as above. Peaks were called using MACS2 (version 2.2.9.1) with default parameters. For the Quantseq, only read (*1.fq.gz) from PE150 bp data was used for downstream analysis. Reads were trimmed using cutadapt (version 1.18) and were mapped to the genome using STAR (version 2.7.10b) to the TAIR10 genome (--quantMode GeneCounts --alignIntronMax 10000 --outSAMmultNmax 20).
Assembly: TAIR10 for everything except for analysis relating to Figure 3, for which the Col-CEN assembly was used.
Supplementary files format and content: BigWig trackes were generated in DeepTools (version 3.5.1) using bamCoverage (--normalizeUsing RPGC, --effectiveGenomeSize 135000000 --binSize 10) with multicopy regions blacklisted (--blackListFileName) using the regions identified in (Klasfeld et al., 2022). For the QuantSeq genecount data, in accordance with the manufacturer’s (Lexogen) instructions, only read (*1.fq.gz) from PE150 bp data was used for downstream analysis. Briefly, reads were trimmed using cutadapt (version 1.18) and were mapped to the genome using STAR (version 2.7.10b) to the TAIR10 genome (--quantMode GeneCounts --alignIntronMax 10000 --outSAMmultNmax 20).

source_name: seedling

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under 16h light: 8h dark condition on soil or plates.

extract_protocol:
All the material for ChIP used in this paper were from pooled 10-12 day old seedlings grown on Murashinge and Skoog agar plates (1/2X MS, 1.5% agar, pH5.7). 2-4g of seedling tissue was used for each sample. Samples were ground in liquid nitrogen and crosslinked for 10 or 12 minutes at room temperature in Nuclei Isolation buffer (50mM Hepes pH8, 1M sucrose, 5mM KCl, 5mM MgCl2, 0.6% triton X-100, 0.4 mM PMSF, 5 mM benzamidine hydrochloride, cOmplete EDTA-free Protease Inhibitor Cocktail (Roche)) containing 1% formaldehyde. The crosslinking reactions were stopped with 125 mM glycine by incubation at room temperature for 10 minutes. Crosslinked nuclei were filtered through one layer of miracloth, washed with Extraction Buffer 2, centrifuged through a layer of Extraction Buffer 3 and lysed with Nuclei lysis buffer (buffer compositions are described in the published protocol (Villar and Kohler, 2018)). Chromatin was sheared using a Bioruptor Plus (Diagenode) (20 cycles of 30 seconds on and 30 seconds off) and immunoprecipitated overnight at 4°C with antibody. 7 µl of anti-HA (3F10, Merck) and 5 µl of anti-H3K4me3 (ab8580, abcam) were added to up to 2 ml of sheared chromatin per sample for pulldown. . 25 µl each of Protein A and Protein G magnetic Dynabeads (Invitrogen) were added to each sample and incubated for 2 more hours at 4°C. The immunoprecipitated chromatin was washed with Low Salt (2X), High Salt, LiCl and TE buffers, for 5 minutes each at 4°C (buffer compositions are described in the published protocol (Villar and Kohler, 2018)) and eluted twice with 250 µl of elution buffer (1% SDS and 0.1 M NaHCO3) in a thermomixer at 65°C and 1000 rpm, 20 minutes for each elution. Reverse crosslinking was performed overnight at 65°C in 0.2 M NaCl, and proteins were degraded by proteinase K treatment at 45°C for 5h. The DNA fragments were purified using phenol:chloroform and ethanol precipitated overnight at -20°C. For the RNA-seq, plant material was extracted using the Direct-zol RNA miniprep kit (Zymo R2052) according to manufacturers instructions, including the in column DNase I treatment.
ChIP-seq libraries were generated using NuGen Ovation Ultra Low System V2 kits according to manufacturer’s instructions. Quantseq libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) according to manufacturer’s instructions.

value: seedling

tag: chip antibody

value: anti-H3K4me3 (ab8580, abcam)


title: CBO-MOK20070-WT4, WT

description:
Library name: WT4_Day8_GT24-08521_CTACGACA-TTGGACTC_S65_L007
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: day 8

value: Cortical brain (dorsal forebrain patterning)


title: Cas9_PTPN2_Donor3

description:
Library name: 274
normalized_counts_CO065.csv

value: primary


title: CRISPRoff_AAVS1_Guide2_Day7_Donor3

description:
Library name: 272
normalized_counts_CO065.csv


description: Library name: ChIPseq_SetB_antiH3K4me3_StSDG2g4_lineCB12_rep1


description: Library name: ChIPseq_SetB_antiH3K4me3_StSDG2g4_lineCB10_rep2


title: CRISPRoff_AAVS1_Guide1_Day7_Donor3

description:
Library name: 271
normalized_counts_CO065.csv


title: CRISPRoff_RASA2_pool_Day7_Donor3

description:
Library name: 269
normalized_counts_CO065.csv


title: CRISPRoff_MED12_pool_Day7_Donor3

description:
Library name: 270
normalized_counts_CO065.csv


title: CRISPRoff_RC3H1_Guide2_Day7_Donor3

description:
Library name: 267
normalized_counts_CO065.csv


title: CBO-MOK20070-WT1, WT

description:
Library name: WT1_Day8_GT24-08519_GATTCTGC-CTCTCGTC_S64_L007
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable


title: CBO-MOK20070-WT2, WT

description:
Library name: WT2_Day8_GT24-08520_TCGTAGTG-CCAAGTCT_S48_L007
KOLF2.2J differentiated to cortical brain organoid


title: CRISPRoff_SUV39H1_Guide2_Day7_Donor3

description:
Library name: 268
normalized_counts_CO065.csv


description: Library name: ChIPseq_SetB_antiH3K4me3_StSDG2g4_lineCB10_rep1


title: ChIPseq_SetB_antiH3K4me3_rdr6_rep2

description: Library name: ChIPseq_SetB_antiH3K4me3_rdr6_rep2


title: CRISPRoff_PTPN2_Guide6_Day7_Donor3

description:
Library name: 266
normalized_counts_CO065.csv


title: CRISPRoff_FAS_Guide1_Day7_Donor3

description:
Library name: 265
normalized_counts_CO065.csv


title: ChIPseq_SetB_antiH3K4me3_rdr6_rep1

description: Library name: ChIPseq_SetB_antiH3K4me3_rdr6_rep1


title: CBO-MOK20070P-D11, KO

description:
Library name: FOXG1_PTC_D11_Day8_GT24-08517_CGTTAGAA-GACCTGAA_S55_L007
KOLF2.2J derived knockout cell line, FOXG1 PTC, differentiated to cortical brain organoid


title: CRISPRoff_FAS_SUV39H1_RC3H1_Donor2

description:
Library name: 257
normalized_counts_CO065.csv


title: CBO-MOK20070P-G12, KO

description:
Library name: FOXG1_PTC_G12_Day8_GT24-08518_AGCCTCAT-TCTCTACT_S58_L007
KOLF2.2J derived knockout cell line, FOXG1 PTC, differentiated to cortical brain organoid


title: CRISPRoff_NTC_multiplexing_Donor2

description:
Library name: 251
normalized_counts_CO065.csv


title: CRISPRoff_FAS_SUV39H1_RC3H1_Donor1

description:
Library name: 243
normalized_counts_CO065.csv


title: QuantSeq_SetE_StSDG2noG_rep2

description: Library name: QuantSeq_SetE_StSDG2noG_rep2

tag: ecotype


title: QuantSeq_SetE_StSDG2noG_rep3

description: Library name: QuantSeq_SetE_StSDG2noG_rep3


title: CBO-MOK20070P-C11, KO

description:
Library name: FOXG1_PTC_C11_Day8_GT24-08516_TACCGAGG-AGTTCAGG_S47_L007
KOLF2.2J derived knockout cell line, FOXG1 PTC, differentiated to cortical brain organoid

tag: cell type


title: CRISPRoff_NTC_multiplexing_Donor1

description:
Library name: 237
normalized_counts_CO065.csv

tag: genotype


title: Cas9_AAVS1_Guide1_Donor2

description:
Library name: 235
normalized_counts_CO065.csv


title: Cas9_MED12_Donor2

description:
Library name: 234
normalized_counts_CO065.csv


title: Cas9_RASA2_Donor2

description:
Library name: 233
normalized_counts_CO065.csv


title: CBO-MOK20069-WT4, WT

description:
Library name: WT4_Day14_GT24-08513_TTACAGGA-GCTTGTCA_S61_L007
KOLF2.2J differentiated to cortical brain organoid

value: day 14


title: Cas9_AAVS1_Guide2_Donor2

description:
Library name: 236
normalized_counts_CO065.csv


title: Cas9_RC3H1_Donor2

description:
Library name: 231
normalized_counts_CO065.csv


title: QuantSeq_SetE_StSDG2noG_rep1

description: Library name: QuantSeq_SetE_StSDG2noG_rep1


title: QuantSeq_SetE_StSDG2g4_rep3

description: Library name: QuantSeq_SetE_StSDG2g4_rep3


title: CBO-MOK20069-WT2, WT

description:
Library name: WT2_Day14_GT24-08512_CCGTGAAG-ATCCACTG_S67_L007
KOLF2.2J differentiated to cortical brain organoid


title: CBO-MOK20069-WT1, WT

description:
Library name: WT1_Day14_GT24-08511_TCCAACGC-AAGTCCAA_S70_L007
KOLF2.2J differentiated to cortical brain organoid


title: QuantSeq_SetE_StSDG2g4_rep2

description: Library name: QuantSeq_SetE_StSDG2g4_rep2


title: CBO-MOK20069P-F09, KO

description:
Library name: EMX2_PTC_F09_Day14_GT24-08510_CTTGGTAT-GGACTTGG_S59_L007
KOLF2.2J derived knockout cell line, EMX2 PTC, differentiated to cortical brain organoid


title: CRISPRoff_AAVS1_Guide2_Day7_Donor2

description:
Library name: 228
normalized_counts_CO065.csv


title: QuantSeq_SetE_StSDG2g4_rep1

description: Library name: QuantSeq_SetE_StSDG2g4_rep1


title: CBO-MOK20069P-E08, KO

description:
Library name: EMX2_PTC_E08_Day14_GT24-08509_GTCGGAGC-TTATAACC_S37_L006
KOLF2.2J derived knockout cell line, EMX2 PTC, differentiated to cortical brain organoid


title: CRISPRoff_MED12_pool_Day7_Donor2

description:
Library name: 226
normalized_counts_CO065.csv


title: Cas9_SUV39H1_Donor2

description:
Library name: 232
normalized_counts_CO065.csv


title: CRISPRoff_SUV39H1_Guide2_Day7_Donor2

description:
Library name: 224
normalized_counts_CO065.csv


title: CRISPRoff_RASA2_pool_Day7_Donor2

description:
Library name: 225
normalized_counts_CO065.csv


title: CRISPRoff_RC3H1_Guide2_Day7_Donor2

description:
Library name: 223
normalized_counts_CO065.csv


title: CRISPRoff_FAS_Guide1_Day7_Donor2

description:
Library name: 221
normalized_counts_CO065.csv


title: HEK293T_Acyclovir_500uM_Rep3

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description:
Library name: HEK293T_Acyclovir_500uM_Rep3
Total RNA with rRNA depletion

data_processing:
Raw FASTQ files were processed using nf-core/rnasplice (v1.0.4), a standardized and reproducible Nextflow-based pipeline (v24.10.0). Reads were aligned to the GRCh38 human genome reference, and all pipeline parameters—including trimming, alignment, quantification, and splicing analysis—were retained at their default settings.
For alternative splicing analysis, rMATS results from nf-core/rnasplice were used to compare branaplam-treated samples to branaplam controls and acyclovir-treated samples to acyclovir controls. Splicing events were quantified from rMATS output files reporting inclusion junction counts (IJC) and skipping junction counts (SJC) for each event. Events were retained if either condition had all replicates with IJC and SJC counts ≥ 10, ensuring robust splicing metric estimation. Significant alternative splicing events were defined as those with FDR < 0.05 and |ΔPSI| > 0.1. Individual splicing patterns were visualized using ggSashimi by merging triplicates and displaying mean coverage based on STAR-aligned BAM files and genomic coordinates extracted from the rMATS results.
For differential gene expression analysis, raw read count data were obtained from featureCounts output files generated by nf-core/splice. Raw counts were processed to retain only Ensembl gene identifiers. Counts for each gene were aggregated across samples and merged into a single count matrix for analysis with DESeq2. Genes with low expression (row sum ≤10) were removed prior to analysis. Differentially expressed genes were defined as those with an adjusted p-value < 0.05 and |log2 fold change| > 1.
All software versions, parameters, and computational workflows are fully documented in the nf-core/rnasplice pipeline. Complete DGE and rMATS datasets for branaplam- and acyclovir-treated samples are provided as additional files.
Assembly: GRCH38
Supplementary files format and content: "RNA-seq_DGE_raw_reads_count.xlsx"-RNAseq raw reads for all samples; raw reads count for each sample is in its subsheet, "RNA-seq_rMATS_acyclovir_250uM_vs_DMSO_250uM.xlsx"-rMATS output; each splicing type is in its subsheet, "RNA-seq_rMATS_acyclovir_500uM_vs_DMOS_500uM.xlsx"-rMATS output; each splicing type is in its subsheet, "RNA-seq_rMATS_branaplam_100nM_vs_DMSO_100nM.xlsx"-rMATS output; each splicing type is in its subsheet.

growth_protocol: HEK293T cells (ATCC CRL-3216) were maintained at 37 °C in a humidified 5 % CO₂ incubator in Dulbecco’s Modified Eagle Medium (DMEM, Thermo 11995065) supplemented with 10 % heat-inactivated fetal bovine serum, 100 U mL⁻¹ penicillin, and 100 µg mL⁻¹ streptomycin. Cells were sub-cultured at 70–80 % confluence by trypsinisation, counted with a TC20™ Automated Cell Counter, and seeded into 10 cm dishes at 2 × 10⁶ cells dish⁻¹ 24 h before drug treatment.

extract_protocol:
Total RNA was isolated with TRIzol LS (Invitrogen 10296010) according to the manufacturer’s instructions. RNA pellets were resuspended in RNase-free H₂O, treated with 1 U DNase I (NEB M0303) 10 min at 37 °C, and purified with the RNA Clean & Concentrator-25 kit (Zymo R1018). RNA integrity (RIN > 9) was verified on an Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded Total RNA Library Preparation Kit (with rRNA depletion) at the Weill Cornell Medicine Genomics Resources Core Facility. Sequencing was performed on an Illumina NovaSeq X Plus platform, generating ≥70million 150 bp paired-end reads per sample. The 500 µM acyclovir group generated ≥ 32 million 150 bp paired-end reads per sample.

treatment_protocol: Six conditions in biological triplicate: (1) 250uM DMSO (vehicle for 250uM acyclovir), (2) 100nM DMSO (vehicle for 100nM branaplam), (3) acyclovir 250 uM, (4) branaplam 100 nM, (5) 500uM DMSO, (6) acyclovir 500 uM. Drugs or vehicle were added directly to culture medium; cells were incubated 72 h before harvest.

value: human embryonic kidney cells

value: Acyclovir 500uM for 3 days


title: QuantSeq_SetE_rdr6_rep1

description: Library name: QuantSeq_SetE_rdr6_rep1


title: QuantSeq_SetA_StPRDM9noG_rep2

description: Library name: QuantSeq_SetA_StPRDM9noG_rep2


title: Cas9_MED12_Donor1

description:
Library name: 218
normalized_counts_CO065.csv


title: HEK293T_Acyclovir_500uM_Rep1

description:
Library name: HEK293T_Acyclovir_500uM_Rep1
Total RNA with rRNA depletion


title: QuantSeq_SetE_rdr6_rep2

description: Library name: QuantSeq_SetE_rdr6_rep2


title: Cas9_RC3H1_Donor1

description:
Library name: 215
normalized_counts_CO065.csv


title: HEK293T_DMSO_500uM_Rep3

description:
Library name: HEK293T_DMSO_500uM_Rep3
Total RNA with rRNA depletion

value: DMSO 500uM for 3 days


title: Cas9_SUV39H1_Donor1

description:
Library name: 216
normalized_counts_CO065.csv


title: CRISPRoff_PTPN2_Guide6_Day7_Donor2

description:
Library name: 222
normalized_counts_CO065.csv


title: Cas9_PTPN2_Donor2

description:
Library name: 230
normalized_counts_CO065.csv


title: HEK293T_DMSO_500uM_Rep2

description:
Library name: HEK293T_DMSO_500uM_Rep2
Total RNA with rRNA depletion


title: Cas9_FAS_Donor2

description:
Library name: 229
normalized_counts_CO065.csv


title: Cas9_AAVS1_Guide1_Donor1

description:
Library name: 219
normalized_counts_CO065.csv


title: Cas9_RASA2_Donor1

description:
Library name: 217
normalized_counts_CO065.csv


title: QuantSeq_SetA_StPRDM9noG_rep1

description: Library name: QuantSeq_SetA_StPRDM9noG_rep1


title: CBO-MOK20069P-A08, KO

description:
Library name: EMX2_PTC_A08_Day14_GT24-08508_ACTAAGAT-CCGCGGTT_S31_L006
KOLF2.2J derived knockout cell line, EMX2 PTC, differentiated to cortical brain organoid


title: CRISPRoff_AAVS1_Guide1_Day7_Donor2

description:
Library name: 227
normalized_counts_CO065.csv


title: Cas9_PTPN2_Donor1

description:
Library name: 214
normalized_counts_CO065.csv


title: QuantSeq_SetE_rdr6_rep3

description: Library name: QuantSeq_SetE_rdr6_rep3


title: QuantSeq_SetA_StPRDM9g4_rep3

description: Library name: QuantSeq_SetA_StPRDM9g4_rep3


title: QuantSeq_SetA_StPRDM9noG_rep3

description: Library name: QuantSeq_SetA_StPRDM9noG_rep3


title: Cas9_AAVS1_Guide2_Donor1

description:
Library name: 220
normalized_counts_CO065.csv


title: HEK293T_DMSO_500uM_Rep1

description:
Library name: HEK293T_DMSO_500uM_Rep1
Total RNA with rRNA depletion


title: HEK293T_Acyclovir_500uM_Rep2

description:
Library name: HEK293T_Acyclovir_500uM_Rep2
Total RNA with rRNA depletion


title: HEK293T_Branaplam_100nM_Rep3

description:
Library name: HEK293T_Branaplam_100nM_Rep3
Total RNA with rRNA depletion

value: Branaplam 100 nM for 3 days


title: CRISPRoff_AAVS1_Guide2_Day7_Donor1

description:
Library name: 212
normalized_counts_CO065.csv

value: Day 18


title: CRISPRoff_RASA2_pool_Day7_Donor1

description:
Library name: 209
normalized_counts_CO065.csv

value: Bulk T cells


title: HEK293T_Branaplam_100nM_Rep2

description:
Library name: HEK293T_Branaplam_100nM_Rep2
Total RNA with rRNA depletion


title: QuantSeq_SetA_StPRDM9g4_rep1

description: Library name: QuantSeq_SetA_StPRDM9g4_rep1


title: CRISPRoff_RC3H1_Guide2_Day7_Donor1

description:
Library name: 207
normalized_counts_CO065.csv

value: CRISPRoff


title: CRISPRoff_SUV39H1_Guide2_Day7_Donor1

description:
Library name: 208
normalized_counts_CO065.csv


title: QuantSeq_SetA_rdr6_rep3

description: Library name: QuantSeq_SetA_rdr6_rep3


title: QuantSeq_SetA_rdr6_rep2

description: Library name: QuantSeq_SetA_rdr6_rep2


title: CRISPRoff_FAS_Guide1_Day7_Donor1

description:
Library name: 205
normalized_counts_CO065.csv


title: HEK293T_DMSO_100nM_Rep3

description:
Library name: HEK293T_DMSO_100nM_Rep3
Total RNA with rRNA depletion

value: DMSO 100nM for 3 days


title: CRISPRoff_PTPN2_Guide6_Day7_Donor1

description:
Library name: 206
normalized_counts_CO065.csv


title: HEK293T_Branaplam_100nM_Rep1

description:
Library name: HEK293T_Branaplam_100nM_Rep1
Total RNA with rRNA depletion

value: WT


title: QuantSeq_SetA_rdr6_rep1

description: Library name: QuantSeq_SetA_rdr6_rep1

value: seedling


title: HEK293T_DMSO_100nM_Rep2

description:
Library name: HEK293T_DMSO_100nM_Rep2
Total RNA with rRNA depletion


title: dTAG-NUDT21 HCT116 cells with dTAGV1+JTE-607 treatment, replicate 4

city: Pittsburgh

first: Hun-Way

last: Hwang

state: PA

address: 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

description: Library name: Sample 8

data_processing:
Raw FASTQ files underwent quality assessment with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), evaluating per-base/tile sequence quality, adapter content, and duplication levels. Reads were preprocessed using fastp to trim auto-detected adapters and remove duplicates; sequences shorter than 25 bases after trimming were discarded. Clean reads were aligned to the Ensembl human reference genome (GRCh38, release 113) using STAR. Gene-level counts were obtained with HTSeq by counting uniquely mapped reads overlapping annotated exonic regions.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each sample

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen).
Library preparation was carried out by using the Lexogen 3′ mRNA-Seq QuantSeq FWD V2 Kit according to manufacturer’s instructions

value: cancer cell line


title: dTAG-NUDT21 HCT116 cells with dTAGV1+JTE-607 treatment, replicate 3

description: Library name: Sample 7


title: dTAG-NUDT21 HCT116 cells with dTAGV1+JTE-607 treatment, replicate 2

description: Library name: Sample 6


title: Cas9_FAS_Donor1

description:
Library name: 213
normalized_counts_CO065.csv

value: Day 7


title: dTAG-NUDT21 HCT116 cells with dTAGV1+JTE-607 treatment, replicate 1

description: Library name: Sample 5


title: QuantSeq_SetA_StPRDM9g4_rep2

description: Library name: QuantSeq_SetA_StPRDM9g4_rep2


title: ChIPseq_SetD_antiHA_StPRDM9g4_line2

description: Library name: ChIPseq_SetD_antiHA_StPRDM9g4_line2

value: anti-HA (3F10, Merck)


title: dTAG-NUDT21 HCT116 cells with DMSO+JTE-607 treatment, replicate 3

description: Library name: Sample 3


title: ChIPseq_SetD_antiHA_StPRDM9g4_line1

description: Library name: ChIPseq_SetD_antiHA_StPRDM9g4_line1


title: HEK293T_DMSO_100nM_Rep1

description:
Library name: HEK293T_DMSO_100nM_Rep1
Total RNA with rRNA depletion


title: dTAG-NUDT21 HCT116 cells with DMSO+JTE-607 treatment, replicate 4

description: Library name: Sample 4


title: CRISPRoff_AAVS1_Guide1_Day7_Donor1

description:
Library name: 211
normalized_counts_CO065.csv


title: HEK293T_Acyclovir_250uM_Rep3

description:
Library name: HEK293T_Acyclovir_250uM_Rep3
Total RNA with rRNA depletion

value: Acyclovir 250uM for 3 days


title: CRISPRoff_MED12_pool_Day7_Donor1

description:
Library name: 210
normalized_counts_CO065.csv

value: primary


title: dTAG-NUDT21 HCT116 cells with DMSO+JTE-607 treatment, replicate 1

description: Library name: Sample 1


title: dTAG-NUDT21 HCT116 cells with DMSO+JTE-607 treatment, replicate 2

description: Library name: Sample 2


title: ChIPseq_SetD_antiHA_rdr6_rep1

description: Library name: ChIPseq_SetD_antiHA_rdr6_rep1