title: Dual-sgRNA target D20_rep1

description:
Library name: D20_rep1
Alias column: D20_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D18_rep1

status: Public on Apr 23 2026

type: SRA

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: D18_rep1
Alias column: D18_rep1
SIQ outcomes for dual-sgRNA sites.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.

tag: tissue

value: skeletal muscle

tag: strain

tag: age

value: 6 weeks

tag: sample group

value: Dual-sgRNA target


title: control for D1

description:
Library name: control for D1
control for D1

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.


title: KYSE30 with RBM28 knockout, bio rep 2

city: Beijing

first: Tao

last: Xiang

state: Beijing

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

country: China

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

description: Library name: KO2

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

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

tag: cell type

value: esophageal cancer cells

tag: genotype

value: RBM28 knockout


title: control for D2

description:
Library name: control for D2
control for D2


title: CRISPRnSEC_S007_D1_CD69_high

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St

country: USA

institute: UCSF Gladstone Institutes

description:
Library name: CRISPRnSEC_S007_D1_CD69_high
Pooled CRISPRn secondary in activated primary human CD4+ T cells; assay: CD69 surface expression; bin: high.

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.

source_name: blood

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: blood

value: CD4+ T cell

tag: treatment

value: FACS sorted for CD69 high

tag: batch

value: CRISPRn-secondary


title: CRISPRnSEC_S006_D1_CD25_low

description:
Library name: CRISPRnSEC_S006_D1_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: control for S44

description:
Library name: control for S44
control for S44


title: CRISPRnSEC_S011_D1_CXCR4_high

description:
Library name: CRISPRnSEC_S011_D1_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 D17_rep2

description:
Library name: D17_rep2
Alias column: D17_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S008_D1_CD69_low

description:
Library name: CRISPRnSEC_S008_D1_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: control for S43

description:
Library name: control for S43
control for S43


title: CRISPRnSEC_S005_D1_CD25_high

description:
Library name: CRISPRnSEC_S005_D1_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: AMs, BODIPY low, 3

city: Nanjing

first: Xinmei

last: Huang

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

description:
Library name: Sample 6
P13

data_processing:
Raw sequencing reads were first assessed for quality using FastQC.
Adapters and low-quality reads were trimmed using Trim Galore (v0.6.6).
Clean reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner (v2.7.9a).
Gene expression quantification was performed using featureCounts (Subread v2.0.1) with GENCODE annotation.
Differential expression analysis was conducted using DESeq2 (v1.30.1) in R.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include normalized gene expression matrices of all samples.
Supplementary files format and content: Files are provided in Excel (.xlsx) format.

molecule: total RNA

source_name: Bronchoalveolar lavage fluid

growth_protocol: Alveolar macrophages were isolated from bronchoalveolar lavage fluid (BALF) collected from patients with pulmonary alveolar proteinosis (PAP) during routine clinical procedures. Cells were maintained ex vivo in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2 until sorting.

extract_protocol:
Total RNA was extracted from sorted alveolar macrophages using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol, followed by purification with the RNeasy Mini Kit (Qiagen). RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions. Briefly, poly(A)+ mRNA was enriched using oligo(dT) beads, fragmented, and reverse-transcribed into cDNA. After adaptor ligation and PCR amplification, libraries were quantified and sequenced on an Illumina platform.

treatment_protocol: No experimental treatment was applied. Alveolar macrophages were stained with BODIPY 493/503 to assess intracellular lipid content and subsequently sorted by fluorescence-activated cell sorting (FACS) into BODIPY^high (foamy) and BODIPY^low (non-foamy) populations for downstream RNA-seq analysis.

value: Bronchoalveolar lavage fluid

value: Primary alveolar macrophages

value: Alveolar macrophages

value: BODIPY low

value: FACS sorting


title: Dual-sgRNA target D17_rep1

description:
Library name: D17_rep1
Alias column: D17_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle

value: 6 weeks


title: KYSE30 with RBM28 knockout, bio rep 1

description: Library name: KO1

value: esophageal cancer cells


title: Dual-sgRNA target D16_rep2

description:
Library name: D16_rep2
Alias column: D16_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: Dual-sgRNA target


title: CRISPRnSEC_S003_D1_HIV_LM_GFP_positive

description:
Library name: CRISPRnSEC_S003_D1_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: blood

value: HIV-GFP infection and FACS sorting


title: CRISPRnSEC_S004_D1_HIV_LM_GFP_negative

description:
Library name: CRISPRnSEC_S004_D1_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


title: control for S41

description:
Library name: control for S41
control for S41


title: Dual-sgRNA target D16_rep1

description:
Library name: D16_rep1
Alias column: D16_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: AMs, BODIPY low, 2

description:
Library name: Sample 5
P12


title: control for S38, S39, S40

description:
Library name: control for S38, S39, S40
control for S38, S39, S40


title: AMs, BODIPY low, 1

description:
Library name: Sample 4
P11


title: CRISPRnSEC_S001_D1_HIV_HM_GFP_positive

description:
Library name: CRISPRnSEC_S001_D1_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.

value: CRISPRn-secondary


title: control for S42

description:
Library name: control for S42
control for S42


title: Dual-sgRNA target D15_rep2

description:
Library name: D15_rep2
Alias column: D15_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: CRISPRnSEC_S002_D1_HIV_HM_GFP_negative

description:
Library name: CRISPRnSEC_S002_D1_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 D15_rep1

description:
Library name: D15_rep1
Alias column: D15_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: AMs, BODIPY high, 3

description:
Library name: Sample 3
P23

value: BODIPY high


title: control for S36

description:
Library name: control for S36
control for S36


title: AMs, BODIPY high, 2

description:
Library name: Sample 2
P22


title: control for S35

description:
Library name: control for S35
control for S35


title: control for S37

description:
Library name: control for S37
control for S37


title: WT_CDK1as_H3K9me3_G2(biol rep1)_Input_ChIP-Seq_Kimura

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: Library name: H3K9me3_G2_1_IN_Kimura

data_processing:
Read adapters trimmed with Cutadapt v1.18  --minimum-length 20  --nextseq-trim=20
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Removal of secondary (0x100), supplementary (0x800), and unmapped (0x4) reads (-F 2304)
BigWig tracks were generated using deepTools v3.5.0 bamCoverage to compute normalised coverage in bins of 1 bp using the BPM (bins per million reads) method.
Assembly: GCA_024206055.2
Supplementary files format and content: bigWig of read coverage

organism: Gallus gallus

source_name: Bursa

growth_protocol: RPMI1640, 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenchng and cell lysis, chromatin was shear using Diagenode Biorupter.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) according to the manufacturer’s protocol. The library size distribution was analysed by Agilent Bioanalyzer with High Sensitivity DNA chip and submitted for Illumina deep sequencing (100 bp pair-end) at the Edinburgh Clinical Research Facility. Sequencing was performed on the NextSeq 2000 platform using the NextSeq 1000/2000 P2 Reagents (100 cycles).

treatment_protocol: Cells were blocked at G2 with 1NMPP1 (G2).

value: Bursa

value: lymphoblast


title: Dual-sgRNA target D14_rep2

description:
Library name: D14_rep2
Alias column: D14_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_H3K9me3_G2(biol rep2)_Input_ChIP-Seq_Kimura

description: Library name: H3K9me3_G2_2_IN_Kimura


title: Dual-sgRNA target D14_rep1

description:
Library name: D14_rep1
Alias column: D14_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: AMs, BODIPY high, 1

description:
Library name: Sample 1
P21


title: AMs, Control3

description: Library name: Sample 6

growth_protocol: Alveolar macrophages were isolated from bronchoalveolar lavage fluid (BALF) obtained from patients with pulmonary alveolar proteinosis (PAP) and age-matched healthy donors. Cells were maintained ex vivo in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37°C with 5% CO2 until RNA extraction.

value: Control


title: control for S34

description:
Library name: control for S34
control for S34


title: WT_CDK1as_H3K9me3_G2(biol rep1)_ChIP-Seq_Kimura

description: Library name: H3K9me3_G2_1_Kimura

tag: antibody


title: WT_CDK1as_H3K9me3_G2(biol rep2)_ChIP-Seq_Kimura

description: Library name: H3K9me3_G2_2_Kimura


title: AMs, Control2

description: Library name: Sample 5

value: Bronchoalveolar lavage fluid


title: control for S30, S31

description:
Library name: control for S30, S31
control for S30, S31


title: AMs, Control1

description: Library name: Sample 4

value: Primary alveolar macrophages


title: Dual-sgRNA target D13_rep1

description:
Library name: D13_rep1
Alias column: D13_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: AMs, PAP3

description: Library name: Sample 3

value: Alveolar macrophages

value: PAP


title: control for S28, S29

description:
Library name: control for S28, S29
control for S28, S29


title: Dual-sgRNA target D13_rep2

description:
Library name: D13_rep2
Alias column: D13_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_CENP-H_G2(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: CENP-H_G2_2_spike-in_IN

data_processing:
Read adapters trimmed with Cutadapt v1.18  --minimum-length 20  --nextseq-trim=20
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Alignment to Chicken T2T genome GCA_024206055.2 with BWA-MEM v0.7.16 and -M parameter
Removal of secondary (0x100), supplementary (0x800), and unmapped (0x4) reads (-F 2304), retention of properly paired reads (-f 3)
BigWig tracks were generated using deepTools v3.5.0 bamCoverage to compute normalised coverage in bins of 1 bp using the BPM (bins per million reads) method.
Assembly: GCA_024206055.2
Supplementary files format and content: bigWig of read coverage

treatment_protocol: Cells were blocked at G2 with 1NMPP1 (G2). After 1NMPP1 washout, cells were collected at 5 min, 7.5 min, 15 min and 30 min.

tag: time


title: AMs, PAP2

description: Library name: Sample 2


title: Dual-sgRNA target D12_rep1

description:
Library name: D12_rep1
Alias column: D12_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S27

description:
Library name: control for S27
control for S27


title: control for S32, S33

description:
Library name: control for S32, S33
control for S32, S33


title: Dual-sgRNA target D12_rep2

description:
Library name: D12_rep2
Alias column: D12_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D11_rep2

description:
Library name: D11_rep2
Alias column: D11_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_H3K9me3_G2(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K9me3_G2_2_IN


title: WT_CDK1as_H3K9me3_G2(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K9me3_G2_1_IN


title: AMs, PAP1

description: Library name: Sample 1


title: WT_CDK1as_H3T3ph_30min(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_30min_2_spike-in_IN


title: Dual-sgRNA target D11_rep1

description:
Library name: D11_rep1
Alias column: D11_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S24, S25

description:
Library name: control for S24, S25
control for S24, S25


title: Dual-sgRNA target D10_rep2

description:
Library name: D10_rep2
Alias column: D10_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S22

description:
Library name: control for S22
control for S22


title: A498_SETD2 addback-rep 2

city: Charleston

first: Aguirre

last: de Cubas

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: Medical University of South Carolina

description: Library name: 10282-MR-0015-4

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling, and analysis was completed using MultiQC v1.7.
Sequencing reads were aligned against the human GENCODE  genome, hg38 GRCh38 (Version 28), using the Spliced Transcripts Alignment to a Reference (STAR) software.
Annotated and quantified using featureCounts using default parameters.
Normalization and differential expression analyses were performed using DESeq2.
Assembly: GENCODE  genome, hg38 GRCh38 (Version 28
Supplementary files format and content: Counts, text files

source_name: Kidney cancer

growth_protocol: RPMI with 10% FBS with Penn Strep and Glutamine

extract_protocol:
Total RNA extracted using Trizol
Poly-A library
RNAseq libraries were prepared using 350 ng of total RNA and the NEBNext Ultra II RNA Library Prep (NEB, E7765S) per manufacturer’s instructions, with messenger RNA (mRNA) enriched via poly-A selection using Oligo(dT) beads. The libraries were sequenced using the NovaSeq 6000 with 150 base pair (bp) paired end reads.

treatment_protocol: Cells were treated with DMSO or 100nM A1331852 or nothing. After 72 hours cells were harvested for RNA extraction

value: Kidney cancer

value: Kidney Cancer

value: SETD2 WT


title: WT_CDK1as_H3T3ph_30min(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_30min_1_spike-in_IN


title: control for S26

description:
Library name: control for S26
control for S26

value: skeletal muscle


title: WT_CDK1as_CENP-H_G2(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: CENP-H_G2_1_spike-in_IN


title: WT_CDK1as_H3T3ph_15min(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_15min_2_spike-in_IN


title: A498_SETD2 addback-rep 1

description: Library name: 10282-MR-0015-3


title: control for S19, S20

description:
Library name: control for S19, S20
control for S19, S20


title: A498_SETD2 deficient-rep 2

description: Library name: 10282-MR-0015-2

value: SETD2 null


title: Dual-sgRNA target D10_rep1

description:
Library name: D10_rep1
Alias column: D10_rep1
SIQ outcomes for dual-sgRNA sites.xlsx

value: 6 weeks

value: Dual-sgRNA target


title: Dual-sgRNA target D9_rep2

description:
Library name: D9_rep2
Alias column: D9_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_15min(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_15min_1_spike-in_IN


title: control for S18

description:
Library name: control for S18
control for S18


title: control for S21, S23

description:
Library name: control for S21, S23
control for S21, S23


title: 786-O SETD2 KO_DMSO treated-rep 2

description: Library name: 7166-MR-145-8

value: DMSO


title: Dual-sgRNA target D9_rep1

description:
Library name: D9_rep1
Alias column: D9_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D8_rep2

description:
Library name: D8_rep2
Alias column: D8_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: 786-O SETD2 KO_DMSO treated-rep 1

description: Library name: 7166-MR-145-7


title: control for S17

description:
Library name: control for S17
control for S17


title: A498_SETD2 deficient-rep 1

description: Library name: 10282-MR-0015-1


title: WT_CDK1as_H3T3ph_7.5min(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_7.5min_2_spike-in_IN


title: 786-O SETD2 WT_DMSO treated-rep 2

description: Library name: 7166-MR-145-4


title: control for S16

description:
Library name: control for S16
control for S16


title: WT_CDK1as_H3T3ph_7.5min(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_7.5min_1_spike-in_IN


title: Dual-sgRNA target D8_rep1

description:
Library name: D8_rep1
Alias column: D8_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_5min(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_5min_2_spike-in_IN


title: WT_CDK1as_H3T3ph_5min(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_5min_1_spike-in_IN


title: Dual-sgRNA target D7_rep1

description:
Library name: D7_rep1
Alias column: D7_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S14

description:
Library name: control for S14
control for S14


title: 786-O SETD2 WT_DMSO treated-rep 1

description: Library name: 7166-MR-145-3


title: Dual-sgRNA target D7_rep2

description:
Library name: D7_rep2
Alias column: D7_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_G2(biol rep2)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_G2_2_spike-in_IN


title: 786-O SETD2 KO_A1331852 treated-rep 3

description: Library name: 8457-MR-0092-8


title: Dual-sgRNA target D6_rep2

description:
Library name: D6_rep2
Alias column: D6_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: 786-O SETD2 KO_A1331852 treated-rep 2

description: Library name: 8457-MR-0092-7


title: Dual-sgRNA target D6_rep1

description:
Library name: D6_rep1
Alias column: D6_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S12, S13

description:
Library name: control for S12, S13
control for S12, S13


title: WT_CDK1as_H3T3ph_G2(biol rep1)_spike-in_InPut_ChIP-Seq

description: Library name: H3T3ph_G2_1_spike-in_IN


title: control for S15

description:
Library name: control for S15
control for S15


title: control for S10, S11

description:
Library name: control for S10, S11
control for S10, S11


title: WT_CDK1as_H3T3ph_30min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3T3ph_30min_2_IN


title: Dual-sgRNA target D4_rep2

description:
Library name: D4_rep2
Alias column: D4_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S9

description:
Library name: control for S9
control for S9


title: control for S8

description:
Library name: control for S8
control for S8


title: Dual-sgRNA target D4_rep1

description:
Library name: D4_rep1
Alias column: D4_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: 786-O SETD2 KO_DMSO treated-rep 3

description: Library name: 8457-MR-0092-5


title: 786-O SETD2 WT_A1331852 treated-rep 3

description: Library name: 8457-MR-0092-4


title: 786-O SETD2 KO_A1331852 treated-rep 1

description: Library name: 8457-MR-0092-6


title: Dual-sgRNA target D3_rep2

description:
Library name: D3_rep2
Alias column: D3_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: 786-O SETD2 WT_A1331852 treated-rep 2

description: Library name: 8457-MR-0092-3


title: WT_CDK1as_H3T3ph_30min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3T3ph_30min_1_IN


title: WT_CDK1as_H3T3ph_15min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3T3ph_15min_1_IN


title: control for S2, S3, S4, S5

description:
Library name: control for S2, S3, S4, S5
control for S2, S3, S4, S5


title: Dual-sgRNA target D3_rep1

description:
Library name: D3_rep1
Alias column: D3_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: control for S6, S7

description:
Library name: control for S6, S7
control for S6, S7


title: WT_CDK1as_H3T3ph_7.5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3T3ph_7.5min_2_IN


title: control for S1

description:
Library name: control for S1
control for S1


title: Dual-sgRNA target D2_rep1

description:
Library name: D2_rep1
Alias column: D2_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: 786-O SETD2 WT_DMSO treated-rep 3

description: Library name: 8457-MR-0092-1


title: 786-O SETD2 WT_A1331852 treated-rep 1

description: Library name: 8457-MR-0092-2


title: ccRCC tumor, Lenvatinib/Pembrolizumab treated, sc50

city: New York

first: Fengshen

last: Kuo

state: New York

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: sc50T
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: single cell barcodes
Supplementary files format and content: features.tsv.gz: gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Primary Tumor

extract_protocol:
Tumors were coarsely minced using a scalpel and enzymatically dissociated using the human tumor dissociation kit (Miltenyi) for 25mins at 37c using the Octo-dissociator (Miltenyi). Digested cells were neutralized in DMEM + 10% FBS and successively washed in PBS and strained through 100um, 70μm and 45μm cell strainers with an RBC lysis step in between (Ack lysis buffer; Gibco). Single cell suspensions were stained with DAPI (BD Pharmingen) and calcein AM (Invitrogen) and FACS sorted for live single cells. Cells were counted using a hemocytometer and up to 10,000 cells were loaded into the Chromium Controller (10x genomics).
Cells were processed using the Next GEM 5’ mRNA V2 kit (10x genomics) with strict adherence to manufacturer’s protocols. Gene expression libraries were sequenced at a target depth of 200 million reads per sample.

treatment_protocol: Advanced ccRCC tumors surgically resected following various tyrosine kinase inhibitor (TKI) or immune checkpoint blockade (ICB) therapy combinations.

value: Primary Tumor

tag: histopathology

value: ccRCC

tag: pre-surgery treatment

value: Lenvatinib/Pembrolizumab

tag: pathological response

value: PR

tag: age at_time_of_surgery

tag: Sex

value: M


title: 26757X4 1311G KNH R2

city: Salt lake City

first: Headtlove

last: Essel Dadzie

state: UT

address: 2000 circle of Hope

department: Oncological Sciences

institute: University of Utah

description: Library name: 26757X4

data_processing:
Adapters were trimmed using Trim Galore v0.6.6 and quality was assessed using FastQC v0.12.1.
Reads were aligned to mouse genome mm10 using Bowtie2 v2.2.9.
Aligned reads were sorted and indexed using Samtools v1.16 and duplicate reads removed using Picard v2.22.0.
Peaks were called using MACS2 v2.2.7.
Coverage tracks were generated as RPM normalized bigWig files using MACS2 and deepTools v3.5.1.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: organoids

growth_protocol: 3D organoid lines were cultured in 50% L-WRN conditioned media.

extract_protocol:
ATAC-seq was performed on organoids using an Omni-ATAC-based protocol adapted from published methods. Organoids were dissociated into single cells using established protocol, depleted of dead cells by two sequential rounds of magnetic separation using the Dead cell removal kit from (Miltenyl Biotec), and washed in PBS. Cell viability exceeded 90% for all samples. Cells were manually counted, and  100,000 cells per condition were pelleted at 500g for 5 minutes at 4°C in PBS supplemented with 1% BSA. For nuclei isolation, cell pellets were resuspended in cold lysis buffer and incubated on ice for 3 minutes. After addition of wash buffer, nuclei were pelleted at 500g for 10 minutes at 4°C and gently resuspended in transposition mix lacking Tn5. Nuclei were counted, and 50,000 nuclei per reaction were used for transposition. Transposition was performed with 2.5uL of Illumina Tn5 and incubated at 37°C for 30 minutes with shaking at 1,000 rpm. Transposed DNA was purified using Zymo DNA Clean and Concentrator and eluted in 21 µL elution buffer.
Libraries were amplified using Q5 Hot Start High-Fidelity Master Mix (NEB) and Nextera barcoded primers. Initial amplification was performed for five cycles, followed by SYBR Green–based qPCR on 10% of each library to determine the minimum number of additional cycles required. Final libraries were purified using Zymo DNA Clean and Concentrator. Library concentration was quantified by Qubit, and size distribution was assessed by Tape Station. Libraries were sequenced using paired-end 150 bp reads on an Illumina platform.

treatment_protocol: 1311G#5 were transiently treated with AD5-Cmv-Cre to delete HNF4α in vitro.

value: organoids

value: KNH


title: 26757X3 1311G KNH R1

description: Library name: 26757X3


title: WT_CDK1as_H3T3ph_7.5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3T3ph_7.5min_1_IN

value: Bursa

value: lymphoblast


title: WT_CDK1as_H3T3ph_5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3T3ph_5min_1_IN


title: WT_CDK1as_H3T3ph_5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3T3ph_5min_2_IN


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc48

description:
Library name: sc48T
10x Genomics

value: rhabdoid ccRCC

value: Axitinib/Pembrolizumab

value: F


title: Dual-sgRNA target D2_rep2

description:
Library name: D2_rep2
Alias column: D2_rep2
SIQ outcomes for dual-sgRNA sites.xlsx

value: skeletal muscle


title: WT_CDK1as_H3T3ph_15min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3T3ph_15min_2_IN


title: Dual-sgRNA target D1_rep2

description:
Library name: D1_rep2
Alias column: D1_rep2
SIQ outcomes for dual-sgRNA sites.xlsx


title: Dual-sgRNA target D1_rep1

description:
Library name: D1_rep1
Alias column: D1_rep1
SIQ outcomes for dual-sgRNA sites.xlsx


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc46

description:
Library name: sc46T
10x Genomics

value: Ipilimumab/Nivolumab


title: WT_CDK1as_H3T3ph_G2(biol rep2)_InPut_ChIP-Seq

description: Library name: H3T3ph_G2_2_IN


title: Single sgRNA target S44_rep2

description:
Library name: S44_rep2
Alias column: S44_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks

value: Single sgRNA target


title: 26757X2 1311G KN R2

description: Library name: 26757X2

value: KN

value: Control


title: Single sgRNA target S44_rep1

description:
Library name: S44_rep1
Alias column: S44_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_G2(biol rep1)_InPut_ChIP-Seq

description: Library name: H3T3ph_G2_1_IN


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc44

description:
Library name: sc44T
10x Genomics

value: Primary Tumor

value: ccRCC

value: CR


title: Runx3 WT

first: Jun Hyung

last: Sin

address: 513 Parnassus Ave S-1076

department: Pediatrics

institute: University of California, San Francisco

description: Library name: Sample 2

data_processing:
FASTQ files were converted into single-cell matrices using 10x Cell Ranger. Matrices were then log transformed into a Seurat object using the Seurat package in R. Initial exclusion criteria included features that were present in fewer than 200 cells and cells where fewer than 1000 features were detected. Samples were merged and integrated using 2000 variable features and dimensions 1:20. Cells with greater than 50% ribosomal RNA, greater than 10% mitochondrial RNA, and greater than 4000 features were excluded. Principal components analysis was performed using 30 principal components, and UMAPs were generated using dimensions 1:20. Cluster identities were assigned cell types and differential gene expression analysis was performed in Seurat.
Assembly: mm10
Supplementary files format and content: barcode, feature, matrix files

source_name: thymus

extract_protocol:
Freshly FACS sorted EpCAM+ TECs from three to four mice of each genotype were pooled and FACS sorted into 1.5 ml Eppendorf tubes containing 500 ul of DMEM with 2% FBS. Approximately 20,000 cells per 100 ul were sent to the UCSF Genomics Core for processing. Single cells were captured using the 10X Chromium microfluidics system (10x Genomics).
The cells were then barcoded complementary DNA libraries and sequenced on the NovaSeq (Illumina).

value: thymus

value: mTEC

value: WT


title: Single sgRNA target S43_rep2

description:
Library name: S43_rep2
Alias column: S43_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me3_30min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me3_30min_2_IN

value: Bursa


title: Runx3 KO

description: Library name: Sample 1

value: KO


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc24.

description:
Library name: sc24T
10x Genomics

value: sarcomatoid ccRCC

value: PR

value: M


title: Single sgRNA target S43_rep1

description:
Library name: S43_rep1
Alias column: S43_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle


title: WT_CDK1as_H3K4me3_15min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me3_15min_2_IN

value: lymphoblast


title: Single sgRNA target S42_rep2

description:
Library name: S42_rep2
Alias column: S42_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc16

description:
Library name: sc16T
10x Genomics

value: Ipilimumab/Nivolumab


title: ccRCC tumor, Cabozantinib treated, sc21

description:
Library name: sc21T
10x Genomics

value: Cabozantinib

value: F


title: 26757X1 1311G KN R1

description: Library name: 26757X1

value: organoids

value: KN

value: Control


title: WT_CDK1as_H3K4me3_30min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me3_30min_1_IN


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc10, medial

description:
Library name: sc10T_M
10x Genomics

source_name: Primary Tumor (Multiple regions)

value: Primary Tumor (Multiple regions)

value: CR


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc30

description:
Library name: sc30T
10x Genomics

source_name: Recurrent metastasis (vena cava)

value: Recurrent metastasis (vena cava)

value: Axitinib/Pembrolizumab


title: Atf7ip KO3

description: Library name: Sample6

data_processing:
Sequence alignment was performed using STAR (version 2.7.9a). Mappings were restricted to those that were uniquely assigned to the mouse genome, and unique read alignments were used to quantify expression and aggregated on a per-gene basis using the Ensembl (GRCm39) annotation. Differentially expressed genes between experimental groups were then determined using DESeq2 (V4.0.3)
Assembly: GRCm39
Supplementary files format and content: CSV File

source_name: Tumor

extract_protocol:
Approximately 500 intratumoral P14+/Atf7ip-sufficient or 500 intratumoral P14+/Atf7ip-deficient CD8+ T cells per sample were sorted directly into lysis buffer from the SMART-seq v4 [Takara Bio] kit. Lysed cells were given to the UCSF Genomics COLAB for Library Preparation. Libraries prepared by the core were submitted to the UCSF Center for Advanced Technology for single-end sequencing.
Libraries were prepared by the UCSF Center for Advanced Technology Core for single-end sequencing

value: Tumor

value: KO


title: Atf7ip KO2

description: Library name: Sample5


title: WT_CDK1as_H3K4me3_15min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me3_15min_1_IN

value: Bursa


title: WT_CDK1as_H3K4me3_7.5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me3_7.5min_2_IN


title: Single sgRNA target S42_rep1

description:
Library name: S42_rep1
Alias column: S42_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: Single sgRNA target


title: Single sgRNA target S41_rep2

description:
Library name: S41_rep2
Alias column: S41_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle


title: Single sgRNA target S41_rep1

description:
Library name: S41_rep1
Alias column: S41_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc10, lateral

description:
Library name: sc10T_L
10x Genomics

value: sarcomatoid ccRCC

value: M


title: WT_CDK1as_H3K4me3_7.5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me3_7.5min_1_IN

value: lymphoblast


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc10, center

description:
Library name: sc10T_C
10x Genomics

value: Ipilimumab/Nivolumab


title: Atf7ip KO1

description: Library name: Sample4


title: Atf7ip Het3

description: Library name: Sample3

value: Wildtype


title: Atf7ip Het1

description: Library name: Sample1


title: WT_CDK1as_H3K4me3_5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me3_5min_2_IN


title: Single sgRNA target S40_rep2

description:
Library name: S40_rep2
Alias column: S40_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: WT_CDK1as_H3K4me3_5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me3_5min_1_IN


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc08, near

description:
Library name: sc08T_N
10x Genomics

value: ccRCC


title: Atf7ip Het2

description: Library name: Sample2


title: WT_CDK1as_H3K4me3_G2(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me3_G2_2_IN


title: Atf7ip KO CD8

description: Library name: Sample2

extract_protocol:
For scRNA-seq, P14+/CD8+ T cells from three to four mice of each genotype were pooled and FACS sorted into 1.5 ml Eppendorf tubes containing 500 ul of DMEM with 2% FBS. Approximately 20,000 cells per 100 ul were sent to the UCSF Genomics Core for processing. Single cells were captured using the 10X Chromium microfluidics system (10x Genomics).
The cells were then barcoded complementary DNA libraries and sequenced on the NovaSeq (Illumina).


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc08, far

description:
Library name: sc08T_F
10x Genomics


title: Single sgRNA target S39_rep2

description:
Library name: S39_rep2
Alias column: S39_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S39_rep1

description:
Library name: S39_rep1
Alias column: S39_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Runx1 WT

description: Library name: Sample2

data_processing:
Fastq files were processed with 10X Cell Ranger and made into Seurat objects in R
Assembly: mm10
Supplementary files format and content: 10X Cell Ranger output (Barcodes, features, matrix files)

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: mTEC

value: WT


title: WT_CDK1as_H3K4me3_G2(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me3_G2_1_IN


title: WT_CDK1as_H3K4me2_30min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me2_30min_2_IN


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc06, near

description:
Library name: sc06T_N
10x Genomics

value: Primary Tumor (Multiple regions)

value: PR


title: Single sgRNA target S38_rep2

description:
Library name: S38_rep2
Alias column: S38_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Runx1 KO

description: Library name: Sample1


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc06, far

description:
Library name: sc06T_F
10x Genomics


title: Single sgRNA target S40_rep1

description:
Library name: S40_rep1
Alias column: S40_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S38_rep1

description:
Library name: S38_rep1
Alias column: S38_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me2_30min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me2_30min_1_IN


title: CD4_Subject_05-P16-Unstimulated

city: Boston

first: Rene

last: Bermea

state: MA

address: 55 Fruit St

department: Pulmonary and Critical Care Medicine

institute: Massachusetts General Hospital

description: Library name: CD4_Subject_05-P16-Unstimulated

data_processing:
Sequence reads were trimmed with Trimmomatic (v0.39)
Trimmed sequence reads were mapped to Homo sapiens Genome assembly GRCH38 with Kallisto (v0.50.1)
Assembly: Homo sapiens Genome assembly GRCh38
Supplementary files format and content: Tab-delimited text file output by Kallisto. Includes transcript counts for each sample
Supplementary files format and content: H5 file output by Kallisto. Includes transcript counts for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Plus Mini kit
The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations.

value: Blood

tag: individual

value: CD4 T Cells

tag: guide

value: Unstimulated


title: CD4_Subject_05-P16-Stimulated

description: Library name: CD4_Subject_05-P16-Stimulated

tag: tissue

value: Stimulated


title: Atf7ip Het CD8

description: Library name: Sample1

value: Tumor


title: Single sgRNA target S37_rep2

description:
Library name: S37_rep2
Alias column: S37_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle

tag: strain

tag: age

value: Single sgRNA target


title: WT_CDK1as_H3K4me2_15min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me2_15min_1_IN

value: Bursa

tag: cell line

value: lymphoblast


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc06, center

description:
Library name: sc06T_C
10x Genomics

value: Ipilimumab/Nivolumab

value: M


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc08, center

description:
Library name: sc08T_C
10x Genomics

value: ccRCC


title: CD4_Subject_05-DG-Unstimulated

description: Library name: CD4_Subject_05-DG-Unstimulated

tag: cell type

value: DG


title: WT_CDK1as_H3K4me2_7.5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me2_7.5min_2_IN


title: Single sgRNA target S37_rep1

description:
Library name: S37_rep1
Alias column: S37_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks

tag: sample group


title: ccRCC tumor, untreated, sc03, near

description:
Library name: sc03T_N
10x Genomics

value: Untreated

value: F


title: Single sgRNA target S36_rep2

description:
Library name: S36_rep2
Alias column: S36_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC tumor, untreated, sc03, far

description:
Library name: sc03T_F
10x Genomics

value: Primary Tumor (Multiple regions)


title: WT_CDK1as_H3K4me2_15min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me2_15min_2_IN

tag: treatment


title: ccRCC tumor, untreated, sc03, center

description:
Library name: sc03T_C
10x Genomics


title: Single sgRNA target S36_rep1

description:
Library name: S36_rep1
Alias column: S36_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me2_7.5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me2_7.5min_1_IN


title: CD4_Subject_04-P16-Unstimulated

description: Library name: CD4_Subject_04-P16-Unstimulated

value: Blood


title: CD4_Subject_05-DG-Stimulated

description: Library name: CD4_Subject_05-DG-Stimulated

value: CD4 T Cells


title: ccRCC tumor, untreated, sc02, upper

description:
Library name: sc02T_U
10x Genomics


title: Single sgRNA target S35_rep2

description:
Library name: S35_rep2
Alias column: S35_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S34_rep2

description:
Library name: S34_rep2
Alias column: S34_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S35_rep1

description:
Library name: S35_rep1
Alias column: S35_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me2_5min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me2_5min_2_IN


title: ccRCC tumor, untreated, sc02, center

description:
Library name: sc02T_C
10x Genomics


title: CD4_Subject_04-P16-Stimulated

description: Library name: CD4_Subject_04-P16-Stimulated


title: WT_CDK1as_H3K4me2_5min(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me2_5min_1_IN


title: CD4_Subject_04-DG-Stimulated

description: Library name: CD4_Subject_04-DG-Stimulated


title: ccRCC tumor, untreated, sc02, lower

description:
Library name: sc02T_L
10x Genomics


title: CD4_Subject_04-DG-Unstimulated

description: Library name: CD4_Subject_04-DG-Unstimulated

value: Unstimulated


title: WT_CDK1as_H3K4me2_G2(biol rep1)_InPut_ChIP-Seq

description: Library name: H3K4me2_G2_1_IN


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc27

description:
Library name: sc27T_ST
10x Genomics

data_processing:
Raw sequencing data were procesed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger's default settings
Gene expression counts per spot were log transformed using the Python library Squidpy, and spots with fewer than 1,000 UMIs were excluded from further analysis.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: spatial spot barcodes
Supplementary files format and content: features.tsv.gz: gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of teh tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factor in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial spot barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Tumors were formalin fixed and paraffin embedded, and 5um sections were cut.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions.

value: Primary Tumor

value: sarcomatoid ccRCC

value: Axitinib/Pembrolizumab

value: CR


title: Single sgRNA target S34_rep1

description:
Library name: S34_rep1
Alias column: S34_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle

value: Single sgRNA target


title: WT_CDK1as_H3K4me2_G2(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me2_G2_2_IN

value: Bursa

value: lymphoblast


title: CD4_Subject_02-P16-Unstimulated

description: Library name: CD4_Subject_02-P16-Unstimulated


title: WT_CDK1as_H3K4me1_30min(biol rep2)_InPut_ChIP-Seq

description: Library name: H3K4me1_30min_2_IN


title: CD4_Subject_02-P16-Stimulated

description: Library name: CD4_Subject_02-P16-Stimulated

value: Stimulated


title: ccRCC tumor, Axitinib/Pembrolizumab treated, sc24

description:
Library name: sc24T_ST
10x Genomics

value: PR

value: M


title: ccRCC tumor, Ipilimumab/Nivolumab treated, sc06

description:
Library name: sc06T_ST
10x Genomics

value: ccRCC

value: Ipilimumab/Nivolumab


title: WT_CDK1as_H3K4me1_30min(biol rep1)_Input_ChIP-Seq

description: Library name: H3K4me1_30min_1_IN


title: Single sgRNA target S33_rep1

description:
Library name: S33_rep1
Alias column: S33_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: CD4_Subject_02-DG-Unstimulated

description: Library name: CD4_Subject_02-DG-Unstimulated

value: Blood

value: DG


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 17

description:
Library name: TKI_IO_post_17
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

data_processing:
RNA-seq sequencing reads were aligned against human genome assembly hg19 by STAR 2-pass alignment. Gene level raw read count values were computed by using the R package GenomicAlignments over aligned reads with UCSC KnownGene in hg19 as the base gene model. The Union counting mode was used and only mapped paired reads after alignment quality filtering were considered. Finally, gene level FPKM (Fragments Per Kilobase Million) values were computed by the R package DESeq2. Batch corrected FPKM expression matrix was derived by the ComBat function implemented by the R package sva.
Assembly: hg19
Supplementary files format and content: Tab-delimited files including raw count file, FPKM count file, and batch-corrected FPKM count file

source_name: primary tumor

extract_protocol:
For snap frozen tissues, 20-30mg frozen tissue was homogenized in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 µL input. Samples were eluted in 15-16 µL RNase-free water. For FFPE tissues, sections were deparaffinized using the mineral oil method. Briefly, 800µL mineral oil was mixed with the sections and the sample was incubated at 65°C for 10 minutes. Phases were separated by centrifugation in 360µL Buffer PKD and Proteinase K was added for digestion. After a three-step incubation (65°C for 45’, 80°C for 15’, 65°C for 30’) and additional centrifugation, the aqueous phase containing RNA was removed and DNase treated. The RNA was then extracted using the RNeasy FFPE Kit (QIAGEN catalog # 73504) according to the manufacturer’s instructions.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 432ng-1µg of total RNA with DV200 values from 24-83% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR.

value: primary tumor

value: clear cell renal cell carcinoma

tag: first-line treatment

value: Cabozantinib + Nivolumab

tag: tumor grade

tag: batch

value: TFH


title: WT_CDK1as_H3K4me1_15min(biol rep2)_Input_ChIP-Seq

description: Library name: H3K4me1_15min_2_IN

tag: antibody

tag: time


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 16

description:
Library name: TKI_IO_post_16
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

source_name: metastatic tumor

value: metastatic tumor

tag: histopathology

value: Lenvatinib + Pembrolizumab


title: Single sgRNA target S32_rep2

description:
Library name: S32_rep2
Alias column: S32_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle

value: Single sgRNA target


title: WT_CDK1as_H3K4me1_15min(biol rep1)_Inut_ChIP-Seq

description: Library name: H3K4me1_15min_1_IN

value: Bursa

value: lymphoblast


title: Single sgRNA target S33_rep2

description:
Library name: S33_rep2
Alias column: S33_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S32_rep1

description:
Library name: S32_rep1
Alias column: S32_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CD8_Subject_03_P16_Unstimulated

description: Library name: CD8_Subject_03_P16_Unstimulated

value: CD8 T Cells

value: Unstimulated


title: CD4_Subject_02-DG-Stimulated

description: Library name: CD4_Subject_02-DG-Stimulated

value: CD4 T Cells

value: Stimulated


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 15

description:
Library name: TKI_IO_post_15
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Axitinib + Pembrolizumab


title: CD8_Subject_03_P16_Stimulated

description: Library name: CD8_Subject_03_P16_Stimulated

value: Blood


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 13

description:
Library name: TKI_IO_post_13
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me1_7.5min(biol rep2)_Input_ChIP-Seq

description: Library name: H3K4me1_7.5min_2_IN


title: WT_CDK1as_H3K4me1_7.5min(biol rep1)_Input_ChIP-Seq

description: Library name: H3K4me1_7.5min_1_IN


title: Single sgRNA target S30_rep2

description:
Library name: S30_rep2
Alias column: S30_rep2
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 14

description:
Library name: TKI_IO_post_14
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Axitinib + Avelumab


title: Single sgRNA target S31_rep2

description:
Library name: S31_rep2
Alias column: S31_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S31_rep1

description:
Library name: S31_rep1
Alias column: S31_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CD8_Subject_03_Dummy_Guide_Unstimulated

description: Library name: CD8_Subject_03_Dummy_Guide_Unstimulated


title: WT_CDK1as_H3K4me1_5min(biol rep2)_Input_ChIP-Seq

description: Library name: H3K4me1_5min_2_IN


title: WT_CDK1as_H3K4me1_5min(biol rep1)_Input_ChIP-Seq

description: Library name: H3K4me1_5min_1_IN


title: CD8_Subject_03_Dummy_Guide_Stimulated

description: Library name: CD8_Subject_03_Dummy_Guide_Stimulated


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 12

description:
Library name: TKI_IO_post_12
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: clear cell renal cell carcinoma


title: CD8_Subject_02_P16_Unstimulated

description: Library name: CD8_Subject_02_P16_Unstimulated


title: WT_CDK1as_H3K4me1_G2(biol rep2)_Input_ChIP-Seq

description: Library name: H3K4me1_G2_2_IN


title: Single sgRNA target S30_rep1

description:
Library name: S30_rep1
Alias column: S30_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me1_G2(biol rep1)_Input_ChIP-Seq

description: Library name: H3K4me1_G2_1_IN


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 11

description:
Library name: TKI_IO_post_11
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S29_rep2

description:
Library name: S29_rep2
Alias column: S29_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 10

description:
Library name: TKI_IO_post_10
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CD8_Subject_02_Dummy_Guide_Unstimulated

description: Library name: CD8_Subject_02_Dummy_Guide_Unstimulated


title: Single sgRNA target S29_rep1

description:
Library name: S29_rep1
Alias column: S29_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 8

description:
Library name: TKI_IO_post_8
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_CENP-H_G2(biol rep2)_spike-in_ChIP-Seq

description: Library name: CENP-H_G2_2_spike-in

value: Halo-Trap Agarose affinity beads


title: Single sgRNA target S28_rep2

description:
Library name: S28_rep2
Alias column: S28_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 9

description:
Library name: TKI_IO_post_9
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CD8_Subject_02_P16_Stimulated

description: Library name: CD8_Subject_02_P16_Stimulated


title: CD8_Subject_01_P16_Unstimulated

description: Library name: CD8_Subject_01_P16_Unstimulated


title: WT_CDK1as_CENP-H_G2(biol rep1)_spike-in_ChIP-Seq

description: Library name: CENP-H_G2_1_spike-in


title: Single sgRNA target S28_rep1

description:
Library name: S28_rep1
Alias column: S28_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CD8_Subject_02_Dummy_Guide_Stimulated

description: Library name: CD8_Subject_02_Dummy_Guide_Stimulated


title: Single sgRNA target S27_rep2

description:
Library name: S27_rep2
Alias column: S27_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: CD8_Subject_01_P16_Stimulated

description: Library name: CD8_Subject_01_P16_Stimulated


title: WT_CDK1as_H3K9me3_G2(biol rep2)_ChIP-Seq

description: Library name: H3K9me3_G2_2


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 6

description:
Library name: TKI_IO_post_6
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K9me3_G2(biol rep1)_ChIP-Seq

description: Library name: H3K9me3_G2_1


title: CD8_Subject_01_Dummy_Guide_Unstimulated

description: Library name: CD8_Subject_01_Dummy_Guide_Unstimulated


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 5

description:
Library name: TKI_IO_post_5
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: primary tumor


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 7

description:
Library name: TKI_IO_post_7
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S26_rep2

description:
Library name: S26_rep2
Alias column: S26_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_30min(biol rep2)_spike-in_ChIP-Seq

description: Library name: H3T3ph_30min_2_spike-in


title: Single sgRNA target S27_rep1

description:
Library name: S27_rep1
Alias column: S27_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S26_rep1

description:
Library name: S26_rep1
Alias column: S26_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CD8_Subject_01_Dummy_Guide_Stimulated

description: Library name: CD8_Subject_01_Dummy_Guide_Stimulated


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 3

description:
Library name: TKI_IO_post_3
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: metastatic tumor


title: WT_CDK1as_H3T3ph_30min(biol rep1)_spike-in_ChIP-Seq

description: Library name: H3T3ph_30min_1_spike-in


title: Single sgRNA target S25_rep2

description:
Library name: S25_rep2
Alias column: S25_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_15min(biol rep2)_spike-in_ChIP-Seq

description: Library name: H3T3ph_15min_2_spike-in


title: CRISPRaGW_S018_D3_HIV_CalB_uninfected

description:
Library name: CRISPRaGW_S018_D3_HIV_CalB_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: uninfected.

value: blood

value: CD4+ T cell

value: HIV-GFP infection and FACS sorting

value: CRISPRa-gw


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 2

description:
Library name: TKI_IO_post_2
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Lenvatinib + Pembrolizumab


title: WT_CDK1as_H3T3ph_15min(biol rep1)_spike-in_ChIP-Seq

description: Library name: H3T3ph_15min_1_spike-in

value: Bursa

value: lymphoblast


title: Single sgRNA target S25_rep1

description:
Library name: S25_rep1
Alias column: S25_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle

value: Single sgRNA target


title: CRISPRaGW_S016_D3_HIV_CalB_GFP_negative

description:
Library name: CRISPRaGW_S016_D3_HIV_CalB_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-negative.


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 4

description:
Library name: TKI_IO_post_4
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Cabozantinib + Nivolumab


title: WT_CDK1as_H3T3ph_7.5min(biol rep2)_spike-in_ChIP-Seq

description: Library name: H3T3ph_7.5min_2_spike-in


title: Single sgRNA target S24_rep2

description:
Library name: S24_rep2
Alias column: S24_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_7.5min(biol rep1)_spike-in_ChIP-Seq

description: Library name: H3T3ph_7.5min_1_spike-in


title: CRISPRaGW_S014_D2_HIV_CalB_GFP_positive

description:
Library name: CRISPRaGW_S014_D2_HIV_CalB_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-positive.


title: CRISPRaGW_S017_D3_HIV_CalB_GFP_positive

description:
Library name: CRISPRaGW_S017_D3_HIV_CalB_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-positive.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 44

description:
Library name: TKI_IO_pre_44
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: TFH


title: Single sgRNA target S24_rep1

description:
Library name: S24_rep1
Alias column: S24_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 42

description:
Library name: TKI_IO_pre_42
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CRISPRaGW_S015_D2_HIV_CalB_uninfected

description:
Library name: CRISPRaGW_S015_D2_HIV_CalB_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: uninfected.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 43

description:
Library name: TKI_IO_pre_43
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CRISPRaGW_S012_D1_HIV_CalB_uninfected

description:
Library name: CRISPRaGW_S012_D1_HIV_CalB_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: uninfected.


title: Single sgRNA target S23_rep1

description:
Library name: S23_rep1
Alias column: S23_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaGW_S013_D2_HIV_CalB_GFP_negative

description:
Library name: CRISPRaGW_S013_D2_HIV_CalB_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-negative.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 41

description:
Library name: TKI_IO_pre_41
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Axitinib + Pembrolizumab


title: Single sgRNA target S23_rep2

description:
Library name: S23_rep2
Alias column: S23_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S22_rep2

description:
Library name: S22_rep2
Alias column: S22_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_5min(biol rep1)_spike-in_ChIP-Seq

description: Library name: H3T3ph_5min_1_spike-in


title: WT_CDK1as_H3T3ph_5min(biol rep2)_spike-in_ChIP-Seq

description: Library name: H3T3ph_5min_2_spike-in


title: WT_CDK1as_H3T3ph_G2(biol rep2)_spike-in_ChIP-Seq

description: Library name: H3T3ph_G2_2_spike-in


title: WT_CDK1as_H3T3ph_G2(biol rep1)_spike-in_ChIP-Seq

description: Library name: H3T3ph_G2_1_spike-in


title: ccRCC, post-treatment tumor, TKI/IO treatment group, sample 1

description:
Library name: TKI_IO_post_1
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: clear cell renal cell carcinoma


title: CRISPRaGW_S011_D1_HIV_CalB_GFP_positive

description:
Library name: CRISPRaGW_S011_D1_HIV_CalB_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-positive.


title: Single sgRNA target S22_rep1

description:
Library name: S22_rep1
Alias column: S22_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaGW_S010_D1_HIV_CalB_GFP_negative

description:
Library name: CRISPRaGW_S010_D1_HIV_CalB_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalB; bin: GFP-negative.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 40

description:
Library name: TKI_IO_pre_40
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 39

description:
Library name: TKI_IO_pre_39
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CRISPRaGW_S009_D3_HIV_CalA_uninfected

description:
Library name: CRISPRaGW_S009_D3_HIV_CalA_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: uninfected.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 38

description:
Library name: TKI_IO_pre_38
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Ipilimumab + Nivolumab


title: Single sgRNA target S21_rep2

description:
Library name: S21_rep2
Alias column: S21_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_30min(biol rep1)_ChIP-Seq

description: Library name: H3T3ph_30min_1


title: Single sgRNA target S21_rep1

description:
Library name: S21_rep1
Alias column: S21_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaGW_S008_D3_HIV_CalA_GFP_positive

description:
Library name: CRISPRaGW_S008_D3_HIV_CalA_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-positive.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 37

description:
Library name: TKI_IO_pre_37
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S20_rep2

description:
Library name: S20_rep2
Alias column: S20_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_30min(biol rep2)_ChIP-Seq

description: Library name: H3T3ph_30min_2


title: WT_CDK1as_H3T3ph_15min(biol rep2)_ChIP-Seq

description: Library name: H3T3ph_15min_2


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 36

description:
Library name: TKI_IO_pre_36
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Lenvatinib + pembrolizumab


title: CRISPRaGW_S006_D2_HIV_CalA_uninfected

description:
Library name: CRISPRaGW_S006_D2_HIV_CalA_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: uninfected.


title: Single sgRNA target S19_rep2

description:
Library name: S19_rep2
Alias column: S19_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 35

description:
Library name: TKI_IO_pre_35
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: primary tumor


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 34

description:
Library name: TKI_IO_pre_34
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3T3ph_7.5min(biol rep2)_ChIP-Seq

description: Library name: H3T3ph_7.5min_2


title: Single sgRNA target S20_rep1

description:
Library name: S20_rep1
Alias column: S20_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S19_rep1

description:
Library name: S19_rep1
Alias column: S19_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3T3ph_7.5min(biol rep1)_ChIP-Seq

description: Library name: H3T3ph_7.5min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 33

description:
Library name: TKI_IO_pre_33
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3T3ph_5min(biol rep2)_ChIP-Seq

description: Library name: H3T3ph_5min_2


title: CRISPRaGW_S007_D3_HIV_CalA_GFP_negative

description:
Library name: CRISPRaGW_S007_D3_HIV_CalA_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-negative.

value: blood


title: CRISPRaGW_S004_D2_HIV_CalA_GFP_negative

description:
Library name: CRISPRaGW_S004_D2_HIV_CalA_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-negative.

value: CD4+ T cell


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 32

description:
Library name: TKI_IO_pre_32
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3T3ph_15min(biol rep1)_ChIP-Seq

description: Library name: H3T3ph_15min_1


title: Single sgRNA target S18_rep2

description:
Library name: S18_rep2
Alias column: S18_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaGW_S002_D1_HIV_CalA_GFP_positive

description:
Library name: CRISPRaGW_S002_D1_HIV_CalA_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-positive.

value: HIV-GFP infection and FACS sorting


title: CRISPRaGW_S003_D1_HIV_CalA_uninfected

description:
Library name: CRISPRaGW_S003_D1_HIV_CalA_uninfected
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: uninfected.

value: CRISPRa-gw


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 31

description:
Library name: TKI_IO_pre_31
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: Lenvatinib + Pembrolizumab


title: CRISPRaGW_S005_D2_HIV_CalA_GFP_positive

description:
Library name: CRISPRaGW_S005_D2_HIV_CalA_GFP_positive
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-positive.


title: WT_CDK1as_H3T3ph_G2(biol rep2)_ChIP-Seq

description: Library name: H3T3ph_G2_2

value: Bursa


title: Single sgRNA target S17_rep2

description:
Library name: S17_rep2
Alias column: S17_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRaGW_S001_D1_HIV_CalA_GFP_negative

description:
Library name: CRISPRaGW_S001_D1_HIV_CalA_GFP_negative
Pooled CRISPRa genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); CalA; bin: GFP-negative.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 30

description:
Library name: TKI_IO_pre_30
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: metastatic tumor


title: Single sgRNA target S17_rep1

description:
Library name: S17_rep1
Alias column: S17_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: skeletal muscle


title: WT_CDK1as_H3T3ph_5min(biol rep1)_ChIP-Seq

description: Library name: H3T3ph_5min_1

value: lymphoblast


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 29

description:
Library name: TKI_IO_pre_29
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: CRISPRnGW_S009_D3_control_uninfected

description:
Library name: CRISPRnGW_S009_D3_control_uninfected
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: control; bin: uninfected.

value: control condition

value: CRISPRn-gw


title: Single sgRNA target S18_rep1

description:
Library name: S18_rep1
Alias column: S18_rep1
SIQ outcomes for single-sgRNA sites.xlsx

value: 6 weeks

value: Single sgRNA target


title: WT_CDK1as_H3K4me3_30min(biol rep2)_ChIP-Seq

description: Library name: H3K4me3_30min_2


title: Single sgRNA target S16_rep2

description:
Library name: S16_rep2
Alias column: S16_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: CRISPRnGW_S006_D2_control_uninfected

description:
Library name: CRISPRnGW_S006_D2_control_uninfected
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: control; bin: uninfected.


title: CRISPRnGW_S007_D3_HIV_GFP_negative

description:
Library name: CRISPRnGW_S007_D3_HIV_GFP_negative
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-negative.


title: CRISPRnGW_S008_D3_HIV_GFP_positive

description:
Library name: CRISPRnGW_S008_D3_HIV_GFP_positive
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-positive.


title: WT_CDK1as_H3K4me3_15min(biol rep2)_ChIP-Seq

description: Library name: H3K4me3_15min_2


title: WT_CDK1as_H3T3ph_G2(biol rep1)_ChIP-Seq

description: Library name: H3T3ph_G2_1


title: WT_CDK1as_H3K4me3_15min(biol rep1)_ChIP-Seq

description: Library name: H3K4me3_15min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 28

description:
Library name: TKI_IO_pre_28
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: clear cell renal cell carcinoma


title: WT_CDK1as_H3K4me3_7.5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me3_7.5min_2


title: CRISPRnGW_S004_D2_HIV_GFP_negative

description:
Library name: CRISPRnGW_S004_D2_HIV_GFP_negative
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-negative.


title: WT_CDK1as_H3K4me3_30min(biol rep1)_ChIP-Seq

description: Library name: H3K4me3_30min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 27

description:
Library name: TKI_IO_pre_27
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S16_rep1

description:
Library name: S16_rep1
Alias column: S16_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 26

description:
Library name: TKI_IO_pre_26
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S15_rep1

description:
Library name: S15_rep1
Alias column: S15_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S15_rep2

description:
Library name: S15_rep2
Alias column: S15_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me3_5min(biol rep2)_ChIP-Seq

description: Library name: H3K4me3_5min_2


title: CRISPRnGW_S005_D2_HIV_GFP_positive

description:
Library name: CRISPRnGW_S005_D2_HIV_GFP_positive
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-positive.


title: CRISPRnGW_S002_D1_HIV_GFP_positive

description:
Library name: CRISPRnGW_S002_D1_HIV_GFP_positive
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-positive.


title: WT_CDK1as_H3K4me3_7.5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me3_7.5min_1


title: CRISPRnGW_S001_D1_HIV_GFP_negative

description:
Library name: CRISPRnGW_S001_D1_HIV_GFP_negative
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: HIV infection (GFP reporter); bin: GFP-negative.


title: CRISPRnGW_S003_D1_control_uninfected

description:
Library name: CRISPRnGW_S003_D1_control_uninfected
Pooled CRISPRn genome-wide in activated primary human CD4+ T cells; assay: control; bin: uninfected.


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 24

description:
Library name: TKI_IO_pre_24
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Single sgRNA target S13_rep1

description:
Library name: S13_rep1
Alias column: S13_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me3_G2(biol rep1)_ChIP-Seq

description: Library name: H3K4me3_G2_1


title: Single sgRNA target S14_rep2

description:
Library name: S14_rep2
Alias column: S14_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S14_rep1

description:
Library name: S14_rep1
Alias column: S14_rep1
SIQ outcomes for single-sgRNA sites.xlsx


title: WT_CDK1as_H3K4me3_G2(biol rep2)_ChIP-Seq

description: Library name: H3K4me3_G2_2


title: Single sgRNA target S10_rep2

description:
Library name: S10_rep2
Alias column: S10_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: Single sgRNA target S13_rep2

description:
Library name: S13_rep2
Alias column: S13_rep2
SIQ outcomes for single-sgRNA sites.xlsx


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 23

description:
Library name: TKI_IO_pre_23
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 22

description:
Library name: TKI_IO_pre_22
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me3_5min(biol rep1)_ChIP-Seq

description: Library name: H3K4me3_5min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 25

description:
Library name: TKI_IO_pre_25
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: Primary Schlemm's canal cells, siPROX1, replicate 1

city: Chicago

first: Benjamin

middle: R

last: Thomson

state: IL

address: 303 E Superior St. SQ8-500

department: Feinberg Cardiovascular and Renal Research Institute

institute: Northwestern University Feinberg School of Medicine

description: Library name: S68SC-siPROX1-1

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: tab-delimited text file with raw counts for each sample, generated with htseq

source_name: Schlemm's canal endothelium

extract_protocol:
Total RNA was isolated using the RNEasy Mini Kit (Qiagen) according to manufacturer's directions
Libraries were generated by the NUSeq core at Northwestern University using the Illumina TruSeq kit

value: Schlemm's canal endothelium

value: Primary human endothelial cells


title: Primary Schlemm's canal cells, siPROX1, replicate 3

description: Library name: S68SC-siPROX1-3


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 18

description:
Library name: TKI_IO_pre_18
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)

value: primary tumor


title: Primary Schlemm's canal cells, siControl, replicate 3

description: Library name: S68SC-siCtr-3

value: siControl


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 21

description:
Library name: TKI_IO_pre_21
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me2_15min(biol rep1)_ChIP-Seq

description: Library name: H3K4me2_15min_1


title: WT_CDK1as_H3K4me2_30min(biol rep1)_ChIP-Seq

description: Library name: H3K4me2_30min_1


title: ccRCC, pretreatment tumor, TKI/IO treatment group, sample 16

description:
Library name: TKI_IO_pre_16
Library name is used as column ID (sample) and NCBI Entrez ID is used as row ID (gene) in both BulkRNAseq.raw.maskid.txt (raw read counts) and BulkRNAseq.BatchCorrected.fpkm.maskid.txt (batch corrected FPKM values)


title: WT_CDK1as_H3K4me2_15min(biol rep2)_ChIP-Seq

description: Library name: H3K4me2_15min_2