title: WT.IP.rep1

description: sRNAseq of ALG-1 IP

data_processing:
Small RNAseq reads were checked for quality before and after filtering using FastQC v0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Cutadapt tool was used to clip the adapter sequence from 3’ end (-a ATCTCGTATGCCGTCTTCTGCTTG -e 0.1).
Reads were split into libraries using fastx barcode splitter utility (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and the remaining 3’ end and 5’ adapter sequences were clipped.
The randomers were trimmed and the reads with a final length range of 17-29 nt were selected for further analysis.
Reads were mapped to C. elegans genome (WS279) using bowtie v1.2.2 (7, 8) allowing three mismatches in the alignment.
Mature miRNA expression was quantified using the miRDeep2 pipeline (9).
The DESeq2 package in R was used to perform differential expression analysis
Assembly: WS279
Supplementary files format and content: xlsx

extract_protocol:
Total (“input”) lysates and “IP” samples were subjected to RNA preparation as described above. Purified RNA was subjected to gel-based size selection.
NEXTflex Small RNA Library Prep kit v3 (PerkinElmer, cat# NOVA-5132) was used to prepare libraries according to the manufacturer’s instructions, followed by size selection of final PCR products. Libraries were sequenced using the Illumina Nextseq500 platform at the Kansas State University Integrated Genomics Facility.


title: null.IP.rep2

status: Public on Dec 30 2023

type: SRA

city: Worcester

first: Ye

last: Duan

state: MA

address: 373 Plantation Street, Biotech Two, Suite 306

country: USA

institute: Umass Medical School

description: sRNAseq of ALG-1 IP

library_source: transcriptomic

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were cultured on nematode growth medium (NGM) and fed with E. coli HB101. To obtain populations of synchronized developing worms, gravid adults were collected and washed twice with water. Pellets of centrifuged worms were treated with 5 ml 1N NaOH and 1% (v/v) sodium hypochlorite for 4 min with shaking to obtain embryos, and the embryos were rinsed with M9 buffer three times. The embryos were hatched in 10 ml M9 buffer at 20°C for 16-18 hrs with mild shaking. Hatched L1 larvae were transferred to plates at 30-50 worms per plate and replicate plates were cultured at 20°C for defined periods of time; samples of the population were examined by microscopy to confirm the developmental stages at the time of harvest.

treatment_protocol: Synchronized populations of developing worms were cultured at 20 °C for 45 hrs after feeding. Harvested worms were washed with water three times and incubated at room temperature for 10 min to allow digestion of intestinal bacteria. Worms were then pelleted by centrifuge at 4,500 rcf for 2 min at room temperature and residual water was removed until the total volumes were twice as the worm pellets. The samples were then flashed frozen by liquid nitrogen and stored at -80 °C.

tag: tissue

value: whole animal

tag: genotype


title: WT.IP.rep2

description: sRNAseq of ALG-1 IP


title: WJL1317_RLF_N019_WT_G2

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

library_source: genomic

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS

molecule: genomic DNA

organism: Mus musculus

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. Indicated inhibitors were added to some of the samples the same day as STI-571.

tag: cell line

value: vAbl-ProB

tag: cell type

value: pro-B cells

value: WT

tag: treatment

tag: well

tag: bait

tag: sample type

value: TAK-700 (Orteronel)


title: null.IP.rep1

description: sRNAseq of ALG-1 IP


title: H751L.IP.rep2

description: sRNAseq of ALG-1 IP


title: WJL1315_RLF_N019_WT_F12

value: Cycling


title: V254I.IP.rep2

description: sRNAseq of ALG-1 IP


title: WJL1314_RLF_N019_WT_F11

value: Vardenafil HCl Trihydrate


title: WJL1313_RLF_N019_WT_F10

value: Clarithromycin


title: G199S.IP.rep2

description: sRNAseq of ALG-1 IP


title: V254I.IP.rep1

description: sRNAseq of ALG-1 IP


title: G199S.rep2.RNAseq

description: mRNA (by rRNA depletion)

data_processing:
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA removal by Bowtie2/2.3.5.1 using C. elegans genome WS279
RPF were mapped to Genome WS279 by Star/2.7.6a with default setting
Gene counting by featureCounts(subread/1.6.2)
Assembly: WS279
Supplementary files format and content: comma-seperated values of gene counts

extract_protocol:
Harvested worms were washed with M9 medium, centrifuged, and the worm pellets were flash-frozen in liquid nitrogen. The worm pellets were thawed and lysed by adding 4X volumes of QIAzol (Qiagen, Cat: 79306) and shaking vigorously at room temperature for 15 min. The total RNA was extracted by the addition of 0.85X volume chloroform, centrifugation, and recovery of the aqueous phase, which was then re-extracted with 1 volume phenol:chloroform:isoamyl alcohol (25:24:1, pH = 5.5). Total RNA was then precipitated by add 1 volume of isopropanol and 0.5 µl GlycoBlue (Invitrogen, Cat: AM9516), followed by incubation at -80oC for at least 30 min, and recovery by centrifugation at 25,000 rcf for 10 min at 4 °C. The supernatants were then removed, and the RNA pellets were subsequently washed twice by 70% (v/v) ethanol, dried in air for 5 min, dissolved in water, and stored at -80 °C. Worm samples for RNA-seq were aliquoted from the ribosome profiling harvests before the lysis step and frozen separately. The total RNA was extracted as described above. To enrich for mRNA, rRNA was depleted as described in detail elsewhere (Duan et al., 2020b). rRNA-depleted mRNA samples were then purified by RNA Clean & Concentrator-5 Kit (ZYMO, Cat: R1015)
Libraries were constructed by NEBNext Ultra II RNA Library Prep kit (NEB, Cat: E7775, E7335, E7500) and sequenced by Illumina NextSeq 500 system
RNAseq (rRNA depletion)


title: G199S.IP.rep1

description: sRNAseq of ALG-1 IP


title: WJ1753_RLF_N020_WT_B4

value: Captopril


title: WJL1312_RLF_N019_WT_F9

value: Sildenafil Citrate


title: WJL1323_RLF_N019_WT_G8

value: Mycophenolate Mofetil


title: WJL1311_RLF_N019_WT_F8

value: Voriconazole


title: WJL1319_RLF_N019_WT_G4

value: Rolipram


title: F180del.rep1.RNAseq

description: mRNA (by rRNA depletion)


title: WJL1322_RLF_N019_WT_G7

value: Avanafil


title: F180del.IP.rep2

description: sRNAseq of ALG-1 IP


title: WJL1309_RLF_N019_WT_F6

value: Apremilast (CC-10004)


title: WJL1316_RLF_N019_WT_G1

value: Pioglitazone HCl


title: F180del.IP.rep1

description: sRNAseq of ALG-1 IP


title: H751L.IP.rep1

description: sRNAseq of ALG-1 IP


title: WJL1308_RLF_N019_WT_F5

value: Ketoconazole


title: WT.total.rep2

description: sRNAseq of total miRNA

value: whole animal


title: WJL1307_RLF_N019_WT_F4

value: vAbl-ProB

value: Cobicistat (GS-9350)


title: WT.total.rep1

description: sRNAseq of total miRNA


title: null.total.rep1

description: sRNAseq of total miRNA


title: H751L.total.rep2

description: sRNAseq of total miRNA


title: WJL1305_RLF_N019_WT_F2

value: pro-B cells

value: WT

value: Ciprofibrate


title: null.total.rep2

description: sRNAseq of total miRNA


title: WJL1303_RLF_N019_WT_E12


title: WJL1302_RLF_N019_WT_E11

value: Rosiglitazone maleate


title: WJL1310_RLF_N019_WT_F7

value: Roflumilast


title: H751L.total.rep1

description: sRNAseq of total miRNA


title: WJL1306_RLF_N019_WT_F3

value: Rosiglitazone HCl


title: V254I.total.rep2

description: sRNAseq of total miRNA


title: WJL1304_RLF_N019_WT_F1

value: Rosiglitazone


title: V254I.total.rep1

description: sRNAseq of total miRNA


title: WJL1301_RLF_N019_WT_E10

value: Abiraterone


title: G199S.total.rep1

description: sRNAseq of total miRNA


title: WJL1300_RLF_N019_WT_E9

value: Amuvatinib (MP-470, HPK 56)


title: WJL1298_RLF_N019_WT_E7

value: Cyclophosphamide monohydrate


title: G199S.total.rep2

description: sRNAseq of total miRNA


title: F180del.total.rep1

description: sRNAseq of total miRNA


title: WJL1297_RLF_N019_WT_E6

value: Tipifarnib (Zarnestra)


title: WJL1299_RLF_N019_WT_E8

value: Methylprednisolone


title: F180del.total.rep2

description: sRNAseq of total miRNA


title: WJL1295_RLF_N019_WT_E4

value: Birinapant (TL32711)


title: WT.rep3.riboseq

description: ribosome protected fragment

data_processing:
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA removal by Bowtie2/2.3.5.1 using C. elegans genome WS279
RPF were mapped to Genome WS279 by Star/2.7.6a with default setting
RPF p-offset and monosome periodosity calculation by olastid/0.4.8
Gene counting by plastid_cs/0.4.8
Assembly: WS279
Supplementary files format and content: comma-seperated values of gene counts
Library strategy: ribosome profiling (Ribo-seq)

extract_protocol:
Concentrated lysis buffer was add to each frozen sample to final concentration of 20 mM Tris-HCl (pH = 7.4), 150 mM NaCl, 5 mM MgCl2, 0.5X Protease Inhibitor (Sigma, Cat:P2714), 1 mM DTT, 0.1 mg/ml cycloheximide (Millipore, Cat:C4859), 1% (v/v) Triton X100 and 5 U/ml Turbo DNase (Invitrogen, Cat:AM2238), and worm pellets were kept on ice until fully thawed. Suspended worms were transferred to 400 µm silica beads tube (OPS Diagnostic, Cat: PFAW-400-100-04) and lysed in bead beater homogenizer for 3 min at 4 °C. Lysates were then centrifuged at 25,000 rcf for 10 min at 4 °C, and supernatants were collected. To generate monosomes, RNase I (Invitrogen, Cat: AM2294) was added to a final concentration of 0.2 U per µl of harvested worm pellet. The digestion was incubated at room temperature for 40 min with gentle rotation and then quenched by adding SUPERase RNase inhibitor (Invitrogen, Cat: AM2694) at 4 U per RNase I unit. The lysates were then loaded onto 5-40 % (m/v) sucrose gradients prepared with lysis buffer without Triton X100 and centrifuged at 32,000 rpm for 3 hrs at 4 °C in an SW41Ti rotor (Beckman Coulter, Cat:331362). The sucrose gradients were fractionated using BR-188 Density Gradient Fractionation System with 60% (m/v) sucrose as chase solution, and monosome fractions were collected according to OD254 profiles. 3.5 X volumes of QIAzol reagent was added to the gradient fractions containing monosomes, and RNA was extracted and separated by 17.5 % denaturing PAGE. A synthetic RNA oligonucleotide with the length of 30 nt was used as a size marker. The gel was stained by Sybr Gold (Invitrogen, Cat: S11494) at room temperature for 10 min, and a gel slice containing RNA of approximately 30 nt was excised and ground by an RNase-free pellet pestle (Fisher Scientific, Cat: 12-141-364). RNA was extracted from the gel slice by adding 500 µl of 300 mM NaAc (pH = 5.5), 1 mM EDTA, and 0.25% (m/v) SDS and mildly shaking overnight at room temperature. The gel granules were excluded using Spin-X tube filter (Millipore, Cat: CLS8160) and the RNA was then concentrated by ethanol precipitation, dissolved in water, and stored at -80 oC. 5’ phosphorylation and 3’ dephosphorylation were performed with T4 PNK (NEB, Cat: M0201S) following the manufacturer’s instructions, and the products were subjected to phenol/chloroform extraction and ethanol precipitation.
Libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB E7300) following the manufacturer’s instructions,  and sequencing was performed using Illumina NextSeq 500 system.


title: WT.rep2.riboseq

description: ribosome protected fragment


title: WJL1294_RLF_N019_WT_E3

value: Thalidomide


title: WJL1293_RLF_N019_WT_E2

value: Pomalidomide (CC-4047)


title: WJL1291_RLF_N019_WT_D12

value: vAbl-ProB


title: null.rep3.riboseq

description: ribosome protected fragment

value: whole animal


title: WJL1292_RLF_N019_WT_E1

value: pro-B cells

value: Lenalidomide (CC-5013)


title: null.rep1.riboseq

description: ribosome protected fragment


title: WJL1288_RLF_N019_WT_D9

value: WT

value: Resveratrol


title: WJL1290_RLF_N019_WT_D11

value: 2-Methoxyestradiol (2-MeOE2)


title: WJL1289_RLF_N019_WT_D10


title: H751L.rep3.riboseq

description: ribosome protected fragment


title: WJL1287_RLF_N019_WT_D8


title: null.rep2.riboseq

description: ribosome protected fragment


title: H751L.rep1.riboseq

description: ribosome protected fragment


title: H751L.rep2.riboseq

description: ribosome protected fragment


title: WJL1283_RLF_N019_WT_D4


title: WJL1286_RLF_N019_WT_D7

value: Thioguanine


title: V254I.rep1.riboseq

description: ribosome protected fragment


title: V254I.rep2.riboseq

description: ribosome protected fragment


title: WJL1296_RLF_N019_WT_E5


title: G199S.rep2.riboseq

description: ribosome protected fragment


title: WJL1285_RLF_N019_WT_D6

value: Entacapone


title: G199S.rep3.riboseq

description: ribosome protected fragment


title: WJL1284_RLF_N019_WT_D5

value: Iniparib (BSI-201)


title: G199S.rep1.riboseq

description: ribosome protected fragment


title: WJL1282_RLF_N019_WT_D3


title: WT.rep1.riboseq

description: ribosome protected fragment


title: V254I.rep3.riboseq

description: ribosome protected fragment


title: F180del.rep3.riboseq

description: ribosome protected fragment


title: F180del.rep2.riboseq

description: ribosome protected fragment


title: WJL1280_RLF_N019_WT_D1


title: F180del.rep1.riboseq

description: ribosome protected fragment


title: WJL1281_RLF_N019_WT_D2

value: BMN 673


title: WJL1279_RLF_N019_WT_C12

value: DMSO


title: WJL1275_RLF_N019_WT_C8

value: Tofacitinib (CP-690550) Citrate


title: WJL1278_RLF_N019_WT_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJL1273_RLF_N019_WT_C6

value: VX-680 (MK-0457,Tozasertib)


title: WJL1277_RLF_N019_WT_C10

value: Tofacitinib (CP-690550,Tasocitinib)


title: d5LNJ2

city: Raleigh

first: Shelly

last: Nolin

state: NC

address: 147 Scott Hall, 2711 Founders, Ashwell Lab

department: Prestage Dept of Poultry Science

institute: NC State University

library_source: other

data_processing:
CLC Genomics Workbench v20 was used for sequence processing
Adapters were trimmed and sequences were checked for quality during import into CLC Genomics Workbench v11
Reads passing quality control grouped into operational taxonomic units (OTUs) based on 97% sequence similarity to reference database SILVA SSU 99 version 138.1
Counts of OTU for each sample were determined and representative sequences were selected from each OTU for taxonomic assignment.
Assembly: SILVA SSU 99 version 138.1
Supplementary files format and content: Text tab delimited Abundance
Library strategy: 16S amplicon sequencing

molecule: other

organism: Gallus gallus

source_name: jejunum

extract_protocol:
Microbial DNA was isolated from intestinal contents using the QiaAmp DNA Stool Mini Kit kit (Qiagen, Hilden, Germany) using the manufacturer protocols.
Libraries for Roche 454 pyrosequencing were constructed at the UNC Microbiome Center based on manufacturer protocol.

value: jejunum

tag: genetic line

value: Low Antibody Selected


title: WJL1274_RLF_N019_WT_C7

value: vAbl-ProB

value: Barasertib (AZD1152-HQPA)


title: d5LNJ6


title: WJL1276_RLF_N019_WT_C9

value: pro-B cells


title: d5LNJ1


title: d5LNJ4


title: WJL1272_RLF_N019_WT_C5

value: WT

value: MLN8237 (Alisertib)


title: d5LNJ3


title: d5LNJ5


title: d5HNJ4

value: High Antibody Selected


title: WJL1269_RLF_N019_WT_C2


title: d5HNJ6


title: d5HNJ3


title: d5HNJ2


title: d5HNJ5


title: WJL1268_RLF_N019_WT_C1

value: Belinostat (PXD101)


title: d5HNJ1


title: WJL1270_RLF_N019_WT_C3

value: Valproic acid sodium salt (Sodium valproate)


title: WJL1267_RLF_N019_WT_B12


title: d5.LNI.6

source_name: ileum

value: ileum


title: d5.LNI.5


title: WJL1266_RLF_N019_WT_B11

value: Pracinostat (SB939)


title: d5.LNI.4

description: Did not pass QC, was not procesed


title: WJL1271_RLF_N019_WT_C4

value: Sodium Phenylbutyrate


title: WJL1262_RLF_N019_WT_B7

value: Rocilinostat (ACY-1215)


title: d5.LNI.3


title: WJL1263_RLF_N019_WT_B8

value: Vorinostat (SAHA, MK0683)


title: WJL1264_RLF_N019_WT_B9

value: Mocetinostat (MGCD0103, MG0103)


title: d5.LNI.2


title: WJL1258_RLF_N019_WT_B3


title: d5.HNI.6


title: WJL1260_RLF_N019_WT_B5

value: Moxonidine


title: d5.HNI.5


title: WJL1259_RLF_N019_WT_B4

value: Captopril


title: WJL1261_RLF_N019_WT_B6

value: Olmesartan medoxomil


title: d5.LNI.1

description: Did not pass QC, was not procesed

value: Low Antibody Selected


title: d5.HNI.3


title: WJL1255_RLF_N019_WT_A12

value: vAbl-ProB


title: d5.HNI.4


title: WJL1257_RLF_N019_WT_B2

value: pro-B cells

value: Raltegravir (MK-0518)


title: WJL1256_RLF_N019_WT_B1

value: WT

value: Empty


title: d5.HNI.2

value: High Antibody Selected


title: d5.LND.6

source_name: duodenum

value: duodenum


title: d5.LND.5


title: WJL1254_RLF_N019_WT_A11

value: Fluorouracil (Adrucil)


title: WJL1253_RLF_N019_WT_A10

value: Elvitegravir (GS-9137)


title: d5.LND.3


title: d5.HNI.1

value: ileum


title: WJL1252_RLF_N019_WT_A9


title: d5.LND.4


title: d5.HND.6

description: Did not pass QC, was not procesed


title: WJL1249_RLF_N019_WT_A6


title: d5.LND.2


title: WJL1250_RLF_N019_WT_A7

value: Doxycycline hyclate


title: WJL1265_RLF_N019_WT_B10


title: WJL1248_RLF_N019_WT_A5

value: Marimastat


title: d5.HND.5


title: d5.HND.2


title: WJL1245_RLF_N019_WT_A2

value: Vildagliptin (LAF-237)


title: d5.LND.1


title: WJL813_RLF_N015_WT_H12

value: Cycling


title: WJL1244_RLF_N019_WT_A1

value: Sitagliptin phosphate monohydrate


title: WJL4141_RLF_N033

state: California

address: 269 Campus Drive

institute: Stanford Medicine

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads from human and mouse were mapped to the hg19 and mm9 reference genomes, respectively, using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Assembly: hg19, mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)
Library strategy: LAM-HTGTS, JoinT-seq

organism: Homo sapiens

source_name: HCT116 DNA-PKcs KD/-

growth_protocol: K562 and its derived cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).  The DNA-PKcs-modified HCT116 cell lines were cultured at 37°C and 5% CO2 in Hyclone α-minimum Eagle's medium supplemented with 5% newborn calf serum, 5% fetal bovine serum (Sigma), and 1× penicillin/streptomycin (Gibco). DNA-PKcs catalytically dead v-Abl cells were cultured in same condition as K562 cells but for the DMEM base medium.

treatment_protocol: G1/G0-arrested K562-Bcl2, K562-Bcl2 PKcs-/- and K562-iCas9 cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with pX330-Cas9-sgRNA or pMCB320-sgRNA to generated twined  DSBs in different compound-treated conditions. The v-Abl cells were arrested by STI-571 for four days to induce V(D)J recombination.

value: HCT116 DNA-PKcs KD/-

value: colorectal carcinoma cells

value: DNA-PKcs KD/-

tag: dsb induction_(bait_site)

tag: dsb induction_(prey_sites)


title: WJL811_RLF_N015_WT_H10

value: vAbl-ProB

value: pro-B cells

value: Anagrelide HCl


title: WJL812_RLF_N015_WT_H11

value: WT

value: Pyrimethamine


title: WJL810_RLF_N015_WT_H9

value: Pralatrexate


title: WJL4139_RLF_N033


title: d5.HND.4

description: Did not pass QC, was not procesed

value: duodenum

value: High Antibody Selected


title: WJL4138_RLF_N033

source_name: HCT116 DNA-PKcs -/-

value: HCT116 DNA-PKcs -/-

value: DNA-PKcs -/-


title: d5.HND.3


title: WJL1247_RLF_N019_WT_A4

value: Atazanavir sulfate (BMS-232632-05)


title: WJL4140_RLF_N033


title: WJL809_RLF_N015_WT_H8

value: S- (+)-Rolipram


title: WJL1251_RLF_N019_WT_A8


title: WJL4136_RLF_N033


title: d5.HND.1


title: WJL1246_RLF_N019_WT_A3

value: Alogliptin (SYR-322)


title: WJL806_RLF_N015_WT_H5

value: Aminophylline


title: WJL803_RLF_N015_WT_H2

value: Gimeracil


title: WJL4137_RLF_N033

value: colorectal carcinoma cells


title: WJL807_RLF_N015_WT_H6

value: Methotrexate


title: WJL801_RLF_N015_WT_G12

value: vAbl-ProB

value: Cycling


title: WJL3718_RLF_N032

value: epithelial-like cells


title: WJL3716_RLF_N032


title: WJL799_RLF_N015_WT_G10

value: pro-B cells

value: WT

value: Rivaroxaban


title: WJL3715_RLF_N032

value: DMSO


title: WJL805_RLF_N015_WT_H4

value: Ozagrel


title: WJL3713_RLF_N032


title: WJL798_RLF_N015_WT_G9

value: Cilostazol


title: WJL4134_RLF_N033

source_name: HCT116 DNA-PKcs +/-

value: HCT116 DNA-PKcs +/-

value: DNA-PKcs +/-


title: WJL796_RLF_N015_WT_G7

value: Avanafil


title: WJL3710_RLF_N032

value: lymphoblast cells


title: WJL804_RLF_N015_WT_H3

value: Dyphylline


title: WJL794_RLF_N015_WT_G5

value: Cilomilast


title: WJL3709_RLF_N032


title: WJL4133_RLF_N033

value: colorectal carcinoma cells


title: WJL792_RLF_N015_WT_G3

value: Tadalafil


title: WJL808_RLF_N015_WT_H7

value: vAbl-ProB

value: Trilostane


title: WJL3707_RLF_N032


title: WJL802_RLF_N015_WT_H1

value: Apixaban


title: WJL788_RLF_N015_WT_F11

value: pro-B cells

value: Vardenafil HCl Trihydrate


title: WJL800_RLF_N015_WT_G11

value: WT

value: Pimobendan


title: WJL3717_RLF_N032

value: epithelial-like cells


title: WJL3714_RLF_N032

value: DMSO


title: WJL3702_RLF_N032


title: WJL786_RLF_N015_WT_F9

value: Sildenafil Citrate


title: WJL3703_RLF_N032


title: WJL3701_RLF_N032


title: WJL797_RLF_N015_WT_G8

value: Mycophenolate Mofetil


title: WJL3712_RLF_N032


title: WJL795_RLF_N015_WT_G6

value: Isotretinoin


title: WJL784_RLF_N015_WT_F7

value: Roflumilast


title: WJL3700_RLF_N032

value: lymphoblast cells

value: Pal + ART558


title: WJL793_RLF_N015_WT_G4

value: Rolipram


title: WJL791_RLF_N015_WT_G2

value: TAK-700 (Orteronel)


title: WJL3706_RLF_N032


title: WJL783_RLF_N015_WT_F6

value: vAbl-ProB

value: Apremilast (CC-10004)


title: WJL3704_RLF_N032


title: WJL3705_RLF_N032


title: WJL790_RLF_N015_WT_G1

value: Pioglitazone HCl


title: WJL3708_RLF_N032


title: WJL789_RLF_N015_WT_F12

value: pro-B cells

value: Cycling


title: WJL787_RLF_N015_WT_F10

value: WT

value: Clarithromycin


title: WJL785_RLF_N015_WT_F8

value: Voriconazole


title: WJL777_RLF_N015_WT_E12


title: WJL776_RLF_N015_WT_E11

value: Rosiglitazone maleate


title: WJL3698_RLF_N032


title: WJL775_RLF_N015_WT_E10

value: Abiraterone


title: WJL3711_RLF_N032


title: WJL3697_RLF_N032


title: WJL3690_RLF_N032

value: Pal + Nu7441-5µM


title: WJL780_RLF_N015_WT_F3

value: Rosiglitazone HCl


title: WJL782_RLF_N015_WT_F5

value: Ketoconazole


title: WJL3695_RLF_N032

value: lymphoblast cells


title: WJL3694_RLF_N032

value: Pal + AZD7648


title: WJL781_RLF_N015_WT_F4

value: Cobicistat (GS-9350)


title: WJL3692_RLF_N032


title: WJL3693_RLF_N032


title: WJL3689_RLF_N032


title: WJL3696_RLF_N032


title: WJL778_RLF_N015_WT_F1

value: Rosiglitazone


title: WJL773_RLF_N015_WT_E8

value: vAbl-ProB

value: Methylprednisolone


title: WJL3686_RLF_N032

value: Pal + Nu7026


title: WJL3691_RLF_N032


title: WJL3699_RLF_N032

value: Pal + ART558


title: WJL3685_RLF_N032

value: Pal + DMSO


title: WJL774_RLF_N015_WT_E9

value: pro-B cells

value: WT

value: Amuvatinib (MP-470, HPK 56)


title: WJL3688_RLF_N032


title: WJL779_RLF_N015_WT_F2

value: Ciprofibrate


title: WJL771_RLF_N015_WT_E6

value: Tipifarnib (Zarnestra)


title: WJL770_RLF_N015_WT_E5


title: WJL3683_RLF_N032


title: WJL768_RLF_N015_WT_E3

value: Thalidomide


title: WJL3684_RLF_N032


title: WJL3687_RLF_N032


title: WJL772_RLF_N015_WT_E7

value: Cyclophosphamide monohydrate


title: WJL762_RLF_N015_WT_D9

value: Resveratrol


title: WJL764_RLF_N015_WT_D11

value: 2-Methoxyestradiol (2-MeOE2)


title: WJL766_RLF_N015_WT_E1

value: Lenalidomide (CC-5013)


title: WJL767_RLF_N015_WT_E2

value: Pomalidomide (CC-4047)


title: CS114_RLF_N032

value: lymphoblast cells

value: Olaparib


title: WJL760_RLF_N015_WT_D7

value: vAbl-ProB

value: Thioguanine


title: WJL763_RLF_N015_WT_D10


title: CS111_RLF_N032

value: DMSO


title: CS120_RLF_N032


title: CS113_RLF_N032


title: CS118_RLF_N032


title: CS119_RLF_N032


title: WJL4135_RLF_N033

value: HCT116 DNA-PKcs +/-

value: colorectal carcinoma cells

value: DNA-PKcs +/-


title: IFNL+IL22 24h-3

city: Gainesville

first: Megan

last: Stanifer

state: FL

address: 1200 Newell Dr

institute: University of Florida

description:
22L-24h-3_S53_R1_00
T84_IL22_INFL_filtered_counts-2.csv

data_processing:
Raw RNA sequencing reads (fastq) were aligned to the Ensembl humanGRCh38genome reference using Rsubread with default settings.
Read summarization was done using featureCounts.
Sequencing and alignment quality was assessed using MultiQC
Differential gene expression analysis was performed using DSeq2
r log transformed data was used for multi-dimensional scaling (MDS) and unsupervised hierarchical clustering analyses.
Assembly: Ensembl humanGRCh38genome
Supplementary files format and content: raw counts for each sample

growth_protocol: T84 cell are grown in 50:50 DMEM:F12, 10% FBS, 1% Pen/Strep at 37oC 21% O2

extract_protocol:
RNA was extracted using a Machery-Nagel RNA isolation kits
500ng of RNA was sent to Genewiz who prepared the library

treatment_protocol: Cells were treated with IFNL, IL_22 or a combination and harvested at 3,6,12 and 24h post-treatment.

value: human colon carcinoma

value: WT


title: IFNL+IL22 24h-2

description:
22L-24h-2_S52_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL+IL22 24h-1

description:
22L-24h-1_S51_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: CS112_RLF_N032


title: WJL761_RLF_N015_WT_D8

value: pro-B cells


title: CS110_RLF_N032


title: WJL759_RLF_N015_WT_D6

value: Entacapone


title: WJL758_RLF_N015_WT_D5

value: Iniparib (BSI-201)


title: WJL769_RLF_N015_WT_E4

value: Birinapant (TL32711)


title: IFNL+IL22 12h-3

description:
22L-12h-3_S50_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: CS109_RLF_N032


title: IFNL+IL22 12h-2

description:
22L-12h-2_S49_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL752_RLF_N015_WT_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJL753_RLF_N015_WT_C12


title: WJL751_RLF_N015_WT_C10

value: Tofacitinib (CP-690550,Tasocitinib)


title: IFNL+IL22 6h-3

description:
22L-6h-3_S47_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL749_RLF_N015_WT_C8

value: Tofacitinib (CP-690550) Citrate


title: IFNL+IL22 3h-3

description:
22L-3h-3_S44_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL765_RLF_N015_WT_D12


title: WJL756_RLF_N015_WT_D3


title: IFNL+IL22 12h-1

description:
22L-12h-1_S48_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL750_RLF_N015_WT_C9


title: WJL748_RLF_N015_WT_C7

value: Barasertib (AZD1152-HQPA)


title: WJL757_RLF_N015_WT_D4


title: WJL755_RLF_N015_WT_D2

value: BMN 673


title: WJL754_RLF_N015_WT_D1

value: vAbl-ProB


title: IFNL+IL22 6h-2

description:
22L-6h-2_S46_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 24h-1

description:
IL-22-24h-1_S39_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 12h-3

description:
IL-22-12h-3_S38_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: WJL743_RLF_N015_WT_C2


title: IL22 24h-2

description:
IL-22-24h-2_S40_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 12h-1

description:
IL-22-12h-1_S36_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 6h-3

description:
IL-22-6h-3_S35_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL+IL22 6h-1

description:
22L-6h-1_S45_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL742_RLF_N015_WT_C1

value: Belinostat (PXD101)


title: IFNL+IL22 3h-2

description:
22L-3h-2_S43_R1_00
T84_IL22_INFL_filtered_counts-2.csv


title: WJL741_RLF_N015_WT_B12

value: DMSO


title: WJL739_RLF_N015_WT_B10


title: WJL745_RLF_N015_WT_C4

value: Sodium Phenylbutyrate


title: WJL746_RLF_N015_WT_C5

value: MLN8237 (Alisertib)


title: WJL747_RLF_N015_WT_C6

value: VX-680 (MK-0457,Tozasertib)


title: IFNL+IL22 3h-1

description:
22L-3h-1_S42_R1_00
T84_IL22_INFL_filtered_counts-2.csv

value: human colon carcinoma


title: IL22 12h-2

description:
IL-22-12h-2_S37_R1_001.
T84_IL22_INFL_filtered_counts-2.csv

value: WT


title: WJL744_RLF_N015_WT_C3

value: pro-B cells

value: Valproic acid sodium salt (Sodium valproate)


title: WJL738_RLF_N015_WT_B9

value: Mocetinostat (MGCD0103, MG0103)


title: WJL737_RLF_N015_WT_B8

value: Vorinostat (SAHA, MK0683)


title: WJL736_RLF_N015_WT_B7

value: Rocilinostat (ACY-1215)


title: WJL735_RLF_N015_WT_B6

value: Olmesartan medoxomil


title: IL22 6h-1

description:
IL-22-6h-1_S33_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 3h-3

description:
IL-22-3h-3_S32_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 24h-3

description:
IL-22-24h-3_S41_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: WJL740_RLF_N015_WT_B11

value: Pracinostat (SB939)


title: IFNL 24h-3

description:
IFN-L-24h-3_S29_R1_001
T84_IL22_INFL_filtered_counts-2.csv

value: 100ng/mL INFL1-3


title: IL22 3h-1

description:
IL-22-3h-1_S30_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: WJL732_RLF_N015_WT_B3


title: IFNL 24h-1

description:
IFN-L-24h-1_S27_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL734_RLF_N015_WT_B5

value: Moxonidine


title: IL22 3h-2

description:
IL-22-3h-2_S31_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: WJL733_RLF_N015_WT_B4

value: vAbl-ProB

value: Captopril


title: IFNL 24h-2

description:
IFN-L-24h-2_S28_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL731_RLF_N015_WT_B2

value: Raltegravir (MK-0518)


title: WJL727_RLF_N015_WT_A10

value: Elvitegravir (GS-9137)


title: IFNL 12h-1

description:
IFN-L-12h-1_S24_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL 6h-2

description:
IFN-L-6h-2_S22_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL729_RLF_N015_WT_A12


title: IFNL 12h-3

description:
IFN-L-12h-3_S26_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL 3h-3

description:
IFN-L-3h-3_S20_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: IL22 6h-2

description:
IL-22-6h-2_S34_R1_001.
T84_IL22_INFL_filtered_counts-2.csv


title: WJL730_RLF_N015_WT_B1

value: Empty


title: WJL723_RLF_N015_WT_A6


title: WJL728_RLF_N015_WT_A11

value: Fluorouracil (Adrucil)


title: IFNL 12h-2

description:
IFN-L-12h-2_S25_R1_001
T84_IL22_INFL_filtered_counts-2.csv

value: human colon carcinoma


title: IFNL 6h-3

description:
IFN-L-6h-3_S23_R1_001
T84_IL22_INFL_filtered_counts-2.csv

value: WT


title: mock 24h-3

description:
Mock-24h-3_S17_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL721_RLF_N015_WT_A4

value: pro-B cells

value: Atazanavir sulfate (BMS-232632-05)


title: IFNL 6h-1

description:
IFN-L-6h-1_S21_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL726_RLF_N015_WT_A9


title: WJL725_RLF_N015_WT_A8


title: mock 24h-1

description:
Mock-24h-1_S15_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL719_RLF_N015_WT_A2

value: Vildagliptin (LAF-237)


title: mock 12h-3

description:
Mock-12h-6_S14_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL718_RLF_N015_WT_A1

value: Sitagliptin phosphate monohydrate


title: mock 12h-2

description:
Mock-12h-4_S13_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL722_RLF_N015_WT_A5

value: Marimastat


title: WJL501_RLF_N013_WT_H9

value: Pralatrexate


title: mock 24h-2

description:
Mock-24h-2_S16_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: mock 6h-2

description:
Mock-6h-2_S10_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL 3h-1

description:
IFN-L-3h-1_S18_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL720_RLF_N015_WT_A3

value: Alogliptin (SYR-322)


title: mock 6h-1

description:
Mock-6h-1_S9_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL504_RLF_N013_WT_H12

value: Cycling


title: mock 3h-2

description:
Mock-3h-2_S7_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: mock 12h-1

description:
Mock-12h-1_S12_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL500_RLF_N013_WT_H8

value: S- (+)-Rolipram


title: mock 6h-3

description:
Mock-6h-4_S11_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: IFNL 3h-2

description:
IFN-L-3h-2_S19_R1_001
T84_IL22_INFL_filtered_counts-2.csv

value: 100ng/mL INFL1-3


title: WJL494_RLF_N013_WT_H2

value: vAbl-ProB

value: Gimeracil


title: WJL502_RLF_N013_WT_H10

value: Anagrelide HCl


title: WJL724_RLF_N015_WT_A7

value: Doxycycline hyclate


title: mock 3h-3

description:
Mock-3h-3_S8_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: mock 3h-1

description:
Mock-3h-1_S6_R1_001
T84_IL22_INFL_filtered_counts-2.csv


title: WJL497_RLF_N013_WT_H5

value: Aminophylline


title: WJL496_RLF_N013_WT_H4

value: Ozagrel


title: WJL492_RLF_N013_WT_G12

value: WT


title: WJL499_RLF_N013_WT_H7

value: pro-B cells

value: Trilostane


title: WJL498_RLF_N013_WT_H6

value: Methotrexate


title: WJ1737_RLF_N020_Bcl2_G1/G0_C12

description: paired DSBs

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Assembly: hg19
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

growth_protocol: K562-Bcl2 cell lines were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing
LAM-HTGTS, JoinT-seq

treatment_protocol: Cycling or G1/G0-arrested K562-Bcl2 cells were transduced with pX330-Cas9-sgRNA or pMCB320-sgRNA to generated twined or genome-wide DSBs in different conditions.

value: lymphoblast cells

value: Palbociclib

tag: compound

value: w/o cutting

tag: well position

tag: number of_raw_reads

tag: number of_filtered_reads


title: WJ1733_RLF_N020_Bcl2_G1/G0_C8

description: paired DSBs


title: WJ1732_RLF_N020_Bcl2_G1/G0_C7

description: paired DSBs

value: Belinostat (PXD101)


title: WJ1729_RLF_N020_Bcl2_G1/G0_C4

description: paired DSBs

value: Mocetinostat (MGCD0103, MG0103)


title: WJL490_RLF_N013_WT_G10

value: Rivaroxaban


title: WJL491_RLF_N013_WT_G11

value: Pimobendan


title: WJL495_RLF_N013_WT_H3

value: vAbl-ProB

value: Dyphylline


title: WJ1731_RLF_N020_Bcl2_G1/G0_C6

description: paired DSBs

value: Pracinostat (SB939)


title: WJL493_RLF_N013_WT_H1

value: Apixaban


title: WJ1730_RLF_N020_Bcl2_G1/G0_C5

description: paired DSBs


title: WJL487_RLF_N013_WT_G7

value: Avanafil


title: WJL503_RLF_N013_WT_H11

value: Pyrimethamine


title: WJ1727_RLF_N020_Bcl2_G1/G0_C2

description: paired DSBs


title: WJ1728_RLF_N020_Bcl2_G1/G0_C3

description: paired DSBs

value: Vorinostat (SAHA, MK0683)


title: WJL489_RLF_N013_WT_G9

value: pro-B cells

value: WT

value: Cilostazol


title: WJ1719_RLF_N020_Bcl2_G1/G0_B6

description: paired DSBs

value: lymphoblast cells


title: WJL484_RLF_N013_WT_G4

value: Rolipram


title: WJ1720_RLF_N020_Bcl2_G1/G0_B7

description: paired DSBs


title: WJ1726_RLF_N020_Bcl2_G1/G0_C1

description: paired DSBs


title: WJ1717_RLF_N020_Bcl2_G1/G0_B4

description: paired DSBs


title: WJL488_RLF_N013_WT_G8

value: Mycophenolate Mofetil


title: WJL480_RLF_N013_WT_F12

value: Cycling


title: WJ1725_RLF_N020_Bcl2_G1/G0_B12

description: paired DSBs

value: Palbociclib

value: w/o cutting


title: WJL482_RLF_N013_WT_G2

value: TAK-700 (Orteronel)


title: WJL478_RLF_N013_WT_F10

value: vAbl-ProB

value: Clarithromycin


title: WJ1715_RLF_N020_Bcl2_G1/G0_B2

description: paired DSBs


title: WJ1721_RLF_N020_Bcl2_G1/G0_B8

description: paired DSBs


title: WJL486_RLF_N013_WT_G6

value: Isotretinoin


title: WJL485_RLF_N013_WT_G5

value: Cilomilast


title: WJL483_RLF_N013_WT_G3

value: Tadalafil


title: WJ1718_RLF_N020_Bcl2_G1/G0_B5

description: paired DSBs


title: WJ1716_RLF_N020_Bcl2_G1/G0_B3

description: paired DSBs


title: WJL477_RLF_N013_WT_F9

value: Sildenafil Citrate


title: WJL475_RLF_N013_WT_F7

value: Roflumilast


title: WJ1706_RLF_N020_Bcl2_G1/G0_A5

description: paired DSBs


title: WJ1707_RLF_N020_Bcl2_G1/G0_A6

description: paired DSBs

value: Pracinostat (SB939)


title: WJ1705_RLF_N020_Bcl2_G1/G0_A4

description: paired DSBs

value: Mocetinostat (MGCD0103, MG0103)


title: WJ1713_RLF_N020_Bcl2_G1/G0_A12

description: paired DSBs


title: WJL476_RLF_N013_WT_F8

value: pro-B cells

value: WT

value: Voriconazole


title: WJ1709_RLF_N020_Bcl2_G1/G0_A8

description: paired DSBs

value: lymphoblast cells


title: WJL474_RLF_N013_WT_F6

value: Apremilast (CC-10004)


title: WJ1708_RLF_N020_Bcl2_G1/G0_A7

description: paired DSBs

value: Belinostat (PXD101)


title: WJL473_RLF_N013_WT_F5

value: Ketoconazole


title: WJ1714_RLF_N020_Bcl2_G1/G0_B1

description: paired DSBs


title: WJL481_RLF_N013_WT_G1

value: Pioglitazone HCl


title: WJL479_RLF_N013_WT_F11

value: vAbl-ProB

value: Vardenafil HCl Trihydrate


title: WJ1699_RLF_N020_Bcl2_H10

description: paired DSBs

value: Anagrelide HCl


title: WJ1701_RLF_N020_Bcl2_H12

description: paired DSBs

value: w/o cutting


title: WJ1702_RLF_N020_Bcl2_G1/G0_A1

description: paired DSBs


title: WJ1703_RLF_N020_Bcl2_G1/G0_A2

description: paired DSBs


title: WJ1704_RLF_N020_Bcl2_G1/G0_A3

description: paired DSBs

value: Vorinostat (SAHA, MK0683)


title: WJL470_RLF_N013_WT_F2

value: Ciprofibrate


title: WJL471_RLF_N013_WT_F3

value: Rosiglitazone HCl


title: WJL472_RLF_N013_WT_F4

value: Cobicistat (GS-9350)


title: WJ1700_RLF_N020_Bcl2_H11

description: paired DSBs

value: Pyrimethamine


title: WJL469_RLF_N013_WT_F1

value: pro-B cells

value: Rosiglitazone


title: WJ1698_RLF_N020_Bcl2_H9

description: paired DSBs

value: Pralatrexate


title: WJL467_RLF_N013_WT_E11

value: WT

value: Rosiglitazone maleate


title: WJ1696_RLF_N020_Bcl2_H7

description: paired DSBs

value: lymphoblast cells

value: Trilostane


title: WJL464_RLF_N013_WT_E8

value: Methylprednisolone


title: WJL463_RLF_N013_WT_E7

value: vAbl-ProB

value: Cyclophosphamide monohydrate


title: WJL466_RLF_N013_WT_E10

value: Abiraterone


title: WJL468_RLF_N013_WT_E12


title: WJL465_RLF_N013_WT_E9

value: Amuvatinib (MP-470, HPK 56)


title: WJL462_RLF_N013_WT_E6

value: Tipifarnib (Zarnestra)


title: WJ1697_RLF_N020_Bcl2_H8

description: paired DSBs

value: S- (+)-Rolipram


title: WJ1695_RLF_N020_Bcl2_H6

description: paired DSBs

value: Methotrexate


title: WJL460_RLF_N013_WT_E4

value: Birinapant (TL32711)


title: WJL458_RLF_N013_WT_E2

value: Pomalidomide (CC-4047)


title: WJ1693_RLF_N020_Bcl2_H4

description: paired DSBs

value: Ozagrel


title: WJL459_RLF_N013_WT_E3

value: pro-B cells

value: Thalidomide


title: WJ1688_RLF_N020_Bcl2_G11

description: paired DSBs

value: Pimobendan


title: WJ1691_RLF_N020_Bcl2_H2

description: paired DSBs

value: Gimeracil


title: WJL461_RLF_N013_WT_E5

value: WT


title: WJ1690_RLF_N020_Bcl2_H1

description: paired DSBs

value: lymphoblast cells

value: Apixaban


title: WJL454_RLF_N013_WT_D10

value: vAbl-ProB


title: WJL457_RLF_N013_WT_E1

value: Lenalidomide (CC-5013)


title: WJ1692_RLF_N020_Bcl2_H3

description: paired DSBs

value: Dyphylline


title: WJ1689_RLF_N020_Bcl2_G12

description: paired DSBs

value: w/o cutting


title: WJ1682_RLF_N020_Bcl2_G5

description: paired DSBs

value: Cilomilast


title: WJL450_RLF_N013_WT_D6

value: Entacapone


title: WJL456_RLF_N013_WT_D12


title: WJ1687_RLF_N020_Bcl2_G10

description: paired DSBs

value: Rivaroxaban


title: WJL455_RLF_N013_WT_D11

value: 2-Methoxyestradiol (2-MeOE2)


title: WJL449_RLF_N013_WT_D5

value: Iniparib (BSI-201)


title: WJ1686_RLF_N020_Bcl2_G9

description: paired DSBs

value: Cilostazol


title: WJ1680_RLF_N020_Bcl2_G3

description: paired DSBs

value: Tadalafil


title: WJ1678_RLF_N020_Bcl2_G1

description: paired DSBs

value: Pioglitazone HCl


title: WJ1679_RLF_N020_Bcl2_G2

description: paired DSBs

value: TAK-700 (Orteronel)


title: WJ1685_RLF_N020_Bcl2_G8

description: paired DSBs

value: Mycophenolate Mofetil


title: WJ1681_RLF_N020_Bcl2_G4

description: paired DSBs

value: Rolipram


title: WJL448_RLF_N013_WT_D4

value: pro-B cells

value: WT


title: WJL451_RLF_N013_WT_D7

value: vAbl-ProB

value: Thioguanine


title: WJ1683_RLF_N020_Bcl2_G6

description: paired DSBs

value: lymphoblast cells

value: Isotretinoin


title: WJ1694_RLF_N020_Bcl2_H5

description: paired DSBs

value: Aminophylline


title: WJL444_RLF_N013_WT_C12

value: DMSO


title: WJ1676_RLF_N020_Bcl2_F11

description: paired DSBs

value: Vardenafil HCl Trihydrate


title: WJL453_RLF_N013_WT_D9

value: Resveratrol


title: WJ1684_RLF_N020_Bcl2_G7

description: paired DSBs

value: Avanafil


title: WJL447_RLF_N013_WT_D3


title: WJ1677_RLF_N020_Bcl2_F12

description: paired DSBs

value: w/o cutting


title: WJL445_RLF_N013_WT_D1


title: WJ1675_RLF_N020_Bcl2_F10

description: paired DSBs

value: Clarithromycin


title: WJL443_RLF_N013_WT_C11

value: Baricitinib (LY3009104, INCB028050)


title: WJL442_RLF_N013_WT_C10

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJL440_RLF_N013_WT_C8

value: Tofacitinib (CP-690550) Citrate


title: WJL439_RLF_N013_WT_C7

value: Barasertib (AZD1152-HQPA)


title: WJL441_RLF_N013_WT_C9

value: pro-B cells


title: WJ1671_RLF_N020_Bcl2_F6

description: paired DSBs

value: Apremilast (CC-10004)


title: WJ1673_RLF_N020_Bcl2_F8

description: paired DSBs

value: Voriconazole


title: WJ1670_RLF_N020_Bcl2_F5

description: paired DSBs

value: Ketoconazole


title: WJ1672_RLF_N020_Bcl2_F7

description: paired DSBs

value: lymphoblast cells

value: Roflumilast


title: WJL435_RLF_N013_WT_C3

value: vAbl-ProB

value: WT

value: Valproic acid sodium salt (Sodium valproate)


title: WJ1669_RLF_N020_Bcl2_F4

description: paired DSBs

value: Cobicistat (GS-9350)


title: WJL434_RLF_N013_WT_C2


title: WJL437_RLF_N013_WT_C5

value: MLN8237 (Alisertib)


title: WJL436_RLF_N013_WT_C4

value: Sodium Phenylbutyrate


title: WJ1668_RLF_N020_Bcl2_F3

description: paired DSBs

value: Rosiglitazone HCl


title: WJ1665_RLF_N020_Bcl2_E12

description: paired DSBs


title: WJ1666_RLF_N020_Bcl2_F1

description: paired DSBs

value: Rosiglitazone


title: WJ1667_RLF_N020_Bcl2_F2

description: paired DSBs

value: Ciprofibrate


title: WJ1674_RLF_N020_Bcl2_F9

description: paired DSBs

value: Sildenafil Citrate


title: WJL431_RLF_N013_WT_B11

value: Pracinostat (SB939)


title: WJ1663_RLF_N020_Bcl2_E10

description: paired DSBs

value: Abiraterone


title: WJL438_RLF_N013_WT_C6

value: pro-B cells

value: VX-680 (MK-0457,Tozasertib)


title: WJ1664_RLF_N020_Bcl2_E11

description: paired DSBs

value: Rosiglitazone maleate


title: WJL432_RLF_N013_WT_B12

value: DMSO


title: WJ1662_RLF_N020_Bcl2_E9

description: paired DSBs

value: lymphoblast cells

value: Amuvatinib (MP-470, HPK 56)


title: WJ1661_RLF_N020_Bcl2_E8

description: paired DSBs

value: Methylprednisolone


title: WJL429_RLF_N013_WT_B9

value: vAbl-ProB

value: WT

value: Mocetinostat (MGCD0103, MG0103)


title: WJL430_RLF_N013_WT_B10


title: WJL428_RLF_N013_WT_B8

value: Vorinostat (SAHA, MK0683)


title: WJ1660_RLF_N020_Bcl2_E7

description: paired DSBs

value: Cyclophosphamide monohydrate


title: WJ1658_RLF_N020_Bcl2_E5

description: paired DSBs


title: WJ1659_RLF_N020_Bcl2_E6

description: paired DSBs

value: Tipifarnib (Zarnestra)


title: WJL425_RLF_N013_WT_B5

value: Moxonidine


title: WJ1657_RLF_N020_Bcl2_E4

description: paired DSBs

value: Birinapant (TL32711)


title: WJL427_RLF_N013_WT_B7

value: Rocilinostat (ACY-1215)


title: WJ1656_RLF_N020_Bcl2_E3

description: paired DSBs

value: Thalidomide


title: WJL423_RLF_N013_WT_B3

value: pro-B cells


title: WJL426_RLF_N013_WT_B6

value: Olmesartan medoxomil


title: WJL433_RLF_N013_WT_C1

value: Belinostat (PXD101)


title: WJL424_RLF_N013_WT_B4

value: Captopril


title: WJ1654_RLF_N020_Bcl2_E1

description: paired DSBs

value: lymphoblast cells

value: Lenalidomide (CC-5013)


title: WJL421_RLF_N013_WT_B1

value: Empty


title: WJL420_RLF_N013_WT_A12

value: vAbl-ProB


title: WJ1653_RLF_N020_Bcl2_D12

description: paired DSBs


title: WJ1655_RLF_N020_Bcl2_E2

description: paired DSBs

value: Pomalidomide (CC-4047)


title: WJ1652_RLF_N020_Bcl2_D11

description: paired DSBs

value: 2-Methoxyestradiol (2-MeOE2)


title: WJL419_RLF_N013_WT_A11

value: WT

value: Fluorouracil (Adrucil)


title: WJ1651_RLF_N020_Bcl2_D10

description: paired DSBs


title: WJ1650_RLF_N020_Bcl2_D9

description: paired DSBs

value: Resveratrol


title: WJ1649_RLF_N020_Bcl2_D8

description: paired DSBs


title: WJL416_RLF_N013_WT_A8


title: WJL415_RLF_N013_WT_A7

value: Doxycycline hyclate


title: WJ1646_RLF_N020_Bcl2_D5

description: paired DSBs

value: Iniparib (BSI-201)


title: WJL417_RLF_N013_WT_A9


title: WJ1648_RLF_N020_Bcl2_D7

description: paired DSBs

value: Thioguanine


title: WJ1644_RLF_N020_Bcl2_D3

description: paired DSBs


title: WJL414_RLF_N013_WT_A6


title: WJL418_RLF_N013_WT_A10

value: Elvitegravir (GS-9137)


title: WJ1643_RLF_N020_Bcl2_D2

description: paired DSBs

value: BMN 673


title: WJL422_RLF_N013_WT_B2

value: pro-B cells

value: Raltegravir (MK-0518)


title: WJL413_RLF_N013_WT_A5

value: Marimastat


title: WJ1642_RLF_N020_Bcl2_D1

description: paired DSBs

value: lymphoblast cells


title: WJL410_RLF_N013_WT_A2

value: Vildagliptin (LAF-237)


title: WJL411_RLF_N013_WT_A3

value: Alogliptin (SYR-322)


title: WJ1641_RLF_N020_Bcl2_C12

description: paired DSBs

value: DMSO


title: WJL412_RLF_N013_WT_A4

value: vAbl-ProB

value: Atazanavir sulfate (BMS-232632-05)


title: WJ1647_RLF_N020_Bcl2_D6

description: paired DSBs

value: Entacapone


title: WJ1640_RLF_N020_Bcl2_C11

description: paired DSBs

value: Baricitinib (LY3009104, INCB028050)


title: vAbl-ProB_Lig4-/-_H12

value: Proof-of-Principle


title: WJ1638_RLF_N020_Bcl2_C9

description: paired DSBs


title: WJL409_RLF_N013_WT_A1

value: WT

value: Sitagliptin phosphate monohydrate


title: vAbl-ProB_Lig4-/-_H11


title: WJ1639_RLF_N020_Bcl2_C10

description: paired DSBs

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJ1645_RLF_N020_Bcl2_D4

description: paired DSBs


title: vAbl-ProB_Lig4-/-_H10


title: WJ1637_RLF_N020_Bcl2_C8

description: paired DSBs

value: Tofacitinib (CP-690550) Citrate


title: vAbl-ProB_Lig4-/-_H9


title: WJ1636_RLF_N020_Bcl2_C7

description: paired DSBs

value: Barasertib (AZD1152-HQPA)


title: WJ1635_RLF_N020_Bcl2_C6

description: paired DSBs

value: VX-680 (MK-0457,Tozasertib)


title: vAbl-ProB_Ku70-/-_H7

value: pro-B cells


title: vAbl-ProB_Ku70-/-_H5


title: WJ1634_RLF_N020_Bcl2_C5

description: paired DSBs

value: MLN8237 (Alisertib)


title: vAbl-ProB_Ku70-/-_H6


title: WJ1632_RLF_N020_Bcl2_C3

description: paired DSBs

value: lymphoblast cells

value: Valproic acid sodium salt (Sodium valproate)


title: vAbl-ProB_WT_H3


title: WJ1631_RLF_N020_Bcl2_C2

description: paired DSBs


title: vAbl-ProB_WT_H2


title: vAbl-ProB_WT_H1


title: WJ1628_RLF_N020_Bcl2_B11

description: paired DSBs

value: Pracinostat (SB939)


title: WJ1629_RLF_N020_Bcl2_B12

description: paired DSBs

value: DMSO


title: WJ1627_RLF_N020_Bcl2_B10

description: paired DSBs


title: vAbl-ProB_Lig4-/-_G12

value: vAbl-ProB


title: vAbl-ProB_Lig4-/-_G10


title: WJ1626_RLF_N020_Bcl2_B9

description: paired DSBs

value: Mocetinostat (MGCD0103, MG0103)


title: vAbl-ProB_Lig4-/-_G11


title: vAbl-ProB_Lig4-/-_G9


title: WJ1624_RLF_N020_Bcl2_B7

description: paired DSBs

value: Rocilinostat (ACY-1215)


title: vAbl-ProB_Ku70-/-_H8


title: vAbl-ProB_Ku70-/-_G8


title: WJ1622_RLF_N020_Bcl2_B5

description: paired DSBs

value: Moxonidine


title: vAbl-ProB_Ku70-/-_G7

value: Proof-of-Principle


title: vAbl-ProB_WT_H4

value: WT


title: WJ1633_RLF_N020_Bcl2_C4

description: paired DSBs

value: Sodium Phenylbutyrate


title: WJ1630_RLF_N020_Bcl2_C1

description: paired DSBs

value: Belinostat (PXD101)


title: vAbl-ProB_Ku70-/-_G5


title: vAbl-ProB_WT_G4


title: WJ1620_RLF_N020_Bcl2_B3

description: paired DSBs


title: vAbl-ProB_WT_G3


title: WJ1618_RLF_N020_Bcl2_B1

description: paired DSBs

value: Empty


title: WJ1619_RLF_N020_Bcl2_B2

description: paired DSBs

value: Raltegravir (MK-0518)


title: WJ1625_RLF_N020_Bcl2_B8

description: paired DSBs

value: Vorinostat (SAHA, MK0683)


title: WJ1617_RLF_N020_Bcl2_A12

description: paired DSBs


title: vAbl-ProB_WT_G2

value: pro-B cells


title: vAbl-ProB_Lig4-/-_F12


title: WJ1616_RLF_N020_Bcl2_A11

description: paired DSBs

value: Fluorouracil (Adrucil)


title: WJ1615_RLF_N020_Bcl2_A10

description: paired DSBs

value: lymphoblast cells

value: Elvitegravir (GS-9137)


title: vAbl-ProB_WT_G1


title: WJ1614_RLF_N020_Bcl2_A9

description: paired DSBs


title: vAbl-ProB_Lig4-/-_F10


title: WJ1623_RLF_N020_Bcl2_B6

description: paired DSBs

value: Olmesartan medoxomil


title: WJ1613_RLF_N020_Bcl2_A8

description: paired DSBs


title: vAbl-ProB_Ku70-/-_F8


title: vAbl-ProB_Lig4-/-_F9


title: vAbl-ProB_Ku70-/-_G6


title: WJ1621_RLF_N020_Bcl2_B4

description: paired DSBs

value: Captopril


title: WJ1612_RLF_N020_Bcl2_A7

description: paired DSBs

value: Doxycycline hyclate


title: vAbl-ProB_Ku70-/-_F7

value: vAbl-ProB


title: WJL446_RLF_N013_WT_D2

value: BMN 673


title: vAbl-ProB_Ku70-/-_F6


title: WJ1608_RLF_N020_Bcl2_A3

description: paired DSBs

value: Alogliptin (SYR-322)


title: WJ1611_RLF_N020_Bcl2_A6

description: paired DSBs


title: vAbl-ProB_WT_F4

value: Proof-of-Principle


title: WJL452_RLF_N013_WT_D8

value: WT


title: WJ1609_RLF_N020_Bcl2_A4

description: paired DSBs

value: Atazanavir sulfate (BMS-232632-05)


title: vAbl-ProB_WT_F2


title: vAbl-ProB_WT_F1


title: vAbl-ProB_WT_F3


title: WJL927_RLF_N016_Bcl2_H11

description: paired DSBs

value: Pyrimethamine


title: WJ1606_RLF_N020_Bcl2_A1

description: paired DSBs

value: Sitagliptin phosphate monohydrate


title: WJL928_RLF_N016_Bcl2_H12

description: paired DSBs

value: w/o cutting


title: WJL926_RLF_N016_Bcl2_H10

description: paired DSBs

value: Anagrelide HCl


title: vAbl-ProB_Lig4-/-_E12

value: pro-B cells


title: vAbl-ProB_Lig4-/-_E10


title: vAbl-ProB_Lig4-/-_F11


title: WJL924_RLF_N016_Bcl2_H8

description: paired DSBs

value: S- (+)-Rolipram


title: vAbl-ProB_Lig4-/-_E9


title: WJL923_RLF_N016_Bcl2_H7

description: paired DSBs

value: lymphoblast cells

value: Trilostane


title: WJL922_RLF_N016_Bcl2_H6

description: paired DSBs

value: Methotrexate


title: vAbl-ProB_Ku70-/-_E8


title: WJ1610_RLF_N020_Bcl2_A5

description: paired DSBs

value: Marimastat


title: WJL921_RLF_N016_Bcl2_H5

description: paired DSBs

value: Aminophylline


title: vAbl-ProB_Ku70-/-_E7

value: vAbl-ProB


title: vAbl-ProB_Ku70-/-_E6


title: vAbl-ProB_Ku70-/-_F5


title: WJL920_RLF_N016_Bcl2_H4

description: paired DSBs

value: Ozagrel


title: WJ1607_RLF_N020_Bcl2_A2

description: paired DSBs

value: Vildagliptin (LAF-237)


title: vAbl-ProB_Ku70-/-_E5

value: Proof-of-Principle


title: WJL919_RLF_N016_Bcl2_H3

description: paired DSBs

value: Dyphylline


title: vAbl-ProB_WT_E4

value: WT


title: vAbl-ProB_Lig4-/-_E11


title: WJL925_RLF_N016_Bcl2_H9

description: paired DSBs

value: Pralatrexate


title: WJL917_RLF_N016_Bcl2_H1

description: paired DSBs

value: Apixaban


title: WJL918_RLF_N016_Bcl2_H2

description: paired DSBs

value: Gimeracil


title: vAbl-ProB_WT_E2


title: WJL916_RLF_N016_Bcl2_G12

description: paired DSBs

value: w/o cutting


title: WJL915_RLF_N016_Bcl2_G11

description: paired DSBs

value: Pimobendan


title: vAbl-ProB_Lig4-/-_D11

value: pro-B cells


title: vAbl-ProB_WT_E1


title: vAbl-ProB_Lig4-/-_D10


title: vAbl-ProB_WT_E3


title: vAbl-ProB_Lig4-/-_D9


title: WJL911_RLF_N016_Bcl2_G7

description: paired DSBs

value: lymphoblast cells

value: Avanafil


title: WJL912_RLF_N016_Bcl2_G8

description: paired DSBs

value: Mycophenolate Mofetil


title: WJL913_RLF_N016_Bcl2_G9

description: paired DSBs

value: Cilostazol


title: vAbl-ProB_Lig4-/-_D12


title: vAbl-ProB_Ku70-/-_D8


title: WJL910_RLF_N016_Bcl2_G6

description: paired DSBs

value: Isotretinoin


title: vAbl-ProB_Ku70-/-_D6

value: vAbl-ProB


title: vAbl-ProB_Ku70-/-_D7


title: WJL909_RLF_N016_Bcl2_G5

description: paired DSBs

value: Cilomilast


title: WJL908_RLF_N016_Bcl2_G4

description: paired DSBs

value: Rolipram


title: vAbl-ProB_Ku70-/-_D5

value: Proof-of-Principle


title: vAbl-ProB_WT_D4


title: WJL907_RLF_N016_Bcl2_G3

description: paired DSBs

value: Tadalafil


title: WJL906_RLF_N016_Bcl2_G2

description: paired DSBs

value: TAK-700 (Orteronel)


title: vAbl-ProB_WT_D3

value: WT


title: WJL905_RLF_N016_Bcl2_G1

description: paired DSBs

value: Pioglitazone HCl


title: WJL904_RLF_N016_Bcl2_F12

description: paired DSBs


title: vAbl-ProB_WT_D2


title: vAbl-ProB_Lig4-/-_C11


title: WJL914_RLF_N016_Bcl2_G10

description: paired DSBs

value: Rivaroxaban


title: vAbl-ProB_Lig4-/-_C10


title: WJL903_RLF_N016_Bcl2_F11

description: paired DSBs

value: Vardenafil HCl Trihydrate


title: vAbl-ProB_WT_D1


title: WJL899_RLF_N016_Bcl2_F7

description: paired DSBs

value: Roflumilast


title: WJL898_RLF_N016_Bcl2_F6

description: paired DSBs

value: Apremilast (CC-10004)


title: vAbl-ProB_Ku70-/-_C8

value: pro-B cells


title: vAbl-ProB_Ku70-/-_C7


title: WJL900_RLF_N016_Bcl2_F8

description: paired DSBs

value: lymphoblast cells

value: Voriconazole


title: WJL902_RLF_N016_Bcl2_F10

description: paired DSBs

value: Clarithromycin


title: vAbl-ProB_Lig4-/-_C9


title: vAbl-ProB_Lig4-/-_C12


title: vAbl-ProB_WT_C3


title: WJL897_RLF_N016_Bcl2_F5

description: paired DSBs

value: Ketoconazole


title: WJL893_RLF_N016_Bcl2_F1

description: paired DSBs

value: Rosiglitazone


title: vAbl-ProB_WT_C1

value: vAbl-ProB


title: WJL896_RLF_N016_Bcl2_F4

description: paired DSBs

value: Cobicistat (GS-9350)


title: vAbl-ProB_Ku70-/-_C5

value: Proof-of-Principle


title: WJL894_RLF_N016_Bcl2_F2

description: paired DSBs

value: Ciprofibrate


title: vAbl-ProB_WT_C4


title: WJL891_RLF_N016_Bcl2_E11

description: paired DSBs

value: Rosiglitazone maleate


title: vAbl-ProB_Lig4-/-_B12


title: WJL895_RLF_N016_Bcl2_F3

description: paired DSBs

value: Rosiglitazone HCl


title: WJL890_RLF_N016_Bcl2_E10

description: paired DSBs

value: Abiraterone


title: WJL892_RLF_N016_Bcl2_E12

description: paired DSBs


title: vAbl-ProB_Lig4-/-_B10


title: WJL901_RLF_N016_Bcl2_F9

description: paired DSBs

value: Sildenafil Citrate


title: vAbl-ProB_Lig4-/-_B11


title: vAbl-ProB_Ku70-/-_C6


title: WJL887_RLF_N016_Bcl2_E7

description: paired DSBs

value: Cyclophosphamide monohydrate


title: vAbl-ProB_Ku70-/-_B8


title: WJL888_RLF_N016_Bcl2_E8

description: paired DSBs

value: Methylprednisolone


title: vAbl-ProB_Ku70-/-_B6


title: WJL884_RLF_N016_Bcl2_E4

description: paired DSBs

value: Birinapant (TL32711)


title: WJL886_RLF_N016_Bcl2_E6

description: paired DSBs

value: Tipifarnib (Zarnestra)


title: vAbl-ProB_Lig4-/-_B9

value: pro-B cells


title: vAbl-ProB_Ku70-/-_B5


title: vAbl-ProB_Ku70-/-_B7


title: vAbl-ProB_WT_B4

value: WT


title: WJL883_RLF_N016_Bcl2_E3

description: paired DSBs

value: lymphoblast cells

value: Thalidomide


title: WJL885_RLF_N016_Bcl2_E5

description: paired DSBs


title: vAbl-ProB_WT_C2


title: vAbl-ProB_WT_B3


title: WJL881_RLF_N016_Bcl2_E1

description: paired DSBs

value: Lenalidomide (CC-5013)


title: vAbl-ProB_WT_B2

value: vAbl-ProB


title: vAbl-ProB_WT_B1


title: vAbl-ProB_Lig4-/-_A12


title: WJL889_RLF_N016_Bcl2_E9

description: paired DSBs

value: Amuvatinib (MP-470, HPK 56)


title: WJL877_RLF_N016_Bcl2_D9

description: paired DSBs

value: Resveratrol


title: vAbl-ProB_Lig4-/-_A11

value: Proof-of-Principle


title: WJL876_RLF_N016_Bcl2_D8

description: paired DSBs


title: WJL880_RLF_N016_Bcl2_D12

description: paired DSBs


title: WJL879_RLF_N016_Bcl2_D11

description: paired DSBs

value: 2-Methoxyestradiol (2-MeOE2)


title: vAbl-ProB_Ku70-/-_A8


title: vAbl-ProB_Lig4-/-_A9


title: vAbl-ProB_Ku70-/-_A7


title: WJL882_RLF_N016_Bcl2_E2

description: paired DSBs

value: Pomalidomide (CC-4047)


title: vAbl-ProB_Lig4-/-_A10


title: vAbl-ProB_Ku70-/-_A6


title: WJL875_RLF_N016_Bcl2_D7

description: paired DSBs

value: Thioguanine


title: WJL870_RLF_N016_Bcl2_D2

description: paired DSBs

value: BMN 673


title: WJL873_RLF_N016_Bcl2_D5

description: paired DSBs

value: Iniparib (BSI-201)


title: WJL878_RLF_N016_Bcl2_D10

description: paired DSBs


title: WJL872_RLF_N016_Bcl2_D4

description: paired DSBs


title: WJL867_RLF_N016_Bcl2_C11

description: paired DSBs

value: Baricitinib (LY3009104, INCB028050)


title: Wt-7 Heart, E14.5

city: Hangzhou

first: Ying

middle: Ying

last: Lin

state: Zhejiang

address: 88 Jiefang Road

department: Department of Cardiology

country: China

institute: Zhejiang University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads. Then about 49 million clean reads for each sample were retained for subsequent analyses. 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. Differential expression genes (DEGs) analysis was performed using the DESeq2. P value<0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly DEGs. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. Based on the hypergeometric distribution, pathway enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0) using database of Go, KEGG and Rectome respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and enrichment analysis circle diagram of the significant enrichment term.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
Embryonic hearts of E14.5 were collected respectively and total RNA were isolated using TRIzol Reagent (Invitrogen, Carlsbad, USA). NanoDrop 2000 spectrophotometer was applied to evaluate the purity and quantity of RNA. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: heart

tag: developmental stage


title: vAbl-ProB_Ku70-/-_A5


title: WJL871_RLF_N016_Bcl2_D3

description: paired DSBs


title: WJL874_RLF_N016_Bcl2_D6

description: paired DSBs

value: Entacapone


title: vAbl-ProB_WT_A4

value: pro-B cells


title: Wt-6 Heart, E14.5

value: WT


title: vAbl-ProB_WT_A3


title: vAbl-ProB_WT_A2


title: WJL868_RLF_N016_Bcl2_C12

description: paired DSBs

value: lymphoblast cells

value: DMSO


title: vAbl-ProB_WT_A1


title: WJL862_RLF_N016_Bcl2_C6

description: paired DSBs

value: VX-680 (MK-0457,Tozasertib)


title: WJL865_RLF_N016_Bcl2_C9

description: paired DSBs


title: Wt-2 Heart, E14.5


title: WJL860_RLF_N016_Bcl2_C4

description: paired DSBs

value: Sodium Phenylbutyrate


title: WJL866_RLF_N016_Bcl2_C10

description: paired DSBs

value: Tofacitinib (CP-690550,Tasocitinib)


title: WJL869_RLF_N016_Bcl2_D1

description: paired DSBs


title: Wt-5 Heart, E14.5


title: Mu-3 Heart, E14.5


title: WJL864_RLF_N016_Bcl2_C8

description: paired DSBs

value: Tofacitinib (CP-690550) Citrate


title: WJL863_RLF_N016_Bcl2_C7

description: paired DSBs

value: Barasertib (AZD1152-HQPA)


title: WJL858_RLF_N016_Bcl2_C2

description: paired DSBs


title: Wt-3 Heart, E14.5


title: Wt-4 Heart, E14.5


title: Mu-2 Heart, E14.5


title: Wt-1 Heart, E14.5


title: WJL861_RLF_N016_Bcl2_C5

description: paired DSBs

value: MLN8237 (Alisertib)


title: WJL857_RLF_N016_Bcl2_C1

description: paired DSBs

value: Belinostat (PXD101)


title: WJL859_RLF_N016_Bcl2_C3

description: paired DSBs

value: Valproic acid sodium salt (Sodium valproate)


title: Mu-4 Heart, E14.5


title: Ko-3 Heart, E14.5


title: Ko-2 Heart, E14.5


title: Ko-1 Heart, E14.5


title: Mu-1 Heart, E14.5


title: WJL855_RLF_N016_Bcl2_B11

description: paired DSBs

value: Pracinostat (SB939)


title: WJL853_RLF_N016_Bcl2_B9

description: paired DSBs

value: Mocetinostat (MGCD0103, MG0103)


title: WJL854_RLF_N016_Bcl2_B10

description: paired DSBs


title: WJL851_RLF_N016_Bcl2_B7

description: paired DSBs

value: Rocilinostat (ACY-1215)


title: wtgl6.3077-biol rep 2

city: Montreal

first: Jiannis

last: Ragoussis

state: Quebec

address: 740, Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Sequences were aligned using Hisat first against the mouse transcriptome as defined by Gencode gene models M16, with default parameters and the remaining unmapped genes to the Ensembl GRCm38 reference mouse genome .  Aligned reads from multiple read groups belonging to the same sample were indexed, sorted, and merged using sambamba v0.5.4 , a faster implementation of the Samtools algorithms . Amplification duplicates were removed using Picard tools v1.128. Various quality controls from the RNASEQC package were used, including the genes detected, mapping rates, duplication rates, and intronic rate, based on metrics collected for each sample used . HTSeq Count  was applied to enumerate the counts for each gene using the Gencode M16 GTF. All statistical analyses were carried out with R v3.6.2.
Differential expression, and principal component analysis (PCA) was performed using Deseq2 and R standard packages.
Assembly: GRCm38
Supplementary files format and content: raw_counts.csv.gz contains the raw counts, expression matrix, obtained from the alignment pipeline (primary analysis)
Supplementary files format and content: normalized_counts_merge.csv.gz contains the normalized count matrix used for differential expression analysis (secondary analysis)

source_name: Mammary Gland

extract_protocol:
Primary tissues (tumor or gland) were isolated from mammary by stepwise mechanical disruption and enzymatic digestion according to our published protocols. Tissues (tumor or gland) were harvested from 6- to 10-wk-old mice, minced with a scalpel, and incubated for digestion for 2 h at 37 °C with gentle rocking in FBS free DMEM (Multicell, Wisent Inc., St. Bruno, Quebec, Canada) supplemented with 2.4 mg/ml collagenase B and 5U/ml Dispase II (4942078001, Roche, Switzerland). Tissue fragments were washed with PBS, centrifuged, and resuspended in DMEM with 10 % Fetal Bovine Serum (Gibco, US Origin), 100 IU/mL penicillin and 100 ug/mL streptomycin (Multicell, Wisent Inc., St. Bruno, Quebec, Canada).
Ribosomal RNA (rRNA) depletion was achieved using an Illumina Ribo-Zero Magnetic kit. First strand cDNA synthesis used Super strand synthesis Act D kit containing random primers and Super Script II reverse transcriptase to convert the original mRNA to complementary cDNA. Second strand cDNA synthesis involves removal of the original RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. After cDNA synthesis, a single “A” nucleotide is added to the 3’ ends of the blunt fragments to prevent them from ligating to one another during the adapter ligation reaction. During adapter ligation process, each sample has a different RNA adapter index for the identification in subsequent data analyses (Illumina® Nextera™ DNA Unique Dual Indexes). AMPure XP beads were used to purify the ds cDNA from the second strand reaction mix and leaving exclusively the blunt-ended cDNA for the subsequent DNA enrichment. The PCR was performed with a PCR primer cocktail that anneals to the ends of the adapters in order to exclusively enrich and amplify those DNA fragments that have adapter molecules on both ends. Only the first strand cDNAs were amplified in this step. Quantification by LightCycler® 96 Instrument with KAPA library quantification kit.
The RNAseq transcriptome strand library was prepared by following the TruSeqTM Stranded Total RNA kit from Illumina (San Diego, CA, USA) using 100 ng of total RNA for each sample. Paired-end RNA-seq library was sequenced with Illumina NovaSeq6000 at McGill Genome Center according to the standard protocol.

value: Mammary Gland

tag: collection weeks

value: mammary epithelium

value: Pthrpwt/wt


title: wt10tu.3070-biol rep 3

source_name: Breast cancer

tag: tissue

value: Breast cancer


title: WJL852_RLF_N016_Bcl2_B8

description: paired DSBs

value: lymphoblast cells

tag: genotype

value: Vorinostat (SAHA, MK0683)


title: WJL850_RLF_N016_Bcl2_B6

description: paired DSBs

tag: cell line

value: Olmesartan medoxomil


title: wtgl10.3069-biol rep 2

tag: cell type


title: WJL849_RLF_N016_Bcl2_B5

description: paired DSBs

tag: treatment

value: Moxonidine


title: wtgl8.3065-biol rep 2


title: wtgl6.3048-biol rep 1


title: WJL848_RLF_N016_Bcl2_B4

description: paired DSBs

value: Captopril


title: WJL847_RLF_N016_Bcl2_B3

description: paired DSBs


title: kotu10_3041-biol rep 3

value: Pthrpflox/flox


title: WJL846_RLF_N016_Bcl2_B2

description: paired DSBs

value: Raltegravir (MK-0518)


title: WJL845_RLF_N016_Bcl2_B1

description: paired DSBs

value: Empty


title: kotu10_3040-biol rep 2


title: wttu6.3045-biol rep 3


title: Ko-4 Heart, E14.5

value: heart


title: kotu10_3039-biol rep 1


title: WJL842_RLF_N016_Bcl2_A10

description: paired DSBs

value: Elvitegravir (GS-9137)


title: WJL843_RLF_N016_Bcl2_A11

description: paired DSBs

value: Fluorouracil (Adrucil)


title: WJL844_RLF_N016_Bcl2_A12

description: paired DSBs


title: WJL841_RLF_N016_Bcl2_A9

description: paired DSBs


title: WJL856_RLF_N016_Bcl2_B12

description: paired DSBs

value: DMSO


title: WJL840_RLF_N016_Bcl2_A8

description: paired DSBs


title: kogl8_3035-biol rep 2


title: KO, scRNA-seq

city: Charlottesville

first: Uma Devi

last: Paila

address: 1335 Lee St

institute: University of Virginia

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 7.0
Seurat R package v4.3 was used for downstream analysis; Data was filtered to include features that were detected in at least three cells, and cells were selected based on their expression of at least 200 features.
Assembly: mm10
Supplementary files format and content: Hierarchical Data Format (HDF5) for the filtered feature-barcode matrices from the Cell Ranger output

molecule: polyA RNA

source_name: P5, RETINAL

extract_protocol:
Retinal endothelial cells from P5 Alk1fl/fl, Alk1fl/fl treated with CDK4/6i, Alk1ECiKO, and Alk1ECiKO treated with CDK4/6i animals were isolated using a previously described and published method optimized for purification and viability. Dissected retinas were digested with Collagenase Type II (1.0 mg/mL, Gibco Cat# 17101015) in DMEM (Gibco Cat# 21013024) and 10% FBS (Gibco Cat# 26140079) for 20 min, washed, immunolabeled with anti-CD31 and anti-CD45 in staining buffer (HBSS with 10% FBS, 20 mM HEPES, 1 mg/mL D-Glucose), then resuspended in FACS buffer (PBS with 1% FBS). FACS-purified live single cell suspensions were submitted to the University of Virginia Genome Analysis and Technology Core (RRID:SCR_018883) for single cell RNA library preparation and next-generation sequencing.
Single cell RNA libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (PN-1000121) and Chromium Controller. Next-generation sequencing was performed using an Illumina NextSeq 2000 Sequencing System on the P3 flow cell with a 100 bp paired-end sequencing reagent kit.

value: P5, RETINAL

value: Endothelial

value: KO


title: CONTROL, scRNA-seq

value: CONTROL


title: kotu8_3033-biol rep 2

value: Breast cancer

value: mammary epithelium


title: kotu8_3036-biol rep 3


title: wttu6.3030-biol rep 2

value: Pthrpwt/wt


title: CONTROL-CDKi, scRNA-seq

value: CONTROL-CDKi


title: KO-CDKi, scRNA-seq

value: KO-CDKi


title: WJL838_RLF_N016_Bcl2_A6

description: paired DSBs

value: lymphoblast cells


title: wttu12.3029-biol rep 1


title: WJL836_RLF_N016_Bcl2_A4

description: paired DSBs

value: Atazanavir sulfate (BMS-232632-05)


title: WJL837_RLF_N016_Bcl2_A5

description: paired DSBs

value: Marimastat


title: wtgl12.3027-biol rep 2

value: Mammary Gland


title: kogl10_3038-biol rep 2

value: Pthrpflox/flox


title: US-1467250_6-VIS05-D37_L5.D707

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw read counts for all the detected genes

source_name: PBMC

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq; 51bp PE

value: PBMC

tag: subject id

tag: time point

value: One week after 2nd vaccination


title: US-1574033_9-VIS02-D0_L6.D702

value: PreVac


title: US-1467247_15-VIS05-D37_L8.D702


title: US-1574064_14-VIS02-D0_L6.D709


title: US-1467245_16-VIS05-D37_L8.D705


title: US-1574058_7-VIS02-D0_L5.D708


title: US-1467249_2-VIS05-D37_L2.D706


title: US-1467243_15-VIS04-D31_L8.D701

value: One day after 2nd vaccination


title: US-1467242_2-VIS04-D31_L2.D705


title: WJL835_RLF_N016_Bcl2_A3

description: paired DSBs

value: Alogliptin (SYR-322)

tag: bait


title: kogl8_3034-biol rep 1


title: wtgl12.3026-biol rep 1


title: US-1467240_20-VIS02-D0_L2.D701


title: WJL834_RLF_N016_Bcl2_A2

description: paired DSBs

value: Vildagliptin (LAF-237)


title: kotu12_3015-biol rep 3


title: WJL839_RLF_N016_Bcl2_A7

description: paired DSBs

value: Doxycycline hyclate


title: US-1467234_7-VIS05-D37_L4.D710


title: kotu12_3013-biol rep 2

value: Breast cancer


title: WJL833_RLF_N016_Bcl2_A1

description: paired DSBs

value: Sitagliptin phosphate monohydrate


title: US-1467231_8-VIS05-D37_L6.D701


title: US-1467226_1-VIS05-D37_L2.D703


title: Z-138, PRMT5 Sensitive  [Z-138_R-Control]

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

description:
ZS
Z-138_R-Control

data_processing:
library strategy: WES
Alignment to hg38 by bwa mem, variant calling by Sentieon against the hg38 reference using the Twist Exome panel
Variant annotation by dbSNP 138 and Mills & 1000 genomes. Somatic variants were called with Sentieon TNscope in between different groups, taking one sample as "germline" and the other as "tumor".
Assembly: hg38
Supplementary files format and content: tab-delimited text files

source_name: lymphoma

extract_protocol: Total DNA was extracted using the Monarch® Genomic DNA Purification Kit (NEB Cat# T3010S) and integrity integrity was verified using the Qubit 4 Fluorometer and the Tapestation Genomic DNA Bioanalyzer.

value: lymphoma

value: Mantle Cell Lymphoma

value: MCL

value: Vehicle Control


title: wttu6.3002-biol rep 1

value: mammary epithelium

value: Pthrpwt/wt


title: US-1467225_17-VIS02-D0_L1.D706


title: kotu8_2971-biol rep 1


title: Z-138, PRMT5 Resistant [Z-138_PR]

description:
ZR
Z-138_PR


title: US-1467217_4-VIS02-D0_L3.D711


title: US-1467220_6-VIS02-D0_L4.D705


title: US-1467215_2-VIS02-D0_L2.D704


title: US-1467218_17-VIS05-D37_L8.D708


title: US-1467221_17-VIS04-D31_L8.D707


title: kotu12_2944-biol rep 1


title: SP53, PRMT5 Sensitive  [SP53_R-Control]

description:
SS
SP53_R-Control


title: kogl12_2945-biol rep 2

value: Mammary Gland


title: SP53, PRMT5 Resistant [SP53-R]

description:
SR
SP53-R


title: US-1467209_4-VIS04-D31_L3.D712


title: US-1467192_6-VIS04-D31_L4.D706


title: US-1467198_7-VIS04-D31_L4.D709


title: US-1467203_8-VIS04-D31_L5.D712


title: CCMCL, PRMT5 Resistant [CCMCL-R]

description:
CR
CCMCL-R

value: CCMCL


title: US-1467190_1-VIS02-D0_L2.D701

value: PBMC


title: Rec-1, PRMT5 Sensitive [Rec-1_R-Control]

description:
RS
Rec-1_R-Control


title: wttu8.2880-biol rep 3


title: US-1467188_15-VIS02-D0_L7.D712


title: wttu8.2875-biol rep 2


title: US-1467232_8-VIS02-D0_L5.D711


title: CCMCL, PRMT5 Sensitive  [CC1]

description:
CS
CC1


title: US-1467186_20-VIS04-D31_L1.D702


title: kogl10_2862-biol rep 1

value: Pthrpflox/flox


title: US-1467183_4-VIS05-D37_L4.D701

value: One week after 2nd vaccination


title: PDX MCL, PRMT5 Short-term treated 2 [PDX_AA_Sentinel_C-1]

description:
PRTS2
PDX_AA_Sentinel_C-1

value: PDX AA MCL


title: US-1467211_16-VIS02-D0_L1.D703

value: PreVac


title: Rec-1, PRMT5 Resistant [Rec-1]

description:
RR
Rec-1


title: US-1467176_20-VIS05-D37_L2.D703


title: US-1465329_22-VIS02-D0_L2.D704


title: US-1465325_14-VIS05-D37_L7.D711


title: US-1465331_19-VIS05-D37_L2.D711


title: PDX MCL, PRMT5 Short-term treated 1 [P6_13]

description:
PRTS1
P6_13


title: wttu8.2849-biol rep 1


title: PDX MCL, Untreated 1 [P6_8]

description:
U
P6_8


title: wttu10.2781-biol rep 2


title: wtgl8.2882-biol rep 1


title: US-1465321_14-VIS04-D31_L7.D710

value: One day after 2nd vaccination


title: PDX MCL, PRMT5 Resistant treated 1 [P6_1 ]

description:
PRTR1
P6_1


title: US-1465322_3-VIS05-D37_L3.D709


title: wtgl10.2771--biol rep 1


title: US-1465315_22-VIS04-D31_L2.D705


title: US-1465313_5-VIS02-D0_L4.D702


title: Rec-1, PRMT5 Sensitive Treated 3

description:
Rec-1 PRT 3
RSPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

data_processing:
STAR two-pass alignment and featureCounts
Pairwise comparisons within each cell type for treatment vs control with DESeq2
Assembly: hg38 and Gencode v33
Supplementary files format and content: tab-delimited text files

growth_protocol: PDX in vivo

extract_protocol:
Total RNA was extracted using the Total RNA Purification Kit (Norgen Cat#17200) and QIAshredder Columns (Qiagen Cat#79654). RNA integrity was interrogated using the Agilent 2100 Bioanalyzer.
TrueSeq stranded mRNA libraries were prepared with Poly-A selection Ribodepletion library prep


title: US-1465308_13-VIS04-D31_L6.D707


title: wttu10.2770-biol rep 1


title: Rec-1, PRMT5 Sensitive Treated 2

description:
Rec-1 PRT 2
RSPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: US-1465300_22-VIS05-D37_L2.D706


title: US-1465297_13-VIS02-D0_L7.D706


title: Rec-1, PRMT5 Sensitive Treated 1

description:
Rec-1 PRT 1
RSPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: YC5-OE-setdb1, 24h,rep3

city: yangling

first: guo

last: ming

state: shanxi province

address: 22 Xinong Road, Yangling Demonstration Zone, Yangling District, Xianyang City

department: College of Animal Science and Technology

institute: Northwest Agriculture & Forestry University

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination
And After removed the low quality bases and undetermined bases ,we used HISAT2 software  to map reads to the genome ,The mapped reads of each sample were assembled using StringTie  with default parameters
The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf output.gtf-lsample input.bam)
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM

extract_protocol:
Total RNA was using Trizol regent(Invitrogen,CA,USA) following the manufacture's.The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard I11umina protocols

value: spermatogonia cells

tag: time


title: US-1465291_19-VIS02-D0_L1.D709


title: YC5-OE-setdb1, 24h,rep2


title: US-1465290_9-VIS05-D37_L7.D704


title: kogl12_2857-biol rep 1


title: Rec-1, PRMT5 Sensitive Untreated 3

description:
Rec-1 DMSO 3
RSU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: DMSO


title: US-1465285_5-VIS05-D37_L5.D704


title: YC5-OE-setdb1, 24h,rep1


title: US-1465282_26-VIS04-D31_L3.D708


title: US-1465277_3-VIS04-D31_L3.D708


title: YC5-OE-CTR, 24h,rep3


title: Rec-1, PRMT5 Sensitive Untreated 2

description:
Rec-1 DMSO 2
RSU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: YC5-OE-CTR, 24h,rep2


title: Rec-1, PRMT5 Sensitive Untreated 1

description:
Rec-1 DMSO 1
RSU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: US-1465303_5-VIS04-D31_L5.D703


title: US-1465259_26-VIS02-D0_L3.D707


title: YC5-OE-CTR, 24h,rep1


title: US-1465261_9-VIS04-D31_L6.D703


title: YC5, 24h,rep3


title: Rec-1, PRMT5 Resistant Treated 2

description:
Rec-1 PR PRT 2
RRPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: YC5, 24h,rep2


title: US-1457772_13-VIS05-D37_L6.D708


title: Placenta E10.5 Female 3 RRBS

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Trimming of adapter and poor quality reads with trim_galore (v0.3.3)
Align to genome and get methylation calls with bsmap (2.90)
Assembly: mm10
Supplementary files format and content: tab-delimited files including CpG sites coordinate, coverage, methylation values
Supplementary files format and content: Input files for the methylKit package

source_name: Placenta

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen) following manufacturer's recommendations
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published prototol (Legault, LM. Bio-Protocol, 2019). Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing. Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplificaton.

value: Placenta

tag: gender

value: female


title: Placenta E10.5 Female 2 RRBS


title: US-1456725_1-VIS04-D31_L2.D702


title: YC5, 24h,rep1


title: Rec-1, PRMT5 Resistant Untreated 3

description:
Rec-1 PR DMSO 3
RRU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: lymphoma

value: Mantle Cell Lymphoma


title: Rec-1, PRMT5 Resistant Treated 3

description:
Rec-1 PR PRT 3
RRPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt

value: MCL


title: Rec-1, PRMT5 Resistant Untreated 2

description:
Rec-1  PR DMSO 2
RRU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Placenta E10.5 Male 3 RRBS

value: male


title: GC1, 24h,rep3

value: WT


title: US-1465275_3-VIS02-D0_L3.D707


title: US-1465266_19-VIS04-D31_L1.D710


title: Placenta E10.5 Male 2 RRBS


title: Z-138, PRMT5 Sensitive Treated 3

description:
Z-138 PRT 3
ZSPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Placenta E10.5 Male 1 RRBS


title: Rec-1, PRMT5 Resistant Untreated 1

description:
Rec-1 PR DMSO 1
RRU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: US-1465251_26-VIS05-D37_L3.D709


title: US-1456777_16-VIS04-D31_L8.D704


title: Z-138, PRMT5 Sensitive Treated 2

description:
Z-138 PRT 2
ZSPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Rec-1, PRMT5 Resistant Treated 1

description:
Rec-1 PR PRT 1
RRPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: GC1, 24h,rep1


title: IRE1_KO_ITD_GMP_rep1

first: Akanksha

last: Verma

address: 1300, York Avenue

department: Department of Physiology and Biophysics

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

extract_protocol:
Total RNA from cells was isolated using the TRIzol reagent
Libraries were prepared using the SMART-Seq v4 UltraTM Low Input kit (Takara Bio, #634891) followed by Illumina’s Nextera XT DNA Library Preparation kit (FC-131-1096, Illumina)

treatment_protocol: Cells were FACS-sorted from bone marrow and assayed subsequently by RNA-Seq

tag: strain background

tag: genotype/variation

value: bone marrow (BM)


title: IRE1_KO_ITD_LSK_rep2

value: Lin-Sca1+cKit+ (LSK)


title: IRE1_KO_ITD_GMP_rep2


title: IRE1_KO_ITD_LSK_rep3


title: IRE1_KO_ITD_GMP_rep3


title: Z-138, PRMT5 Sensitive Treated 1

description:
Z-138 PRT 1
ZSPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: IRE1_KO_GMP_rep1

value: Ern1(fl/fl)-VavCre (IRE1_KO)


title: Z-138, PRMT5 Sensitive Untreated 2

description:
Z-138 DMSO 2
ZSU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: 5XFAD, TCR, rep2

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: Gross Hall, 845 Health Sciences Rd

institute: University of California, Irvine

description:
5XFAD-2 RNA enriched for T cell receptor sequences, T cells from a pool of 3 female 5XFAD mouse brains. WT-2 and 5XFAD-2 samples were sequenced in a separate run from the rest of the samples.
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
5XFAD-2_TCR

data_processing:
Gene expression and V(D)J FASTQ files from each sample were aligned to the GRCm38 (mm10) mouse transcriptome with the 10x Genomics Cell Ranger 6.0.1 multi command, using references provided by 10x Genomics (“refdata-gex-mm10-2020-A” for gene expression and “refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0” for V(D)J alignment). For cellranger multi, “expect-cells” was set to 10,000 and all other arguments were set to default. Results from all samples were combined using cellranger aggr, with “normalize” set to none.
Assembly: GRCm38 (mm10)
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, & matrix.mtx.gz: Gzipped tab-separated files which together provide RNA count information for all samples. These are generated by CellRanger and is the filtered matrix (containing only barcodes that CellRanger determined are likely to be a cell and not background). Barcode ending numbers correspond to samples as follows: 1 = WT-1, 2 = WT-2, 3 = 5XFAD-1, 4 = 5XFAD-2, 5 = PS19, 6 = PS-5X
Supplementary files format and content: csv files are comma-separated files describing clonotype information. Barcodes in these files correspond to barcodes in the count matrix. See https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/output/annotation for file descriptions.

source_name: Brain parenchyma

growth_protocol: All mice were group housed on a 12h/12h light/dark cycle with access to food and water ad libitum. PS19 transgenic mice (Strain #:008169; B6C3F1/J) and 5XFAD mice (Strain #034848, C57BL6 congenic) were purchased from the Jackson Laboratories. PS19 mice express mutant human microtubule-associated protein tau (MAPT) driven by the mouse prion protein promoter. Hemizygous PS19 and hemizygous 5XFAD mice were crossed to create a colony of mice that carried one of four genotypes; WT/WT, bigenic PS19+/0/5XFAD+/0, PS19+/0/WT, or WT/5XFAD+/0.  The colony was subsequently expanded via additional crosses of PS19 and 5XFAD hemizygous F1 progeny. Strain-matched female littermates from each of the four genotypes were used for single cell experiments.

extract_protocol:
Female WT, 5XFAD, PS19, and PS-5X mice were sacrificed at 9 months of age by carbon dioxide asphyxiation and spleen, deep cervical lymph nodes, and blood were gently removed prior to intracardiac perfusion with 0.01M phosphate buffered saline (PBS). Half-brains were immediately placed in complete RPMI medium, cut into fine pieces and placed in dissociation tubes along with Collagenase IV+ DNase1 in complete RPMI. Tissue was then placed into a gentleMACS Dissociator for 30 mins on the ABDK setting at 37°C and then filtered through 70μm strainers. Further removal of myelin and debris was conducted using 23% Percoll density gradient centrifugation. For sorting, cells were then stained with the following antibodies: APC-CD8, APC-Cy7-CD45, FITC-CD4, PE-TCRg/d, BV421-CD11b, and PI (all with 1:200 dilution). CD4+, CD8+, and γδ+ T cells were then sorted on a BD FACSAria II and cells from multiple mice were pooled for each genotype into 2 samples each for WT and 5XFAD and 1 sample each of PS19 and PS-5X: n=10 WT#1, n=8 WT#2, n=4 5XFAD#1, n=3 5XFAD#2, n=4 PS19, n=4 PS-5X.
Single cell 5’ gene expression libraries and single cell V(D)J enriched libraries were prepared according to the 10x Genomics Chromium Single Cell 5' Reagent Kits User Guide v2 (Dual Index) (CG000331 Rev C). The 10x Genomics workflow was followed according to the manufacturer protocol and libraries were pooled at equimolar concentrations for sequencing on an Illumina NovaSeq 6000, targeting 50,000 reads per cell for gene expression and 5,000 reads per cell for TCR expression.

value: Brain parenchyma

value: CD3+ T cells


title: IRE1_KO_GMP_rep2


title: PS19, TCR

description:
PS19 RNA enriched for T cell receptor sequences, T cells from a pool of 4 female PS19 mouse brains
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
PS19_TCR


title: GC1, 24h,rep2


title: IRE1_KO_ITD_LSK_rep1


title: 5XFAD, TCR, rep1

description:
5XFAD-1 RNA enriched for T cell receptor sequences, T cells from a pool of 4 female 5XFAD mouse brains
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
5XFAD-1_TCR


title: IRE1_KO_LSK_rep2


title: IRE1_KO_GMP_rep3


title: PS-5X, TCR

description:
PS-5X RNA enriched for T cell receptor sequences, T cells from a pool of 4 female PS-5X mouse brains
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
PS-5X_TCR


title: Z-138, PRMT5 Sensitive Untreated 1

description:
Z-138 DMSO 1
ZSU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: WT, TCR, rep2

description:
WT-2 RNA enriched for T cell receptor sequences, T cells from a pool of 8 female WT mouse brains. WT-2 and 5XFAD-2 samples were sequenced in a separate run from the rest of the samples.
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
WT-2_TCR


title: Z-138, PRMT5 Sensitive Untreated 3

description:
Z-138 DMSO 3
ZSU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: WT, TCR, rep1

description:
WT-1 RNA enriched for T cell receptor sequences, T cells from a pool of 10 female WT mouse brains
filtered_contig_annotations.csv
consensus_annotations.csv
clonotypes.csv
WT-1_TCR


title: Z-138, PRMT5 Resistant Treated 3

description:
Z-138 PR PRT 3
ZRPRT3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: IRE1_KO_LSK_rep1


title: ITD_LSK_rep1

value: Flt3-ITD (ITD)


title: PS19, RNA

description:
PS19 whole-cell RNA, T cells from a pool of 4 female PS19 mouse brains
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
PS19_GEX


title: ITD_GMP_rep1


title: ITD_GMP_rep3


title: ITD_GMP_rep2


title: Z-138, PRMT5 Resistant Untreated 3

description:
Z-138 PR DMSO 3
ZRU3
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Placenta E10.5 Female 1 RRBS


title: 5XFAD, RNA, rep2

description:
5XFAD-2 whole-cell RNA, T cells from a pool of 3 female 5XFAD mouse brains. WT-2 and 5XFAD-2 samples were sequenced in a separate run from the rest of the samples.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
5XFAD-2_GEX


title: Z-138, PRMT5 Resistant Untreated 2

description:
Z-138  PR DMSO 2
ZRU2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Z-138, PRMT5 Resistant Treated 2

description:
Z-138 PR PRT 2
ZRPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Z-138, PRMT5 Resistant Untreated 1

description:
Z-138 PR DMSO 1
ZRU1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: Z-138, PRMT5 Resistant Treated 1

description:
Z-138 PR PRT 1
ZRPRT1
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: ITD_LSK_rep2


title: PS-5X, RNA

description:
PS-5X whole-cell RNA, T cells from a pool of 4 female PS-5X mouse brains
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
PS-5X_GEX


title: WT, RNA, rep2

description:
WT-2 whole-cell RNA, T cells from a pool of 8 female WT mouse brains. WT-2 and 5XFAD-2 samples were sequenced in a separate run from the rest of the samples.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
WT-2_GEX


title: WT_GMP_rep3

value: wild type


title: WT_LSK_rep2


title: WT_GMP_rep1


title: WT_LSK_rep1


title: WT, RNA, rep1

description:
WT-1 whole-cell RNA, T cells from a pool of 10 female WT mouse brains
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
WT-1_GEX


title: 5XFAD, RNA, rep1

description:
5XFAD-1 whole-cell RNA, T cells from a pool of 4 female 5XFAD mouse brains
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
5XFAD-1_GEX


title: SP53, PRMT5 Sensitive Treated 2

description:
SP53 PRT 2
SSPRT2
MCL_PRMT5i_star_featureCounts.countSymbol.txt
MCL_PRMT5i_star_featureCounts.tpmSymbol.txt


title: IRE1_KO_LSK_rep3


title: KB_Infected_Brain_Neutrophils, scRNA seq

city: Riverside

first: Emma

middle: Harriet

last: Wilson

address: 900 University Avenue

institute: UC Riverside

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mus musculus Reference Genome
Supplementary files format and content: cloupe files, used to visualize and analyze data using Cloupe Browser

source_name: Purified from murine brain

extract_protocol:
Neutrophils were sorted from brain and spleen based on CD11b/Ly6G positivity. BMNCs and splenocytes were harvested as above at 4wpi. To obtain a large enough number of neutrophils for sequencing, 3 naïve and 3 infected mice were pooled for naïve and infected neutrophil splenocyte samples, and 7 infected mice were pooled for neutrophil BMNC sample. 3 separate infected mice were pooled for an unsorted BMNC control sample. Cells were incubated in fluorescent-conjugated antibodies for CD11b APCCy7 (Invitrogen) and Ly6G PE or PerCPCy5.5 (Clone 1A8; Invitrogen), rinsed, and resuspended at 1.0 x 107 concentration in FACS buffer with 10% FBS to minimize cell death during sorting. Neutrophils were sorted from pooled samples based on gating strategy of Ly6G+CD11b+ cells using a MoFlo Astrios EQ Cell Sorter at 3-4% pressure to maximize cell survival. Sorted cells were re-counted to determine viability, and a minimum of 1.0 x 104 sorted cells were used for single cell sequencing.   10x Sequencing and Analysis. Sorted Ly6G+CD11b+ cells and unsorted BMNC control sample were processed for single cell RNA sequencing according to 10x sample prep protocols for Steps 1-3 (Manual: CG000204 RevD); instructions were followed exactly. Time spent before loading sorted cells onto 10x Chromium controller for Step 1 was <1hr. Processed samples were analyzed after Steps 2 and 3 via Bioanalyzer by the UCR Genomics Core facility for viability and concentration before proceeding to next steps. Upon completion of the 10x protocol, samples were sent to the UC San Diego IGM Genomics Center for sequencing (500 million reads/sample).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Purified from murine brain

value: neutrophils