title: Lig4-KO_rep8

description:
Library name: Lig4-KO_rep8
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep8
SIQ outcomes for in vivo perturbation.xlsx


title: DIPGXIII, AZD4573+sertraline, rep3

status: Public on Apr 23 2026

type: SRA

city: Houston

first: Rebecca

middle: Lauren

last: Murdaugh

state: Texas

address: One Baylor Plaza

department: Neurosurgery

country: USA

institute: Baylor College of Medicine

description:
Library name: RNAseq_DIPGXIII_AZD+sert_REP3
AZD4573+sertraline_rep3

library_source: transcriptomic

data_processing:
Reads were aligned to the genome with STAR.
DESeq2 was used to identify differentially expressed genes.
Assembly: hg38
Supplementary files format and content: count tables for each RNA-seq dataset

molecule: polyA RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: Tumor samples were isolated from xenograft NSG mice bearing SU-DIPGXIIIP*+ZsGreen/luciferase tumors. SU-DIPGXIII cells were passaged weekly with TrypLE Express Enzyme dissociation reagent and grown as neurospheres at 37C and 5% CO2 in glioma stem cell media glioma stem cell media consisting of 1:1 DMEM/F12 and Neurobasal A, 20 µg/mL human EGF, 20 µg/mL FGF-154, B27 without vitamin A, heparin sulfate, sodium pyruvate, HEPES buffer, GlutaMAX, and Antibiotic-Antimycotic at 1X each.

extract_protocol:
Tumor samples were isolated by dissociating whole brains, depleting mouse cells, and using the human cell fraction for bulk RNA-seq. Neurospheres were dissociated to single cells with TrypLE Express Enzyme, washed with 1X HBSS, counted, and prepared for CUT&RUN with 250,000 cells/sample. RNA was extracted with Trizol and used to generate cDNA from mRNA.
Sequencing libraries were prepared from cDNA following Illumina protocols.

treatment_protocol: Mice bearing SU-DIPGXIIIP*+ZsGreen/luciferase tumors were treated for 3 weeks with vehicle or 15 mg/kg zotiraciclib 3 times per weekSU-DIPGXIII cells were treated for 24 hours with DMSO, 20 nM zotiraciclib, 6 nM AZD4573, 5 𝛍M sertraline, 20 nM zotiraciclib + 5 𝛍M sertraline, or 6 nM AZD4573 + 5 𝛍M sertraline in biological triplicates.

tag: tissue

value: cell line

tag: cell line

value: SU-DIPGXIII

tag: cell type

value: patient-derived tumor cell line

tag: genotype

tag: treatment

tag: time

value: 24 hours


title: Kidney, DKD replicate 1, proximal tubule region 2, healthy

city: Calgary

first: Justin

last: Chun

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description:
Library name: DKD-DKD1-PT-011-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

data_processing:
FASTQ files were processed into gene count data for each sample using the GeoMx NGS Pipeline. Read depth was performed with total transcripts identified across nuclei, corresponding to an average of transcripts per nucleus.
Assembly: GRCh38
Supplementary files format and content: Processed data files are supplied as RDS objects aggregating all samples pre and post data processing.
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: Kidney cortex

extract_protocol:
5 um sectioned tissue samples from 2 FFPE transplant control pre-implantation biopsies and 3 DKD (class III) biopsies were prepared on slides.
Nanostring GeoMx Human Whole Transcriptome Atlas probes were hybridized to the tissue overnight. The fluorescent conjugated morphology markers used were CD10, PanCK, and SYTO 13 nucleic acid stain. Regions of interest were selected on the GeoMx Digital Spatial Profiler. RNA-ID and UMI-containing oligonucleotide tags were UV-cleaved from the WTA panel within the chosen ROIs and collected in a 96-well collection plate. Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to index each ara of illumination uniquely.

value: Kidney cortex

tag: disease state

value: DKD class III

tag: group

value: DKD

tag: region

value: PT

tag: marker

value: Healthy


title: Kidney, DKD replicate 1, glomerulus region 2

description:
Library name: DKD-DKD1-Glom-008-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Glom


title: Kidney, DKD replicate 1, proximal tubule region 3, healthy

description:
Library name: DKD-DKD1-PT-012-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, zotiraciclib+sertraline, rep2

description:
Library name: RNAseq_DIPGXIII_ZTR+sert_REP2
zotiraciclib+sertraline_rep2

value: zotiraciclib+sertraline


title: Kidney, DKD replicate 1, proximal tubule region 1, healthy

description:
Library name: DKD-DKD1-PT-010-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, DKD replicate 1, proximal tubule region 4, injured

description:
Library name: DKD-DKD1-PT-013-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Ctrl-for-Lig4_rep3

city: Hong Kong

first: Yang

last: Fu

address: Prince of Wales Hospital, N.T, H.K, 32 Ngan Shing St, Sha Tin

department: Department of Orthopaedics and Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Library name: Ctrl-for-Lig4_rep3
SgCtrl vs. sgLig4 spreadsheet: Alias column: Ctrl_rep3
SIQ outcomes for in vivo perturbation.xlsx

library_source: genomic

data_processing:
All sequencing data for single-sgRNA groups were generated in-house, except for samples S12, which were sourced from published paper. In house scripts were developed to extract NGS reads containing target-specific primer sequences. Quality filtering was performed using Trimmomatic (v0.39) with the parameter AVGQUAL:30 to eliminate low-quality reads. In instances where paired reads exhibited significant quality disparities, only the higher-quality end was retained. The processed reads were then analyzed using SIQ (v1.3) through a two-stage workflow: (i) merging overlapping paired-end reads and (ii) aligning the merged consensus sequences to target references for variant detection, utilizing default parameters (Min support: 2; Max base error: 0.08; TINS search distance: 100). While most analyses relied on paired-end data, single-end processing was employed in three specific scenarios: (i) when targets exceeded 300 bp, (ii) in cases of insufficient merge efficiency, or (iii) due to substantial quality discordance between read pairs (Supplementary Table 2).
All sequencing data for dual-sgRNA groups were generated in-house, except for samples D5 and D32, which were sourced from published paper. For data analysis, primer-specific reads were extracted and quality control was performed on the NGS data for each dual-sgRNA site (Supplementary Table 1), following the same workflow applied to single-sgRNA sites. Next, a two-stage alignment approach, adapted from Chakrabarti et al, was implemented. In the initial stage, reads were aligned to the reference genome using BBMap (v39.01). During this phase, reads that aligned as proper pairs were discarded, and only the remaining reads were retained for further analysis using Samtools (v1.6). In the second stage, these remaining reads were aligned to the reference genome using BBMap (v39.01) with a threshold that permitted indels of up to 3000 bp. Finally, unmapped reads and secondary alignments were filtered out utilizing Samtools (v1.6) and Sambamba (v1.0.0). Indels were detected and characterized using R scripts adapted from Chakrabarti et al., with positions and lengths determined through CIGAR string parsing. For each target's two cut sites (3 bp upstream of NGG PAMs), indels overlapping the ±10 bp window surrounding either cut site were analyzed. Reads containing these indels were classified as edited reads and were categorized into three types: type 1, which includes indels spanning the windows of both cut sites; type 2, consisting of indels that overlap the window of only one cut site; and type 3, involving concurrent indels that overlap the windows of both cut sites without spanning. Type 1 is prioritized over the other types. Unedited reads were defined as: (i) quality-trimmed reads before alignment, excluding the remaining reads from the initial alignment, and (ii) reads whose indels fell completely outside both cut site windows. For type 1 analysis, type 1 reads were extracted to SIQ (v1.3) and precisely ligated sequences were utilized as references to explore the accurate ligation (Supplementary Table 2).
Assembly: Target sequences (Supplementary Table 1)
Supplementary files format and content: Table S3. SIQ outcomes for single-sgRNA sites.xlsx is the indel profiles for GSM9129596 to GSM9129681.
Supplementary files format and content: Table S5. SIQ outcomes for dual-sgRNA sites is the indel profiles for GSM9129682 to GSM9129779.
Supplementary files format and content: Table S8. SIQ outcomes for AAV dose groups is the indel profiles for GSM9129780 to GSM9129797.
Supplementary files format and content: Table S9. SIQ outcomes for in vivo perturbation is the indel profiles for GSM9129798 to GSM9129853.

molecule: genomic DNA

organism: Mus musculus

source_name: skeletal muscle

extract_protocol:
MuSCs were isolated by fluorescence-activated cell sorting (FACS) based on established protocols. Briefly, hindlimb muscles from Pax7Cas9 mice were collected and digested with collagenase II (1000 U/ml; Worthington) for 90 minutes at 37°C. The tissue suspension was then washed in washing medium [Ham’s F-10 medium (Sigma-Aldrich), 10% heat-inactivated horse serum (HIHS) (Gibco), penicillin/streptomycin (1×, Gibco)]. MuSCs were further liberated by collagenase II (1000 U/ml) and dispase (11 U/ml) treatment for 40 minutes at 37°C. Mononuclear cells were filtered through a 40 μm cell strainer, and GFP+ MuSCs were sorted using a BD FACSAria Fusion cell sorter (BD Biosciences).
Genomic DNA from MuSCs infected with AAV9-sgRNA or AAV9-dual sgRNA was amplified using the Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and subjected to library preparation with the NEBNext® Ultra™ II DNA Library Preparation Kit (NEB). Barcoded libraries were pooled and sequenced on the Illumina HiSeq 1500 platform.

value: skeletal muscle

tag: strain

tag: age

value: 6 weeks

tag: sample group


title: Lig4-KO_rep9

description:
Library name: Lig4-KO_rep9
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep9
SIQ outcomes for in vivo perturbation.xlsx


title: Lig4-KO_rep7

description:
Library name: Lig4-KO_rep7
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep7
SIQ outcomes for in vivo perturbation.xlsx


title: DIPGXIII, AZD4573+sertraline, rep1

description:
Library name: RNAseq_DIPGXIII_AZD+sert_REP1
AZD4573+sertraline_rep1


title: Kidney, DKD replicate 1, glomerulus region 3

description:
Library name: DKD-DKD1-Glom-009-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 1, proximal tubule region 3, healthy

description:
Library name: Normal-Normal1-PT-006-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Non-diseased control

value: Normal


title: DIPGXIII, AZD4573+sertraline, rep2

description:
Library name: RNAseq_DIPGXIII_AZD+sert_REP2
AZD4573+sertraline_rep2


title: DIPGXIII, sertraline, rep3

description:
Library name: RNAseq_DIPGXIII_sert_REP3
sertraline_rep3

value: sertraline


title: Kidney, DKD replicate 1, glomerulus region 1

description:
Library name: DKD-DKD1-Glom-007-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal 1, proximal tubule region 2, healthy

description:
Library name: Normal-Normal1-PT-005-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Kidney, normal1, proximal tubule region 1, healthy

description:
Library name: Normal-Normal1-PT-004-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: Lig4-KO_rep5

description:
Library name: Lig4-KO_rep5
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep5
SIQ outcomes for in vivo perturbation.xlsx


title: Kidney, normal 1, Glomerulus region 3

description:
Library name: Normal-Normal1-Glom-003-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS


title: DIPGXIII, sertraline, rep1

description:
Library name: RNAseq_DIPGXIII_sert_REP1
sertraline_rep1


title: Muscle, pre-exercise training, Patient 9

city: San Diego

first: Pura

last: Muñoz-Cánoves

state: CA

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Library name: RNA_HMuscle_PreP9
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PreP9

data_processing:
Sequencing data was processed using the Nextflow nf-core pipeline. Raw reads were trimmed using Trimgalore (v.0.6.10) and quantified using Salmon (v.1.10.3) with the reference genome GRCh38. Counts were summarized using tximport (v1.30.0).
Assembly: GRCh38
Supplementary files format and content: human_gene_24H_exercise_tpm.tsv: tab separated text file with TPM counts for the 24h exercise and control samples
Supplementary files format and content: human_gene_6weeks_tpm.tsv: tab separated text file with TPM counts for the pre- and post-6 weeks exercise training

source_name: quadriceps femoris muscle

extract_protocol:
Extraction was performed using Qiagen.
Libraries were generated using the Watchmaker mRNA Library Prep Kit v1.1.0823 (for 24 h samples) or SMART-Seq mRNA LP kit (Takara Bio #634768) (for 6 weeks samples) and sequenced on an Illumina NextSeq 2000 platform (paired-end, 51 bp read length, ~250 million reads per run).

value: quadriceps femoris muscle

value: pre-6 weeks Exercise

tag: batch


title: Lig4-KO_rep6

description:
Library name: Lig4-KO_rep6
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep6
SIQ outcomes for in vivo perturbation.xlsx


title: Lig4-KO_rep4

description:
Library name: Lig4-KO_rep4
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep4
SIQ outcomes for in vivo perturbation.xlsx


title: Lig4-KO_rep3

description:
Library name: Lig4-KO_rep3
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep3
SIQ outcomes for in vivo perturbation.xlsx


title: DIPGXIII, zotiraciclib, rep3

description:
Library name: RNAseq_DIPGXIII_ZTR_REP3
zotiraciclib_rep3

value: cell line

value: SU-DIPGXIII

value: zotiraciclib


title: Lig4-KO_rep2

description:
Library name: Lig4-KO_rep2
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep2
SIQ outcomes for in vivo perturbation.xlsx


title: DIPGXIII, zotiraciclib, rep2

description:
Library name: RNAseq_DIPGXIII_ZTR_REP2
zotiraciclib_rep2

value: patient-derived tumor cell line

value: 24 hours


title: Kidney, normal 1, Glomerulus region 1

description:
Library name: Normal-Normal1-Glom-001-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Kidney cortex


title: Muscle, pre-exercise training, Patient 16

description:
Library name: RNA_HMuscle_PreP16
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PreP16


title: Muscle, pre-exercise training, Patient 11

description:
Library name: RNA_HMuscle_PreP11
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PreP11


title: Muscle, post-6 weeks of exercise, Patient 9

description:
Library name: RNA_HMuscle_PostP9
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PostP9

value: post-6 weeks Exercise


title: Lig4-KO_rep1

description:
Library name: Lig4-KO_rep1
SgCtrl vs. sgLig4 spreadsheet: Alias column: Lig4_rep1
SIQ outcomes for in vivo perturbation.xlsx


title: DIPGXIII, zotiraciclib, rep1

description:
Library name: RNAseq_DIPGXIII_ZTR_REP1
zotiraciclib_rep1


title: single high dose rep3

description:
Library name: S12-05-rep3
Single-sgRNA spreadsheet: Alias column: S12-05-rep3
SIQ outcomes for AAV dose groups.xlsx

value: single high dose


title: DIPGXIII, AZD4573, rep3

description:
Library name: RNAseq_DIPGXIII_AZD_REP3
AZD4573_rep3


title: DIPGXIII, sertraline, rep2

description:
Library name: RNAseq_DIPGXIII_sert_REP2
sertraline_rep2


title: Muscle, post-6 weeks of exercise, Patient 11

description:
Library name: RNA_HMuscle_PostP11
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PostP11


title: Muscle, 24 hours post-exercise, rep1

description:
Library name: Exercise24H_RNA_S5
Column name in human_gene_24H_exercise_tpm.tsv: Exercise24H_RNA_S5

source_name: vastus lateralis muscle

value: vastus lateralis muscle

value: 24h Exercise


title: Kidney, normal 1, Glomerulus region 2

description:
Library name: Normal-Normal1-Glom-002-Full
01_initSet.GeoMx.RDS
02_finalSet.GeoMx.RDS

value: Glom

value: Healthy


title: single high dose rep2

description:
Library name: S12-05-rep2
Single-sgRNA spreadsheet: Alias column: S12-05-rep2
SIQ outcomes for AAV dose groups.xlsx

value: skeletal muscle

value: 6 weeks


title: DIPGXIII, AZD4573, rep2

description:
Library name: RNAseq_DIPGXIII_AZD_REP2
AZD4573_rep2


title: Muscle, control, rep4

description:
Library name: CTR_RNA_S4
Column name in human_gene_24H_exercise_tpm.tsv: CTR_RNA_S4

value: Control


title: Muscle, 24 hours post-exercise, rep3

description:
Library name: Exercise24H_RNA_S7
Column name in human_gene_24H_exercise_tpm.tsv: Exercise24H_RNA_S7


title: Muscle, control, rep3

description:
Library name: CTR_RNA_S3
Column name in human_gene_24H_exercise_tpm.tsv: CTR_RNA_S3


title: Muscle, post-6 weeks of exercise, Patient 16

description:
Library name: RNA_HMuscle_PostP16
Column name in human_gene_6weeks_tpm.tsv: RNA_HMuscle_PostP16

value: quadriceps femoris muscle


title: Muscle, 24 hours post-exercise, rep2

description:
Library name: Exercise24H_RNA_S6
Column name in human_gene_24H_exercise_tpm.tsv:  Exercise24H_RNA_S6


title: Muscle, control, rep2

description:
Library name: CTR_RNA_S2
Column name in human_gene_24H_exercise_tpm.tsv: CTR_RNA_S2


title: DIPGXIII, AZD4573, rep1

description:
Library name: RNAseq_DIPGXIII_AZD_REP1
AZD4573_rep1


title: Muscle, control, rep1

description:
Library name: CTR_RNA_S1
Column name in human_gene_24H_exercise_tpm.tsv: CTR_RNA_S1


title: single middle dose rep2

description:
Library name: S12-01-rep2
Single-sgRNA spreadsheet: Alias column: S12-01-rep2
SIQ outcomes for AAV dose groups.xlsx

value: single middle dose


title: WT5

city: San Francisco

first: Jun Hyung

last: Sin

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

description: Library name: Sample3

data_processing:
Reads were aligned to mm10 using Bowtie2 and peaks were called using MAC2 peak calling software
Assembly: mm10
Supplementary files format and content: BigWig files aligned with Bowtie2 and peak calling done against IgG control with MACS2
Library strategy: CUT&Run

source_name: Thymus

extract_protocol:
Freshly FACS sorted EpCAM+ TECs were collected into eppendorf tubes with DMEM+2% FBS
Per UCSF Genomics Core

value: Thymus

value: medullary thymic epithelial cell

value: WT


title: WT3

description: Library name: Sample2


title: single middle dose rep3

description:
Library name: S12-01-rep3
Single-sgRNA spreadsheet: Alias column: S12-01-rep3
SIQ outcomes for AAV dose groups.xlsx


title: single high dose rep1

description:
Library name: S12-05-rep1
Single-sgRNA spreadsheet: Alias column: S12-05-rep1
SIQ outcomes for AAV dose groups.xlsx


title: DIPGXIII, DMSO, rep2

description:
Library name: RNAseq_DIPGXIII_DMSO_REP2
DMSO_rep2

value: cell line

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: DMSO


title: DIPGXIII, DMSO, rep1

description:
Library name: RNAseq_DIPGXIII_DMSO_REP1
DMSO_rep1

value: 24 hours


title: WT1

description: Library name: Sample1


title: single middle dose rep1

description:
Library name: S12-01-rep1
Single-sgRNA spreadsheet: Alias column: S12-01-rep1
SIQ outcomes for AAV dose groups.xlsx


title: long-read S28_rep1

description:
Library name: long-read S28_rep1
long-read S28_rep1

data_processing:
Nanopore R10 sequencing data were processed by filtering for reads with a quality score ≥ 10. High-quality reads were further screened using custom scripts to extract sequences containing both flanking primers. The VAULT tool43 was utilized with default parameters for variant analysis, applying an additional length filter of 50-20,000 bp. Among filtered variants, all single-nucleotide variants and any indels falling outside a ±30 bp window of the cut site were re-classified as wild type. For indels overlapping this window, variants were categorized as insertions if the insertion length exceeded the deletion length, and as deletions if the deletion length was greater. Specifically, insertions ≥ 20 bp were classified as LIs, while deletions ≥ 50 bp were classified as LDs. For the four edited samples, background indels identified in control samples were excluded. The reference amplicon size is from 1928 bp to 2039 bp. The mutant amplicon we analyzed ranged from 115 to 19,996 bp.
Assembly: Not applicable.
Supplementary files format and content: Excel file showing indels from long-read IDM-Seq.

extract_protocol:
Target DNA molecules were labeled using a UMI-containing oligonucleotide pool comprising three functional regions: a 3′ gene-specific sequence for targeting the edited locus, a central random UMI sequence for unique molecule tagging, and a 5′ universal primer binding site, facilitating uniform amplification of all UMI-labeled DNA molecules for Nanopore long read sequencing.
Genomic DNA from unedited MuSCs or MuSCs infected with AAV9-sgRNA was subjected to UMI labeling via one round of UMI oligonucleotide priming, using the following thermal cycling program: initial denaturation at 98 °C for 70 seconds, gradient annealing from 70 to 65 °C at a ramp rate of 1 °C/5 seconds, extension at 72 °C for 7 minutes, and a final hold at 4 °C. The UMI-labeled DNA was purified using 0.8× DNA clean beads (Vazyme, N411-01) to remove unlabeled UMI oligonucleotides, then mixed with a universal primer and a target site-specific reverse primer for amplification with Q5 High-Fidelity 2× Master Mix (NEB). The resulting amplicon was further purified and used for Nanopore library preparation with the Ligation Sequencing Kit (Oxford Nanopore Technologies) according to the manufacturer's standard protocol, followed by sequencing on the Nanopore platform. The sequences of the primers used are listed in Table S10.


title: DIPGXIIIP*xenograft, zotiraciclib, rep2

description:
Library name: RNAseq_xeno_DIPGXIIIP*_ZTR_REP2
ZTR_rep2

source_name: xenograft

value: xenograft

value: SU-DIPGXIIIP*+ZsGreen/luciferase

value: xenografted patient-derived tumor cell line

value: zotiraciclib

value: 3 weeks


title: long-read S28_repwt

description:
Library name: long-read S28_repwt
long-read S28_repwt

value: skeletal muscle


title: long-read S7_rep1

description:
Library name: long-read S7_rep1
long-read S7_rep1


title: long-read S18_rep1

description:
Library name: long-read S18_rep1
long-read S18_rep1


title: long-read S18_repwt

description:
Library name: long-read S18_repwt
long-read S18_repwt


title: single low dose rep3

description:
Library name: S12-002-rep3
Single-sgRNA spreadsheet: Alias column: S12-002-rep3
SIQ outcomes for AAV dose groups.xlsx

value: 6 weeks

value: single low dose


title: long-read S18_rep2

description:
Library name: long-read S18_rep2
long-read S18_rep2


title: single low dose rep1

description:
Library name: S12-002-rep1
Single-sgRNA spreadsheet: Alias column: S12-002-rep1
SIQ outcomes for AAV dose groups.xlsx


title: DIPGXIIIP*xenograft, zotiraciclib, rep3

description:
Library name: RNAseq_xeno_DIPGXIIIP*_ZTR_REP3
ZTR_rep3


title: DIPGXIIIP*xenograft, zotiraciclib, rep1

description:
Library name: RNAseq_xeno_DIPGXIIIP*_ZTR_REP1
ZTR_rep1


title: long-read S28_rep2

description:
Library name: long-read S28_rep2
long-read S28_rep2


title: dual high dose rep3

description:
Library name: Myc_10_3
Dual-sgRNA spreadsheet: Alias column: Myc_10_3
SIQ outcomes for AAV dose groups.xlsx

value: dual high dose


title: DIPGXIII, DMSO, rep3

description:
Library name: RNAseq_DIPGXIII_DMSO_REP3
DMSO_rep3


title: DIPGXIIIP*xenograft, DMSO, rep3

description:
Library name: RNAseq_xeno_DIPGXIIIP*_DMSO_REP3
DMSO_rep3


title: long-read S1_rep1

description:
Library name: long-read S1_rep1
long-read S1_rep1


title: long-read S7_rep2

description:
Library name: long-read S7_rep2
long-read S7_rep2


title: long-read S7_repwt

description:
Library name: long-read S7_repwt
long-read S7_repwt


title: dual high dose rep2

description:
Library name: Myc_10_2
Dual-sgRNA spreadsheet: Alias column: Myc_10_2
SIQ outcomes for AAV dose groups.xlsx


title: long-read S1_repwt

description:
Library name: long-read S1_repwt
long-read S1_repwt


title: single low dose rep2

description:
Library name: S12-002-rep2
Single-sgRNA spreadsheet: Alias column: S12-002-rep2
SIQ outcomes for AAV dose groups.xlsx


title: dual high dose rep1

description:
Library name: Myc_10_1
Dual-sgRNA spreadsheet: Alias column: Myc_10_1
SIQ outcomes for AAV dose groups.xlsx


title: DIPGXIIIP*xenograft, DMSO, rep2

description:
Library name: RNAseq_xeno_DIPGXIIIP*_DMSO_REP2
DMSO_rep2


title: long-read S1_rep2

description:
Library name: long-read S1_rep2
long-read S1_rep2


title: dual middle dose rep3

description:
Library name: Myc_5_3
Dual-sgRNA spreadsheet: Alias column: Myc_5_3
SIQ outcomes for AAV dose groups.xlsx

value: dual middle dose


title: CRISPRnGW_S010_plasmid

first: Alexander

last: Marson

address: 1650 Owens St

institute: UCSF Gladstone Institutes

description:
Library name: CRISPRnGW_S010_plasmid
Sequencing of pooled sgRNA plasmid library.

library_source: other

data_processing:
Demultiplexed FASTQ files were processed to quantify sgRNA read counts per sample by aligning reads to the relevant sgRNA reference library.
For each screen, sgRNA count tables were generated (rows = sgRNAs; columns = samples) and used as input for downstream statistical testing.
Differential sgRNA and gene enrichment between paired conditions (e.g., GFP-positive vs GFP-negative; marker-high vs marker-low) was computed using MAGeCK (RRA).
Statistical outputs include gene-level and sgRNA-level summary tables containing effect direction, p-values, and FDR for each comparison.
Assembly: Not applicable (sgRNA amplicon sequencing; reads aligned to sgRNA reference libraries, not to a genome)
Supplementary files format and content: Processed files include tab-delimited sgRNA count matrices for each screen and corresponding sgRNA library annotation files mapping sgRNA IDs/sequences to target genes.
Supplementary files format and content: MAGeCK output tables are provided at both gene and sgRNA resolution for all genome-wide and secondary CRISPRn/CRISPRa screens, including p-values and FDR as reported by MAGeCK.

molecule: other

organism: synthetic construct

source_name: plasmid library

growth_protocol: Primary human CD4+ T cells were isolated from healthy donor leukopaks by negative selection and cultured in complete RPMI. Cells were activated with anti-CD3/CD28 stimulation prior to pooled screen transduction and infection.

extract_protocol:
After sorting, cell pellets were processed for genomic DNA extraction. Integrated sgRNA cassettes were PCR-amplified from genomic DNA for next-generation sequencing.
sgRNA amplicons were generated by PCR, purified, pooled, and sequenced on Illumina instruments as single-end reads.

treatment_protocol: Activated CD4+ T cells transduced with pooled CRISPR knockout (CRISPRn) or CRISPR activation (CRISPRa) libraries were challenged with replication-competent GFP-reporter HIV. For secondary screens, additional conditions included different HIV inoculum concentrations, VSV-G pseudotyped HIV-GFP, and FACS-based marker assays (e.g., CD4, CXCR4, CD25, CD69). Cells were sorted into the indicated bins (e.g., GFP-positive/GFP-negative or marker-high/marker-low) for sequencing-based quantification of sgRNA representation.

value: plasmid library

value: plasmid DNA library sequencing

value: CRISPRn-gw


title: CRISPRaGW_S019_CalA_plasmid

description:
Library name: CRISPRaGW_S019_CalA_plasmid
Sequencing of pooled sgRNA plasmid library.

value: CRISPRa-gw


title: CRISPRaGW_S020_CalB_plasmid

description:
Library name: CRISPRaGW_S020_CalB_plasmid
Sequencing of pooled sgRNA plasmid library.


title: CRISPRaSEC_S045_D3_control_uninfected

description:
Library name: CRISPRaSEC_S045_D3_control_uninfected
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.

source_name: blood

value: blood

value: CD4+ T cell

value: control condition

value: CRISPRa-secondary


description:
Library name: CRISPRaSEC_S044_D3_HIV_VSVG_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-negative.

value: HIV-GFP infection and FACS sorting


title: CRISPRaSEC_S042_D3_HIV_LM_GFP_negative

description:
Library name: CRISPRaSEC_S042_D3_HIV_LM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-negative.


description:
Library name: CRISPRaSEC_S043_D3_HIV_VSVG_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-positive.


title: dual middle dose rep1

description:
Library name: Myc_5_1
Dual-sgRNA spreadsheet: Alias column: Myc_5_1
SIQ outcomes for AAV dose groups.xlsx


title: dual low dose rep3

description:
Library name: Myc_1_3
Dual-sgRNA spreadsheet: Alias column: Myc_1_3
SIQ outcomes for AAV dose groups.xlsx

value: dual low dose


title: CRISPRaSEC_S040_D3_HIV_HM_GFP_negative

description:
Library name: CRISPRaSEC_S040_D3_HIV_HM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-negative.


title: DIPGXIIIP*xenograft, DMSO, rep1

description:
Library name: RNAseq_xeno_DIPGXIIIP*_DMSO_REP1
DMSO_rep1

value: xenograft

value: SU-DIPGXIIIP*+ZsGreen/luciferase

value: xenografted patient-derived tumor cell line

value: DMSO


title: CRISPRaSEC_S039_D3_HIV_HM_GFP_positive

description:
Library name: CRISPRaSEC_S039_D3_HIV_HM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-positive.


title: CRISPRaSEC_S038_D2_control_uninfected

description:
Library name: CRISPRaSEC_S038_D2_control_uninfected
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.


description:
Library name: CRISPRaSEC_S037_D2_HIV_VSVG_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-negative.


title: dual low dose rep2

description:
Library name: Myc_1_2
Dual-sgRNA spreadsheet: Alias column: Myc_1_2
SIQ outcomes for AAV dose groups.xlsx

value: skeletal muscle

value: 6 weeks


title: dual middle dose rep2

description:
Library name: Myc_5_2
Dual-sgRNA spreadsheet: Alias column: Myc_5_2
SIQ outcomes for AAV dose groups.xlsx

value: dual middle dose


title: DIPGXIII, H3K4me3Q5dop, zotiraciclib+sertraline, rep2

description: Library name: CUT_RUN_H3K4me3Q5dop_DIPGXIII_ZTR.sertraline_REP2

data_processing:
Reads were processed with trimgalore.
Reads were aligned to the genome with bowtie2.
Peaks were called with MACS2.
Differential peak analysis was done with diffbind.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Library strategy: CUT&Run

source_name: SU-DIPGXIII

growth_protocol: SU-DIPGXIII cells were passaged weekly with TrypLE Express Enzyme dissociation reagent and grown as neurospheres at 37C and 5% CO2 in glioma stem cell media glioma stem cell media consisting of 1:1 DMEM/F12 and Neurobasal A, 20 µg/mL human EGF, 20 µg/mL FGF-154, B27 without vitamin A, heparin sulfate, sodium pyruvate, HEPES buffer, GlutaMAX, and Antibiotic-Antimycotic at 1X each.

extract_protocol:
Neurospheres were dissociated to single cells with TrypLE Express Enzyme, washed with 1X HBSS, counted, and prepared for CUT&RUN with 500,000 cells/sample. CUT&RUN-enriched DNA was prepared using the Cell Signaling Technologies CUT&RUN Kit (catalog# 86652) following the manufacturer's protocol using the following antibodies: pS2-Pol2 (Anti-RNA polymerase II subunit B1 phospho CTD Ser-2, clone 3E10; MilliporeSigma), H3K4me3 (Anti-Histone H3 tri methyl K4; Abcam, ab8580), H3K4me3Q5dop (Anti-H3K4me3Q5dopaminyl; MilliporeSigma, ABE2590), and IgG (Anti-IgG Rabbit; DIAgenode, cat# C15410206). Yeast spike-in DNA (S. cerevisiae; Cell Signaling Technology) was added at 0.5% to each reaction following chromatin digestion.
Sequencing libraries were prepared from 3 ng of enriched DNA using the SMARTer ThruPLEX Plasma-seq kit (Takara Bio, cat# R400681) with dual indexes (Takara Bio, cat# DX34752) according to the manufacturer's protocol. Adapter-ligated libraries were amplified for 11 PCR cycles, purified using AMPure XP beads (Beckman Coulter), and evaluated for fragment size distribution on an Agilent 2100 Bioanalyzer. Library molar concentrations were determined by quantitiative PCR with the KAPA Library Quantification Kit (Roche) before pooling for sequencing on an Illumina NovaSeq 6000 to generate 150-bp paired-end reads.

treatment_protocol: SU-DIPGXIII cells were treated for 24 hours with DMSO or 20 nM zotiraciclib + 5 𝛍M sertraline in biological duplicates.

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: zotiraciclib+sertraline

value: 24 hours


title: DIPGXIII, H3K4me3Q5dop, DMSO, rep2

description: Library name: CUT_RUN_H3K4me3Q5dop_DIPGXIII_DMSO_REP2


title: CRISPRaSEC_S041_D3_HIV_LM_GFP_positive

description:
Library name: CRISPRaSEC_S041_D3_HIV_LM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-positive.

value: blood


title: DIPGXIII, IgG, DMSO, rep1

description: Library name: CUT_RUN_IgG_DIPGXIII_DMSO_REP1


title: dual low dose rep1

description:
Library name: Myc_1_1
Dual-sgRNA spreadsheet: Alias column: Myc_1_1
SIQ outcomes for AAV dose groups.xlsx


title: DIPGXIII, IgG, zotiraciclib+sertraline, rep1

description: Library name: CUT_RUN_IgG_DIPGXIII_ZTR.sertraline_REP1


title: DIPGXIII, H3K4me3Q5dop, zotiraciclib+sertraline, rep1

description: Library name: CUT_RUN_H3K4me3Q5dop_DIPGXIII_ZTR.sertraline_REP1


description:
Library name: CRISPRaSEC_S036_D2_HIV_VSVG_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-positive.

value: CD4+ T cell


title: Dual-sgRNA target D51_rep2

description:
Library name: D51_rep2
Alias column: D51_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: CRISPRaSEC_S033_D2_HIV_HM_GFP_negative

description:
Library name: CRISPRaSEC_S033_D2_HIV_HM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-negative.

value: CRISPRa-secondary


title: CRISPRaSEC_S032_D2_HIV_HM_GFP_positive

description:
Library name: CRISPRaSEC_S032_D2_HIV_HM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-positive.

value: HIV-GFP infection and FACS sorting


title: Dual-sgRNA target D51_rep1

description:
Library name: D51_rep1
Alias column: D51_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: DIPGXIII, H3K4me3Q5dop, DMSO, rep1

description: Library name: CUT_RUN_H3K4me3Q5dop_DIPGXIII_DMSO_REP1


title: DIPGXIII, H3K4me3, zotiraciclib+sertraline, rep2

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_ZTR.sertraline_REP2


title: CRISPRaSEC_S035_D2_HIV_LM_GFP_negative

description:
Library name: CRISPRaSEC_S035_D2_HIV_LM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-negative.


title: Dual-sgRNA target D50_rep2

description:
Library name: D50_rep2
Alias column: D50_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRaSEC_S034_D2_HIV_LM_GFP_positive

description:
Library name: CRISPRaSEC_S034_D2_HIV_LM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-positive.


title: CRISPRaSEC_S031_D1_control_uninfected

description:
Library name: CRISPRaSEC_S031_D1_control_uninfected
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.

value: control condition


title: DIPGXIII, H3K4me3, zotiraciclib+sertraline, rep1

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_ZTR.sertraline_REP1


description:
Library name: CRISPRaSEC_S030_D1_HIV_VSVG_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-negative.


title: DIPGXIII, H3K4me3, DMSO, rep2

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_DMSO_REP2


title: DIPGXIII, H3K4me3, DMSO, rep1

description: Library name: CUT_RUN_H3K4me3_DIPGXIII_DMSO_REP1


title: Single-nucleus ATAC-seq of Macaca fascicularis pineal gland, rep 1

city: Shanghai

first: jihong

last: zheng

state: Shanghai

address: XinSongjiang Road, Songjiang District

country: China

institute: Shanghai General Hospital

description:
Library name: Mf_Pineal_snATAC_rep1
10X Genomics

library_source: genomic single cell

data_processing:
For snRNA-seq, the sequencing data were processed using Cell Ranger v7.1.0, where the raw data were aligned to the Macaca fascicularis_6.0 genome to generate a UMI count matrix. Data were quality-controlled by removing cells with UMI counts >25,000, retaining cells with between 200–7,000 detected genes. Doublets were removed using DoubletFinder, and SCTransform normalization was applied. The Seurat package was used for analysis, identifying seven distinct cell populations, which were annotated using marker genes from the NHPCA dataset. The snRNA-seq data were integrated with the NHPCA reference dataset using Canonical Correlation Analysis (CCA), and the harmonized expression matrix was visualized using UMAP.
For snATAC-seq, the data were processed with Cell Ranger ATAC v2.0.0, where the raw data were aligned to the Macaca fascicularis_6.0 reference genome to generate a fragment count matrix. Quality control steps included filtering based on TSS enrichment, fragment counts per cell (1,000–10,000), and fragment lengths (10–2,000 bp). Doublets were removed using the addDoubletScores and filterDoublets functions. Downstream analysis was performed using ArchR, including dimensionality reduction with Iterative LSI and clustering using the Louvain algorithm. The data were integrated with snRNA-seq data, and five major cell types were identified and annotated.
Spatial transcriptomic data were aligned to the Macaca fascicularis_6.0 genome using BSTMatrix (v2.4). Gene expression matrices were generated using aggregation-based superspot strategies, with Level-5 resolution (25 μm diameter) selected for optimal transcript detection sensitivity.
Assembly: Macaca fascicularis_6.0
Supplementary files format and content: Mf_Pineal_snRNA_barcodes.tsv.gz: A tab-delimited file containing the spatial barcodes corresponding to individual cells or nuclei.
Supplementary files format and content: Mf_Pineal_snRNA_features.tsv.gz: A tab-delimited file listing gene IDs (features) that were measured during the experiment.
Supplementary files format and content: Mf_Pineal_snRNA_matrix.mtx.gz: A Matrix Market Exchange Format (MTX) file containing gene expression count data. Rows represent genes, and columns represent cells or nuclei, with values indicating the UMI counts.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_barcodes.tsv: A tab-delimited file containing spatial barcode information for each nucleus or spot.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_peaks.bed: A BED file describing the genomic regions accessible in the sampled nuclei (based on ATAC-seq data).
Supplementary files format and content: Mf_Pineal_snATAC_rep1_matrix.mtx: A Matrix Market file containing gene accessibility data for the peaks identified in the peaks.bed file.
Supplementary files format and content: A CSV file containing metadata for each cell, with columns for various quality control metrics and feature counts. Key columns include barcode (cell identifier), total (total mapped reads), duplicate (duplicate reads), unmapped (unmapped fragments), mitochondrial (mitochondrial fragments), passed_filters (fragments passing quality control), and is__cell_barcode (indicates if the barcode is valid, with 1 = valid and 0 = invalid).
Supplementary files format and content: Mf_Pineal_snATAC_rep1_filtered_peak_bc_matrix.h5: A compressed HDF5 file containing the matrix of peaks versus cell barcodes, with filtered data.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_fragments.tsv.gz: A compressed file containing the transposed fragments from the ATAC-seq data.
Supplementary files format and content: Mf_Pineal_snATAC_rep1_fragments.tsv.gz.tbi: A tabix index file for Mf_Pineal_snATAC_rep1_fragments.tsv.gz, allowing for efficient querying and retrieval of specific fragment data.
Supplementary files format and content: For rep2 (Mf_Pineal_snATAC_rep2), the files follow the same structure as for rep1, with different batch or experimental replicate names:  Mf_Pineal_snATAC_rep2_barcodes.tsv  Mf_Pineal_snATAC_rep2_peaks.bed  Mf_Pineal_snATAC_rep2_matrix.mtx  Mf_Pineal_snATAC_rep2_singlecell.csv  Mf_Pineal_snATAC_rep2_filtered_peak_bc_matrix.h5  Mf_Pineal_snATAC_rep2_fragments.tsv.gz  Mf_Pineal_snATAC_rep2_fragments.tsv.gz.tbi
Supplementary files format and content: Mf_Pineal_Spatial_fluorescence_HE.txt: A text file containing information about fluorescence and H&E stained tissue regions.
Supplementary files format and content: Mf_Pineal_Spatial_fluorescence.tif: A high-resolution TIFF image showing fluorescence of the tissue for spatial analysis.
Supplementary files format and content: Mf_Pineal_Spatial_HE.tif: A high-resolution TIFF image of the H&E stained tissue for anatomical context.
Supplementary files format and content: Mf_Pineal_Spatial_scalefactors_json.json: A JSON file containing scale factors used for aligning spatial coordinates between tissue images and gene expression data.
Supplementary files format and content: Mf_Pineal_Spatial_tissue_lowres_image.png: A low-resolution image of the tissue used for visualization and spatial mapping.
Supplementary files format and content: Mf_Pineal_Spatial_tissue_positions_list.csv: A CSV file mapping the spatial barcode positions to coordinates of tissue spots.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_barcodes_pos.tsv.gz: A compressed tab-delimited file containing spatial barcodes and their corresponding positions on the tissue.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_barcodes.tsv.gz: A compressed tab-delimited file containing a list of spatial barcodes for the dataset.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_features.tsv.gz: A compressed tab-delimited file listing the genes detected in the spatial transcriptomics dataset.
Supplementary files format and content: Mf_Pineal_Spatial_level_5_matrix.mtx.gz: A Matrix Market file containing gene expression count data, formatted as a sparse matrix.

organism: Macaca fascicularis

source_name: Pineal gland

extract_protocol:
In this experiment, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used to construct the single-nucleus RNA-seq library. The tissue was processed to extract single nuclei, ensuring that the nuclei quality met the standards for downstream snRNA-seq analysis. The extracted nuclei were encapsulated with barcoded gel beads (GEMs) using the 10X Genomics Chromium Single Cell 3' Reagent Kit v3.1, enabling the capture and labeling of poly(A)+ RNA for downstream sequencing.
For snATAC-seq, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was used as the source material. The tissue was processed to extract high-quality nuclei. Tn5 transposase was used to cleave the DNA in open chromatin regions within the nuclei, inserting sequencing adapters. The transposition products were encapsulated with ATAC reagents in GEMs on a microfluidic chip, allowing for the capture of chromatin accessibility information for subsequent analysis.
For spatial transcriptomics, pineal gland tissue from the Crab Monkey (Macaca fascicularis) was prepared using the BMKMANU Spatial Transcriptomics Gene Expression Kit. The tissue was sectioned into 10 μm slices, which were then transferred to a BMKMANU S3000 Gene Expression Slide for further processing. After fixation and H&E staining, permeabilization was performed, followed by imaging to determine the optimal conditions for library construction.
For snRNA-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus.
For snATAC-seq, Illumina adapters (P7 and Index sequences) were added to the transposed DNA, followed by PCR amplification to construct the library. The libraries were quantified using Qubit 4.0 to ensure that the concentration met the necessary specifications. The libraries were then sequenced on the Illumina NovaSeq 6000 platform using a PE150 sequencing strategy to ensure sufficient read depth for each nucleus.
For spatial transcriptomics, libraries were constructed following the TruSeq Illumina library preparation method. Illumina adapters were added to the library, followed by PCR amplification. The libraries were quantified using Qubit 4.0. After ensuring the library quality, sequencing was conducted on the Illumina NovaSeq X Plus platform using the PE150 strategy, targeting at least 150,000 read pairs per spatial point.

value: Pineal gland

value: Mixed:Pinealocytes, Astrocytes, Microglia, Oligodendrocytes, Oligodendrocyte Precursor Cells (OPCs), Neurons, Endothelial cells, and Vascular Leptomeningeal Cells (VLMCs).

value: wild type

value: 4 to 5 years

tag: Sex

value: mixed


title: Single-nucleus RNA-seq of Macaca fascicularis pineal gland

description:
Library name: Mf_Pineal_snRNA
10X Genomics

library_source: transcriptomic single cell


title: Dual-sgRNA target D49_rep2

description:
Library name: D49_rep2
Alias column: D49_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle

value: 6 weeks


description:
Library name: CRISPRaSEC_S029_D1_HIV_VSVG_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: VSV-G pseudotyped HIV infection (GFP reporter); bin: GFP-positive.


title: 6-LPS

city: Xi'an

first: Zhang

last: Siyu

state: ShanXi

address: GaoQiao

institute: Xi'an Jiaotong University

description: Library name: Sample 6

data_processing:
The raw image data files acquired via high-throughput sequencing platforms (DNBSEQ) and undergo base calling analysis using CASAVA software to generate sequencing raw data. The project utilized DESeq2 software for differential expression analysis, with a significance threshold set at P-value < 0.05 and a minimum fold-change requirement of ≥2 (|log2FC| ≥ 1) as the criteria for statistically significant differences.
KEGG database and GO enrichment analysis was conducted using a cutoff of P-value ≤ 0.05. The P values were adjusted using Benjamini–Hochberg multiple-testing correction.
Assembly: NCBI genome build number.
Supplementary files format and content: geneID_symbol_fpkm.txt

source_name: hippocampus

extract_protocol: The hippocampal tissues of three mice per group were isolated carefully and immediately flash-freeze samples in liquid nitrogen for 1-2 hours. Ship samples on dry ice to Company (Tsingke) for RNA sequencing.

value: hippocampus

value: WT

value: LPS from Salmonella enterica serotype typhimurium, Sigma, L2630


title: Dual-sgRNA target D49_rep1

description:
Library name: D49_rep1
Alias column: D49_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Single-nucleus ATAC-seq of Macaca fascicularis pineal gland, rep 2

description:
Library name: Mf_Pineal_snATAC_rep2
10X Genomics


title: 5-LPS

description: Library name: Sample 5


title: CRISPRaSEC_S027_D1_HIV_LM_GFP_positive

description:
Library name: CRISPRaSEC_S027_D1_HIV_LM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-positive.


title: DIPGXIII, pS2-Pol2, zotiraciclib+sertraline, rep2

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_ZTR.sertraline_REP2

value: SU-DIPGXIII

value: patient-derived tumor cell line

value: zotiraciclib+sertraline

value: 24 hours


title: CRISPRaSEC_S028_D1_HIV_LM_GFP_negative

description:
Library name: CRISPRaSEC_S028_D1_HIV_LM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-negative.

value: blood

value: CD4+ T cell

value: CRISPRa-secondary


title: 3-ctr

description: Library name: Sample 3

value: sterile saline


title: CRISPRaSEC_S026_D1_HIV_HM_GFP_negative

description:
Library name: CRISPRaSEC_S026_D1_HIV_HM_GFP_negative
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-negative.

value: HIV-GFP infection and FACS sorting


title: Dual-sgRNA target D48_rep2

description:
Library name: D48_rep2
Alias column: D48_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: 4-LPS

description: Library name: Sample 4


title: DIPGXIII, pS2-Pol2, zotiraciclib+sertraline, rep1

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_ZTR.sertraline_REP1


title: Dual-sgRNA target D48_rep1

description:
Library name: D48_rep1
Alias column: D48_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D50_rep1

description:
Library name: D50_rep1
Alias column: D50_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: DIPGXIII, pS2-Pol2, DMSO, rep2

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_DMSO_REP2

value: DMSO


title: CRISPRaSEC_S025_D1_HIV_HM_GFP_positive

description:
Library name: CRISPRaSEC_S025_D1_HIV_HM_GFP_positive
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-positive.


title: DIPGXIII, pS2-Pol2, DMSO, rep1

description: Library name: CUT_RUN_pS2-Pol2_DIPGXIII_DMSO_REP1


title: 2-ctr

description: Library name: Sample 2


title: CRISPRaSEC_S024_D3_CXCR4_high

description:
Library name: CRISPRaSEC_S024_D3_CXCR4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: high.

value: FACS sorted for CXCR4 high


title: Dual-sgRNA target D47_rep1

description:
Library name: D47_rep1
Alias column: D47_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle


title: Dual-sgRNA target D47_rep2

description:
Library name: D47_rep2
Alias column: D47_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks


title: DIPGXIII, zotiraciclib+sertraline, 24hr, rep3

description: Library name: ATACseq_DIPGXIII_ZTR.sertraline_REP3

data_processing:
Reads were processed with trimgalore.
Reads were aligned to the genome with BWA.
Peaks were called with MACS2.
Differential peak analysis was done with csaw.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample

extract_protocol:
Neurospheres were dissociated to single cells with TrypLE Express Enzyme, washed with 1X HBSS, counted, and prepared for CUT&RUN with 500,000 cells/sample.
Sequencing libraries were prepared using following Illumina protocols.

treatment_protocol: SU-DIPGXIII cells were treated for 24 hours with DMSO or 20 nM zotiraciclib + 5 𝛍M sertraline in biological triplicates.

value: cell line


title: 1-ctr

description: Library name: Sample 1

value: hippocampus

value: WT


title: DIPGXIII, zotiraciclib+sertraline, 24hr, rep2

description: Library name: ATACseq_DIPGXIII_ZTR.sertraline_REP2

value: SU-DIPGXIII


title: CRISPRaSEC_S022_D3_CD4_high

description:
Library name: CRISPRaSEC_S022_D3_CD4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.

value: FACS sorted for CD4 high


title: CRISPRaSEC_S023_D3_CXCR4_low

description:
Library name: CRISPRaSEC_S023_D3_CXCR4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.

value: FACS sorted for CXCR4 low


description:
Library name: Deep-seq of enLI donor site in S15 control
Deep-seq of enLI donor site in S15 control

data_processing:
All sequencing data for edited single-sgRNA groups were generated in-house, except for samples S12, which were sourced from published paper.31 In house scripts were developed to extract NGS reads containing target-specific primer sequences. Quality filtering was performed using Trimmomatic (v0.39)53 with the parameter AVGQUAL:30 to eliminate low-quality reads. In instances where paired reads exhibited significant quality disparities, only the higher-quality end was retained. The processed reads were then analyzed using Sequence Interrogation and Quantification (SIQ) (v1.3)54 through a two-stage workflow: (i) merging overlapping paired-end reads and (ii) aligning the merged consensus sequences to target references for variant detection, utilizing default parameters (Min support: 2; Max base error: 0.08; TINS search distance: 100). While most analyses relied on paired-end data, single-end processing was employed in three specific scenarios: (i) when targets exceeded 300 bp, (ii) in cases of insufficient merge efficiency, or (iii) due to substantial quality discordance between read pairs (Table S2). The outcomes were classified into the following categories: wild-type (WT), single-nucleotide variant (SNV), insertion, deletion, delins (an insertion coinciding with a deletion), TINS (a deletion accompanied by an insertion sourced from the adjacent sequence within 100 bp of the cut site), tandem duplication (TD), and TD compound (a TD that incorporates additional insertions). For each event, the fraction, position, and size of indels, as well as the MH for deletions were provided. In terms of relative mutation positioning, SIQ defines the canonical cut site as position 0, with positions to the left of the cut site assigned negative values and those to the right assigned positive values. Given that targets vary in length, we ensured a fair evaluation of on-target editing by defining a 60 bp window centered on the canonical cut site for all target sites. Events overlapping with this window (delRelativeStart ≤ 30 and delRelativeEnd ≥ -30) were included in the subsequent analysis, with their corresponding fractions adjusted accordingly. The mutant amplicon we analyzed ranged from 40 to 290 bp. Indel events—including insertion, deletion, delins, TINS, TD, and TD compound—were classified as edited events, while SNVs were categorized as WT events. The mutations from control samples were excluded from downstream analyses. Target genomic locations were displayed using the R package “RIdeogram”.55
Supplementary files format and content: An excel file showing indel profiles of enLI samples.
Supplementary files format and content: Table S3. SIQ outcomes for single-sgRNA sites.xlsx is the indel profiles for GSM9129596 to GSM9129681.
Supplementary files format and content: Table S5. SIQ outcomes for dual-sgRNA sites is the indel profiles for GSM9129682 to GSM9129779.
Supplementary files format and content: Table S8. SIQ outcomes for AAV dose groups is the indel profiles for GSM9129780 to GSM9129797.
Supplementary files format and content: Table S9. SIQ outcomes for in vivo perturbation is the indel profiles for GSM9129798 to GSM9129853.

extract_protocol:
MuSCs were isolated by fluorescence-activated cell sorting (FACS) based on established protocols.49 Briefly, hindlimb muscles from Pax7Cas9 mice were collected and digested with collagenase II (1000 U/ml; Worthington) for 90 minutes at 37°C. The tissue suspension was then washed in washing medium [Ham’s F-10 medium (Sigma-Aldrich), 10% heat-inactivated horse serum (HIHS) (Gibco), penicillin/streptomycin (1×, Gibco)]. MuSCs were further liberated by collagenase II (1000 U/ml) and dispase (11 U/ml) treatment for 40 minutes at 37°C. Mononuclear cells were filtered through a 40 μm cell strainer, and GFP+ MuSCs were sorted using a BD FACSAria Fusion cell sorter (BD Biosciences).
Targeted deep sequencing was performed as previously described.31 Briefly, genomic DNA from unedited MuSCs, MuSCs infected with AAV9-sgRNA or AAV9-dual sgRNA was amplified using the Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and subjected to library preparation with the NEBNext® Ultra™ II DNA Library Preparation Kit (NEB). Barcoded libraries were pooled and sequenced on the Illumina HiSeq 1500 or NovaSeq X platform. The primers used for Deep-seq are listed in Table S1.


description:
Library name: Deep-seq of enLI donor site in S8 control
Deep-seq of enLI donor site in S8 control


title: Dual-sgRNA target D46_rep2

description:
Library name: D46_rep2
Alias column: D46_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: DIPGXIII, DMSO, 24hr, rep3

description: Library name: ATACseq_DIPGXIII_DMSO_REP3

value: patient-derived tumor cell line

value: 24 hours


title: DIPGXIII, zotiraciclib+sertraline, 24hr, rep1

description: Library name: ATACseq_DIPGXIII_ZTR.sertraline_REP1

value: zotiraciclib+sertraline


title: Dual-sgRNA target D45_rep1

description:
Library name: D45_rep1
Alias column: D45_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D46_rep1

description:
Library name: D46_rep1
Alias column: D46_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D45_rep2

description:
Library name: D45_rep2
Alias column: D45_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


description:
Library name: Deep-seq of enLI donor site in edited S8
Deep-seq of enLI donor site in edited S8


title: CRISPRaSEC_S020_D3_CD69_high

description:
Library name: CRISPRaSEC_S020_D3_CD69_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.

value: blood

value: CD4+ T cell

value: FACS sorted for CD69 high

value: CRISPRa-secondary


title: CRISPRaSEC_S021_D3_CD4_low

description:
Library name: CRISPRaSEC_S021_D3_CD4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.

value: FACS sorted for CD4 low


title: DIPGXIII, DMSO, 24hr, rep2

description: Library name: ATACseq_DIPGXIII_DMSO_REP2

value: DMSO


title: control for D50

description:
Library name: control for D50
control for D50

data_processing:
All sequencing data for edited single-sgRNA groups were generated in-house, except for samples S12, which were sourced from published paper.31 In house scripts were developed to extract NGS reads containing target-specific primer sequences. Quality filtering was performed using Trimmomatic (v0.39)53 with the parameter AVGQUAL:30 to eliminate low-quality reads. In instances where paired reads exhibited significant quality disparities, only the higher-quality end was retained. The processed reads were then analyzed using Sequence Interrogation and Quantification (SIQ) (v1.3)54 through a two-stage workflow: (i) merging overlapping paired-end reads and (ii) aligning the merged consensus sequences to target references for variant detection, utilizing default parameters (Min support: 2; Max base error: 0.08; TINS search distance: 100). While most analyses relied on paired-end data, single-end processing was employed in three specific scenarios: (i) when targets exceeded 300 bp, (ii) in cases of insufficient merge efficiency, or (iii) due to substantial quality discordance between read pairs (Table S2). The outcomes were classified into the following categories: wild-type (WT), single-nucleotide variant (SNV), insertion, deletion, delins (an insertion coinciding with a deletion), TINS (a deletion accompanied by an insertion sourced from the adjacent sequence within 100 bp of the cut site), tandem duplication (TD), and TD compound (a TD that incorporates additional insertions). For each event, the fraction, position, and size of indels, as well as the MH for deletions were provided. In terms of relative mutation positioning, SIQ defines the canonical cut site as position 0, with positions to the left of the cut site assigned negative values and those to the right assigned positive values. Given that targets vary in length, we ensured a fair evaluation of on-target editing by defining a 60 bp window centered on the canonical cut site for all target sites. Events overlapping with this window (delRelativeStart ≤ 30 and delRelativeEnd ≥ -30) were included in the subsequent analysis, with their corresponding fractions adjusted accordingly. The mutant amplicon we analyzed ranged from 40 to 290 bp. Indel events—including insertion, deletion, delins, TINS, TD, and TD compound—were classified as edited events, while SNVs were categorized as WT events. The mutations from control samples were excluded from downstream analyses. Target genomic locations were displayed using the R package “RIdeogram”.55
All sequencing data for edited dual-sgRNA groups were generated in-house, except for samples D5 and D32, which were sourced from published paper.31 For data analysis, primer-specific reads were extracted, and quality control was performed on the NGS data for each dual-sgRNA site (Table S1), following the same workflow applied to single-sgRNA sites. Next, a two-stage alignment approach, adapted from Chakrabarti et al,37 was implemented. In the initial stage, reads were aligned to the reference genome using BBMap (v39.01).65 During this phase, reads that aligned as proper pairs were discarded, and only the remaining reads were retained for further analysis using Samtools (v1.6).57 In the second stage, these remaining reads were aligned to the reference genome using BBMap (v39.01)65 with a threshold that permitted indels of up to 3000 bp. Finally, unmapped reads and secondary alignments were filtered out utilizing Samtools (v1.6)57 and Sambamba (v1.0.0).58 Indels were detected and characterized using R scripts adapted from Chakrabarti et al.37 with positions and lengths determined through CIGAR string parsing. For each target's two cut sites (3 bp upstream of NGG PAMs), indels overlapping the ±10 bp window surrounding either cut site were analyzed, with background indels from control samples removed. Reads containing these indels were classified as edited reads and were categorized into three types: type 1, which includes indels spanning the windows of both cut sites; type 2, consisting of indels that overlap the window of only one cut site; and type 3, involving concurrent indels that overlap the windows of both cut sites without spanning. Type 1 is prioritized over the other types. Unedited reads were defined as: (i) quality-trimmed reads before alignment, excluding the remaining reads from the initial alignment, and (ii) reads whose indels fell completely outside both cut site windows. For type 1 analysis, type 1 reads were extracted to SIQ (v1.3)54 and precisely ligated sequences were utilized as references to explore the accurate ligation (Table S2). For subsequent analysis, only targets with a total event count exceeding 100 were considered. SNVs and WT were classified as accurate events, and PAM orientations were assigned as 'W' for NGG and 'C' for CCN. For TI analysis, 1 bp TIs were defined as insertions matching either the -3 or -4 nucleotide upstream of either PAM. 2 bp TIs were defined as insertions that matched either the -3:-2 or -5:-4 dinucleotides of either PAM, or any of the four combinations consisting of one nucleotide from the -3 or -4 position of PAM1 and one nucleotide from the -3 or -4 position of PAM2.
Assembly: Not applicable.
Supplementary files format and content: Excel files showing indels for each site.

extract_protocol:
MuSCs were isolated by fluorescence-activated cell sorting (FACS) based on established protocols.49 Briefly, hindlimb muscles from Pax7Cas9 mice were collected and digested with collagenase II (1000 U/ml; Worthington) for 90 minutes at 37°C. The tissue suspension was then washed in washing medium [Ham’s F-10 medium (Sigma-Aldrich), 10% heat-inactivated horse serum (HIHS) (Gibco), penicillin/streptomycin (1×, Gibco)]. MuSCs were further liberated by collagenase II (1000 U/ml) and dispase (11 U/ml) treatment for 40 minutes at 37°C. Mononuclear cells were filtered through a 40 μm cell strainer, and GFP+ MuSCs were sorted using a BD FACSAria Fusion cell sorter (BD Biosciences).
Targeted deep sequencing was performed as previously described. Briefly, genomic DNA from unedited MuSCs, MuSCs infected with AAV9-sgRNA or AAV9-dual sgRNA was amplified using the Q5 High-Fidelity 2× Master Mix (NEB). PCR products were purified using the QIAquick PCR Purification Kit (Qiagen) and subjected to library preparation with the NEBNext® Ultra™ II DNA Library Preparation Kit (NEB). Barcoded libraries were pooled and sequenced on the Illumina HiSeq 1500 or NovaSeq X platform. The primers used for Deep-seq are listed in Table S1.

value: skeletal muscle


title: CRISPRaSEC_S018_D3_CD25_high

description:
Library name: CRISPRaSEC_S018_D3_CD25_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: high.

value: FACS sorted for CD25 high


description:
Library name: Deep-seq of enLI donor site in edited S15
Deep-seq of enLI donor site in edited S15


title: Dual-sgRNA target D44_rep2

description:
Library name: D44_rep2
Alias column: D44_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: CRISPRaSEC_S019_D3_CD69_low

description:
Library name: CRISPRaSEC_S019_D3_CD69_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: low.

value: FACS sorted for CD69 low


title: control for D51

description:
Library name: control for D51
control for D51


title: Muscle, PAN, rep5

description:
Library name: PAN_Sample_5
Column name in tmm_all.csv: PAN_S5

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v2.20.0) and preprocessed with fastp (v0.21.0). Gene abundances were quantified using Salmon (v1.5.2). Counts were normalized using the Trimmed Mean of M values (TMM) method implemented in edgeR (v3.34.1) for downstream visualization.
Assembly: GRCh38
Supplementary files format and content: tmm_all.csv: comma separated text file with TMM counts for each sample

source_name: gastrocnemius

extract_protocol:
Muscle samples were immediately flash-frozen upon biopsy and stored at -80ºC. They were then transported on dry ice to the NIH, where they were uniformly processed. RNA extraction was performed using TRIzol.
Libraries were prepared either using the NeoPrep system with the TruSeq Stranded mRNA Library Prep protocol (Illumina, San Diego, CA) or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490 and #E7760).

value: gastrocnemius

value: Polyarteritis nodosa


title: DIPGXIII, DMSO, 24hr, rep1

description: Library name: ATACseq_DIPGXIII_DMSO_REP1

value: cell line

value: SU-DIPGXIII


title: Dual-sgRNA target D44_rep1

description:
Library name: D44_rep1
Alias column: D44_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Muscle, PAN, rep4

description:
Library name: PAN_Sample_4
Column name in tmm_all.csv: PAN_S4


title: control for D49

description:
Library name: control for D49
control for D49


title: Dual-sgRNA target D43_rep2

description:
Library name: D43_rep2
Alias column: D43_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRaSEC_S017_D3_CD25_low

description:
Library name: CRISPRaSEC_S017_D3_CD25_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: low.

value: FACS sorted for CD25 low


title: CRISPRaSEC_S016_D2_CXCR4_high

description:
Library name: CRISPRaSEC_S016_D2_CXCR4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: high.

value: FACS sorted for CXCR4 high


title: Dual-sgRNA target D43_rep1

description:
Library name: D43_rep1
Alias column: D43_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D48

description:
Library name: control for D48
control for D48


title: CRISPRaSEC_S015_D2_CXCR4_low

description:
Library name: CRISPRaSEC_S015_D2_CXCR4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.

value: blood

value: FACS sorted for CXCR4 low


title: Muscle, PAN, rep2

description:
Library name: PAN_Sample_2
Column name in tmm_all.csv: PAN_S2


title: Muscle, PAN, rep1

description:
Library name: PAN_Sample_1
Column name in tmm_all.csv: PAN_S1


title: CRISPRaSEC_S014_D2_CD4_high

description:
Library name: CRISPRaSEC_S014_D2_CD4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.

value: CD4+ T cell

value: FACS sorted for CD4 high


title: Dual-sgRNA target D42_rep1

description:
Library name: D42_rep1
Alias column: D42_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Muscle, PAN, rep3

description:
Library name: PAN_Sample_3
Column name in tmm_all.csv: PAN_S3


title: control for D46

description:
Library name: control for D46
control for D46


title: transform Follicular Lymphoma 4 Peripheral Blood

city: Toulouse

first: Marie

last: Tosolini

address: 2 avenue Hubert Curien

department: CRCT

country: France

institute: INSERM

description: Library name: tFL4_PB1

data_processing:
Raw data were aligned using Cellranger (v8.0.1, 10x Genomics) with the Chromium Human Transcriptome Probe Set reference (v1.0.1_GRCh38-2020-A)
Assembly: GRCh38
Supplementary files format and content: sparse matrix

molecule: nuclear RNA

source_name: Peripheral blood

extract_protocol:
Dissociated cryopreserved cells from R/R B-NHL patient samples were prepared according to 10X Genomics protocol.
Cell and nuclei fixation were performed according to the Chromium Fixed RNA Profiling protocol (CG000478 – Rev D)

value: Peripheral blood


title: CRISPRaSEC_S013_D2_CD4_low

description:
Library name: CRISPRaSEC_S013_D2_CD4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.

value: FACS sorted for CD4 low

value: CRISPRa-secondary


title: Diffuse Large B-Cell Lymphomas 6 Lymph Node

description: Library name: DLBCL6_LN1

source_name: Lymph node

value: Lymph node


title: Follicular Lymphoma 11 Lymph Node

description: Library name: FL11_LN1


title: Dual-sgRNA target D41_rep1

description:
Library name: D41_rep1
Alias column: D41_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle

value: 6 weeks


title: Dual-sgRNA target D42_rep2

description:
Library name: D42_rep2
Alias column: D42_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: CRISPRaSEC_S012_D2_CD69_high

description:
Library name: CRISPRaSEC_S012_D2_CD69_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.

value: FACS sorted for CD69 high


title: control for D44

description:
Library name: control for D44
control for D44


title: control for D43

description:
Library name: control for D43
control for D43


title: Dual-sgRNA target D41_rep2

description:
Library name: D41_rep2
Alias column: D41_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D45

description:
Library name: control for D45
control for D45


title: CRISPRaSEC_S011_D2_CD69_low

description:
Library name: CRISPRaSEC_S011_D2_CD69_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: low.

value: FACS sorted for CD69 low


title: Follicular Lymphoma 10 Lymph Node

description: Library name: FL10_LN2


title: Dual-sgRNA target D40_rep1

description:
Library name: D40_rep1
Alias column: D40_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D40_rep2

description:
Library name: D40_rep2
Alias column: D40_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D47

description:
Library name: control for D47
control for D47


title: CRISPRaSEC_S010_D2_CD25_high

description:
Library name: CRISPRaSEC_S010_D2_CD25_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: high.

value: FACS sorted for CD25 high


title: Follicular Lymphoma 8 Lymph Node

description: Library name: FL8_LN1


title: CRISPRaSEC_S009_D2_CD25_low

description:
Library name: CRISPRaSEC_S009_D2_CD25_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: low.


title: Dual-sgRNA target D39_rep2

description:
Library name: D39_rep2
Alias column: D39_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D41

description:
Library name: control for D41
control for D41


title: control for D42

description:
Library name: control for D42
control for D42


title: CRISPRaSEC_S008_D1_CXCR4_high

description:
Library name: CRISPRaSEC_S008_D1_CXCR4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: high.


title: Follicular Lymphoma 5 Peripheral Blood

description: Library name: FL5_PB1


title: Follicular Lymphoma 3 Lymph Node

description: Library name: FL3_LN1


title: CRISPRaSEC_S006_D1_CD4_high

description:
Library name: CRISPRaSEC_S006_D1_CD4_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.


title: Dual-sgRNA target D38_rep2

description:
Library name: D38_rep2
Alias column: D38_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D39

description:
Library name: control for D39
control for D39


title: CRISPRaSEC_S005_D1_CD4_low

description:
Library name: CRISPRaSEC_S005_D1_CD4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.


title: Follicular Lymphoma 6 Peripheral Blood

description: Library name: FL6_PB1


title: control for D40

description:
Library name: control for D40
control for D40


title: control for D37

description:
Library name: control for D37
control for D37


title: Dual-sgRNA target D39_rep1

description:
Library name: D39_rep1
Alias column: D39_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D36

description:
Library name: control for D36
control for D36


title: CRISPRaSEC_S004_D1_CD69_high

description:
Library name: CRISPRaSEC_S004_D1_CD69_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.


title: Dual-sgRNA target D37_rep1

description:
Library name: D37_rep1
Alias column: D37_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Follicular Lymphoma 1 Lymph Node

description: Library name: FL1_LN2


title: Dual-sgRNA target D37_rep2

description:
Library name: D37_rep2
Alias column: D37_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D38_rep1

description:
Library name: D38_rep1
Alias column: D38_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D36_rep2

description:
Library name: D36_rep2
Alias column: D36_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Follicular Lymphoma 1 Peripheral Blood

description: Library name: FL1_PB1


title: control for D38

description:
Library name: control for D38
control for D38


title: control for D35

description:
Library name: control for D35
control for D35


title: Follicular Lymphoma 2 Peripheral Blood

description: Library name: FL2_PB1


title: crc_dmmr_tumor_s30

city: Southampton

first: Stephen

middle: Mark

last: Thirdborough

state: Hants

address: Tremona Road

department: School of Cancer Sciences

country: United Kingdom

institute: University of Southampton

description:
Library name: CRG.033.18
Column name in gene_expression_cpm.txt

data_processing:
Data was demultiplexed using bcl2fastq, trimmed with trimmomatic, and aligned to GRCh38/p13 using STAR.
Reads were mapped to the reference genome using featureCounts, and raw read counts were subsequently filtered, normalized, and transformed to log-CPM using edgeR.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes log-CPM values from edgeR for each sample
Supplementary files format and content: tab-delimited text file includes rawcounts from featureCounts for each sample

source_name: Tumor

extract_protocol:
Snap-frozen tumor samples were sectioned to 14-22nm, and RNA extracted using the RNeasy Plus Mini kit.
mRNA was purified, double-stranded cDNA was generated, and libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit.

value: Tumor

tag: gender

value: F

tag: msi status

value: MSI (d MLH1/PMS2)

tag: tumor type

value: Adenocarcinoma

tag: differentiation

value: T1-Well/mod; T2-Well/mod


title: Dual-sgRNA target D36_rep1

description:
Library name: D36_rep1
Alias column: D36_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

tag: tissue


title: CRISPRaSEC_S003_D1_CD69_low

description:
Library name: CRISPRaSEC_S003_D1_CD69_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: low.

value: blood

tag: cell type

value: CD4+ T cell


title: Follicular Lymphoma 3 Peripheral Blood

description: Library name: FL3_PB1

value: Peripheral blood


title: CRISPRaSEC_S007_D1_CXCR4_low

description:
Library name: CRISPRaSEC_S007_D1_CXCR4_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.

tag: treatment

value: FACS sorted for CXCR4 low


title: CRISPRaSEC_S002_D1_CD25_high

description:
Library name: CRISPRaSEC_S002_D1_CD25_high
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: high.

value: CRISPRa-secondary


title: CRISPRaSEC_S001_D1_CD25_low

description:
Library name: CRISPRaSEC_S001_D1_CD25_low
Pooled CRISPRa secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: low.

value: FACS sorted for CD25 low


title: control for D34

description:
Library name: control for D34
control for D34

value: skeletal muscle


title: Dual-sgRNA target D35_rep2

description:
Library name: D35_rep2
Alias column: D35_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks


title: crc_dmmr_tumor_s29

description:
Library name: CRA.834.19
Column name in gene_expression_cpm.txt

value: MSI (d MSH6)

value: Well/mod


title: control for D33

description:
Library name: control for D33
control for D33


title: CRISPRnSEC_S039_D3_control_uninfected

description:
Library name: CRISPRnSEC_S039_D3_control_uninfected
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.

value: control condition

value: CRISPRn-secondary


title: Dual-sgRNA target D35_rep1

description:
Library name: D35_rep1
Alias column: D35_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: crc_dmmr_tumor_s28

description:
Library name: CRA.833.19
Column name in gene_expression_cpm.txt

value: Tumor

value: M


title: control for D32

description:
Library name: control for D32
control for D32


title: Dual-sgRNA target D34_rep2

description:
Library name: D34_rep2
Alias column: D34_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S038_D3_CXCR4_low

description:
Library name: CRISPRnSEC_S038_D3_CXCR4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.


title: control for D31

description:
Library name: control for D31
control for D31


title: Dual-sgRNA target D34_rep1

description:
Library name: D34_rep1
Alias column: D34_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D30

description:
Library name: control for D30
control for D30


title: CRISPRnSEC_S037_D3_CXCR4_high

description:
Library name: CRISPRnSEC_S037_D3_CXCR4_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: high.

value: FACS sorted for CXCR4 high


title: Dual-sgRNA target D33_rep2

description:
Library name: D33_rep2
Alias column: D33_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S035_D3_CD4_high

description:
Library name: CRISPRnSEC_S035_D3_CD4_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.

value: FACS sorted for CD4 high


title: crc_dmmr_tumor_s27

description:
Library name: CRA.832.19
Column name in gene_expression_cpm.txt

value: MSI (d PMS2 & MSH6)

value: Adenocarcinoma

value: Moderate


title: crc_dmmr_tumor_s25

description:
Library name: CRA.810.18
Column name in gene_expression_cpm.txt

value: MSI (d MLH1/PMS2)


title: crc_dmmr_tumor_s24

description:
Library name: CRA.801.18
Column name in gene_expression_cpm.txt

value: MSI (d MSH2/MSH6)


title: control for D29

description:
Library name: control for D29
control for D29


title: crc_dmmr_tumor_s26

description:
Library name: CRA.823.18
Column name in gene_expression_cpm.txt

value: F

value: T1-poor; T2-well/mod; T3-well/mod


title: control for D27

description:
Library name: control for D27
control for D27

value: skeletal muscle


title: CRISPRnSEC_S034_D3_CD69_low

description:
Library name: CRISPRnSEC_S034_D3_CD69_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: low.

value: blood

value: CD4+ T cell

value: FACS sorted for CD69 low


title: CRISPRnSEC_S036_D3_CD4_low

description:
Library name: CRISPRnSEC_S036_D3_CD4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.

value: FACS sorted for CD4 low

value: CRISPRn-secondary


title: control for D26

description:
Library name: control for D26
control for D26


title: Dual-sgRNA target D33_rep1

description:
Library name: D33_rep1
Alias column: D33_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: Dual-sgRNA target D31_rep1

description:
Library name: D31_rep1
Alias column: D31_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D28

description:
Library name: control for D28
control for D28


title: crc_dmmr_tumor_s23

description:
Library name: CRA.794.18
Column name in gene_expression_cpm.txt

value: Tumor

value: Mod/poor


title: CRISPRnSEC_S033_D3_CD69_high

description:
Library name: CRISPRnSEC_S033_D3_CD69_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.

value: FACS sorted for CD69 high


title: Dual-sgRNA target D31_rep2

description:
Library name: D31_rep2
Alias column: D31_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S032_D3_CD25_low

description:
Library name: CRISPRnSEC_S032_D3_CD25_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: low.

value: FACS sorted for CD25 low


title: Dual-sgRNA target D30_rep2

description:
Library name: D30_rep2
Alias column: D30_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D25

description:
Library name: control for D25
control for D25


title: crc_dmmr_tumor_s21

description:
Library name: CRA.780.18
Column name in gene_expression_cpm.txt

value: Adenocarcinoma

value: Well/mod


title: CRISPRnSEC_S031_D3_CD25_high

description:
Library name: CRISPRnSEC_S031_D3_CD25_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: high.

value: FACS sorted for CD25 high


title: crc_dmmr_tumor_s22

description:
Library name: CRA.782.18
Column name in gene_expression_cpm.txt

value: M

value: MSI (d MLH1/PMS2)

value: Mucinous adenocarcinoma

value: Poor


title: CRISPRnSEC_S030_D3_HIV_LM_GFP_negative

description:
Library name: CRISPRnSEC_S030_D3_HIV_LM_GFP_negative
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-negative.

value: blood

value: CD4+ T cell

value: HIV-GFP infection and FACS sorting


title: Dual-sgRNA target D29_rep2

description:
Library name: D29_rep2
Alias column: D29_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle


title: crc_dmmr_tumor_s20

description:
Library name: CRA.761.18
Column name in gene_expression_cpm.txt


title: crc_dmmr_tumor_s19

description:
Library name: CRA.730.17
Column name in gene_expression_cpm.txt

value: F


title: Dual-sgRNA target D29_rep1

description:
Library name: D29_rep1
Alias column: D29_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: CRISPRnSEC_S029_D3_HIV_LM_GFP_positive

description:
Library name: CRISPRnSEC_S029_D3_HIV_LM_GFP_positive
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-positive.

value: CRISPRn-secondary


title: control for D23

description:
Library name: control for D23
control for D23


title: control for D24

description:
Library name: control for D24
control for D24


title: control for D21

description:
Library name: control for D21
control for D21


title: control for D20

description:
Library name: control for D20
control for D20


title: crc_dmmr_tumor_s17

description:
Library name: CRA.673.17
Column name in gene_expression_cpm.txt

value: Tumor


title: CRISPRnSEC_S025_D2_CXCR4_low

description:
Library name: CRISPRnSEC_S025_D2_CXCR4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.

value: FACS sorted for CXCR4 low


title: crc_dmmr_tumor_s15

description:
Library name: CRA.664.17
Column name in gene_expression_cpm.txt

value: Adenocarcinoma


title: CRISPRnSEC_S027_D3_HIV_HM_GFP_positive

description:
Library name: CRISPRnSEC_S027_D3_HIV_HM_GFP_positive
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-positive.


title: Dual-sgRNA target D28_rep1

description:
Library name: D28_rep1
Alias column: D28_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D30_rep1

description:
Library name: D30_rep1
Alias column: D30_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S026_D2_control_uninfected

description:
Library name: CRISPRnSEC_S026_D2_control_uninfected
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.

value: control condition


title: control for D19

description:
Library name: control for D19
control for D19


title: CRISPRnSEC_S028_D3_HIV_HM_GFP_negative

description:
Library name: CRISPRnSEC_S028_D3_HIV_HM_GFP_negative
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-negative.


title: Dual-sgRNA target D28_rep2

description:
Library name: D28_rep2
Alias column: D28_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s16

description:
Library name: CRA.671.17
Column name in gene_expression_cpm.txt

value: MSI (d MSH6)

value: Well/mod


title: Dual-sgRNA target D27_rep2

description:
Library name: D27_rep2
Alias column: D27_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D27_rep1

description:
Library name: D27_rep1
Alias column: D27_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s14

description:
Library name: CRA.644.16
Column name in gene_expression_cpm.txt

value: MSI (d MLH1/PMS2)


title: control for D22

description:
Library name: control for D22
control for D22


title: control for D17

description:
Library name: control for D17
control for D17


title: control for D18

description:
Library name: control for D18
control for D18


title: crc_dmmr_tumor_s18

description:
Library name: CRA.698.17
Column name in gene_expression_cpm.txt

value: MSI (d PMS2, MSH2, MSH6)


title: CRISPRnSEC_S024_D2_CXCR4_high

description:
Library name: CRISPRnSEC_S024_D2_CXCR4_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: high.

value: FACS sorted for CXCR4 high


title: Dual-sgRNA target D26_rep2

description:
Library name: D26_rep2
Alias column: D26_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D26_rep1

description:
Library name: D26_rep1
Alias column: D26_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s13

description:
Library name: CRA.594.15
Column name in gene_expression_cpm.txt

value: Mucinous adenocarcinoma


title: control for D16

description:
Library name: control for D16
control for D16


title: CRISPRnSEC_S023_D2_CD4_low

description:
Library name: CRISPRnSEC_S023_D2_CD4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.

value: blood

value: CD4+ T cell

value: FACS sorted for CD4 low


title: crc_dmmr_tumor_s12

description:
Library name: CRA.585.15
Column name in gene_expression_cpm.txt

value: F


title: Dual-sgRNA target D25_rep2

description:
Library name: D25_rep2
Alias column: D25_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle

value: 6 weeks


title: CRISPRnSEC_S022_D2_CD4_high

description:
Library name: CRISPRnSEC_S022_D2_CD4_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.

value: FACS sorted for CD4 high

value: CRISPRn-secondary


title: control for D15

description:
Library name: control for D15
control for D15


title: Dual-sgRNA target D25_rep1

description:
Library name: D25_rep1
Alias column: D25_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: crc_dmmr_tumor_s11

description:
Library name: CRA.538.15
Column name in gene_expression_cpm.txt

value: Tumor

value: M


title: CRISPRnSEC_S020_D2_CD69_high

description:
Library name: CRISPRnSEC_S020_D2_CD69_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.

value: FACS sorted for CD69 high


title: Dual-sgRNA target D23_rep2

description:
Library name: D23_rep2
Alias column: D23_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D14

description:
Library name: control for D14
control for D14


title: crc_dmmr_tumor_s8

description:
Library name: CRA.522.15
Column name in gene_expression_cpm.txt

value: Adenocarcinoma

value: Poor


title: control for D13

description:
Library name: control for D13
control for D13


title: crc_dmmr_tumor_s9

description:
Library name: CRA.530.15
Column name in gene_expression_cpm.txt

value: MSI (d MLH1/PMS2)

value: Well/mod


title: CRISPRnSEC_S019_D2_CD25_low

description:
Library name: CRISPRnSEC_S019_D2_CD25_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: low.

value: FACS sorted for CD25 low


title: Dual-sgRNA target D24_rep2

description:
Library name: D24_rep2
Alias column: D24_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S018_D2_CD25_high

description:
Library name: CRISPRnSEC_S018_D2_CD25_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD25 surface expression; bin: high.

value: blood

value: FACS sorted for CD25 high


title: Dual-sgRNA target D24_rep1

description:
Library name: D24_rep1
Alias column: D24_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s10

description:
Library name: CRA.537.15
Column name in gene_expression_cpm.txt

value: Moderate


title: Dual-sgRNA target D23_rep1

description:
Library name: D23_rep1
Alias column: D23_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s7

description:
Library name: CRA.515.15
Column name in gene_expression_cpm.txt

value: F


title: control for D11

description:
Library name: control for D11
control for D11

value: skeletal muscle


title: CRISPRnSEC_S017_D2_HIV_LM_GFP_negative

description:
Library name: CRISPRnSEC_S017_D2_HIV_LM_GFP_negative
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-negative.

value: CD4+ T cell

value: HIV-GFP infection and FACS sorting


title: CRISPRnSEC_S016_D2_HIV_LM_GFP_positive

description:
Library name: CRISPRnSEC_S016_D2_HIV_LM_GFP_positive
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); low concentration HIV-GFP; bin: GFP-positive.

value: CRISPRn-secondary


title: control for D12

description:
Library name: control for D12
control for D12


title: crc_dmmr_tumor_s6

description:
Library name: CRA.330.13
Column name in gene_expression_cpm.txt


title: Dual-sgRNA target D22_rep2

description:
Library name: D22_rep2
Alias column: D22_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: crc_dmmr_tumor_s5

description:
Library name: CRA.261.13
Column name in gene_expression_cpm.txt

value: Tumor


title: control for D10

description:
Library name: control for D10
control for D10


title: Dual-sgRNA target D22_rep1

description:
Library name: D22_rep1
Alias column: D22_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s4

description:
Library name: CRA.210.12
Column name in gene_expression_cpm.txt

value: Mucinous adenocarcinoma


title: CRISPRnSEC_S021_D2_CD69_low

description:
Library name: CRISPRnSEC_S021_D2_CD69_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: low.

value: FACS sorted for CD69 low


title: CRISPRnSEC_S014_D2_HIV_HM_GFP_positive

description:
Library name: CRISPRnSEC_S014_D2_HIV_HM_GFP_positive
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-positive.


title: control for D8

description:
Library name: control for D8
control for D8


title: CRISPRnSEC_S015_D2_HIV_HM_GFP_negative

description:
Library name: CRISPRnSEC_S015_D2_HIV_HM_GFP_negative
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); high concentration HIV-GFP; bin: GFP-negative.


title: Dual-sgRNA target D21_rep2

description:
Library name: D21_rep2
Alias column: D21_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for D9

description:
Library name: control for D9
control for D9


title: control for D7

description:
Library name: control for D7
control for D7


title: crc_dmmr_tumor_s3

description:
Library name: CRA.209.12
Column name in gene_expression_cpm.txt

value: MSI (d MSH2/MSH6)


title: control for D6

description:
Library name: control for D6
control for D6


title: Dual-sgRNA target D21_rep1

description:
Library name: D21_rep1
Alias column: D21_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s2

description:
Library name: CRA.186.12
Column name in gene_expression_cpm.txt

value: MSI (d MLH1/PMS2)

value: Adenocarcinoma

value: Poor


title: CRISPRnSEC_S012_D1_CXCR4_low

description:
Library name: CRISPRnSEC_S012_D1_CXCR4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CXCR4 surface expression; bin: low.

value: blood

value: FACS sorted for CXCR4 low


title: control for D5

description:
Library name: control for D5
control for D5


title: CRISPRnSEC_S013_D1_control_uninfected

description:
Library name: CRISPRnSEC_S013_D1_control_uninfected
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: control; bin: uninfected.

value: control condition


title: Dual-sgRNA target D20_rep2

description:
Library name: D20_rep2
Alias column: D20_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: crc_dmmr_tumor_s1

description:
Library name: CRA.185.12
Column name in gene_expression_cpm.txt

value: F

value: Well/mod


title: CRISPRnSEC_S009_D1_CD4_high

description:
Library name: CRISPRnSEC_S009_D1_CD4_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: high.

value: CD4+ T cell

value: FACS sorted for CD4 high


title: control for D3

description:
Library name: control for D3
control for D3

value: skeletal muscle


title: CRISPRnSEC_S010_D1_CD4_low

description:
Library name: CRISPRnSEC_S010_D1_CD4_low
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD4 surface expression; bin: low.

value: FACS sorted for CD4 low

value: CRISPRn-secondary


title: Dual-sgRNA target D19_rep1

description:
Library name: D19_rep1
Alias column: D19_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: KYSE30 without RBM28 knockout, bio rep 3

city: Beijing

first: Tao

last: Xiang

state: Beijing

address: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: NC3

data_processing:
Raw data (raw reads) of fastq format were firstly processed throughfastpsoftware.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-Nandlowquality reads from raw data
Q20, Q30 and GCcontent the clean data were calculated
All the downstream analyses werebasedon the clean data with high quality
RNA-sequencing data were mapped to the GRCh38 human genome by HISAT2 (version 2.0.5). The gene expression matrix of raw read counts after annotation by FeatureCounts (version v1.5.0-p3) was processed using limma (version 3.58.1).
Assembly: GRCh38
Supplementary files format and content: csv files include  count value for each sample

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1.0 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: esophageal cancer cells

tag: genotype

value: WT


title: control for D4

description:
Library name: control for D4
control for D4


title: KYSE30 without RBM28 knockout, bio rep 1

description: Library name: NC1


title: Dual-sgRNA target D19_rep2

description:
Library name: D19_rep2
Alias column: D19_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: KYSE30 without RBM28 knockout, bio rep 2

description: Library name: NC2


title: Dual-sgRNA target D18_rep2

description:
Library name: D18_rep2
Alias column: D18_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: KYSE30 with RBM28 knockout, bio rep 3

description: Library name: KO3

value: RBM28 knockout