title: bl6_kidney_S30_exp2

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from APCmin mice of intestinal cancer

hyb_protocol: 15ug cRNA was used for 2nd-cycle ss-cDNA of which 3ug cDNA was fragmented and hybridized onto Mouse Clariom S HTarrays.

scan_protocol: Scanning was done using the GeneTitan Scanner systems (Thermo Fisher).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

source_name: Kidney, Bl6 Mice healthy

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the Affy WT PLUS Reagent Kit ( ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: ApcMin/+ (C57BL/6J-ApcMin/J, RRID:IMSR_JAX002020) mice were obtained from Jackson Laboratories at approximately eight weeks of age. ApcMin/+ mice carry a heterozygote mutation in the murine Apc (adenomatous polyposis coli) locus, encoding a nonsense mutation at codon 850 and resulting in multiple intestinal neoplasia (Min).

extract_protocol: At sacrifice, intestine, lung, liver, kidney and spleen were aseptically harvested for mRNA extraction and and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Ten-week-old female ApcMin/+ mice received 20 mg of BAMLET in 2 x 200 μl PBS (BAMLET) or 2 x 200 μl of PBS alone (sham) by daily gavage for ten days. The mice were sacrificed two or five weeks after the end of treatment. Alternatively, mice received 20 mg of BAMLET in 5 ml PBS or PBS alone, daily in the drinking water until sacrifice after eight weeks or long-term follow-up.

value: female

tag: mouse strain

value: Kidney

tag: experiment


title: HepG2_coumarin 0.001 μM_rep3

status: Public on Feb 12 2024

type: SRA

city: Beijing

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

country: China

institute: Beijing Proteome Research Center

library_source: transcriptomic

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts and fpkm for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 cells

growth_protocol: About 5×107 HepG2 cells were treated in triplicates using 6 concentrations of coumarin and a control for 6 h.

extract_protocol:
After the culture medium with coumarin was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Coumarin was dissolved in DMEM (100 mM stock solutions). Further dilutions were made with serum-free DMEM. At the time of coumarin exposure, after the FBS-DMEM culture medium was removed, HepG2 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing different concentrations of coumarin (0-100 μM) for 6 h.

tag: cell line

value: HepG2 cells

tag: treatment

value: treated with 0.001 uM coumarin for 6 h


title: UHRF1-AID_WGBS_Day12_Rep3

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

country: France

institute: Epigenetics and Cell Fate Unit

library_source: genomic

data_processing:
As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: hg38
Supplementary files format and content: Processed data files were obtained with above data processing steps. The methylexport data includes chromosome number, cytosine position in CpG, strand, methylated C reads, total C reads in each columns.

molecule: genomic DNA

source_name: Colon

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Genomic DNA was isolated using the DNeasy Tissue & Blood kit (Qiagen) according to the manufacturer's protocol.
The library preparation for WGBS was performed with the tPBAT protocol described previously (Miura F, Nucleic Acids Res, 2012; Miura F, Nucleic Acids Res, 2019). One hundred nanograms of genomic DNA spiked with 1% (w/w) of unmethylated lambda DNA (Promega) was used for the library preparation.

treatment_protocol: To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.

tag: tissue

value: Colon

tag: cell type

value: Colorectal cancer cell

value: Auxin treatment

tag: time point

value: 12 days


title: bl6_kidney_S29_exp2

type: RNA

label: biotin

organism: Mus musculus

tag: gender


title: Apc_kidney_S27_exp2

source_name: Kidney, Apcmin Mice intestinal cancer long term followup 27 weeks of BAMLET in drinking water

value: BAMLET


title: Apc_kidney_S28_exp2


title: UHRF1-AID_WGBS_Day12_Rep1


title: 001-360min-3

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
After the culture medium with 2,4-D was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: About 5×10^7 HepG2 cells were treated in triplicates using 0.001 μM of 2,4-D treated for 0, 10, 30 and 360 min.

value: treated with 0.001 uM 2,4-D for 360 min.


title: 001-360min-2


title: Apc_kidney_S25_exp2

source_name: Kidney, Apcmin Mice intestinal cancer long term followup 15 weeks of PBS in drinking water

value: sham


title: Apc_kidney_S26_exp2


title: HepG2_coumarin 0.001 μM_rep2


title: UHRF1-AID_WGBS_Day8_Rep3

value: 8 days


title: bl6_spleen_S24_exp2

source_name: Spleen, Bl6 Mice intestine healthy

value: Spleen


title: HepG2_coumarin 0.001 μM_rep1


title: 001-30min-3

value: treated with 0.001 uM 2,4-D for 30 min.


title: UHRF1-AID_WGBS_Day8_Rep2


title: HepG2_coumarin 0 μM_rep3

value: untreated


title: 001-30min-2


title: UHRF1-AID_WGBS_Day6_Rep3

value: 6 days


title: HepG2_coumarin 0 μM_rep2


title: UHRF1-AID_WGBS_Day8_Rep1


title: 001-30min-1


title: 001-10min-3

value: treated with 0.001 uM 2,4-D for 10 min.


title: bl6_spleen_S23_exp2

value: female


title: UHRF1-AID_WGBS_Day6_Rep2


title: UHRF1-AID_WGBS_Day6_Rep1


title: IP H3K27me3 Wild Type plant Rep2

city: CLERMONT FERRAND

first: simon

last: amiard

address: 28 place henry dunant

institute: CNRS - UMR 6247 - GRED

data_processing:
reads were pre-processed with Trimagalore to remove Illumina sequencing adapters
Trimmed reads were mapped against the TAIR10 Arabidopsis thaliana genome with Bowtie2
Peaks were called using MACS2
Assembly: TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: seeds were stratified for 2 days at 4°C in the dark, and plants grown under long day conditions (16h light, 8h dark, 23°C). Seeds were sterilized in 70% EtOH / 0.01% SDS and seedlings were grown in vitro on 1x MS plates containing 1% sucrose

extract_protocol:
1g of 7-day old in vitro grown plantlets were fixed in 1% formaldehyde under vacuum twice for 7 min and then quenched in 0.125 M glycine. Nuclei were isolated and lysed, and chromatin sonicated using the Diagenode Bioruptor (set to high intensity, 3 times 7 cyles (30sec ON / 30 sec OFF) or the S220 Focused-ultrasonicator (Covaris) 5 min at peak power 175 W, duty factor 20%, 200 cycles per burst for histone modifications
anti-H3K27me3, Diagenode, #C15410069, Batch A1818P, anti-H3K4me3, Millipore #04-745
DNBSEQ stranded mRNA library

treatment_protocol: No treatment

value: seedlings

tag: genotype

value: Wild Type

tag: ip antibody


title: Apc_spleen_S21_exp2

source_name: Spleen, Apcmin Mice intestinal cancer long term followup 27 weeks of BAMLET in drinking water


title: IP H3K27me3 trb45 plant Rep2


title: 001-360min-1

value: HepG2 cells


title: Apc_spleen_S22_exp2


title: 001-10min-2


title: 001-10min-1


title: UHRF1-AID_WGBS_Day4_Rep3

value: Colon

value: 4 days


title: Apc_spleen_S20_exp2

source_name: Spleen, Apcmin Mice intestinal cancer long term followup 15 weeks of PBS in drinking water


title: bl6_liver_S18_exp2

source_name: Liver, Bl6 Mice healthy

value: Liver


title: IP H3K27me3 trb45 plant Rep1


title: bl6_liver_S17_exp2


title: 001-0min-3


title: UHRF1-AID_WGBS_Day4_Rep2

value: Colorectal cancer cell

value: Auxin treatment


title: HepG2_coumarin 0 μM_rep1


title: IP H3K27me3 Wild Type plant Rep1


title: UHRF1-AID_WGBS_Day4_Rep1


title: 001-0min-2


title: INPUT H3K27me3 Wild Type plant


title: 001-0min-1


title: INPUT H3K27me3 trb45 plant


title: UHRF1-AID_WGBS_Day2_Rep3

value: 2 days


title: Apc_spleen_S19_exp2

value: sham


title: Apc_liver_S16_exp2

source_name: Liver, Apcmin Mice intestinal cancer long term followup 27 weeks of BAMLET in drinking water

value: BAMLET


title: UHRF1-AID_WGBS_Day2_Rep2


title: UHRF1-AID_WGBS_Day2_Rep1


title: IP H3K4me3 trb45 plant Rep2


title: IP H3K4me3 Wild Type plant Rep2


title: Apc_liver_S15_exp2


title: UHRF1-AID_WGBS_Day0_Rep3

value: Before auxin treatment


title: IP H3K4me3 trb45 plant Rep1


title: IP H3K4me3 Wild Type plant Rep1


title: UHRF1-AID_WGBS_Day0_Rep2


title: Apc_liver_S14_exp2

source_name: Liver, Apcmin Mice intestinal cancer long term followup 15 weeks of PBS in drinking water


title: INPUT H3K4me3 trb45 plant


title: bl6_lung_S11_exp2

source_name: Lung, Bl6 Mice healthy

value: Lung


title: bl6_lung_S12_exp2


title: Apc_liver_S13_exp2


title: bl6_intestine_S7_exp1 [HT_MG-430_PM]

description: Gene expression data from healthy C57BL/6 mice

hyb_protocol: 6ug of fragmented and labelled cRNA was hybridized onto Mouse Genome 430 PM array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas systems (Thermo Fisher).

source_name: Intestine, Bl6 Mice healthy

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the GeneChip 3´IVT PLUS Kit ( ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratories at approximately eight weeks of age.

extract_protocol: At sacrifice, bladders were aseptically harvested for mRNA extraction and analysis. Total RNA was extracted (RNeasy Mini kit, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Ten-week-old female C57BL/6 mice received 20 mg of BAMLET in 2 x 200 μl PBS (BAMLET) or 2 x 200 μl of PBS alone by daily gavage for ten days. The mice were sacrificed two or five weeks after the end of treatment. Alternatively, mice received 20 mg of BAMLET in 5 ml PBS or PBS alone, daily in the drinking water until sacrifice after eight weeks. Healthy untreated C57BL/6 mice intestines were used as controls.

value: Intestine


title: Apc_lung_S10_exp2

source_name: Lung, Apcmin Mice intestinal cancer long term followup 27 weeks of BAMLET in drinking water


title: WT_WGBS_Day12_Rep3

value: 12 days


title: bl6_intestine_S6_exp1 [HT_MG-430_PM]

source_name: Intestine, Bl6 Mice healthy 8 weeks BAMLET drinking water


title: INPUT H3K4me3 Wild Type plant


title: bl6_intestine_S8_exp1 [HT_MG-430_PM]


title: WT_WGBS_Day12_Rep2


title: bl6_intestine_S4_exp1 [HT_MG-430_PM]

source_name: Intestine, Bl6 Mice healthy 5 weeks post BAMLET treatment by oral gavage


title: IP GFP TRB4GFP rep2

data_processing:
were pre-processed with Trimagalore to remove Illumina sequencing adapters
Trimmed reads were mapped against the TAIR10 Arabidopsis thaliana genome with Bowtie2
Peaks were called using MACS2
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol:
1g of 7-day old in vitro grown plantlets were fixed in 1% formaldehyde under vacuum twice for 7 min and then quenched in 0.125 M glycine. Nuclei were isolated and lysed, and chromatin sonicated using the Diagenode Bioruptor (set to high intensity, 3 times 7 cyles (30sec ON / 30 sec OFF) or the S220 Focused-ultrasonicator (Covaris) for 20 min at peak power 110 W, duty factor 5%, 200 cycles per burst for TRB4-GFP
anti-GFP, Invitrogen, #A-111222
DNBSEQ stranded mRNA library

value: No


title: Apc_lung_S8_exp2

source_name: Lung, Apcmin Mice intestinal cancer long term followup 15 weeks of PBS in drinking water

value: female


title: WT_WGBS_Day12_Rep1


title: Apc_lung_S7_exp2


title: Apc_lung_S9_exp2


title: UHRF1-AID_WGBS_Day0_Rep1


title: WT_WGBS_Day0_Rep3


title: IP GFP WT rep2

value: seedlings

value: WT


title: bl6_intestine_S3_exp1 [HT_MG-430_PM]


title: wildtype, female, whole fly, replicate 4

city: Kiel

first: Judith

last: Bossen

address: Am Botanischen Garten 3-9

department: Molecular Physiology

country: Germany

institute: CAU Kiel, Zoological Institute

data_processing:
CLC Genomics Workbench 9.5.2
Imported using Illumina Single Read import (FastQ); Quality Score = NCBI/Sanger or Illumina Pipeline 1.8 and later; failed reads were removed
Sequence reads were mapped to gene regions only using the Drosophila melanogaster genome (assembly Release 6 plus ISO1 MT)  (parameters: mismatch cost = 2, insertion cost = 2, deletion cost = 2, length fraction = 0.8, similarity fraction = 0.85, global alignment = no, strand specific = both, maximum number of hits for a read = 10, count paired reads as two = no, expression value = RPKM, calculate RPKM for genes without transcripts = no, use EM estimation = yes)
Differential expression for RNA-Seq was perfomed compairing to a control group (WholeAdults, Larval Trachea )
Assembly: assembly Release 6 plus ISO1 MT
Supplementary files format and content: xlsx files include RPKM values for each Sample

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
RNA was extracted using RNAmagic after manufacturer's protocol (Bio-Budget Technologies GmbH, Germany). cDNA synthesis was performed after Hagemann-Jensen et al. 2020 with minor modifications. Due to low cDNA amount whole length cDNA was amplified via PCR by controlling cycle number to avoid overamplification with LA Taq polymerase (TAKARA BIO INC., Japan).
Library preparation was done  adopted to Picelli et al. 2014. The samples were equimolar pooled and quantified (with Agilent Bioanalyzer, DNA 7500). Sequencing was done on the NextSeq 500 (Illumina) using the High Output Kit v2.5 (75 cycles)

value: whole body

value: adult


title: bl6_intestine_S6_exp2


title: WT_WGBS_Day0_Rep2

source_name: Colon

value: Colon


title: bl6_intestine_S2_exp1 [HT_MG-430_PM]

source_name: Intestine, Bl6 Mice healthy 2 weeks post BAMLET treatment by oral gavage


title: bl6_intestine_S5_exp2


title: bl6_intestine_S5_exp1 [HT_MG-430_PM]


title: bl6_intestine_S1_exp1 [HT_MG-430_PM]


title: wildtype, female, whole fly, replicate 3


title: IP GFP WT rep1


title: WT_WGBS_Day0_Rep1


title: Apc_intestine_S4_exp2

source_name: Intestine, Apcmin Mice intestinal cancer long term followup 27 weeks of BAMLET in drinking water


title: INPUT GFP TRB4GFP

value: INPUT


title: Apc_intestine_S3_exp2


title: IP GFP TRB4GFP rep1


title: shM8-2_2

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trim_galore (version 0.6.7) with the default parameters.
Mapping of RNA-seq reads and reads counting was done using RSEM/bowtie2 (Li and Dewey, 2011) and with parameters: --estimate-rspd  --output-genome-bam and the human gene annotation model GRCh37.
Assembly: hg19
Supplementary files format and content: txt format; raw counts values for three experimental conditions with 3 replicates each.

source_name: Cancer stem cells

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and  FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
A modified NEBNext RNA Ultra protocol is used to prepare the libraries for mRNA sequencing. The first step is selectively purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first strand synthesis reaction. Subsequently, the cDNA is converted to double stranded cDNA in a DNA polymerase based reaction. These DNA molecules are then subjected to a series of enzymatic steps for end repair, A-Tailing and ligation with NEB adapters. Finally, these adapter ligated molecules are enriched in a limited cycle PCR with indexed primers and purified using AMPure beads to create final cDNA library for sequencing.

treatment_protocol: TS543 cells were treated with either with non-targeting or targeting shRNA.

value: Glioblastoma patient derived cancer stem cell

tag: passage


title: 5502, OTV:MALAT1 multidose IV

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

country: USA

institute: Denali Therapeutics

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We created a custom Macaca fascicularis genome index for use with Cellranger (10X Genomics). Genome assembly 6.0 (GCA_011100615.1) and matching gene annotations were downloaded from Ensembl release 106. Ensembl (release 106) annotates the human MALAT1 gene at position 11:65,498,546-65,507,374 (GRCh38.p13). This 20 kb region aligns to position 14:8,898,660-8,903,763 in the Macaca fascicularis genome, which contains the non-coding ENSMFAG00000062016 gene, the Macaca fascicularis MALAT1 ortholog. We observed that alignments from both bulk whole-transcriptome and 3' single-nuclei RNA-seq Macaca fascicularis data extend beyond both ENSMFAG00000062016's 5' and 3' ends, indicating the gene is actually longer than currently annotated. To capture all RNA-seq reads originating from this locus, we expanded the Macaca fascicularis MALAT1 gene region to coordinates 14:8,898,273-8,905,739. The custom Cell Rranger index was created following the instructions provided by 10X Genomics. First, gene annotations were filtered to retain the following gene-biotypes: protein_coding, lncRNA, antisense, IG_LV_gene, IG_V_gene, IG_V_pseudogene, IG_D_gene, IG_J_gene, IG_J_pseudogene, IG_C_gene, IG_C_pseudogene, TR_V_gene, TR_V_pseudogene, TR_D_gene, TR_J_gene, TR_J_pseudogene, TR_C_gene. Afterward, the genome index was created with the cellranger mkref command with default options. Reads were subsequently mapped using this new reference with Cell Ranger v6.1.2.
Raw reads (FASTQ files) were processed with 10X Genomics' cellranger count command (version 6.1.2) with the following arguments: --include-introns --expect-cells=10000. A custom reference was
Filtered counts matrices generated with Cell Ranger were further processed in R using Seurat v4. Nuclei with >=800  and <=6000 genes detected were retained. In addition, nuclei with >30,000 UMIs and >1% ribosomal reads were removed
Filtered gene expression matrices output by Cell Ranger were combined by Canonical Correlation Analysis (CCA) using the FindIntegrationAnchors and IntegrateData functions in Seurat v4 with 2000 shared variable features. Integrated expression values were then scaled and PCA was performed. Dimensionality reduction and clustering were performed in Seurat with default settings. Doublet detection was performed using scDblFinder.
Assembly: Macaca_fascicularis_6.0 (GCA_011100615.1)
Supplementary files format and content: HDF5 files with raw counts per gene per droplet, produced by Cell Ranger (version 6.1.2) as raw_feature_bc_matrix.h5 for each sample
Supplementary files format and content: barcodes.tsv.gz is a gzip compressed TSV file with the cell barcodes, annotating the columns of the matrix.mtx.gz file
Supplementary files format and content: features.tsv.gz is a gzip compressed TSV file with the gene identifiers, annotating the rows of the matrix.mtx.gz file.
Supplementary files format and content: matrix.mtx.gz is a compressed sparse matrix with genes on the rows and cells on the columns. It includes the final, filtered gene expression counts used for the analysis.
Supplementary files format and content: metadata.csv.gz is a gzip compressed CSV file with metadata for each cell/barcode in the matrix.mtx.gz file.

molecule: polyA RNA

organism: Macaca fascicularis

source_name: brain

growth_protocol: Upon receipt at the testing Facility, the animals  were housed in groups of 2, 3, or 4 (single sex) in appropriately sized caging. The monkeys were individually housed when protocol functions required individual data collection, e.g. urine collections. Housing set-up was as specified in the USDA Animal Welfare Act (9 CFR, Parts 1, 2 and 3) and as described in the Guide for the Care and Use of Laboratory Animals. Animals were separated during designated procedures/activities as required for monitoring and/or health purposes, as deemed appropriate by Study Director and/or Clinical Veterinarian. Lab Diet Certified Primate Diet #5048, PMI Nutrition International, Inc. was provided to all animals.

extract_protocol:
Tissues were collected two weeks after the final dose to allow sufficient time for target knockdown. Brain tissue was dissected and frozen for analysis.
Nuclei were isolated from frozen mouse brain tissue samples in a procedure similar to a previously published “Frankenstein” protocol (https://www.protocols.io/view/frankenstein-protocol-for-nuclei-isolation-from-f-bq23mygn). Briefly, frozen tissue samples were placed into chilled Nuclei EZ Lysis Buffer (Sigma Aldrich, # NUC101) and mechanically homogenized using a 2 mL dounce homogenizer by stroking 15-20 times with pestle A followed by 15-20 strokes of pestle B. The lysate was incubated on ice for 5-10 mins, passed through a 70 µm strainer mesh, pellet and resuspended again in Nuclei EZ Lysis Buffer for another 5 mins of incubation on ice. After 3-4 washes to remove debris (500g at 4°C for 5 minutes), nuclei were resuspended in Nuclei Wash Buffer with a final concentration of 0.2 U/uL RNase inhibitor (Ambion, cat. no. AM2682) and 1% BSA in PBS, and then passed through a 30µm strainer.  Using DAPI stain, roughly 25,000 - 35,000 nuclei were FACS sorted on BD FACSAria (Becton Dickinson) directly into 10x Genomics RT master mix for a target recovery of 10,000-15,000 nuclei. RT enzyme was added immediately prior to microfluidic loading on Chromium for nuclei capture, and libraries were prepared per 10X Genomics user guide (CG000204 Rev B). Next-generation sequencing was performed by SeqMatic (Fremont, CA) on an Illumina NovaSeq instrument with a S2 flow cell generating paired-end reads (28x10x10x90 bases).

treatment_protocol: This study includes three treatment groups, each with three animals: 1) Single dose of 4mg MALAT1 ASO intrathecally (“ASO IT”) 2) Four biweekly doses of saline intravenously (“Saline” or “Vehicle”),  3) Four biweekly doses of 30mpk OTV:MALAT1 intravenously (“OTV IV”).

tag: animal id

tag: Sex

value: brain

tag: region

value: thalamus

value: OTV:MALAT1 multidose IV


title: wildtype, larval trachea, replicate 4

source_name: trachea

value: trachea

value: 3rd instar larvae


title: 5503, OTV:MALAT1 multidose IV

description: 10x Genomics


title: shM8-2_3


title: wildtype, female, whole fly, replicate 1


title: wildtype, larval trachea, replicate 3


title: shM8-2_1


title: wildtype, female, whole fly, replicate 2


title: Apc_intestine_S2_exp2

source_name: Intestine, Apcmin Mice intestinal cancer long term followup 15 weeks of PBS in drinking water

value: sham


title: shM8-1_3


title: Apc_intestine_S1_exp2

value: Intestine


title: 5501, OTV:MALAT1 multidose IV

description: 10x Genomics


title: wildtype, larval trachea, replicate 2


title: shM8-1_2


title: 4502, Saline

description: 10x Genomics

value: Saline


title: bl6_intestine_S7_exp1


title: wildtype, adult trachea, replicate 4

description: S04Adult Trachea_4


title: shM8-1_1


title: 4501, Saline

description: 10x Genomics


title: wildtype, larval trachea, replicate 1


title: shNT_3

value: shNT


title: Apc_intestine_S5_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 8 weeks sham drinking water

value: female


title: Apc_intestine_S4_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 5 weeks post BAMLET treatment by oral gavage

value: BAMLET


title: wildtype, adult trachea, replicate 3

description: S03Adult Trachea_3


title: 1503, 4mg MALAT1 ASO IT

description: 10x Genomics

value: 4mg MALAT1 ASO IT


title: 4503, Saline

description: 10x Genomics


title: Apc_intestine_S3_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 5 weeks post sham treatment by oral gavage


title: 1502, 4mg MALAT1 ASO IT

description: 10x Genomics


title: shNT_2


title: 1501, 4mg MALAT1 ASO IT

description: 10x Genomics


title: wildtype, adult trachea, replicate 1

description: S01Adult Trachea_1


title: noAAV_0

status: Public on Feb 11 2024

city: San Francisco

first: Kristen

last: Seim

state: CA

address: 201 Haskins Way

institute: GraphiteBio

data_processing:
Crispresso 2 (v2.1.0) -  quantify the various gene editing outcomes i
R (v4.1.2) and the ggplot2 package - data visualization
Assembly: hg19
Supplementary files format and content: excel/csv file
Supplementary files format and content: recombinary events with frequency
Library strategy: DNA-seq assay

source_name: cell type

extract_protocol:
For this assay, genomic DNA was harvested from cells using a Quick-DNA 96 Plus Kit (Zymo Research). The DNA concentration was measured using a Qubit 1X dsDNA BR assay kit (ThermoFisher). Purified genomic DNA was then used to amplify the HBB locus via polymerase chain reaction (PCR). The PCR products were diluted using nuclease-free water to serve as the template DNA for targeted NGS library prep. An Aglient Tapestation was used to confirm the PCR product for each sample was the expected size (1410bp). A second PCR with primers carrying partial Illumina adapters was performed to amplify a 142 base pair sequence that includes the region of the HBB locus that is to be corrected during the genome correction process. The PCR products were diluted again to serve as templates in a third PCR reaction using Nextera XT index primers. This third PCR reaction was used to assign unique identifiers to each sample and to add the full length adapter sequences necessary for Illumina sequencing. The size of the PCR products was assessed on an Agilent BioAnalyzer. PCR products were then pooled, purified using a Qiagen PCR purification kit, and quantified using PicoGreen in order to ready the PCR products for sequencing.
Quick-DNA 96 Plus Kit (Zymo Research).

value: cell type

value: primary HSPC


title: HBB-snp_4.8828125


title: HBB-snp_2.44140625


title: Apc_intestine_S2_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 2 weeks post BAMLET treatment by oral gavage


title: HBB-snp_19.53125


title: HBB-snp_39.0625


title: Apc_intestine_S1_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 2 weeks post sham treatment by oral gavage


title: HBB-snp_9.765625


title: HBB-snp_78.125


title: HBB-snp_156.25


title: HBB-snp_2500


title: GPH101, MOI_AAV_2500, SK08_S8

value: NoAdditive


title: HBB-snp_1250


title: GPH101, MOI_AAV_2500


title: i53 DM_1.5mg/mL_GPH101_2500

value: DM


title: wildtype, adult trachea, replicate 2

description: S02Adult Trachea_2

value: adult


title: shNT_1

value: Glioblastoma patient derived cancer stem cell


title: 2500_MOI_HBB_snp_his_i53_L67H_3C_protein_006_0_4_2


title: i53_1.5mg/mL_GPH101_2500, SK18_S18


title: i53_1.5mg/mL_GPH101_2500


title: 312_5_MOI_HBB_snp_his_i53_L67H_3C_protein_006_0_4_2


title: Apc_intestine_S6_exp1

source_name: Intestine, Apcmin Mice intestinal cancer 8 weeks BAMLET drinking water


title: 312_5_MOI_HBB_snp_his_i53_L67R_3C_protein_005_0_4_2


title: 312_5_MOI_HBB_snp_i53_Aldevron_Native_011_0_4_2


title: HBB-snp_625


title: 2500_MOI_HBB_snp_his_i53_L67R_3C_protein_005_0_4_2


title: 312_5_MOI_HBB_snp_his_i53_L67R_3C_protein_005_0_4_1


title: HBB-snp_312.5


title: 2500_MOI_HBB_snp_his_i53_L67R_3C_protein_005_0_4_1


title: 2500_MOI_HBB_snp_i53_Aldevron_Native_011_0_4_2


title: 2500_MOI_HBB_snp_i53_dead_010_0_4_1

value: DM MOI2500


title: 312_5_MOI_HBB_snp_i53_Aldevron_Native_011_0_4_1


title: 312_5_MOI_HBB_snp_i53_dead_010_0_4_2

value: DM MOI312.5


title: PD_058_X_UT_on

value: Untreated


title: 312_5_MOI_HBB_snp_i53_dead_010_0_4_1


title: 2500_MOI_HBB_snp_his_i53_L67H_3C_protein_006_0_4_1


title: 312_5_MOI_HBB_snp_his_i53_L67H_3C_protein_006_0_4_1


title: PD_058_X_GB_on

value: RNP+AAV


title: PD_058_X_EP_on

value: EPonly


title: PD_058_X_AAV_on

value: AAVonly


title: PD_058_U_GB_on_on


title: PD_058_U_UT_on


title: PD_058_U_AAV_on


title: PD_058_U_EP_on


title: 2500_MOI_HBB_snp_i53_Aldevron_Native_011_0_4_1


title: 2500_MOI_HBB_snp_i53_dead_010_0_4_2


title: PD_058_X_RNP_on

value: RNPonly


title: 3-rnp-only-2-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_rnp only.2_mcherry_neg

value: RNP only (no AAV, GFP -, NTC shRNA -)


title: 3-rnp-only-1-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_rnp only.2_mcherry_pos

value: RNP only (no AAV, GFP +, NTC shRNA +)


title: 1-rnp-only-2-gfp-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 1_rnp only.2_gfp_neg

value: RNP only (no AAV, GFP -, POLQ shRNA -)


title: 3-HBB-snp-2500-2-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (312.5).2_mcherry_neg

value: MOI 312.5 (GFP -, NTC shRNA -)


title: 3-HBB-snp-312-5-1-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (312.5).1_mcherry_pos

value: MOI 312.5 (GFP +, NTC shRNA +)


title: 3-HBB-snp-312-5-2-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (312.5).2_mcherry_pos

value: primary HSPC


title: 3-HBB-snp-2500-2-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (2500).2_mcherry_pos

value: MOI 2500 (GFP +, NTC shRNA +)


title: 3-HBB-snp-312-5-2-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (2500).1_mcherry_neg

value: MOI 2500 (GFP -, NTC shRNA -)


title: 3-rnp-only-1-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_rnp only.1_mcherry_pos


title: 3-rnp-only-2-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_rnp only.1_mcherry_neg


title: 3-HBB-snp-312-5-1-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (2500).2_mcherry_neg


title: 3-HBB-snp-2500-1-mcherry-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (312.5).1_mcherry_neg


title: 1-HBB-snp-312-5-2-gfp-neg

description:
S3.4E.csv
S3.4D.txt

value: MOI 312.5 (GFP -, POLQ shRNA -)


title: 1-rnp-only-2-gfp-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 1_rnp only.2_gfp_pos

value: RNP only (no AAV, GFP +, POLQ shRNA +)


title: PD_058_U_RNP_on

source_name: cell type

value: cell type


title: 1-rnp-only-1-gfp-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 1_rnp only.1_gfp_pos


title: 1-HBB-snp-312-5-1-gfp-neg

description:
S3.4E.csv
S3.4D.txt


title: 1-HBB-snp-312-5-2-gfp-pos

description:
S3.4E.csv
S3.4D.txt

value: MOI 312.5 (GFP +, POLQ shRNA +)


title: 1-rnp-only-1-gfp-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 1_rnp only.1_gfp_neg


title: 1-HBB-snp-2500-2-gfp-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 1_HBB snp (2500).2_gfp_neg

value: MOI 2500 (GFP -, POLQ shRNA -)


title: 1-HBB-snp-2500-1-gfp-neg

description:
S3.4E.csv
S3.4D.txt

source_name: 1_HBB snp (2500).1_gfp_pos

value: MOI 2500 (GFP +, POLQ shRNA +)


title: 1-HBB-snp-2500-2-gfp-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 1_HBB snp (2500).2_gfp_pos


title: 1-HBB-snp-2500-1-gfp-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 1_HBB snp (2500).1_gfp_neg


title: GCPS8393

source_name: AZD .5uM


title: GCPS8107

source_name: Tox-006-No drug 1-040_gDNA


title: GCPS8104


title: 3-HBB-snp-2500-1-mcherry-pos

description:
S3.4E.csv
S3.4D.txt

source_name: 3_HBB snp (2500).1_mcherry_pos


title: GCPS8100

source_name: Tox-006-No drug 1-041_gDNA


title: GCPS8097


title: GCPS8086


title: GCPS8070


title: GCPS8074


title: GCPS8090


title: GCPS8075


title: GCPS8059


title: GCPS8067


title: GCPS8083


title: GCPS8058


title: GCPS8071


title: GCPS8055


title: GCPS8063


title: GCPS8079


title: GCPS8051


title: 1-HBB-snp-312-5-1-gfp-pos

description:
S3.4E.csv
S3.4D.txt


title: GCPS8054


title: GCPS8087


title: GCPS8047


title: GCPS8043


title: GCPS8405

source_name: GB101 only


title: GCPS7806


title: GCPS7800


title: GCPS7803


title: GCPS7780


title: GCPS7807


title: GCPS7776


title: GCPS7778


title: GCPS7777


title: GCPS7774


title: GCPS7773


title: GCPS7770


title: GCPS7765


title: GCPS7769


title: GCPS7766


title: GCPS7764


title: GCPS7762


title: GCPS7757


title: GCPS7758


title: GCPS7753


title: GCPS7750


title: GCPS7754


title: GCPS7749


title: GCPS7745


title: GCPS7748


title: GCPS7746


title: GCPS7738


title: GCPS7741


title: GCPS7744


title: GCPS7734


title: GCPS7737


title: GCPS7728

description: 3B (% HDR - 312.5).txt


title: GCPS7707

description: 3B (% HDR - 312.5).txt


title: GCPS7708

description: 3B (% HDR - 312.5).txt


title: GCPS7727

description: 3B (% HDR - 312.5).txt


title: GCPS7733


title: GCPS7729

description: 3B (% HDR - 312.5).txt


title: GCPS7761


title: GCPS7760


title: GCPS7692

description: 3B (% HDR - 312.5).txt


title: GCPS7688

description: 3B (% HDR - 312.5).txt


title: GCPS7687

description: 3B (% HDR - 312.5).txt


title: GCPS7691

description: 3B (% HDR - 312.5).txt


title: GCPS7659

description: 3B (% HDR - 312.5).txt


title: GCPS7742


title: GCPS7653

description: 3B (% HDR - 312.5).txt


title: GCPS7651

description: 3B (% HDR - 312.5).txt


title: GCPS7647

description: 3B (% HDR - 312.5).txt


title: GCPS7645

description: 3B (% HDR - 312.5).txt


title: GCPS7641

description: 3B (% HDR - 312.5).txt


title: GCPS7636

description: 3B (% HDR - 312.5).txt


title: GCPS5495

description: S3.2B (MOI 2500, percent of edited alleles).txt


title: GCPS5473


title: GCPS5474


title: GCPS5475


title: GCPS7704

description: 3B (% HDR - 312.5).txt


title: GCPS5470


title: GCPS5467


title: GCPS5468


title: GCPS5466


title: GCPS5463


title: GCPS5469


title: GCPS5464


title: GCPS7703

description: 3B (% HDR - 312.5).txt


title: GCPS5462


title: GCPS7657

description: 3B (% HDR - 312.5).txt


title: GCPS5461


title: GCPS5458


title: GCPS5456


title: GCPS5457


title: GCPS5455


title: GCPS5476


title: GCPS5454


title: GCPS5452


title: GCPS5451


title: GCPS5450


title: GCPS5472


title: GCPS5448


title: GCPS5449


title: GCPS5445


title: GCPS5446


title: GCPS5442


title: GCPS5443


title: GCPS5444


title: GCPS5440


title: GCPS5460


title: GCPS5436


title: GCPS5439


title: GCPS5432


title: GCPS5437


title: GCPS5434


title: GCPS5431


title: GCPS5433


title: GCPS5438


title: GCPS5428


title: GCPS5430


title: GCPS5427


title: GCPS5426


title: GCPS5425


title: GCPS5424


title: GCPS5418


title: GCPS5420


title: GCPS5413


title: GCPS5412


title: GCPS5419


title: GCPS5421


title: GCPS5415


title: GCPS5416


title: GCPS5414


title: GCPS5410


title: GCPS5408


title: GCPS5409


title: GCPS5406


title: GCPS5407


title: GCPS5304

description: S3.2B (MOI 312.5, percent of edited alleles).txt


title: GCPS5307


title: GCPS5308

description:
3B (% HDR - 312.5).txt
S3.2B (MOI 312.5, percent of edited alleles).txt


title: GCPS5310


title: GCPS5309


title: GCPS5302


title: GCPS5303


title: GCPS5291


title: GCPS5290


title: GCPS5422


title: GCPS5306


title: GCPS5301


title: GCPS5300


title: GCPS5285


title: GCPS5284


title: GCPS5282


title: GCPS5283


title: GCPS5279


title: GCPS5280


title: GCPS5278


title: GCPS5273


title: GCPS5276


title: GCPS5277


title: GCPS5272


title: GCPS5274


title: GCPS5268


title: GCPS5266


title: GCPS5271


title: GCPS5267


title: GCPS5265


title: GCPS5264


title: GCPS5261


title: GCPS5260


title: GCPS5258


title: GCPS5259


title: GCPS5262


title: GCPS5254


title: GCPS5255


title: GCPS5256


title: GCPS5286


title: GCPS5252


title: GCPS5251


title: GCPS5249


title: GCPS5250


title: GCPS5147


title: GCPS5145


title: GCPS5146


title: GCPS5144


title: GCPS5248


title: GCPS5270


title: GCPS5143


title: GCPS5136


title: GCPS5137


title: GCPS5132


title: GCPS5130


title: GCPS5126


title: GCPS5134


title: GCPS5128


title: GCPS5124


title: GCPS5129


title: GCPS5122


title: GCPS5125


title: GCPS5118


title: GCPS5120


title: GCPS5117


title: GCPS5116


title: GCPS5114


title: GCPS5113


title: GCPS5119


title: GCPS5112


title: GCPS5111


title: GCPS5123


title: GCPS5108


title: GCPS5104


title: GCPS5110


title: GCPS5102


title: GCPS5105


title: GCPS5131


title: GCPS5135


title: GCPS5100


title: GCPS5096


title: GCPS5098


title: GCPS5093


title: GCPS5094


title: GCPS5101


title: GCPS5107


title: GCPS5088


title: GCPS5099


title: GCPS5087


title: GCPS5090


title: GCPS5084


title: GCPS5082


title: GCPS5086


title: GCPS5092


title: GCPS5089


title: GCPS5080


title: GCPS5081


title: GCPS5106


title: GCPS5083


title: GCPS5077


title: GCPS5074


title: GCPS5076


title: GCPS5072


title: GCPS5071


title: GCPS5070


title: GCPS5075


title: GCPS5095


title: GCPS5069


title: GCPS5068


title: GCPS5065


title: GCPS5059


title: GCPS5058


title: GCPS5057


title: GCPS5062


title: GCPS5060


title: GCPS5064


title: GCPS5056


title: GCPS5054


title: GCPS5053


title: GCPS5078


title: GCPS5052


title: GCPS4363


title: GCPS5050


title: GCPS4364


title: GCPS4339


title: GCPS4337


title: GCPS4362


title: GCPS5051


title: GCPS4332


title: GCPS4334


title: GCPS4333


title: GCPS4335


title: GCPS5063


title: GCPS5066


title: GCPS4331


title: GCPS4330


title: GCPS4365


title: GCPS4329


title: GCPS4327


title: GCPS4324


title: GCPS4325


title: GCPS4328


title: GCPS4326


title: GCPS4323


title: GCPS4321


title: GCPS4338


title: GCPS4322


title: GCPS4336


title: GCPS4317


title: GCPS4314


title: GCPS4320


title: GCPS4318


title: GCPS4319


title: GCPS4310


title: GCPS4309


title: GCPS4302


title: GCPS4305


title: GCPS4304


title: GCPS4303


title: GCPS4301


title: GCPS4300


title: GCPS4298


title: GCPS4299


title: GCPS4315


title: GCPS4312


title: GCPS4316


title: GCPS4313


title: GCPS4297


title: GCPS4296


title: GCPS4295


title: GCPS4294


title: GCPS4311


title: GCPS4266


title: GCPS4293


title: GCPS4265


title: GCPS4269


title: GCPS4267


title: GCPS4268


title: GCPS4261


title: GCPS4264


title: GCPS4263


title: GCPS4262


title: GCPS4257


title: GCPS4255


title: GCPS4259


title: GCPS4253


title: GCPS4254


title: GCPS4258


title: GCPS4256


title: GCPS4260


title: GCPS4251


title: GCPS4270


title: GCPS4247


title: GCPS4250


title: GCPS4249


title: GCPS4248


title: GCPS4246


title: GCPS4243


title: GCPS4242


title: GCPS4244


title: GCPS4241


title: GCPS4239


title: GCPS4240


title: GCPS4235


title: GCPS4237


title: GCPS4238


title: GCPS4234


title: GCPS4236


title: GCPS4233


title: GCPS4232


title: GCPS4231


title: GCPS4147

description:
S4.4B.txt
4B.csv

value: RNP only (no AAV) + AZD7648 (0.5 uM)


title: GCPS4139

description:
S4.4B.txt
4B.csv


title: GCPS4137

description:
S4.4B.txt
4B.csv


title: GCPS4138

description:
S4.4B.txt
4B.csv


title: GCPS4252


title: GCPS4136

description:
S4.4B.txt
4B.csv


title: GCPS4127

description:
S4.4B.txt
4B.csv

value: no nucleofection + L67R (0.8 mg/mL)


title: GCPS4125

description:
S4.4B.txt
4B.csv

value: untreated


title: GCPS4123

description:
S4.4B.txt
4B.csv


title: GCPS4245


title: GCPS4126

description:
S4.4B.txt
4B.csv

value: no nucleofection + AZD7648 (0.5 uM)


title: GCPS4128

description:
S4.4B.txt
4B.csv

value: no nucleofection + AZD7648 (0.5 uM) + L67R (0.8 mg/mL)


title: GCPS4120

description:
S4.4B.txt
4B.csv


title: GCPS4121

description:
S4.4B.txt
4B.csv


title: GCPS4124

description:
S4.4B.txt
4B.csv

value: RNP only (no AAV) + AZD7648 (0.5 uM) + L67R (0.8 mg/mL)


title: GCPS4119

description:
S4.4B.txt
4B.csv


title: GCPS4122

description:
S4.4B.txt
4B.csv


title: GCPS4116

description:
S4.4B.txt
4B.csv


title: GCPS4118

description:
S4.4B.txt
4B.csv

value: RNP only (no AAV) + L67R (0.8 mg/mL)


title: GCPS4111

description:
S4.4B.txt
4B.csv


title: GCPS4112

description:
S4.4B.txt
4B.csv


title: GCPS4115

description:
S4.4B.txt
4B.csv


title: GCPS4114

description:
S4.4B.txt
4B.csv


title: GCPS4117

description:
S4.4B.txt
4B.csv


title: GCPS4113

description:
S4.4B.txt
4B.csv


title: GCPS4106

description:
S4.4B.txt
4B.csv

value: RNP only (no AAV)


title: GCPS4108

description:
S4.4B.txt
4B.csv

value: primary HSPC


title: GCPS4105

description:
S4.4B.txt
4B.csv


title: GCPS4109

description:
S4.4B.txt
4B.csv


title: GCPS4104

description:
S4.4B.txt
4B.csv


title: GCPS4103

description:
S4.4B.txt
4B.csv


title: GCPS4102

description:
S4.4B.txt
4B.csv

value: MOI 625


title: GCPS4091

description:
S4.4B.txt
4B.csv


title: GCPS4099

description:
S4.4B.txt
4B.csv


title: GCPS4089

description:
S4.4B.txt
4B.csv


title: GCPS4092

description:
S4.4B.txt
4B.csv


title: GCPS4101

description:
S4.4B.txt
4B.csv


title: GCPS4097

description:
S4.4B.txt
4B.csv


title: GCPS4096

description:
S4.4B.txt
4B.csv


title: GCPS4095

description:
S4.4B.txt
4B.csv


title: GCPS4090

description:
S4.4B.txt
4B.csv


title: GCPS4088

description:
S4.4B.txt
4B.csv


title: GCPS4098

description:
S4.4B.txt
4B.csv


title: GCPS4083

description:
S4.4B.txt
4B.csv


title: GCPS4100

description:
S4.4B.txt
4B.csv


title: GCPS4087

description:
S4.4B.txt
4B.csv


title: GCPS4086

description:
S4.4B.txt
4B.csv


title: GCPS4084

description:
S4.4B.txt
4B.csv


title: GCPS4082

description:
S4.4B.txt
4B.csv


title: GCPS4107

description:
S4.4B.txt
4B.csv


title: GCPS4081

description:
S4.4B.txt
4B.csv


title: GCPS4078

description:
S4.4B.txt
4B.csv


title: GCPS3075

value: MOI 2500 + DNAPKi (0.5 uM)


title: GCPS4110

description:
S4.4B.txt
4B.csv


title: GCPS3073


title: GCPS4080

description:
S4.4B.txt
4B.csv


title: GCPS3079


title: GCPS4094

description:
S4.4B.txt
4B.csv


title: GCPS4093

description:
S4.4B.txt
4B.csv


title: GCPS4085

description:
S4.4B.txt
4B.csv


title: GCPS1397


title: GCPS1399


title: GCPS1395


title: GCPS4079

description:
S4.4B.txt
4B.csv


title: GCPS1398


title: GCPS1396


title: GCPS1386


title: GCPS1385


title: GCPS1388


title: GCPS1383


title: GCPS1375


title: GCPS1387


title: GCPS1384


title: GCPS1374


title: GCPS1364


title: GCPS1373


title: GCPS1372


title: GCPS1362


title: GCPS1363


title: GCPS1352


title: GCPS1359


title: GCPS1360


title: GCPS1351


title: GCPS1361


title: GCPS1400


title: GCPS1350


title: GCPS1348


title: GCPS1349


title: GCPS1347


title: GCPS1371


title: GCPS1376


title: GCPS1340


title: GCPS1339


title: GCPS1335


title: GCPS1336


title: GCPS1337


title: GCPS12058


title: GCPS1338


title: GCPS12057


title: GCPS12055


title: GCPS12056


title: GCPS12050


title: GCPS12052


title: GCPS12051


title: GCPS12054


title: GCPS12053


title: GCPS12048


title: GCPS12049


title: GCPS12047


title: GCPS12046


title: GCPS12044


title: GCPS12042


title: GCPS12043


title: GCPS12045


title: GCPS11991

description:
5A_HDRonly.txt
5A_NHEJonly.txt
S5.1_MMEJ+HBD.txt

source_name: Donor 3 1250 MOI


title: GCPS11989

source_name: Donor 3 625 MOI


title: GCPS11992

source_name: Donor 3 v1.1 RNP Only


title: GCPS11983

source_name: Donor 3 625 + Booster


title: GCPS11690

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS12059


title: GCPS11689

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11686

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11687

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11688

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11684

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11682

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11685

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11683

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11680

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11677

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11681

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11674

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11679

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11673

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11678

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11672

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11670

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11675

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11669

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11667

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11662

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11664

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11663

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11665

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11661

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11668

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11666

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11660

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11656

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11657

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11676

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11653

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11655

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11659

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11654

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11658

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11651

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11650

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11671

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11649

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11652

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11648

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11646

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11645

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11647

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11644

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11642

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11641

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11639

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11638

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11637

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11634

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11635

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11636

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11633

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11630

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11629

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11632

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11631

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11627

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11628

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11626

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11625

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11624

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11622

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11623

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11643

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11620

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11615

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11621

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11619

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11640

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11617

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11618

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11612

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11614

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11608

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11611

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11613

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11609

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11610

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11606

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11604

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11607

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11605

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11603

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11602

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11601

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11599

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11598

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11597

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11582

description:
5C_S5.5A_S5.5D_HDRonly.txt
5C_S5.5B_NHEJonly.txt


title: GCPS11595

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11596

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11580


title: GCPS11581


title: GCPS11578


title: GCPS11576


title: GCPS11577


title: GCPS11616

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11579


title: GCPS11573


title: GCPS11574


title: GCPS11571


title: GCPS11568


title: GCPS11569


title: GCPS11570


title: GCPS11562


title: GCPS11600

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11560


title: GCPS11558


title: GCPS11559


title: GCPS11561


title: GCPS11556


title: GCPS11557


title: GCPS11555


title: GCPS11554


title: GCPS11575


title: GCPS11553


title: GCPS11551


title: GCPS11550


title: GCPS11552


title: GCPS11543

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11572


title: GCPS11541

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11542

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11539

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11538

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11540

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11535

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11498 OT-1 off targets


title: GCPS11497 OT-1 off targets


title: GCPS11485

description:
5B_ColonySeq.txt
S5.3B_EditFrequencies_fromCFUseq.csv

value: MOI 625 + VHH (T12V.T14H.L67H, 0.8 mg/mL) (CFU-seq)


title: GCPS11486


title: GCPS11484


title: GCPS11482


title: GCPS11480


title: GCPS11481


title: GCPS11483


title: GCPS11549


title: GCPS11479


title: GCPS11473


title: GCPS11475


title: GCPS11474


title: GCPS11537

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11476


title: GCPS11470


title: GCPS11472


title: GCPS11471


title: GCPS11536

description:
3C_HDR.txt
3C_NHEJ.txt
S3.5.csv


title: GCPS11468


title: GCPS11496 OT-1 off targets


title: GCPS11469


title: GCPS11465


title: GCPS11466


title: GCPS11462


title: GCPS11495 OT-1 off targets


title: GCPS11463


title: GCPS11460


title: GCPS11459


title: GCPS11461


title: GCPS11478


title: GCPS11458


title: GCPS11457


title: GCPS11456


title: GCPS11454


title: GCPS11477


title: GCPS11451


title: GCPS11453


title: GCPS11452


title: GCPS11448


title: GCPS11467


title: GCPS11449


title: GCPS11464


title: GCPS11450


title: GCPS11447


title: GCPS11446


title: GCPS11443


title: GCPS11441


title: GCPS11442


title: GCPS11440


title: GCPS11455


title: GCPS11439


title: GCPS11438


title: GCPS11436


title: GCPS11437


title: GCPS11444


title: GCPS11435


title: GCPS11430


title: GCPS11432


title: GCPS11433


title: GCPS11431


title: GCPS11429


title: GCPS11428


title: GCPS11426


title: GCPS11425


title: GCPS11424


title: GCPS11445


title: GCPS11423


title: GCPS11422


title: GCPS11420


title: GCPS11421


title: GCPS11418


title: GCPS11417


title: GCPS11416


title: GCPS11413


title: GCPS11415


title: GCPS11434


title: GCPS11412


title: GCPS11410


title: GCPS11414


title: GCPS11409


title: GCPS11411


title: GCPS11407


title: GCPS11427


title: GCPS11408


title: GCPS11406


title: GCPS11403


title: GCPS11404


title: GCPS11399

value: MOI 1250 (CFU-seq)


title: GCPS11405


title: GCPS11397


title: GCPS11398


title: GCPS11419


title: GCPS11395


title: GCPS11396


title: GCPS11393


title: GCPS11391


title: GCPS11389


title: GCPS11392


title: GCPS11390


title: GCPS11386


title: GCPS11388


title: GCPS11387


title: GCPS11385


title: GCPS11384


title: GCPS11383


title: GCPS11382


title: GCPS11377


title: GCPS11378


title: GCPS11380


title: GCPS11379


title: GCPS11375


title: GCPS11376


title: GCPS11373


title: GCPS11372


title: GCPS11371


title: GCPS11394


title: GCPS11370


title: GCPS11369


title: GCPS11366


title: GCPS11365


title: GCPS11367


title: GCPS11364


title: GCPS11360


title: GCPS11363


title: GCPS11359


title: GCPS11358


title: GCPS11362


title: GCPS11381


title: GCPS11355


title: GCPS11354


title: GCPS11374


title: GCPS11351


title: GCPS11361


title: GCPS11350


title: GCPS11347


title: GCPS11356


title: GCPS11348


title: GCPS11368


title: GCPS11352


title: GCPS11343


title: GCPS11345


title: GCPS11346


title: GCPS11342


title: GCPS11341


title: GCPS11340


title: GCPS11338


title: GCPS11357


title: GCPS11336


title: GCPS11337


title: GCPS11353


title: GCPS11335


title: GCPS11349


title: GCPS11333


title: GCPS11331


title: GCPS11329


title: GCPS11330


title: GCPS11332


title: GCPS11334


title: GCPS11328


title: GCPS11327


title: GCPS11326


title: GCPS11325


title: GCPS11344


title: GCPS11324


title: GCPS11323


title: GCPS11322


title: GCPS11321


title: GCPS11320


title: GCPS11318


title: GCPS11339


title: GCPS11319


title: GCPS11317


title: GCPS11312


title: GCPS11311


title: GCPS11309


title: GCPS11310


title: GCPS11308


title: GCPS11307


title: GCPS11306


title: GCPS11305


title: GCPS11304


title: GCPS11303


title: GCPS11301


title: GCPS11299


title: GCPS11296


title: GCPS11297


title: GCPS11302


title: GCPS11298


title: GCPS11300


title: GCPS11295


title: GCPS11293


title: GCPS11294


title: GCPS11291


title: GCPS11289


title: GCPS11292


title: GCPS11316


title: GCPS11288


title: GCPS11287


title: GCPS11290


title: GCPS11286


title: GCPS11285


title: GCPS11283


title: GCPS11281


title: GCPS11284


title: GCPS11280


title: GCPS11278


title: GCPS11279


title: GCPS11277


title: GCPS11276


title: GCPS11274


title: GCPS11273


title: GCPS11275


title: GCPS11271


title: GCPS11272


title: GCPS11270


title: GCPS11269


title: GCPS11266


title: GCPS11268


title: GCPS11265


title: GCPS11263


title: GCPS11261


title: GCPS11258


title: GCPS11257


title: GCPS11260


title: GCPS11256


title: GCPS11282


title: GCPS11262


title: GCPS11264


title: GCPS11259


title: GCPS11254


title: GCPS11251


title: GCPS11253


title: GCPS11249


title: GCPS11255


title: GCPS11252


title: GCPS11248


title: GCPS11246


title: GCPS11267


title: GCPS11247


title: GCPS11244


title: GCPS11250


title: GCPS11245


title: GCPS11242


title: GCPS11240


title: GCPS11239


title: GCPS11241


title: GCPS11243


title: GCPS11237


title: GCPS11235


title: GCPS11230


title: GCPS11225

value: MOI 625 (CFU-Seq)


title: GCPS11233


title: GCPS11232


title: GCPS11231


title: GCPS11229


title: GCPS11234


title: GCPS11224


title: GCPS11219


title: GCPS11221


title: GCPS11218


title: GCPS11220


title: GCPS11223


title: GCPS11222


title: GCPS11217


title: GCPS11215


title: GCPS11213


title: GCPS11238


title: GCPS11214


title: GCPS11209


title: GCPS11210


title: GCPS11212


title: GCPS11211


title: GCPS11208


title: GCPS11236


title: GCPS11216


title: GCPS11207


title: GCPS11205


title: GCPS11204


title: GCPS11201


title: GCPS11203


title: GCPS11198


title: GCPS11199


title: GCPS11200


title: GCPS11202


title: GCPS11196


title: GCPS11197


title: GCPS11192


title: GCPS11191


title: GCPS11194


title: GCPS11190


title: GCPS11189


title: GCPS11195


title: GCPS11188


title: GCPS11187


title: GCPS11206


title: GCPS11185


title: GCPS11183


title: GCPS11184


title: GCPS11186


title: GCPS11182


title: GCPS11179


title: GCPS11181


title: GCPS11175


title: GCPS11177


title: GCPS11176


title: GCPS11193


title: GCPS11172


title: GCPS11171


title: GCPS11168


title: GCPS11167


title: GCPS11174


title: GCPS11169


title: GCPS11170


title: GCPS11180


title: GCPS11178


title: GCPS11173


title: GCPS11164


title: GCPS11163


title: GCPS11160


title: GCPS11159


title: GCPS11158


title: GCPS11153


title: GCPS11155


title: GCPS11154


title: GCPS11162


title: GCPS11161


title: GCPS11157


title: GCPS11166


title: GCPS11151


title: GCPS11152


title: GCPS11150


title: GCPS11147


title: GCPS11149


title: GCPS11165


title: GCPS11148


title: GCPS11146


title: GCPS11145


title: GCPS11156


title: GCPS11135


title: GCPS11134


title: GCPS11133


title: GCPS11132


title: GCPS11131


title: GCPS11130


title: GCPS11125


title: GCPS11129


title: GCPS11126


title: GCPS11122


title: GCPS11124


title: GCPS11128


title: GCPS11127


title: GCPS11123


title: GCPS11118


title: GCPS11116


title: GCPS11119


title: GCPS11115


title: GCPS11113


title: GCPS11143


title: GCPS11142


title: GCPS11114


title: GCPS11144


title: GCPS11136


title: GCPS11111


title: GCPS11109


title: GCPS11112


title: GCPS11110


title: GCPS11107


title: GCPS11106


title: GCPS11108


title: GCPS11104


title: GCPS11105


title: GCPS11103


title: GCPS11121


title: GCPS11100


title: GCPS11120


title: GCPS11098


title: GCPS11117


title: GCPS11102


title: GCPS11099


title: GCPS11097


title: GCPS11096


title: GCPS11095


title: GCPS11094


title: GCPS11092


title: GCPS11091


title: GCPS11090


title: GCPS11089


title: GCPS11088


title: GCPS11087


title: GCPS11086


title: GCPS11085


title: GCPS11084


title: GCPS11083


title: GCPS11082


title: GCPS11101


title: GCPS11080


title: GCPS11081


title: GCPS11079


title: GCPS11077


title: GCPS11076


title: GCPS11075


title: GCPS11073


title: GCPS11074


title: GCPS11072


title: GCPS11070


title: GCPS11071


title: GCPS11069


title: GCPS11068


title: GCPS11093


title: GCPS11064


title: GCPS11067


title: GCPS11066


title: GCPS11061


title: GCPS11062


title: GCPS11065


title: GCPS11060


title: GCPS11059


title: GCPS11063


title: GCPS11058


title: GCPS11057


title: GCPS11056


title: GCPS11055


title: GCPS11054


title: GCPS11078


title: GCPS11045


title: GCPS11046


title: GCPS11047


title: GCPS11053


title: GCPS11044


title: GCPS11041


title: GCPS11037


title: GCPS11039


title: GCPS11038


title: GCPS11036


title: GCPS11042


title: GCPS11035


title: GCPS11032


title: GCPS11034


title: GCPS11031


title: GCPS11027


title: GCPS11029


title: GCPS11028


title: GCPS11026


title: GCPS11025


title: GCPS11024


title: GCPS11030


title: GCPS11022


title: GCPS11023


title: GCPS11043


title: GCPS11020


title: GCPS11017


title: GCPS11018


title: GCPS11019


title: GCPS11015


title: GCPS11016


title: GCPS11040


title: GCPS11013


title: GCPS11010


title: GCPS11009


title: GCPS11012


title: GCPS11033


title: GCPS11008


title: GCPS11007


title: GCPS11005


title: GCPS11021


title: GCPS11003


title: GCPS11002


title: GCPS11004


title: GCPS11000


title: GCPS11001


title: GCPS10997


title: GCPS10998


title: GCPS11014


title: GCPS10996


title: GCPS10994


title: GCPS11011


title: GCPS10993


title: GCPS10988


title: GCPS10992


title: GCPS10989


title: GCPS10990


title: GCPS10991


title: GCPS10987


title: GCPS11006


title: GCPS10983


title: GCPS10986


title: GCPS10985


title: GCPS10984


title: GCPS10982


title: GCPS10980


title: GCPS10981


title: GCPS10999


title: GCPS10995


title: GCPS10977


title: GCPS10979


title: GCPS10978


title: GCPS10975


title: GCPS10976


title: GCPS10973


title: GCPS10971


title: GCPS10974


title: GCPS10970


title: GCPS10968


title: GCPS10967


title: GCPS10966


title: GCPS10965


title: GCPS10972


title: GCPS10957


title: GCPS10964


title: GCPS10956


title: GCPS10955


title: GCPS10954


title: GCPS10953


title: GCPS10944


title: GCPS10945


title: GCPS10952


title: GCPS10951


title: GCPS10958


title: GCPS10946


title: GCPS10943


title: GCPS10942


title: GCPS10937


title: GCPS10938


title: GCPS10936


title: GCPS10941


title: GCPS10940


title: GCPS10939


title: GCPS10935


title: GCPS10969


title: GCPS10933


title: GCPS10932


title: GCPS10931


title: GCPS10930


title: GCPS10929


title: GCPS10934


title: GCPS10925


title: GCPS10923


title: GCPS10924


title: GCPS10927


title: GCPS10926


title: GCPS10921


title: GCPS10920


title: GCPS10918


title: GCPS10922


title: GCPS10915


title: GCPS10914


title: GCPS10919


title: GCPS10916


title: GCPS10913


title: GCPS10912


title: GCPS10911


title: GCPS10910


title: GCPS10909


title: GCPS10907


title: GCPS10908


title: GCPS10906


title: GCPS10903


title: GCPS10904


title: GCPS10901


title: GCPS10900


title: GCPS10899


title: GCPS10895


title: GCPS10893


title: GCPS10905


title: GCPS10898


title: GCPS10896


title: GCPS10894


title: GCPS10928


title: GCPS10891


title: GCPS10888


title: GCPS10897


title: GCPS10887


title: GCPS10892


title: GCPS10917


title: GCPS10886


title: GCPS10890


title: GCPS10885


title: GCPS10883


title: GCPS10882


title: GCPS10880


title: GCPS10881


title: GCPS10879


title: GCPS10878


title: GCPS10877


title: GCPS10875


title: GCPS10874


title: GCPS10876


title: GCPS10873


title: GCPS10867


title: GCPS10872


title: GCPS10871


title: GCPS10869


title: GCPS10870


title: GCPS10864


title: GCPS10868


title: GCPS10863


title: GCPS10862


title: GCPS10889


title: GCPS10865


title: GCPS10884


title: GCPS10860


title: GCPS10859


title: GCPS10858


title: GCPS10856


title: GCPS10857


title: GCPS10850


title: GCPS10855


title: GCPS10849


title: GCPS10848


title: GCPS10845


title: GCPS10844


title: GCPS10843


title: GCPS10846


title: GCPS10861


title: GCPS10842


title: GCPS10841


title: GCPS10840


title: GCPS10839


title: GCPS10837


title: GCPS10834


title: GCPS10836


title: GCPS10832


title: GCPS10833


title: GCPS10831


title: GCPS10829


title: GCPS10827


title: GCPS10828


title: GCPS10830


title: GCPS10826


title: GCPS10847


title: GCPS10825


title: GCPS10866


title: GCPS10822


title: GCPS10824


title: GCPS10823


title: GCPS10820


title: GCPS10835


title: GCPS10838


title: GCPS10818


title: GCPS10816


title: GCPS10817


title: GCPS10813


title: GCPS10815


title: GCPS10812


title: GCPS10814


title: GCPS10811


title: GCPS10809


title: GCPS10808


title: GCPS10807


title: GCPS10821


title: GCPS10806


title: GCPS10810


title: GCPS10805


title: GCPS10819


title: GCPS10800


title: GCPS10802


title: GCPS10804


title: GCPS10799


title: GCPS10797


title: GCPS10801


title: GCPS10803


title: GCPS10798


title: GCPS10796


title: GCPS10793


title: GCPS10792


title: GCPS10794


title: GCPS10789


title: GCPS10790


title: GCPS10785


title: GCPS10784


title: GCPS10782


title: GCPS10781


title: GCPS10780


title: GCPS10778


title: GCPS10795


title: GCPS10774


title: GCPS10775


title: GCPS10769


title: GCPS10777


title: GCPS10768


title: GCPS10772


title: GCPS10773


title: GCPS10776


title: GCPS10770


title: GCPS10771


title: GCPS10788


title: GCPS10764


title: GCPS10765


title: GCPS10767


title: GCPS10787


title: GCPS10766


title: GCPS10762


title: GCPS10791


title: GCPS10786


title: GCPS10763


title: GCPS10761


title: GCPS10760


title: GCPS10783


title: GCPS10759


title: GCPS10779


title: GCPS10902


title: GCPS10754


title: GCPS10753


title: GCPS10752


title: GCPS10751


title: GCPS10750


title: GCPS10749


title: GCPS10747


title: GCPS10745


title: GCPS10746


title: GCPS10744


title: GCPS10741


title: GCPS10743


title: GCPS10739


title: GCPS10742


title: GCPS10738


title: GCPS10736


title: GCPS10735


title: GCPS10733


title: GCPS10740


title: GCPS10732


title: GCPS10734


title: GCPS10731


title: GCPS10729


title: GCPS10726


title: GCPS10727


title: GCPS10728


title: GCPS10725


title: GCPS10724


title: GCPS10723


title: GCPS10748


title: GCPS10721


title: GCPS10722


title: GCPS10718


title: GCPS10717


title: GCPS10716


title: GCPS10720


title: GCPS10719


title: GCPS10715


title: GCPS10737


title: GCPS10712


title: GCPS10709


title: GCPS10713


title: GCPS10708


title: GCPS10730


title: GCPS10710


title: GCPS10711


title: GCPS10704


title: GCPS10706


title: GCPS10705


title: GCPS10702


title: GCPS10714


title: GCPS10703


title: GCPS10699


title: GCPS10707


title: GCPS10701


title: GCPS10698


title: GCPS10696


title: GCPS10695


title: GCPS10694


title: GCPS10700


title: GCPS10690


title: GCPS10692


title: GCPS10691


title: GCPS10689


title: GCPS10686


title: GCPS10688


title: GCPS10687


title: GCPS10684


title: GCPS10683


title: GCPS10682


title: GCPS10681


title: GCPS10680


title: GCPS10676


title: GCPS10677


title: GCPS10678


title: GCPS10674


title: GCPS10697


title: GCPS10675


title: GCPS10671


title: GCPS10672


title: GCPS10669


title: GCPS10670


title: GCPS10693


title: GCPS10668


title: GCPS10659 OT-1 off targets


title: GCPS10667


title: GCPS10656 OT-1 off targets


title: GCPS10658 OT-1 off targets


title: GCPS10685


title: GCPS10653 OT-1 off targets


title: GCPS10657 OT-1 off targets


title: GCPS10654 OT-1 off targets


title: GCPS10652 OT-1 off targets


title: GCPS10679


title: GCPS10546


title: GCPS10673


title: GCPS10547


title: GCPS10543


title: GCPS10544


title: GCPS10545


title: GCPS10541


title: GCPS10542


title: lib002_bulk

description:
KS_090122_1
S1.5.csv

data_processing:
Fastqc - QC
cutadapt - counting the number of each observed sequence in the NGS data and then removing all unexpected sequence (ie using a prespecified “whitelist” of variants known to be contained in the pool).
R (v4.1.2) and the ggplot2 package - data visualization
Assembly: hg19
Supplementary files format and content: excel/csv file
Supplementary files format and content: variant frequency
Library strategy: i53 assay DNAseq

source_name: primary HSPC

extract_protocol: The construct for the lentiviral-based expression and screening of i53 variants was cloned from a third-generation lentiviral plasmid (Lenti SFFV) purchased from Twist Biosciences.

value: transduced with 67 and 68 combinational library (parent:i53 WT, bulk)


title: lib002_mcpos_gfppos_1-2

description:
KS_090122_1
S1.5.csv

value: transduced with 67 and 68 combinational library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: lib002_mcpos_gfpneg_2

description:
KS_090122_1
S1.5.csv

value: transduced with 67 and 68 combinational library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: lib002_mcpos_gfppos_3

description:
KS_090122_1
S1.5.csv


title: GCPS10655 OT-1 off targets


title: lib002_mcpos_gfpneg_3

description:
KS_090122_1
S1.5.csv


title: lib002_mcpos_gfpneg_1

description:
KS_090122_1
S1.5.csv


title: lib002_mcpos_gfppos_2

description:
KS_090122_1
S1.5.csv


title: GCPS10548


title: Libb02_HBB3_mcpos_gfpneg

description:
KS_072222
S1.5.csv


title: Libb02_bulk

description:
KS_072222
S1.5.csv


title: lib002_mcpos_gfppos_1

description:
KS_090122_1
S1.5.csv


title: lib002_mcpos_gfpneg_1-2

description:
KS_090122_1
S1.5.csv


title: Libb02_HBB2_mcpos_gfpneg

description:
KS_072222
S1.5.csv


title: Libb02_HBB3_mcpos_gfppos

description:
KS_072222
S1.5.csv


title: vallib3_mcpos_gfpneg_3

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfpneg-3.csv

value: transduced with 12.14 validation library (parent:L67H) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: Libb02_HBB2_mcpos_gfppos

description:
KS_072222
S1.5.csv


title: vallib3_mcpos_gfppos_3

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfppos-3.csv

value: transduced with 12.14 validation library (parent:L67H) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: vallib3_mcpos_gfpneg_2

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfpneg-2.csv


title: vallib3_mcpos_gfppos_2

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfppos-2.csv


title: WT-HFD5, Wild type group

city: Fuzhou

first: Changgan

last: Chen

state: --- Select One ---

address: #29 Xinquan Road, Fuzhou 350001, People’s Republic of China

institute: Fujian Medical University Union Hospital

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: After reads ressembled by StringTie2, gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using Cuffcompare software.
Supplementary files format and content: processed data xls file includes  RPKM values for each samples

source_name: tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: tumor

value: pancreatic cancer cell

value: Wild type


title: WT-HFD3, Wild type group


title: vallib3_mcpos_gfppos_1

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfppos-1.csv


title: P9 cells expression after DSF 0.1 uM and MgCl2 1 uM 24h treatment

city: Taipei

first: Ying

last: Kao

address: No.145, Zhengzhou Rd

country: Taiwan

institute: Taipei City Hospital

description: Gene expression data from P9 cells after DSF 0.1 uM and MgCl2 1 uM treatment for 24hr

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: meningioma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: P9 were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with DMSO, CuCl2, DSF, MgCl2 as indicated amount for this experiment.

value: brain

tag: disease state

value: brain tumor

value: DSF 0.1 uM and MgCl2 1 uM

tag: time

value: 24 hr


title: WT-HFD2, Wild type group


title: ANXA1-HFD5, Myeloid-specific ANXA1 deficiency group

value: Myeloid-specific ANXA1 deficiency group


title: lib012_mcpos_gfpneg_3

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfpneg-3.csv

value: primary HSPC

value: transduced with 12 and 14 combinational library (parent:L67H) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: lib012_mcpos_gfppos_3

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfppos-3.csv

value: transduced with 12 and 14 combinational library (parent:L67H) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: P9 cells expression after DSF 0.1 uM and CuCl2 1 uM 6h treatment

description: Gene expression data from P9 cells after DSF 0.1 uM and CuCl2 1 uM treatment for 6hr

value: DSF 0.1 uM and CuCl2 1 uM

value: 6 hr


title: P9 cells expression after DSF 0.1 uM and MgCl2 1 uM 6h treatment

description: Gene expression data from P9 cells after DSF 0.1 uM and MgCl2 1 uM treatment for 6hr


title: P9 cells expression after DSF 0.1 uM 24h treatment

description: Gene expression data from P9 cells after DSF 0.1 uM treatment for 24hr

value: DSF 0.1 uM


title: ANXA1-HFD4, Myeloid-specific ANXA1 deficiency group


title: P9 cells expression after CuCl2 1uM 6h treatment

description: Gene expression data from P9 cells after CuCl2 1 uM treatment for 6hr

value: CuCl2 1uM


title: P9 cells expression after DSF 0.1 uM 6h treatment

description: Gene expression data from P9 cells after DSF 0.1 uM treatment for 6hr


title: P9 cells expression after MgCl2 1uM 24h treatment

description: Gene expression data from P9 cells after MgCl2 1 uM treatment for 24hr

value: MgCl2 1uM


title: lib012_mcpos_gfpneg_2

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfpneg-2.csv


title: ANXA1-HFD3, Myeloid-specific ANXA1 deficiency group


title: lib012_mcpos_gfppos_2

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfppos-2.csv


title: vallib3_mcpos_gfpneg_1

description:
KS_110722_1
S1.5D.txt
S1.5D_vallib3-mcpos-gfpneg-1.csv

value: transduced with 12.14 validation library (parent:L67H) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: 4KO-MN-rep1

city: Chongqing

first: Jie

last: Lan

state: Chongqing

address: No. 1 Yixueyuan Rd, Yuzhong District

department: Bioinformatics

institute: Chongqing medical university

data_processing:
ChIP-seq: The ChIP-seq data were mapped to the Mus musculus genome (mm9) and homo sapiens genome (hg19) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by Samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS. Reads were normalized with fly reference as previous study.
MNase-seq: The MNase-seq data were mapped to the Mus musculus genome (mm9) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by SAMtools and retained the uniquely mapped tags. Enriched peaks were called using MACS.
Assembly: mm9, hg19
Supplementary files format and content: bigwig files

source_name: mouse embryonic stem cells

extract_protocol:
1×107 cells were pelleted in PBS and then lysed in 1ml buffer A (10 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 3 mM MgCl2; 1 mM DTT, 0.1% NP-40) on ice 10 min. Then the cells were centrifuged at 1,000g 5 min and resuspended in 1 ml buffer A without NP-40. The cells were incubated at 37°C 5 min. Digestion was initiated by adding 2 mM CaCl2 (final concentration) and 1 μl 200U/ml MNase and incubated at 37°C. 200 μl digested chromatin was taken out at the time point of 1, 2, 4 min and the reactions were stopped by adding 4μl 500 mM EGTA (final concentration 10 mM). the mixture was treated with RNaseA 1hr at 37℃, and proteinase K 2 hrs at 55℃. DNA was recovered by phenol-chloroform extraction and precipitated by ethanol, and separated by 1.2% agarose gel.
The mononucleosome-sized DNA fragments were recovered by gel extraction kit (Qiagen) and the libraries were generated using the NEB Next ultra DNA library Prep kit for Illumina. The DNA libraries were purified with 1 volume AMpure beads and sequenced on Nova-seq6000 with paired-end 150 bp (Illumina).

value: mouse embryonic stem cells

tag: strain

tag: chip antibody

value: no


title: lib012_mcpos_gfpneg_1

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfpneg-1.csv


title: 4KO-MN-rep2


title: P9 cells expression after DSF 0.1 uM and CuCl2 1 uM 24h treatment

description: Gene expression data from P9 cells after DSF 0.1 uM and CuCl2 1 uM treatment for 24hr


title: lib012_mcpos_gfppos_1

description:
KSOE_092722
1D+S1.4A.csv
1D_S1.4_lib012-mcpos-gfppos-1.csv


title: P9 cells expression after CuCl2 1uM 24h treatment

description: Gene expression data from P9 cells after CuCl2 1 uM treatment for 24hr


title: P9 cells expression at 6 hr

description: Gene expression data from P9 cells without drug treatment for 6h

value: mock


title: P9 cells expression after DMSO 24h treatment

description: Gene expression data from P9 cells after DMSO treatment for 24h

value: brain

value: DMSO


title: P9 cells expression at 0 hr

description: Gene expression data from P9 cells without drug treatment for 0h

value: brain tumor

value: 0 hr


title: R1-MN-rep2

value: Wild type


title: Lib007_bulk

description:
KS_072922
S1.4B.csv

value: primary HSPC

value: transduced with 12 and 14 combinational library (parent:L67R, bulk)


title: R1-MN-rep1


title: KO-Ring1B-rep2

growth_protocol: mESCs were fixed with 2.5 mM ethylene glycol- bis (succinimidylsuccinate) (EGS) for 45 min, then washed twice with PBS and fixed again with 1% formaldehyde for 10 min. 10% of 293T cell chromatin was used as a reference to calculate the relative change of protein enrichment among different samples

extract_protocol:
Fixed mESCs were resuspended in nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors) and sheared to 300- to 500-bp-sized fragments. 100 μl sheared chromatin was diluted using 900 μl ChIP dilution buffer (50 mM Tris-HCl pH 8.0, 0.167 M NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate and protease inhibitors). Diluted chromatin was pre-cleared with Protein A/G beads 1 hour before incubating with antibodies overnight at 4°C. Antibody–chromatin complexes were washed with RIPA150 (50 mM Tris-HCl pH 8.0, 0.15 M NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate and protease inhibitors) once, RIPA500 (50 mM Tris-HCl pH 8.0, 0.5 M NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate and protease inhibitors) twice, RIPA-LiCl (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate, 0.5 M LiCl and protease inhibitors) twice and 1×TE twice. The precipitations were eluted by 200μl NLB (50 mM Tris-HCl pH 8.0, 10 mM EDTA and 1% SDS) at 65°C. Reverse crosslink was performed at 65°C overnight.
The DNA libraries were purified with 1 volume AMpure beads and sequenced on Nova-seq6000 with paired-end 150 bp (Illumina).

treatment_protocol: no

value: RING1B (BML, D139-3)


title: P9 cells expression after DMSO 6h treatment

description: Gene expression data from P9 cells after DMSO treatment for 6h


title: P9 cells expression after MgCl2 1uM 6h treatment

description: Gene expression data from P9 cells after MgCl2 1 uM treatment for 6hr


title: Lib007_HBB2_mcpos_gfpneg

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB2-mcpos-gfpneg.csv

value: transduced with 12 and 14 combinational library (parent:L67R) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: Lib007_HBB2_mcpos_gfppos

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB2-mcpos-gfppos.csv

value: transduced with 12 and 14 combinational library (parent:L67R) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: Lib007_HBB3_mcpos_gfppos

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB3-mcpos-gfppos.csv


title: KO-Ring1B-rep1


title: Lib007_HBB1_mcpos_gfpneg

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB1-mcpos-gfpneg.csv


title: R1-Ring1B-rep2


title: KO-CBX7-rep2

value: CBX7 (Abcam, ab21873)


title: Lib007_HBB3_mcpos_gfpneg

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB3-mcpos-gfpneg.csv


title: R1-Ring1B-rep1


title: vallib2_mcpos_gfpneg_4

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfpneg-4.csv

value: transduced with 67.68 validation library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: Lib007_HBB1_mcpos_gfppos

description:
KS_072922
S1.4B.csv
S1.4_Lib007-HBB1-mcpos-gfppos.csv


title: valib2_bulk

description:
KS_102422_1
S1.5C.txt

value: transduced with 67.68 validation library (parent:i53 WT, bulk)


title: R1-CBX7-rep2


title: KO-CBX7-rep1


title: R1-PCGF2-rep2

value: PCGF2 (Cell Signaling, sc-515329)


title: vallib2_mcpos_gfppos_4

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfppos-4.csv

value: transduced with 67.68 validation library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: R1-JARID2-rep2

value: mouse embryonic stem cells

value: JARID2 (Cell Signaling, 13594)


title: vallib2_mcpos_gfppos_3

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfppos-3.csv


title: vallib2_mcpos_gfpneg_2

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfpneg-2.csv


title: vallib2_mcpos_gfpneg_3

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfpneg-3.csv


title: R1-CBX7-rep1


title: I53A-PCGF2-rep2

value: Ring1b I53A


title: I53A-PCGF2-rep1


title: vallib2_mcpos_gfppos_1

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfppos-1.csv


title: I53A-JARID2-rep2


title: vallib2_mcpos_gfpneg_1

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfpneg-1.csv


title: HBB_02_mcneg_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt

value: untransduced (mCherry-)


title: I53A-PHC1-rep2

value: PHC1 (Cell Signaling, 13768)


title: I53A-JARID2-rep1


title: I53A-PHC1-rep1


title: HBB_01_mcpos_gfpneg

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt

value: transduced with 67 and 68 NNK library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: R1-JARID2-rep1

value: Wild type


title: HBB_02_mcpos_gfpneg

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt

value: primary HSPC


title: HBB_03_mcpos_gfpneg

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt


title: R1-PHC1-rep1


title: R1-PHC1-rep2


title: NIPBL dTAG treated +estradiol 72hrs_RAD21_ChIPSeq

city: SAN DIEGO

first: Indumathi

last: Patta

address: 9500 Gilman Drive, NSB5114A, LaJolla

department: Molecular Biology

institute: UCSD

data_processing:
ChIP-seq reads were aligned to the reference genome mm10 using Bowtie2.
Only the uniquely mapped reads were included for further processing.
MACS2 (PMID: 18798982) were used to call RAD21ChIP-seq peaks in progenitors and NIPBL-depleted progenitors.
Based on the binary peak status in progenitors and NIPBL depleted progenitors, we defined three groups of RAD21 peaks: shared RAD21 peaks, progenitor-specific RAD21 peaks and NIPBL depleted progenitor-specific RAD21 peaks.
Last, we selected promoters and enhancers within progenitor-specific RAD21 peaks and NIPBL depleted progenitor-specific RAD21 peaks, and applied HOMER (PMID: 20513432) with the default settings to perform the motif enrichmentanalysis.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: FKBP12F36V_NIPBL_Ecomg myeloid progenitor cell line

growth_protocol: ECOMG progenitor cells were cultured in RPMI 1640 media supplemented with 10%FBS, glutamine, penicillin and streptomycin, GM-CSF, and β-estradiol.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched with glycine to a final concentration of 125mM for 5 minutes at room temperature. ChIP was performed using ChIP-IT High Sensitivity kit (Active motif) according to the manufacturer’s instructions. Briefly, cells were resuspended in chromatin preparation buffer and incubated on ice for 10 minutes. Nuclei were collected by centrifuging at 1000g for 5 minutes at 4 °C. The nuclear pellets were resuspended in ChIP Buffer and lysates were fragmented using Covaris E220 with the following settings: peak power -140W, duty factor - 5%, 200 cycles per burst, temperature=4°C for 900 seconds. Chromatin immune precipitation was carried out using 4µg of anti-RAD21 antibody (Abcam, #ab992). Protein G agarose beads were used for pulldown protein-DNA complexes.
ChIP-Seq library construction was performed using Truseq ChIP Library Preparation Kit (IP-202-1012) according to the manufacturer’s instructions.

treatment_protocol: ECOMG progenitors expressing NIPBL-FKBP12F36V-EYFP were cultured in the presence or absence of dTAG-13 for 72hrs

value: Myeloid progenitor

value: dTAG treated +estradiol

value: RAD21(Abcam, #ab992)


title: NIPBL dTAG treated +estradiol 72hrs_Input

value: FKBP12F36V_NIPBL_Ecomg myeloid progenitor cell line


title: HBB_03_mcneg_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt


title: HBB_01_mcneg_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt


title: vallib2_mcpos_gfppos_2

description:
KS_102422_1
S1.5C.txt
S1.5C_vallib2-mcpos-gfppos-2.csv


title: HBB_02_mcpos_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt

value: transduced with 67 and 68 NNK library (parent:i53 WT) and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: HBB_03_mcpos_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt


title: R1-PCGF2-rep1


title: NIPBL Untreated +estradiol 72hrs_Input

value: Untreated +estradiol


title: HBB_01_mcpos_gfppos

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt


title: bulktransduced

description:
KS_052622_hdrbooster
1C.txt
S1.3A.txt

value: transduced with mock library (bulk)


title: AID-8h-Input

data_processing:
ChIP-seq: The ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by Samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS. Reads were normalized with fly reference as previous study.
RNA-seq: The RNA-seq data were mapped to the Mus musculus genome (mm9) using HISAT2 with the default parameters and gene counts were extracted by featureCounts. The normalization and differential expression between samples were performed with R package DEseq2.
ATAC-seq: The ATAC-seq data were mapped to the Mus musculus genome (mm9) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by SAMtools and retained the uniquely mapped tags. Enriched peaks were called using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph, bigwig, txt files

growth_protocol: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol: For RING1B, RYBP, HA and FLAG ChIPs, mESCs were fixed with 2.5 mM ethylene glycol- bis(succinimidylsuccinate) (EGS) for 45 min, then washed twice with PBS and fixed again with 1% formaldehyde for 10 min. For the H3K27me3 and RING1B- ChIP experiments , mESCs were only fixed with 1% formaldehyde for 10 min. Fixed mESCs were resuspended in nuclei lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS and protease inhibitors) and sheared to 300- to 500-bp-sized fragments. 100 μl of sheared chromatin was diluted using 900 μl ChIP dilution buffer (50 mM Tris-HCl (pH 8.0), 0.167 M NaCl, 1.1% Triton X-100, 0.11% sodium deoxycholate and protease inhibitors). Diluted chromatin was pre-cleared with Protein A/G beads 1 h before incubating with antibodies overnight at 4 °C. Antibody–chromatin complexes were washed with RIPA150 (50 mM Tris-HCl (pH 8), 0.5 M NaCl, 1 mM EDTA (pH 8), 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate and protease inhibitors) once, RIPA500 twice, RIPA-LiCl (50 mM Tris-HCl (pH 8), 1 mM EDTA (pH 8), 1% NP-40, 0.7% sodium deoxycholate, 0.5 M LiCl and protease inhibitors) twice and 1× TE twice.

value: no


title: npm2 mc+gfp-

description:
OE_0502222_19
S1.2_npm2mc1gfp0.csv
S1.2.csv

value: transduced with mock library and edited with HBB-UBC-GFP (mCherry+, GFP-)


title: NIPBL Untreated +estradiol 72hrs_RAD21_ChIPSeq


title: AID-4h-Input

value: mouse embryonic stem cells


title: npm2 mc+gfp+

description:
OE_0502222_19
S1.2_npm2mc1gfp1.csv
S1.2.csv

value: transduced with mock library and edited with HBB-UBC-GFP (mCherry+, GFP+)


title: npm3 mc+gfp-

description:
OE_0502222_19
S1.2_npm3mc1gfp0.csv
S1.2.csv


title: AID-2h-Input


title: Bulk

description:
OE_0502222_19
S1.2_Bulk.csv


title: HBB3 mc+gfp-

description:
OE_0502222_19
S1.2_HBB3mc1gfp0.csv
S1.2.csv


title: DKO-Input


title: npm3 mc+gfp+

description:
OE_0502222_19
S1.2_npm3mc1gfp1.csv
S1.2.csv


title: AID-0h-Input


title: ATAC-seq_I53A_rep2

extract_protocol:
5×104 viable cells were re-suspended in 50 μl cold ATAC-Resuspension Buffer (10 mM Tris-HCl PH 7.4, 10mM NaCl, 3mM MgCl and 0.1% NP40) and incubated on ice for 3 minutes. The nuclei were pelleted at 500 RCF for 10 min at 4°C, then re-suspended cell pellet in 50 μl of transposition mixture and incubated reaction at 37°C for 30 min in a thermomixer with 1000 rpm mixing.
The ATAC-seq was performed using TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme, China). 200~1000bp fragmented DNA was selected and enriched using AMpure XP (Beckman Coulter, Inc. American).

value: Ring1b I53A


title: HBB3 mc+gfp+

description:
OE_0502222_19
S1.2_HBB3mc1gfp1.csv
S1.2.csv


title: ATAC-seq_WT_rep2

value: WT


title: WT-Input


title: HBB1 mc+gfp+

description:
OE_0502222_19
S1.2_HBB1mc1gfp1.csv
S1.2.csv


title: ChIP-seq_I53A_H1.4_rep2


title: ATAC-seq_WT_rep1


title: ChIP-seq_WT_H1.4_rep1


title: ChIP-seq_RING1B_T8_rep2

value: RING1B (BML, D139-3)


title: Ring1B-I53A-Input


title: ChIP-seq_I53A_H1.4_rep1


title: HBB1 mc+gfp-

description:
OE_0502222_19
S1.2_HBB1mc1gfp0.csv
S1.2.csv


title: ChIP-seq_RING1B_T4_rep2


title: ATAC-seq_I53A_rep1


title: ChIP-seq_RING1B_T4_rep1


title: ChIP-seq_RING1B_T2_rep2


title: ChIP-seq_RING1B_T0_rep2


title: ChIP-seq_RING1B_T2_rep1


title: ChIP-seq_RING1B_T0_rep1


title: ChIP-seq_CBX7_T8_rep2

value: CBX7 (Abcam, ab21873)


title: ChIP-seq_CBX7_T8_rep1


title: ChIP-seq_RING1B_T8_rep1


title: ChIP-seq_CBX7_T4_rep1


title: ChIP-seq_CBX7_T2_rep2


title: ChIP-seq_CBX7_T4_rep2


title: ChIP-seq_CBX7_T2_rep1


title: ChIP-seq_CBX7_T0_rep2


title: ChIP-seq_CBX7_T0_rep1


title: ChIP-seq_DKO_data2_uH2A_rep2


title: ChIP-seq_DKO_data2_uH2A_rep1


title: ChIP-seq_WT_data2_uH2A_rep1

value: Wild type


title: ChIP-seq_DKO_data2_RING1B_rep2


title: ChIP-seq_DKO_data2_RING1B_rep1


title: ChIP-seq_WT_data2_RING1B_rep2


title: tumor-case-58

type: genomic

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained according to manufacturer's protocols.

data_processing: Data was imported into R, normalized (quantile normalization) and failed probes were removed; cross reactive probes and multi-mapped probes were removed as well.

label: Cy3, Cy5

source_name: Skin

label_protocol: As per manufacturer

extract_protocol: As per manufacturer

value: BPDCN

value: tumor

value: male

tag: age

tag: primary location

value: Skin


title: tumor-case-57


title: tumor-case-56

value: female


title: tumor-case-53


title: ChIP-seq_WT_data2_RING1B_rep1


title: tumor-case-44

source_name: Bonemarrow

value: Bonemarrow


title: ChIP-seq_DKO_data2_CBX7_rep2


title: tumor-case-55


title: tumor-case-54


title: tumor-case-46


title: tumor-case-48

source_name: Lymphnode

value: Lymphnode


title: ChIP-seq_DKO_data2_CBX7_rep1


title: tumor-case-43


title: tumor-case-52


title: tumor-case-51


title: tumor-case-38


title: ChIP-seq_WT_data2_CBX7_rep2


title: ChIP-seq_WT_data2_CBX7_rep1


title: tumor-case-41


title: ChIP-seq_DKO_data2_H3K27me3_rep2


title: ChIP-seq_DKO_data2_H3K27me3_rep1


title: tumor-case-40


title: tumor-case-30


title: tumor-case-45


title: ChIP-seq_WT_data2_H3K27me3_rep1


title: tumor-case-37


title: tumor-case-36


title: ChIP-seq_WT_data2_H3K27me3_rep2


title: tumor-case-32


title: tumor-case-31


title: tumor-case-29


title: ChIP-seq_I53A_data1_uH2A_rep1


title: ChIP-seq_I53A_data1_uH2A_rep2


title: ChIP-seq_WT_data1_uH2A_rep2


title: tumor-case-42


title: ChIP-seq_WT_data1_uH2A_rep1


title: tumor-case-34


title: tumor-case-47


title: tumor-case-28

source_name: Mucous membrane

value: Mucous membrane


title: ChIP-seq_I53A_data1_CBX7_rep2


title: ChIP-seq_WT_data1_CBX7_rep2


title: ChIP-seq_I53A_data1_CBX7_rep1


title: ChIP-seq_I53A_data1_H3K27me3_rep1


title: ChIP-seq_WT_data1_CBX7_rep1


title: ChIP-seq_WT_data1_H3K27me3_rep2


title: ChIP-seq_WT_data1_H3K27me3_rep1


title: RNA-seq_data2_QKO_rep3

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions, and complementary DNA was reverse-transcribed using a Perfect Real Time kit (TaKaRa; RR047A).
Libraries were prepared according to the Illumina TruSeq protocol and sequenced using a HiSeq 2000 system at Berry Genomics.


title: tumor-case-25


title: tumor-case-23


title: tumor-case-27


title: RNA-seq_data2_QKO_rep2


title: ChIP-seq_I53A_data1_H3K27me3_rep2


title: RNA-seq_data2_WT_rep3


title: tumor-case-24


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with 4-phenyl butyrate (4-PBA) [Liv_UP8]

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

description: mRNA sequencing

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulat
Genome_build: mice
Supplementary_files_format_and_content: excel sheet of read counts

growth_protocol: 18 weeks old, male c57BL/6j mice into ground-based controls (n = 3) and Hind limb uploaded (HU) mice. HU mice were further divided into two groups and treated with either PBS as the vehicle (HU-v; n = 3) or 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections) (n = 3).

extract_protocol:
Total mRNAs were extracted from liver tissues of the three groups of mice
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directiona

treatment_protocol: HU (n=3) mice were injected with 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections)

value: Liver

tag: agent

value: 4-phenyl butyrate

value: 18 weeks


title: RNA-seq_data2_WT_rep2

value: mouse embryonic stem cells


title: RNA-seq_data2_WT_rep1


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with 4-phenyl butyrate (4-PBA) [Liv_UP7]

description: mRNA sequencing

tag: tissue


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with 4-phenyl butyrate (4-PBA) [Liv_UP5]

description: mRNA sequencing


title: RNA-seq_data2_QKO_rep1

tag: cell type


title: tumor-case-26


title: RNA-seq_data1_I53A_rep3

value: Ring1b I53A


title: RNA-seq_data1_I53A_rep2


title: tumor-case-22


title: tumor-case-19

source_name: Adipose tissue

value: Adipose tissue


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with PBS as vehicle [Liv_U18]

description: mRNA sequencing

value: PBS


title: tumor-case-21


title: tumor-case-16


title: RNA-seq_data1_I53A_rep1


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with PBS as vehicle [Liv_U4]

description: mRNA sequencing


title: RNA-seq_data1_WT_rep3


title: tumor-case-18