title: Type 2 diabetes patient 17

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_8880549_00749


title: Type 2 diabetes patient 36

status: Public on Apr 12 2023

type: genomic

city: Abu Dhabi

first: Habiba

last: Al Safar

state: Abu Dhabi

address: Shakhbout Bin Sultan St

department: Biomedical Engineering

country: United Arab Emirates

institute: Khalifa University

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_8798087_00726

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays.After overnight incubation at 48˚C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XStain BeadChip solution 4 (XC4) and wash buffer (PB1), dried for 1 hour and scanned on iScan System microarray scanner (Illumina).

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Type 2 diabetes

label_protocol: 300 ng of genomic DNA was amplified in an overnigh reaction at 37 ˚C using multi-sample amplification mix 1 (MA1), multi-sample amplification mix 2 (MA2), and multi-sample amplification master mix (MSM). After incubation, the amplified DNA was fragmented with fragmaentation solution (FMS), percipitated with 2-propanol and percipitation solution (PM1), and resuspended in resuspension, hybridization, and wash solution (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using the Qiagen DNA extraction kit per the manufacturer’s instructions.

tag: age

tag: gender

value: Male

tag: bmi

tag: complication type

value: No complications

tag: disease state

value: Type 2 diabetes


title: Type 2 diabetes patient 14

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_10566091_00856

value: Female


title: Type 2 diabetes patient 15

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_8904171_00750

value: Retinopathy


title: Type 2 diabetes patient 35

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_124551696_00735


title: Type 2 diabetes patient 11

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_10500014_00854

value: Retinopathy, Nephropathy


title: Type 2 diabetes patient 12

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_2463938_00855

value: Cardiovascular complications


title: Type 2 diabetes patient 9

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_7121831_00853


title: Type 2 diabetes patient 13

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_5627869_00744

value: Neuropathy


title: Type 2 diabetes patient 8

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_5676711_00865


title: Type 2 diabetes patient 10

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_5570352_00866

value: Nephorpathy


title: Type 2 diabetes patient 5

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_31962360_00851


title: Type 2 diabetes patient 6

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_5554004_00863


title: Type 2 diabetes patient 3

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_7157151_00850


title: Type 2 diabetes patient 4

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_2683253_00862


title: Type 2 diabetes patient 2

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_2440156_00861


title: Type 2 diabetes patient 1

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_2647702_00849


title: diaphragm, mechanical ventilation with PEEP application, rep1

type: SRA

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

country: China

institute: School of Pharmaceutical Sciences, Jilin University

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the oryctolagus cuniculus(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/003/625/GCF_000003625.3_OryCun2.0) reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: OryCun2.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: diaphragm

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

tag: tissue

value: diaphragm

tag: treatment


title: diaphragm, mechanical ventilation without PEEP application, rep3

value: mechanical ventilation


title: diaphragm, control group, rep2

value: control


title: diaphragm, control group, rep1


title: diaphragm, mechanical ventilation with PEEP application, rep3


title: diaphragm, control group, rep3


title: diaphragm, mechanical ventilation without PEEP application, rep2


title: diaphragm, mechanical ventilation without PEEP application, rep1


title: diaphragm, mechanical ventilation with PEEP application, rep2


title: Bead1, KTRs, scRNA-seq

city: seoul

first: Hyunjoo

last: Bae

address: 222, Banpo-daero, Seocho-gu

department: Biomedical Science, Laboratory Medicine

country: South Korea

institute: The Catholic University of Korea, College of Medicine, Seoul St. Mary’s hospital

description: Tag 01, 02, 04 : TOT, scRNA-seq

library_source: transcriptomic single cell

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Supplementary files format and content: Tab-separated values files

source_name: peripheral blood

extract_protocol:
PBMCs from each patient were isolated using Ficoll-Paque Plus (GE Healthcare). Collected cells were cryopreserved in cryopreservation medium containing 90% fetal bovine serum (FBS; Hyclone Laboratories Inc.) and 10% dimethyl sulfoxide (Sigma-Aldrich) and stored in liquid nitrogen. Banked PBMCs were thawed in a 37℃ water bath and transferred to tubes containing warm complete culture medium (RPMI 1640). Cells were centrifuged at 400×g for 5 minutes before red blood cell (RBC) lysis treatment. After RBC lysis (VersaLyse Lysing Solution), waiting for 5 minutes at room temperature, centrifugation (400×g for 5 minutes, room temperature) was performed and cell pellet was resuspended in PBS. After centrifugation again, cell pellet was resuspended in cold sample buffer.
Libraries were prepared using mRNA Targeted, Sample Tags, and BD™ AbSeq Library Preparation (document 23-21335-00) with the BD Rhapsody™ Targeted mRNA and AbSeq Amplification Kit. mRNA, sample tag, and Abseq encoded in Cell Capture Beads were amplified by PCR1. Sample Tag and AbSeq PCR1 products were separated from mRNA target PCR1 products for double-sided size selection. The mRNA target was amplified by PCR2, the PCR2 product was purified and concentrated by index PCR to generate an mRNA target library. Aliquots of AbSeq/Sample Tag PCR1 product were diluted prior to index PCR of AbSeq PCR1 product. The AbSeq PCR1 product requires only index PCR. Undiluted PCR1 product was subjected to PCR2 amplification and index PCR for the Sample Tag library. Index PCR products were purified and quantified according to the qPCR quantification protocol.

value: peripheral blood

tag: cell type

value: peripheral blood mononuclear cell

tag: group

value: TOT, STA, BPAR (mixed samples)

tag: sample tag


title: Bead3, KTRs, scRNA-seq

description: Tag 09 : TOT, scRNA-seq

value: Tag 09:TOT


title: Bead2, KTRs, scRNA-seq

description: Tag 05, 06 : BRAR, Tag 07, 08 : STA, scRNA-seq

value: Tag 05, 06:BRAR, Tag 07, 08:STA


title: Type 2 diabetes patient 7

description:
Genomic DNA extracted from the blood of type 2 diabetes patients was genotyped using Infinium Exome BeadChip (Illumina).
DXB_DDC_21_8822875_00852

value: Male


title: Bead0, KTRs, scRNA-seq


title: mESC TFIIA IAA run9_rep2

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: Life Science Institute

description:
TFIIA_Ctrl_vs_IAA_promoters_filtered.xlsx
TFIIA_vs_Pol2_promoters_filter50_pol2.xlsx
Taf4_vs_TFIIA_promoters_filter50x50.xlsx

library_source: genomic

data_processing:
library strategy: CUT&Tag
Quality Assurance was done using FastQC to check metrics
CUT&Tag reads were aligned to the mm10, k12, and s2 genome using bowtie2 with parameters: --no-unal –local –very-sensitive-local –no-discordant –no-mixed –contain –overlap –dovetail –phred33 -I 10 -X 9999 with PCR duplicates being kept
bigwig generation was done using the E. Coli/ s2 normalization factor determined from Bowtie2 mapping
Heatmaps, IGV tracks, and other downstream analysis were generated from bigwig files using Deeptools/ComputeMatrix
Read counts were generated using featureCounts (for DGE analysis) or bedtools multicov (for scatterplot analysis). DGE read counts were normalized to TMM and Scatterplot read counts were normalized to either the E. Coli scaling factor or s2 scaling factor
Assembly: mm10 and k12
Supplementary files format and content: txt files were generated for read counts that were either normalized to the E. Coli scaling factor or S2 Factor, were summed up or averaged and  log transformed when comparing two different antibodies

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: For all experiments, the mouse ES cell line C64 was used which is a CRISPR genetically modified JM8.N4 cell line that contains an AID tag for TBP. Cells were cultured on gelatin-coated plates in ESC media (Knockout DMEM, 15% FBS, 0.1mM MEM non essential amino acids, 2mM GlutaMAX, 0.1mM 2-mercaptoethanol and 1000 units/ml of ESGRO. ES cells are fed daily, cultured at 37C in a 5% CO2 incubator and passaged every two days via trypsinization.)

extract_protocol:
Extract protocol was done following the CUT&Tag published protocol where cells and DNA were sheared using 10uL 0.5M EDTA, 3uL 10% SDS, 2.5uL 20mg/mL Proteinase followed by phenol chloroform isoamyl extracted
Librarires were prepared following the CUT&Tag protocol. Briefly 21uL(out of 30uL) was used with 2uL Universal i5 primer (10uM) +2uL uniquely barcoded i7 primers (10uM) using a different unique barcode for each sample. 25UL of NEBNext HiFi 2x PCR Master mix (NEB M0541L) was used for the PCR reaction following the PCR protocol for CUT&Tag using 12 cycles. Library was cleaned up using Ampure XP beads using 1.1x volume and samples were pooled by volume and bead cleaned again before sequencing

treatment_protocol: C64 cells were treated with IAA (6 hours, 500uM final IAA concentration), Heat shock (30 minutes at 42C), Heat shock + IAA (6 hours, 500uM final IAA concentration followed by an extra 30 minutes of HS + IAA), Retinoic Acid (16 hours, 25uM final RA concentration), Retinoic Acid + IAA (16 hours 25uM final RA concentration and 16 hours 500uM final IAA concentration)

tag: cell line

tag: cut&tag antibody

value: SCB – sc -25365

value: IAA treated


title: mESC TFIIA WT run9_rep1

value: untreated


title: mESC TFIIA IAA run9_rep1


title: mESC TAF1 IAA run8_rep1

description:
Taf1_Ctrl_vs_IAA_promoter_filtered.ods
Taf1_vs_Pol2_promoters_filter50_pol2.xlsx

value: CST - D6J8B


title: mESC TFIIA WT run9_rep2


title: mESC RNA Pol III IAA run8_rep2

value: SCB – sc-21754


title: mESC TAF1 WT run8_rep1


title: mESC RNA Pol III WT run8_rep2


title: mESC B8 RNA Pol II WT run8_rep2

description:
featurecounts_pol2_B8_ctrl_iaa_bam_6hours.txt
featurecounts_pol2_ctrl_B8_vs_C64_bam.txt

value: CST – D1G3K


title: mESC TAF1 WT run8_rep2


title: mESC B8 RNA Pol II IAA run8_rep1

description: featurecounts_pol2_B8_ctrl_iaa_bam_6hours.txt


title: mESC B8 RNA Pol II WT run8_rep1


title: mESC RNA Pol III WT run8_rep1


title: mESC B8 RNA Pol II IAA run8_rep2


title: mESC B8 IgG WT run7_rep1

value: Abcam ab46540


title: mESC B8 HA WT run7_rep2

value: EpiCypher 13-2010


title: mESC B8 HA WT run7_rep1


title: mESC TAF1 IAA run8_rep2


title: mESC B8 IgG WT run7_rep2


title: mESC RNA Pol III IAA run8_rep1


title: mESC B8 RNA Pol II IAA run6_rep2


title: mESC B8 RNA Pol II WT run6_rep2


title: mESC B8 TBP IAA run6_rep1

value: Abcam – ab51841


title: mESC B8 RNA Pol II IAA run6_rep1


title: mESC B8 TBP IAA run6_rep2


title: mESC B8 TBP WT run6_rep1


title: mESC B8HA RNA Pol II IAA run6_rep1


title: mESC B8HA TBP WT run6_rep1


title: mESC B8HA RNA Pol II WT run6_rep1


title: mESC B8HA RNA Pol II WT run6_rep2


title: mESC B8HA TBP WT run6_rep2


title: mESC B8HA HA IAA run6_rep2


title: mESC B8HA TBP IAA run6_rep1


title: mESC B8HA TBP IAA run6_rep2


title: mESC B8HA HA WT run6_rep1

description:
HA-TRF2_vs_Pol2_promoters.xlsx
HA-TRF2_vs_TBP_promoters.xlsx


title: mESC TAF4 IAA run6_rep2

description:
Taf4_Ctrl_vs_IAA_promoters_filtered.xls
Taf4_vs_Pol2_promoters_filter50_pol2.xlsx
Taf4_vs_TFIIA_promoters_filter50x50.xlsx


title: mESC TAF4 WT run6_rep2


title: mESC TAF4 IAA run6_rep1


title: mESC B8 TBP WT run6_rep2


title: mESC B8HA HA WT run6_rep2


title: mESC B8 RNA Pol II WT run6_rep1


title: mESC TAF4 WT run6_rep1


title: mESC B8HA HA IAA run6_rep1


title: mESC TAF1 IAA run6_rep2


title: mESC TAF1 IAA run6_rep1


title: mESC IgG WT run2_rep1


title: mESC IgG WT run2_rep2


title: mESC IgG WT run3_rep2


title: mESC TBP Retinoic Acid run3_rep2

value: retinoic acid treated


title: mESC TBP Retinoic Acid + IAA run3_rep1

value: retinoic acid + IAA treated


title: mESC TBP Retinoic Acid + IAA run3_rep2


title: mESC TAF1 WT run6_rep1


title: mESC B8HA RNA Pol II IAA run6_rep2


title: mESC TBP Retinoic Acid run3_rep1


title: mESC TBP Heat Shock + IAA run2_rep2

value: heat shock + IAA treated


title: mESC TBP Heat Shock run2_rep1

value: heat shock treated


title: mESC TBP IAA run3_rep2


title: mESC TBP IAA run2_rep2


title: mESC RNA Pol II Retinoic Acid run3_rep1

description:
featurecounts_pol2_ctrl_vs_ra_v2.txt
featurecounts_pol2_ra_vs_raiaa_v2.txt


title: mESC TBP WT run2_rep1

description:
HA-TRF2_vs_TBP_promoters.xlsx
TBP_Ctrl_vs_IAA_promoters_filtered.xls


title: mESC RNA Pol II Retinoic Acid + IAA run3_rep2


title: mESC RNA Pol II Retinoic Acid + IAA run3_rep1


title: mESC TAF1 WT run6_rep2


title: mESC TBP Heat Shock run2_rep2


title: mESC RNA Pol II Retinoic Acid run3_rep2


title: mESC TBP Heat Shock + IAA run2_rep1


title: mESC RNA Pol II Heat Shock + IAA run2_rep1


title: mESC TBP WT run3_rep2


title: mESC TBP WT run3_rep1


title: mESC TBP IAA run3_rep1


title: mESC TBP IAA run2_rep1


title: mESC RNA Pol II Heat Shock + IAA run2_rep2


title: mESC RNA Pol II Heat Shock run2_rep1

description:
featurecounts_pol2_ctrl_vs_hs_v2.txt
featurecounts_pol2_hs_vs_hsiaa_v2.txt


title: mESC RNA Pol II IAA run3_rep2

description: featurecounts_pol2_ctrl_vs_iaa_16hours.txt


title: mESC RNA Pol II IAA run2_rep2

description:
Pol2_con_vs_IAA_promoters_filtered.xls
Taf1_vs_Pol2_promoters_filter50_pol2.xlsx
Taf4_vs_Pol2_promoters_filter50_pol2.xlsx
TFIIA_vs_Pol2_promoters_filter50_pol2.xlsx
featurecounts_pol2_ctrl_vs_iaa_6hours_v2.txt


title: mESC RNA Pol II IAA run3_rep1


title: mESC RNA Pol II Heat Shock run2_rep2


title: mESC RNA Pol II WT run2_rep2

description:
HA-TRF2_vs_Pol2_promoters.xlsx
Pol2_con_vs_IAA_promoters_filtered.xls
Taf1_vs_Pol2_promoters_filter50_pol2.xlsx
Taf4_vs_Pol2_promoters_filter50_pol2.xlsx
TFIIA_vs_Pol2_promoters_filter50_pol2.xlsx
featurecounts_pol2_ctrl_B8_vs_C64_bam.txt
featurecounts_pol2_ctrl_vs_hs_v2.txt
featurecounts_pol2_ctrl_vs_iaa_6hours_v2.txt


title: mESC RNA Pol II WT run3_rep2

description:
featurecounts_pol2_ctrl_vs_iaa_16hours.txt
featurecounts_pol2_ctrl_vs_ra_v2.txt


title: mESC RNA Pol II IAA run2_rep1


title: mESC RNA Pol II WT run3_rep1


title: mESC RNA Pol II WT run2_rep1


title: mESC TBP WT run2_rep2


title: CUT&RUN - WT72_d2 - H3K27me3

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
CUTeRUN_d2_WT72_H3K27me3.stringent.bed
d2_WT_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed

data_processing:
CUT&RUN reads were first trimmed on quality (PHRED > 20) and length (> 20 bp) using TrimGalore! in paired-end mode. Trimmed reads were aligned to GENCODE mm10 GRCm38.p6 using bowtie with specific settings “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700”, specifically for CUT&RUN (33), and deduplicated with Picard MarkDuplicates (v2.23.0) using default settings. The duplication rate was < 1%. SEACR was used to call peaks, using stringent mode and normalized against IgG R (v4.0.5) (44). Diffbind (v3.0.15) was used to define differentially enriched regions using default settings. Genes were associated with differentially enriched H3K27me3 regions using the rGREAT (v1.22.0) package. For visualization, bam files of merged replicates were made into bigwig files using BamCoverage (v3.4.3) with settings “--binSize 20 --smoothLength 60 --minMappingQuality 3 --normalizeUsing BPM”. Profile plots and heatmaps were made uinsg DeepTools (v3.4.3).
Assembly: mm10
Supplementary files format and content: .bed file with called peaks
Supplementary files format and content: .bigwig file for pooled reads
Supplementary files format and content: .bigwig file for sample
Supplementary files format and content: .bed file for loss-in-KO
Supplementary files format and content: .bed file for loss-gain-in-KO
Supplementary files format and content: .bed file for gain-in-KO
Supplementary files format and content: .bed file for gain-in-KO d5+X
Library strategy: CUT&RUN

source_name: mESC B6129S6F1 Tet1<tm1Koh>

growth_protocol: Anterior neural progenitor differentiation was performed as previously described (Cruz-Molina et al., 2017; Gouti et al., 2014; Luo et al., 2020). Feeder depleted serum cultured ESCs were plated on gelatin coated plates at 10,000 cells/cm2 (90,000 cells per well in a 6-well plate) in advanced N2B27 defined media compromising a 1:1 mix of 1:1 DMEM/F12 (Invitrogen, 12634-010, Invitrogen) and Neurobasal medium (Invitrogen, 10888-022) supplemented with 0.5x B27 without vitamin A (Invitrogen, 12587-010), 0.5x N2 (Invitrogen, 17502-048), 2 mM L-glutamine (Invitrogen, 25030-024), 40 mg/ml BSA fraction V (Invitrogen, 15260037), 0.1 mM 2-mercaptoethanol (Invitrogen, 31350-010) and 100:100 units:µg/ml penicillin:streptomycin (Sigma-Aldrich, P4333; or Gibco, 15140122). Cells were supplemented with 10 ng/ml bFGF (Cat#100-18C, Peprotech) from day 0 until day 3. At day 3 the medium was changed to medium without bFGF. In some experiments, 5 µM of the Wnt inhibitor XAV939 (Sigma-Aldrich, X3004), 2.5 µM of the TGF-β receptor inhibitor SB431542 (Sigma-Aldrich, S4317), 0.1 µM BMP inhibitor LDN193189 (Sigma-Aldrich, SML0559), 0.3 µM or 3 μM GSK3 β inhibitor CHIR99021 (Axon Medchem BV,1408), 5 or 25 ng/ml of Activin A (Peprotechm 120-14E), or equivalent amount of DMSO (vehicle control) were added from day 2 until day 5. The medium was changed every day during differentiation, except on day 1. At day 4, 1.5x amount of medium was added. The experimental end-point is day 5.

extract_protocol: CUT&RUN was performed using the CUTANATM KIT (Epicypher, 14-1048) according to the manufacturer’s instructions with minor modifications (33,34). Briefly, 5 x 105 cells were collected as a single cell suspension and washed three times with 100 μl/sample wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and 1 Roche complete tablet/50ml). Cells were then bound to activated Concanavalin A beads and incubated for 10 minutes at RT, followed by incubation with 0.5 μg anti-H3K27me3 (Invitrogen, MA5-11198) antibody or IgG (Epicypher, 18-1401) diluted in antibody buffer on a nutator overnight at 4°C. After 3 washes of magnet-bound beads with digitonin buffer, pAG/MNase was added and incubated for 10 minutes at RT, washed and resuspended in digestion buffer for a 30-minute incubation on ice. The reaction was stopped by addition of STOP buffer and incubated for 10 minutes at 37 °C. The supernatant containing enriched DNA was then extracted using the supplied DNA Clean-up Columns. Libraries were prepared using the NEBNext® Ultra II DNA library Prep Kit for Illumina (New England Biolabs®, NEB E7645L) according to Epicypher’s instructions, and amplified by PCR using NEBNext Dual Index Primers (New England Biolabs, E6440S) with the following settings: 98°C 45 sec; 14 x 98°C 15 sec, 60°C 10 sec; 72°C 1 min. Library concentration was quantified using Qubit HS dsDNA Quant kit (ThermoFisher, Q32851).Quality and size distribution were further assessed on an Agilent 2100 Bioanalyzer using a High Sensitivity DNA Analysis Kit (Agilent, 5067-4626). Libraries were diluted to 4nM and pooled together for PE50 sequencing on NextSeq500 or NextSeq2000 for minimally 5 million reads per sample.

value: mESC B6129S6F1 Tet1<tm1Koh>

value: mESC

tag: genotype

value: WT

tag: chip antibody


title: CUT&RUN - WT72_d0 - IgG

description:
CUTeRUN_d0_WT72_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed

value: IgG


title: CUT&RUN - WT72_d0 - H3K27me3

description:
CUTeRUN_d0_WT72_H3K27me3.stringent.bed
d0_WT_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - WT70_d0 - IgG

description:
CUTeRUN_d0_WT70_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - WT70_d2 - IgG

description:
CUTeRUN_d2_WT70_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - KO25_d2 - H3K27me3

description:
CUTeRUN_d2_WT70_H3K27me3.stringent.bed
d2_WT_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed

value: Tet1 KO


title: CUT&RUN - WT70_d0 - H3K27me3

description:
CUTeRUN_d0_WT70_H3K27me3.stringent.bed
d0_WT_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - KO25_d2 - IgG


title: CUT&RUN - WT70_d2 - H3K27me3


title: CUT&RUN - KO25_d0 - H3K27me3


title: CUT&RUN - KO15_d2 - IgG

description:
CUTeRUN_d2_KO15_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - KO15_d0 - H3K27me3

description:
CUTeRUN_d0_KO15_H3K27me3.stringent.bed
d0_KO_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - KO15_d0 - IgG

description:
CUTeRUN_d0_KO15_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - CM59_d2 - IgG

description:
CUTeRUN_d2_CM59_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed

source_name: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

value: mESC B6129S6F1 Tet1<tm1Koh>; CRISPR HDR

value: Tet1 MUT


title: CUT&RUN - KO15_d2 - H3K27me3

description:
CUTeRUN_d2_KO15_H3K27me3.stringent.bed
d2_KO_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - CM59_d0 - IgG

description:
CUTeRUN_d0_CM59_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - CM59_d0 - H3K27me3

description:
CUTeRUN_d0_CM59_H3K27me3.stringent.bed
d0_CM_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - CM40_d0 - IgG

description:
CUTeRUN_d0_CM40_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - CM40_d2 - H3K27me3

description:
CUTeRUN_d2_CM40_H3K27me3.stringent.bed
d2_CM_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: NET-seq hs rep2

data_processing:
library strategy: NET-seq
NET-seq data was processed as described in Mayer et al. (2015). Reads were trimmed and aligned using STAR (v. 2.4.0). Reverse transcription mispriming events, PCR duplication events, and splicing intermediates were removed using custom Python scripts provided by the Churchman group (https://github.com/churchmanlab).
The bam files of biological replicates were merged and normalized by subsampling each sample by the number of aligned Drosophila reads (used as spike-in) across all samples using SAMtools.
BedGraph coverage files for gene plots were generated from normalized bam files with a custom Python script provided by the Churchman group (https://github.com/churchmanlab) and visualized by IGV.
Bigwig coverage files for heatmaps and TSS plots were generated using deepTools with the following parameters: -bs 1 -- Offset 1
Heatmaps and TSS plots were generated using deepTools with the following parameters: -a 1000 -b 1000 -bs 10 followed by filterValues --max 50.
Read counts across tRNAs were generated from normalized bam files using bedtools.
Read counts used in edgeR analysis were generated from bam files using featureCounts.
Assembly: mm10/dm6
Supplementary files format and content: Matrix table with raw gene counts for every gene for control and IAA-treated samples
Supplementary files format and content: Matrix table with normalized gene counts for tRNAs for control and IAA-treated samples

source_name: embryonic stem cell

growth_protocol: For all experiments, the mouse ES cell line C64 was used. C64 is a CRISPR modified JM8.N4 cell line that contains an AID tag at the TBP locus. Cells were cultured on gelatin-coated plates in ESC media (Knockout DMEM, 15% FBS, 0.1 mM MEM non-essential amino acids, 2mM Glutamax, 0.1 mM 2-mercaptoethanol, and 1000 units/mL of ESGRO. ES cells are fed daily, cultured at 37C in a 5% CO2 incubator and passaged every two days by trypsinization.

extract_protocol:
Nascent RNA extraction was performed as described in Mayer and Churchman (2016). Around 10 million cells were collected per sample, and a 3% spike-in (by cell count) of Drosophila S2 cells was added per sample. Elongating Pol II-associated chromatin was collected by cellular fractionation, and RNA from the insoluble chromatin was extracted with Trizol for library preparation.
NET-seq library preparation was performed as described in Mayer and Churchman (2016). Briefly, RNA was ligated with barcoded DNA linker and subjected to alkaline fragmentation. Fragmented RNA was size selected, purified, and reverse transcribed as first strand cDNA. cDNA was size selected, purified, and circularized. Circularized cDNA containing sequences of a subset of sequenced snRNAs, snoRNAs, and rRNAs were specifically depleted using biotinylated DNA oligos before being amplified with uniquely barcoded sequencing primers. Resulting NET-seq libraries were purified before sequencing.

treatment_protocol: Cells were treated with IAA (6 hours, 500 uM final conc.), heat shock (30 mins at 42C), and heat shock + IAA (6 hours, 500 uM final conc, followed by 30 minutes of heat shock), with two biological replicates for each treatment.

tag: strain

value: embryonic stem cell

value: AID-TBP

value: heat-shocked

tag: molecule subtype

value: nascent RNA


title: CUT&RUN - CM40_d2 - IgG

description:
CUTeRUN_d2_CM40_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: CUT&RUN - WT72_d2 - IgG

description:
CUTeRUN_d2_WT72_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: NET-seq iaahs rep2

value: IAA-treated + heat-shocked


title: NET-seq ctrl rep2

description:
netseq_dge_matrix.txt
netseq_counts_tRNAs.txt

value: untreated


title: NET-seq hs rep1


title: NET-seq iaahs rep1


title: CUT&RUN - CM40_d0 - H3K27me3

description:
CUTeRUN_d0_CM40_H3K27me3.stringent.bed
d0_CM_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: NET-seq iaa rep1

value: IAA-treated


title: NET-seq ctrl rep1


title: CUT&RUN - KO25_d0 - IgG

description:
CUTeRUN_d0_WT70_H3K27me3.stringent.bed
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: MAS patient with ID 200785

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

description:
ScRNASeq-MetaData.xlsx
Patient_Clinical-MetaData.xlsx

data_processing:
Raw FASTQ files were aligned to hg19 reference genome and transcriptome and provided as input for CellRanger version 3 to generate counts matrices for all samples. Seurat integrated analysis was performed on the counts matrices using Seurat version 3 for batch effect correction. We implemented the default VST approach for identifying highly variable genes from each sample and the Canonical correlation approach (CCA) approach on the first 50 CCA dimensions to integrate the samples. We followed the author-recommended workflow to scale the integrated data and performed principal component analysis (PCA) on first 50 dimensions. UMAP was determined from the first 36 PCs, which captured the majority of true signal, based on the elbow plot.  We derived 30 clusters using the cluster resolution set to 0.6. The marker genes of each cluster were determined using the FindAllMarkers function as per Seurat documentation. Unique marker genes for each cluster were selected based on maximum average log fold change value for a gene for a given cluster. Clusters were annotated using Azimuth, which uses an annotated reference dataset  of human PBMCs (Stuart et al., 2019) to automate the processing, analysis, and interpretation of single-cell RNA-seq data with a 'reference-based mapping' pipeline. Count matrices of each sample was provided as input to Azimuth and the default PBMC reference dataset, with 30 clusters, provided on Azimuth’s web application was used. The annotations were refined based on the cluster’s unique marker genes.
Assembly: hg19
Supplementary files format and content: HDF5 sparse matrices and Excel workbooks

source_name: PBMCs

extract_protocol:
sample collection protocol:
This study was approved by the CCHMC institutional review board (IRB# 2018-2408) and written informed consent was obtained from each parent or guardian, and child assent was obtained where appropriate. Clinical and laboratory features were obtained from the electronic medical record using a standardized case report form. All patients were diagnosed with SJIA based on the International League of Associations for Rheumatology (ILAR) criteria (Petty et al., 2004); however, for newly diagnosed patients samples were obtained and treatment initiated with a disease duration <6 months, using the operational definition of SJIA (DeWitt et al., 2012). Inactive disease was defined based on the Wallace criteria (Wallace et al., 2004); conversely patients were considered to have active SJIA if they had any active clinical features including arthritis, rash, fever, adenopathy, hepatosplenomegaly, or elevated c-reactive protein or erythrocyte sedimentation rate. Patients were diagnosed with MAS based on diagnosis of the treating physician. Patients were considered to have SJIA-LD if they had both clinical and radiographic features of lung disease based on definition of probable or definite SJIA-LD (Erkens et al., 2021).
cell isolation protocol:
Frozen PBMCs were thawed and washed twice with PBS. Dead cells were removed with dead cell removal kit following the manufacturer’s instructions (Miltenyi Biotec, Bergisch Gladbach, Germany)), and then resuspended at 700-1,200 cells/μl in PBS (total count 12,800 cells). Samples were then sequenced with 10x Genomics (Pleasanton, CA, USA), version Chromium NextGEM (Chemistry: 3’v3 Assay).
10x Genomics
Chromium NextGEM
Chemistry: 10x Genomics Chromium 3' v3 Assay

tag: age (yrs)

tag: disease subtype

value: MAS


title: CUT&RUN - CM59_d2 - H3K27me3

description:
CUTeRUN_d2_CM59_H3K27me3.stringent.bed
d2_CM_H3K27me3.merged.bw
H3K27me3.loss-loss-in-KO.bed
H3K27me3.loss-gain-in-KO.bed
H3K27me3.gain-gain-in-KO.bed
H3K27me3.gain-in-KO_d5_X.bed


title: MAS patient with ID 2001020


title: LungDisease patient with ID 2001208

value: Lung disease


title: LungDisease patient with ID 200970


title: LungDisease patient with ID 200622


title: LungDisease patient with ID 200758 from a late timepoint


title: Inactive patient with ID 200641

value: Inactive SJIA


title: Inactive patient with ID 200594


title: LungDisease patient with ID 200396


title: NET-seq iaa rep2


title: Inactive patient with ID 200812


title: Control with ID 200967

value: Control


title: Control with ID 200657


title: Control with ID 200974


title: Active patient with ID 2001087

value: Active SJIA (changed, was before inactive)


title: Active patient with ID 2001295

value: Active SJIA


title: Inactive patient with ID 200353


title: Active patient with ID 200805


title: Active patient with ID 200673


title: Active patient with ID 200794


title: Active patient with ID 2001056


title: LungDisease patient with ID 200965


title: HD

city: Pamplona

first: Miren

last: Lasaga

address: Av. de Pío XII, 55

country: Spain

institute: CIMA

data_processing:
Basecalls performed CellRanger version 3.0.1
Reads were aligned to the hg38 genome assembly using CellRanger version 3.0.1
Genome_build: hg 38
Supplementary_files_format_and_content: raw data matrices for SC analysis

source_name: Healthy donor BM CD34+ cells

extract_protocol:
BM aspirate was sequenced in fresh.NEXTGEM Single Cell 3' Reagent Kits v3.1 (10X Genomics) according to the manufacturer's instructions. Between 2.000 and 6.000 CD34+ cells were loaded at a concentration of 700-1,000 cells/µL on a Chromium Controller instrument (10X Genomics)
scRNA libraries were prepared for sequencing using standard 10X protocols

treatment_protocol: Fanconi patients were treated with gene therapy

value: BM

value: CD34+ cell

value: Untreated


title: FA-02008

source_name: Fanconi patient BM CD34+ cells

value: Gene therapy


title: LungDisease patient with ID 200758 from an early timepoint


title: FA-02004


title: FA-02006


title: Inactive patient with ID 200593


title: Control with ID 200609


title: Control with ID 200637


title: NC10MEP

city: Tianjin

first: Coral

last: Tong

address: 288 Nanjing Rd, Heping

institute: Institute of Hematology & Blood Disease Hospital

data_processing:
remove low-quality reads and adapters by trimmomatic
aligning by hisat2
mark and remove duplicates by Picard
quantification by stringtie
Genome_build: hg38(gencode v27)
Supplementary_files_format_and_content: csv

molecule: polyA RNA

growth_protocol: patient samples

extract_protocol:
BMMNCs were stained with a lineage-marker cocktail (biotinylated anti-CD2, -CD3, -CD11b, -CD14, -CD15, -CD16, -CD19, -CD56, -CD123, and -CD235a) and subsequently magnetically labeled with Anti-Biotin MicroBeads (Miltenyi Biotec). Lineage-negative stem and progenitor cells (Lin- cells) were obtained by depleting the magnetically-labeled cells after passing through LS columns (Miltenyi Biotec). Lin- cells were stained with antibodies of PE-cy7-conjugated anti-CD38 (BD Biosciences), APC-conjugated anti-CD34 (BD Biosciences), Percp-cy5-conjugated anti-CD45RA (BD Biosciences) and APC-cy7-conjugated anti-CD123 (BD Biosciences). HSCs (CD34+CD38-CD45RA-CD123-) and MEPs (CD34+CD38+CD45RA-CD123-) were sorted with an Aria III instrument (BD Biosciences)
Briefly, cells were lysed in lysis buffer (Novogene), and the direct first-strand cDNA was synthesized from polyA-selected RNA with a SMARTer® Ultra Low RNA Kit for Illumina® Sequencing (Clontech) (Cat. #. 634888). cDNAs were purified using AMPure XP beads, followed by LD-PCR, to yield the full-length first-strand cDNA. Double-stranded cDNA was synthesized and amplified with an Advantage® 2 PCR kit. After generating the sequencing libraries using the NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: no treatment

tag: sample type

value: healthy donor


title: NC11MEP


title: NC1MEP


title: NC3MEP


title: NC2MEP


title: ET12MEP

value: essential thrombocythemia patient


title: NC9MEP


title: NC8MEP


title: ET11MEP


title: ET7MEP


title: Active patient with ID 200704


title: ET8MEP


title: NC7MEP


title: ET10MEP


title: ET6MEP


title: ET4MEP


title: ET3MEP


title: ET2MEP


title: ET1MEP


title: PV9MEP

value: polycythemia vera patient


title: PV7MEP


title: PV8MEP


title: PV6MEP


title: PV5MEP


title: ET9MEP


title: PV3MEP


title: PV4MEP


title: PV2MEP


title: PV1MEP


title: RNA sequencing of wild-type K562 cells [K562_DMSO_Rep3]

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: Unstranded mRNA library

data_processing:
Sequencing reads were demultiplexed using the bcl2fastq software (Illumina). For calculating TPM of genes, sequencing reads from the unstranded RNA libraries were aligned to the GRCh38 reference genome (Gencode V43) using Salmon (v1.9.0). For the CRISPRoff experiment, reads were aligned to the GRCh38 reference genome and counted against all Ensembl genes using STAR (2.7.6a). Raw counts were analyzed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: K562_WT_TPM.txt contains expression levels of genes in TPM (transcript per million)
Supplementary files format and content: CRISPRoff_RNAseq_count.txt cotains expression levels of genes in raw counts

source_name: RNA sequencing of wild-type K562 cells

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL).

extract_protocol:
Total RNAs were purified from cells using TRIzol LS Reagent (Invitrogen) following manufacturer’s instructions, treated with DNase (QIAGEN or Invitrogen) and cleaned up using RNeasy Mini kit (QIAGEN).
For K562 wild-type cells, 1 ug total RNA (RNA integrity >= 9.7) were used for unstranded mRNA library preparation using the TruSeq RNA Library Prep Kit v2. For the CRISPRoff experiment, 1 ug total RNA (RNA integrity >= 9.9) were used for stranded mRNA library preparation using the Illumina TruSeq® Stranded mRNA Library Prep kit. The RNA libraries were indexed using the Illumina TruSeq RNA UD Indexes.

treatment_protocol: For the CRISPRoff experiment, on Day 0, 2 x 106 clone 5 cells were transfected with CRISPRoff-v2.1 (3,000 ng), pU6-Sp-dual-gRNA (1,000 ng) and pmax-GFP (500 ng, Lonza) using the SF Cell Line 4D-Nucleofector X kit L (Lonza). On Day 2, cells were sorted based on high GFP expression (top 20%) on a flow cytometer and expanded. On Day 11, cells were collected for RNA extraction.

value: lymphoblast

value: Wild type


title: ET5MEP


title: RNA sequencing of wild-type K562 cells [K562_DMSO_Rep1]

description: Unstranded mRNA library


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP123-GFP-neg]

description:
synHEK3 amplicon sequencing library
shrna_freq_table.csv

data_processing:
T7-assisted reporter mapping: Sequencing reads were first demultiplexed using the bcl2fastq software. Under the current library design and sequencing scheme, Read1 started from genomic sequence and extended into the integrated synHEK3 construct, while Read2 contained reporter barcode information. Therefore, 1) for each sequencing read pair, the 16-bp reporter barcode was extracted from Read 2 and attached to the read name of Read 1. 2) Read1 was trimmed using cutadapt (v4.1) with following parameters: --cores=4 --discard-untrimmed -e 0.2 -m 10 -O 8 -a CCCTAGAAAGATAGTCTGCGTAAAATTGACGCATG. The adapter corresponded to the 3’ITR of piggyBac transposon. Since parameter “--discard-untrimmed” was used, only reads spanning insertion junctions were kept and trimmed. 3) Trimmed sequences were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). The “-Y” option was used to enable soft clipping for supplementary alignments. 4) Reads uniquely (without XA:Z tag) and contiguously mapped near putative piggyBac landing pads (TTAA motifs) were kept using samtools (v1.9) and a custom script. 5) Aligned reads were converted to BED format using the sam2bed function in bedops (v2.4.35). Reads aligned to standard chromosomes were kept. 6) Insertion points were calculated for all reads based on strand of alignment. And reads were sorted by the insertion coordinates. 7) The first 8-bp of reads were used as UMIs. A custom script was used to collapse reads at a per-location, per-barcode, per UMI basis. A barcode-location-UMI count table was generated. 8) synHEK3 barcodes <3 Levenshtein Distance at each location were collapsed and barcodes with > 3 UMIs were kept. 9) The count table was converted to a GenomicRanges object in R. Coordinates of the last 4 base pairs of aligned reads were designated as genomic locations of the inserted synHEK3 reporters. 10) “Landing pads” of the mapped synHEK3 reporters were retrieved using the getSeq() function in the BSgenome package. Reporters that didn’t have a TTAA sequence (which could be due to PCR error, mapping error, or the use of non-canonical landing pads) were removed. 11) SynHEK3 barcodes mapped to more than one location were removed.
SynHEK3 amplicon sequencing library: Sequencing reads from the Illumina NextSeq platforms were first demultiplexed using the bcl2fastq software. The 16-bp reporter barcodes were extracted from read and attached to its read name. Sequences around the CRISPR cut site were extracted for all reads. A barcode-editing outcome table was generated. For prime editing experiments, a custom script was used to align sequences to a reference sequence and count mutation frequency for every barcode. For Cas9 mutagenesis analysis, all sequences were aggregated and editing outcomes (alleles) with the highest number of counts were selected. These most frequent alleles were then aligned to reference sequences using needleall with the following parameters: -gapopen 20 -gapextend 0.5 -endopen 20. A custom script was used to annotate the mutational events.
Amplicon sequencing of endogenous genes: Sequencing reads were demultiplexed using the bcl2fastq software (Illumina). A custom script was used to determine frequencies of the introduced substitutions.
Assembly: GRCh38
Supplementary files format and content: T7-500-1_S1_ITR_corrected.txt contains processed, barcode collapsed synHEK3 integration raw counts
Supplementary files format and content: T7-500-1_processed.csv contains fully processed, unique synHEK3 reporters and relevent information
Supplementary files format and content: K562-HEK3-insCTT-DMSO_count.txt contains processed prime editing outcomes of all synHEK3 barcodes
Supplementary files format and content: K562-HEK3-Cas9-Day1-XL281_S68_barcode_edit.txt contains processed Cas9 indel frequency of all synHEK3 barcodes on Day 1
Supplementary files format and content: K562-HEK3-Cas9-Day2-XL281_S70_barcode_edit.txt contains processed Cas9 indel frequency of all synHEK3 barcodes on Day 2
Supplementary files format and content: K562-HEK3-Cas9-Day4-XL281_S72_barcode_edit.txt contains processed Cas9 indel frequency of all synHEK3 barcodes on Day 4
Supplementary files format and content: sg1_top_alleles_count.txt contains Cas9 editing allele count for all synHEK3 barcodes on Day 4
Supplementary files format and content: sg1_top_alleles_info.txt contains annotations of the most frequent alleles for Cas9 editing on Day 4
Supplementary files format and content: CRISPRoff_LRRC8C.csv contains processed prime editing frequencies of synHEK3 reporters in the CRISPRoff experiment, LRRC8C vs. non-targeting control
Supplementary files format and content: CRISPRoff_METTL2A.csv contains processed prime editing frequencies of synHEK3 reporters in the CRISPRoff experiment, METTL2A vs. non-targeting control
Supplementary files format and content: CRISPRoff_USP7.csv contains processed prime editing frequencies of synHEK3 reporters in the CRISPRoff experiment, USP7 vs. non-targeting control
Supplementary files format and content: CRISPRa_CXCR4_IL2RB_EGFR_CDKL5.csv contains prime editing frequencies at endogenous loci before and after CRISPR activation
Supplementary files format and content: shrna_freq_table.csv contains prime editing frequencies of synHEK3 reporters measured in cells transduced with individual shRNAs (GFP positive and GFP negative)

extract_protocol:
gDNA of K562 cells was purified using the DNeasy Blood & Tissue Kit. Alternatively, cells were lysed in a lysis buffer [100 mM Tris-HCl pH8.0, 0.05% SDS and 0.04 mg/mL proteinase K(Thermo Scientific)], and incubated at 50 oC 60 min and 80 oC 30 min.
T7-assisted reporter mapping: gDNA of K562 cells was purified using the DNeasy Blood & Tissue Kit (QIAGEN) and in vitro transcribed with the HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Briefly, each reaction (20 uL) contained 0.3~1 ug gDNA, NTPs (10 mM each) and 2 ul T7 RNA Polymerase Mix. The reaction mixture was incubated at 37 oC for 16 hours. Then, gDNA was digested with 2.5 uL DNase (Qiagen) in a 100 uL reaction at room temperature for 30 min. RNA was extracted with TRIzol LS Reagent (Invitrogen), and aqueous phase was precipitated with 1 volume of isopropanol and 5 ug Glycogen (Invitrogen) at -80 oC for 1 hour. RNA pellet was collected by centrifugation at 21,000 x g at 4 oC for 1 hour. The pellet was washed with 80% ice-cold ethanol and resuspended in 11.5 uL nuclease-free water. For reverse transcription, RNA was incubated with 0.5 uL 100 uM RT primer p6 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNN-3’) and 1 uL 10 mM dNTP at 65 oC for 5 min and cooled on ice. Then, 4 uL 5X RT buffer, 1 uL 100 mM DTT, 1 uL RNaseOUT (40 U/uL) and 1 uL SuperScript IV RT (200 U/uL, Invitrogen) were added and the reaction mixture was incubated at 23 oC for 10 min, 50  oC for 15 min and 80 oC for 10 min. cDNA library was amplified with KAPA2G Robust HotStart polymerase, using primers p7 (5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAAAGGAAGCCCTGCTTCCTCCAGAGGG-3’, 0.5 uM) and p8 (5’- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, 16~18 cycles; and 72 oC 1 min. The PCR product was subjected to double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The resulting product ranged from 200 to 1000 bp. To prepare Illumina sequencing libraries, 5-10 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles. The final PCR product underwent another round of double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The library was sequenced on an Illumina MiSeq in paired-end mode (Read 1: 254 bp; Read2: 55bp).  Amplicon sequencing of synHEK3 reporters: 100~250 ng gDNA or cell lysates were amplified using KAPA2G Robust HotStart ReadyMix with primers p9 (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTACCCCGACCACATGAAGCAGC-3’, 0.5 uM) and p10 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNGACCATGTCATCGCGCTTCTCGT-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 68-N oC 15 s, 72 oC 30 s, for 9 cycles (N was cycle number); 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, for 11 cycles; and 72 oC 1 min. To ensure enough coverage and accurate measurement of editing efficiencies, for the K562 synHEK3 pool, we pooled products from at least 16 PCR reactions. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.   Other amplicon sequencing: Cell lysates were directly used for PCR with the KAPA2G Robust HotStart ReadyMix with primers (0.5 uM each) designed for the endogenous targets. PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 66-N oC 15 s, 72 oC 40 s, for 8 cycles (N was cycle number); 95 oC 15 s, 60 oC 15 s, 72 oC 40 s, for 11 cycles; and 72 oC 1 min. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.

treatment_protocol: T7-assisted reporter mapping: We randomly integrated a complex library of the synHEK3 reporters into a monoclonal K562 cell line constitutively expressing the PE2 prime editor. We further bottlenecked the pool to ~500 clones, each containing a unique combination of randomly inserted reporters, and performed T7-assisted reporter mapping on this population.  SynHEK3 amplicon sequencing for prime editing-mediated CTT insertion and Cas9 editing: the K562 synHEK3 pool was transfected with the pU6-Sp-pegRNA-HEK3-insCTT plasmid or Cas9 RNP using the SF Cell Line 4D-Nucleofector X kit L (Lonza).  CRISPRoff experiments: On Day 0, 2 x 106 clone 5 cells were transfected with CRISPRoff-v2.1 (3,000 ng), pU6-Sp-dual-gRNA (1,000 ng) and pmax-GFP (500 ng, Lonza) using the SF Cell Line 4D-Nucleofector X kit L (Lonza). On Day 2, cells were sorted based on high GFP expression (top 20%) on a flow cytometer and expanded. On Day 11, 4 x 105 cells were transfected with the pU6-Sp-pegRNA-HEK3-insCTT plasmid (1,000 ng) using the SF Cell Line 96-well Nucleofector Kit (Lonza). Program code was FF-120.  CRISPRa experiments: On Day 0, 4 x 105 K562 dCas9-VP64 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (600 ng) and paired pU6-Sp-gRNA-2XMS2 (200 ng each) plasmids targeting the same promoter. On Day2, 4 x 105 cells from the previous transfection were transfected with pCMV-PEmax (Addgene: 174820)11 or  PB-PEmax-P2A-mCherry-EF1a-Puro (800 ng) and the pU6-Sp-pegRNA plasmids (400 ng). All transfections were performed using the SF Cell Line 96-well Nucleofector Kit (Lonza) with program FF-120.  For prime editing in shRNA treated cells: we transduced 2 monoclonal line (Clone 3 and Clone 5) individually with lentiviral shRNAs against candidate genes. After 2 days of doxycycline treatment to induce shRNA and GFP expression. For each shRNA, we pooled the 2 clones and transfected the cells with pegRNAs to induce 6-bp insertions. Cells were sorted into GFP positive and negative populations. Amplicon sequencing were performed on the sorted cells.

value: lentiviral shRNA against HLTF (additional shRNA), GFP negative


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP119-GFP-neg]

value: lentiviral shRNA against PMS2, GFP negative


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP125-GFP-neg]

value: lentiviral shRNA against PMS2 (additional shRNA), GFP negative


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP119-GFP-pos]

value: lentiviral shRNA against PMS2, GFP positive


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP111-GFP-neg]

value: lentiviral shRNA against EP300, GFP negative


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP113-GFP-neg]

value: lentiviral shRNA against FEN1, GFP negative


title: RNA sequencing of wild-type K562 cells [K562_DMSO_Rep2]

description: Unstranded mRNA library


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP123-GFP-pos]

value: lentiviral shRNA against HLTF (additional shRNA), GFP positive


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP117-GFP-neg]

value: lentiviral shRNA against MLH1, GFP negative


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP125-GFP-pos]

value: lentiviral shRNA against PMS2 (additional shRNA), GFP positive


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP117-GFP-pos]

value: lentiviral shRNA against MLH1, GFP positive


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP116-GFP-pos]

value: lentiviral shRNA against HLTF, GFP positive


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP111-GFP-pos]

value: lentiviral shRNA against EP300, GFP positive


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-USP7-Rep1_2]

description:
synHEK3 amplicon sequencing library
CRISPRoff_USP7.csv

value: CRISPRoff v2, USP7


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-LRRC8C-Rep2_2]

description:
synHEK3 amplicon sequencing library
CRISPRoff_LRRC8C.csv

value: CRISPRoff v2, LRRC8C


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-METTL2A-Rep2_2]

description:
synHEK3 amplicon sequencing library
CRISPRoff_METTL2A.csv

value: CRISPRoff v2, METTL2A


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-LRRC8C-Rep1_2]

value: lymphoblast


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-METTL2A-Rep1_2]

value: Wild type


title: Cas9 editing library in synHEK3 reporters (Day 4) [K562-HEK3-Cas9-Day4-XL281_S9]

description: synHEK3 amplicon sequencing library


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-Ctrl-Rep2_2]

description: synHEK3 amplicon sequencing library

value: CRISPRoff v2, Non targeting control


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP116-GFP-neg]

value: lentiviral shRNA against HLTF, GFP negative


title: Cas9 editing library in synHEK3 reporters (Day 2) [K562-HEK3-Cas9-Day2-XL281_S7]

description: synHEK3 amplicon sequencing library


title: Cas9 editing library in synHEK3 reporters (Day 1) [K562-HEK3-Cas9-Day1-XL281_S5]

description: synHEK3 amplicon sequencing library


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-Ctrl-Rep1_2]

description: synHEK3 amplicon sequencing library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12H]

description: sci-RNA-seq3 library

data_processing:
For the sci-RNA-seq3 transcriptome libraries, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. Reads were filtered based on RT and ligation index, by allowing <2 hamming distance from reference. Filtered reads were trimmed with TrimGalore (v0.6.6) with parameters: -a AAAAAAAA --three_prime_clip_R1 1. Reads were then aligned to the GRCh38 reference genome using STAR (v2.7.6a). PCR duplicates were collapsed using the RT index, ligation index, UMI sequence and end coordinate of reads. Reads were further demultiplexed based on the combination of the RT, ligation and PCR index and split into files for individual cells. To generate gene expression count matrices, reads were assigned to the exonic and intronic region of closest genes with HTseq (v.2.0.2). Reads with ambiguous assignments were discarded. Cells were further filtered based on total UMI (> 100) and mitochondrial reads percentage (<10%). Cells with the number of features detected between 10% and 90% percentile of all cells were kept and considered high-quality cells. The single cell analysis was performed using the Seurat (v4.0.0) package in R.
For capture libraries of the synHEK3 and shRNA constructs, sequencing reads from the Illumina NextSeq platforms were first demultiplexed based on PCR index using the bcl2fastq software. A custom script was used to further demultiplex and filter the synHEK3 and shRNA libraries based on the combination of RT, ligation and PCR index (cell ID), by allowing <2 hamming distance from reference. For the synHEK3 library, reporter barcodes (<2 hamming distance to the reference barcode set), prime editing outcomes and read UMIs were extracted. For the shRNA library, shRNA sequences (<2 hamming distance to the reference barcode set) and read UMIs were extracted. UMIs <3 hamming distance were collapsed.   A series of pre-processing steps were applied to the data. 1) We matched cell IDs between the sci-RNA-seq3 transcriptome libraries and the capture libraries, and only kept high-quality cells (number of features between 10% and 90% percentile). 2) For the shRNA library, cells with <3 or >200 UMIs or >20 shRNA were removed. 3) For the synHEK3 library, cells with <4 UMIs were first removed. We counted UMIs for synHEK3 reporters belonging to the two clones and calculated a clone UMI/total UMI ratio. If the ratio was >80% for a specific clone, the cell is assigned to the corresponding clone. Cells with extremely high UMIs (cutoff between 100 and 250 UMIs, depending on library complexity and sequencing depth of the plate) were also removed for downstream analysis. 4) For a cell-synHEK3 barcode combination, if multiple insertion sequences were observed, sequences <3 hamming distance were collapsed. Cell-synHEK3 barcode pairs having conflicting editing outcomes were discarded. 5) A cell-synHEK3 barcode-editing outcome-shRNA matrix was generated for a common set of cells identified by the shRNA and synHEK3 libraries.
Assembly: GRCh38
Supplementary files format and content: cell_synHEK3_shRNA.csv.gz contains a cell-synHEK3-shRNA capture matrix

extract_protocol: We performed a modified version of sci-RNA-seq3 (Martin et al., 2022). In brief, K562 cells were lysed with 5 mL of a hypotonic, PBS-based lysis buffer containing DEPC. The resulting nuclei were fixed with 4 volume of ice-cold methanol. After rehydrating and washing the nuclei carefully in a sucrose/PBS/triton buffer (SPBST), the nuclei were treated with T7 polymerase in an NTP mix buffer at 37oC for 30 min. Then nuclei were washed, sonicated briefly and counted. The nuclei were distributed to a 96-well plate for reverse transcription, with a cocktail of three indexed primers: oligo-dT, HEK3 and CS1 -- specific for the cellular transcriptome, and RNAs produced from the synHEK3 reporter and the shRNA constructs, respectively. After reverse transcription, nuclei were pooled, washed in SPBST and redistributed to 4 fresh plates for ligation of the second index primer with T4 DNA ligase. Nuclei were then again pooled, washed, and redistributed to 4 final plates at two different concentrations (1300 cell per well for 2 plates and 2500 cell per well for 2 plates) for second strand synthesis and extraction. Nuclear lysates were split in half, with one half undergoing normal sci-RNA-seq3 transcriptome library preparation (tagmentation and PCR to add the third index) and the other half subjected to indexed enrichment PCR for both the synHEK3 and shRNA constructs. Products were pooled by PCR plate, size-selected and sequenced on an Illumina Nextseq 2000 or Nextseq 550.

treatment_protocol: Two monoclonal K562 PE2-Puro lines (clone 3 and clone 5) containing multiple randomly integrated chromatin sensors for prime editing (synHEK3) were transduced with Lenti-rtTA-P2A-Blast viruses and selected in 10 ug/mL Blasticidin for 7 days. Monoclonal lines were derived and further transduced with a DNA damage response gene-focused lentiviral shRNA library containing 304 hairpins targeting 76 genes. Cells were transdcued at either low MOI (<1) or high MOI (~10) and selected in 800 ug/mL Geneticin for 7 days. For preparing sci-RNA-seq3 libraries, at the RT step, the low MOI cells are placed in the first 6 columns of the 96-well plate, while the high MOI cells were placed in the 7-12 columns of the 96-well palte. Low MOI and High MOI transduced cells can be distiguished by RT indices.

value: lentiviral transduction of a DDR-focused shRNA library


title: Prime editing library of synHEK3 reporters in two monoclonal lines (Clone 3 and Clone 5) [K562-HEK3-SC-XLP113-GFP-pos]

value: lentiviral shRNA against FEN1, GFP positive


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11H]

description: sci-RNA-seq3 library


title: Prime editing library of syHEK3 reporters in CRISPRoff treated cells [K562-SC1-5-OFF-USP7-Rep2_2]


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-11F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-10C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-12B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-09D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-08B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-07A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-06H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-05B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-04B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-02C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-03C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_2_P1-01F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-12A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-11A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-10B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-08B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-09A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-07C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-06G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-05A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-03A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-02D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-01A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-12A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-11A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-10G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-3_enrich_P1-04B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08B]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07E]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-08A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-06H]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07G]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-09A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-07A]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-06C]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-06F]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-06D]

description: sci-RNA-seq3 library


title: DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate2500-2_TX_P1-05H]

description: sci-RNA-seq3 library