title: MCF10A_RNAseH1OE_72h_rep1

description: Culture under serum medium.

data_processing:
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using BWA (v0.7.15).
Quality control on reads was done using package ATACseqQC.
PCR duplicates were removed using sambamba13 and potential mouse reads were further removed using a custom Java script with the criteria of (1) more than 2 mismatches; (2) human genome alignment score ratio less than 0.67 and mapping quality less than 30.
BigWig files for visualization were created using deeptools with CPM function.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: breast cell line MCF10A

growth_protocol: MCF10A cells were purchased from ATCC and were grown in DMEM/F12 (Gibco) with 5% horse serum, 20 ng/ml EGF, 0.5 mg/ml hydrocortisone, 100 ng/ml Cholera Toxin and 10 μg/ml insulin. BRx82 and BRx142 CTC cell lines were established from primary CTCs, viably isolated from blood specimen of patients with metastatic hormone-receptor positive breast cancer, following microfluidic enrichment using the CTC-iChip. CTC cultures were maintained as anchorage independent clusters under hypoxia, in tumor sphere medium. All the cell lines used in this study were routinely checked for mycoplasma using Mycoalert kit from Lonza and their cell of origin was confirmed using genetic fingerprinting analysis.

extract_protocol:
ATAC-seq was carried out according to the Omni-ATAC-seq protocol published previously. Briefly, cultured or sorted cells were washed with PBS once and subjected to nuclei preparation in ATAC resuspension buffer containing 0.1% NP-40 (Sigma), 0.1% Tween-20 (Sigma), and 0.01% digitonin (Promega) on ice. Transposition reaction was carried out in 50 μl transposition mix containing 25 μl 2x TD buffer (Illumina), 2.5 μl Tn5 transposase (Illumina), 16.5 μl PBS (Gibco), 0.5 μl 1% digitonin (Promega), 0.5 μl 10% Tween-20 (Sigma) and 5 μl H2O at 37°C for 30 minutes with 1000 RPM mixing in a thermomixer.
Transposed DNA fragments were amplified with 6-15 cycles on Thermocycler using 2x NEBNext MasterMix (New England Biolabs) together with sample-specific barcoded primers. After purification with AMPure XP beads (Beckman Coulter), samples were pooled and sequenced on HiSeq X sequencer with 150 bp paired-end reads.

treatment_protocol: RNaseH1 overexpression plasmid encoding RNase H1 fused with GFP was ectopically expressed in MCF10A cells by transfection using 10 μg plasmid in the presence of Lipofectamine 3000 (Invitrogen). Cells were harvested 72 h after transfection, sorted based on the GFP signal and then subjected to ATAC-seq. For the CTC mouse metastasis experiment, all the animal experiments were performed according to the animal protocol reviewed and approved by MGH Subcommittee on Research Animal Care (IACUC). 6-8 week-old female immunodeficient NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice (Jackson Laboratory) were used for mammary fat pad injections and intracardiac injections. Mice were anaesthetized with isoflurane prior to tumor cell injections. For intracardiac injections, the left side of the mouse chest was opened to expose the rib cage and 500,000 BRx142, BRx82 or M231 cells suspended in 100 μl PBS were gently injected into the left ventricle of the heart. The skin was closed and sutured and a 90-day estrogen release pellet (Innovative Research of America) was placed subcutaneously behind the neck of each mouse. Mice were routinely monitored under the IVIS Lumina II imaging system (PerkinElmer) after intraperitoneal injections of D-luciferin substrate (Sigma), and tumor derived bioluminescent signal was measured. Tumors tissue was dissected immediately after sacrificing the mice. Tissues were washed with PBS to remove excessive blood and stromal tissue and were minced with a scalpel. Tissue digestion was performed with collagenase/hyaluronidase cocktail (Stemcell) in DMEM medium at 37°C on a rocker for 2-4 hours. Samples were vortexed every 30 minutes to enhance tissue dissociation/digestion. After digestion, the tissue solution was passed through a 70 μm filter to obtain a single cell suspension, which was then stained with PE-anti-human CD298 antibody (Biolegend) together with DAPI for 30 minutes at 4°C in the dark. Unbound antibody and DAPI were removed by washing with DMEM medium. In addition to the anti-human antibody CD298, CTCs were also tagged with endogenous GFP, and human CTC-derived cells recovered from mouse tissues were identified by double staining for both PE and GFP, as well as being low for DAPI staining (indicating cell viability). Cells were sorted using a FACS Fusion Cell Sorter (BD) into an 1.5 ml Eppendorf tube for bulk ChIP-seq experiments.

value: breast cell line

tag: rnase

value: RNaseH1 overexpression (72h)


title: Input_H3K27ac_MCF10a_serumWD_back1h

status: Public on Nov 03 2021

type: SRA

city: Boston

first: Gabriel

middle: Alejandro

last: Golczer Gatti

state: MA

address: 55 Fruit St

department: MGH Cancer Center

country: USA

institute: Harvard Medical School

description: Serum replenish for 1h

library_source: genomic

data_processing:
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using BWA (v0.7.15).
PCR duplicates were removed using sambamba13 and potential mouse reads were further removed using a custom Java script with the criteria of (1) more than 2 mismatches; (2) human genome alignment score ratio less than 0.67 and mapping quality less than 30.
BigWig files for visualization were created using deeptools with CPM function.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig or bedGraph

molecule: genomic DNA

organism: Homo sapiens

source_name: MCF10A breast epithelial cells

growth_protocol: BRx82 and BRx142 CTC cell lines were established from primary CTCs, viably isolated from blood specimen of patients with metastatic hormone-receptor positive breast cancer, following microfluidic enrichment using the CTC-iChip. CTC cultures were maintained as anchorage independent clusters under hypoxia, in tumor sphere medium.

extract_protocol:
Cell lines cultured in vitro, or tumor xenograft-derived and FACS-sorted single cell suspension were washed with ice-cold PBS, and crosslinked with 1% formaldehyde (Sigma) for 10 minutes (for histone modifications and RNA pol II) or 15 minutes (for transcription factors) at room temperature and quenched with glycine. ChIP was performed using EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore) following the recommended protocol. Briefly, nuclei were isolated with cold nuclei isolation buffer and sheared with Covaris S2 instrument with an optimized program (Duty Cycle: 5%; Intensity: 4; Cycles/Burst: 200; treatment time: 360s) to yield an average fragment size of approximately 300 bp. Chromatin was incubated with Protein A/G Dynabeads (ThermoFisher) together with 5 μg ChIP-grade antibody overnight at 4°C with rotation. The beads were then collected and washed extensively with high- and low-salt buffers. DNA was de-crosslinked and purified through ethanol precipitation. Before immunoprecipitation with Dynabeads and antibody, 10% of chromatin was saved as input control.
Immunoprecipitated DNA from ChIP experiment, together with input DNA were all subjected to end repair, dA-tailing and ligation of Illumina sequencing adapters according to the instructions from KAPA Hyper Prep Kits (Kapa Biosystems). After ligation, the final PCR amplification was performed with KAPA Hifi Hotstart Readymix (2x, Kapa Biosystems), Illumina universal primer and Illumina index primer. Barcoded libraries were pooled and sequenced on Illumina HiSeq X platform with 150 bp paired-end reads.

treatment_protocol: All the animal experiments were performed according to the animal protocol reviewed and approved by MGH Subcommittee on Research Animal Care (IACUC). 6-8 week-old female immunodeficient NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice (Jackson Laboratory) were used for mammary fat pad injections and intracardiac injections. Mice were anaesthetized with isoflurane prior to tumor cell injections. For intracardiac injections, the left side of the mouse chest was opened to expose the rib cage and 500,000 BRx142, BRx82 or M231 cells suspended in 100 μl PBS were gently injected into the left ventricle of the heart. The skin was closed and sutured and a 90-day estrogen release pellet (Innovative Research of America) was placed subcutaneously behind the neck of each mouse. Mice were routinely monitored under the IVIS Lumina II imaging system (PerkinElmer) after intraperitoneal injections of D-luciferin substrate (Sigma), and tumor derived bioluminescent signal was measured. Tumors tissue was dissected immediately after sacrificing the mice. Tissues were washed with PBS to remove excessive blood and stromal tissue and were minced with a scalpel. Tissue digestion was performed with collagenase/hyaluronidase cocktail (Stemcell) in DMEM medium at 37°C on a rocker for 2-4 hours. Samples were vortexed every 30 minutes to enhance tissue dissociation/digestion. After digestion, the tissue solution was passed through a 70 μm filter to obtain a single cell suspension, which was then stained with PE-anti-human CD298 antibody (Biolegend) together with DAPI for 30 minutes at 4°C in the dark. Unbound antibody and DAPI were removed by washing with DMEM medium. In addition to the anti-human antibody CD298, CTCs were also tagged with endogenous GFP, and human CTC-derived cells recovered from mouse tissues were identified by double staining for both PE and GFP, as well as being low for DAPI staining (indicating cell viability). Cells were sorted using a FACS Fusion Cell Sorter (BD) into an 1.5 ml Eppendorf tube for bulk ChIP-seq experiments.

tag: cell line

tag: cell type

value: breast epithelial cell line

tag: gender

value: female

tag: culture condition

value: Serum refeeding (1h)

tag: chip antibody


title: BRx82_day100_ovary

description: Ovary metastasis.

source_name: breast cancer circulating tumor cells

tag: patient id

tag: tissue

value: xenograft ovary metastasis

tag: timepoint

value: day 100

value: breast cancer circulating tumor cells


title: MCF10A_RNAseH1OE_control_rep1

description: Culture under serum medium.

value: Serum

value: RNaseH1 overexpression control


title: H3K27ac_MCF10a_serumWD_24h

description: Serum starve for 24h

value: Serum starvation (24h)

value: H3K27ac (Active motif; Cat#39133)


title: MCF10A_RNAseH1OE_control_rep2

description: Culture under serum medium.


title: BRx82_day64_ovary

description: Ovary metastasis.

value: day 64


title: BRx82_preinjection

description: Culture under serum-free medium.

value: Serum-free


title: MCF10A_RNAseH1OE_72h_rep2

description: Culture under serum medium.


title: BRx142_day110_ovary

description: Ovary metastasis.

value: day 110


title: BRx142_day81_ovary

description: Ovary metastasis.

value: day 81


title: BRx142_day0_ovary

description: Ovary metastasis.

value: day 0


title: BRx142_preinjection

description: Culture under serum-free medium.


title: RNaseH_MCF10A_in_serum

description: Culture under serum condition.

data_processing:
Library strategy: DRIP-seq
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using BWA (v0.7.15).
Quality control on reads was done using package ATACseqQC.
PCR duplicates were removed using sambamba13 and potential mouse reads were further removed using a custom Java script with the criteria of (1) more than 2 mismatches; (2) human genome alignment score ratio less than 0.67 and mapping quality less than 30.
BigWig files for visualization were created using deeptools with CPM function.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

growth_protocol: MDA-MB-231 (M231) and MCF10A cells were all purchased from ATCC. M231 were grown under adherent condition with 10% FBS (Gibco) in DMEM high glucose medium (Gibco). MCF10A cells were grown in DMEM/F12 (Gibco) with 5% horse serum, 20 ng/ml EGF, 0.5 mg/ml hydrocortisone, 100 ng/ml Cholera Toxin and 10 μg/ml insulin. All the cell lines used in this study were routinely checked for mycoplasma using Mycoalert kit from Lonza and their cell of origin was confirmed using genetic fingerprinting analysis.

extract_protocol:
DNA from cultured cells was isolated using phenol/chloroform extraction with phase lock tubes, followed by ethanol precipitation. DNA was digested with a restriction enzyme cocktail (BsrgI, EcoRI, HindIII, SspI and XbaI, all from New England Biolabs) overnight at 37°C. For RNase H in vitro digestion controls, 8 μg digested DNA was incubated with RNase H (New England Biolabs) for 6-8 hours at 37°C before purifying with phenol/chloroform. 1% of digested DNA was saved as input control. 4 μg DNA (with or without RNase H treatment) was incubated with 10 μg S9.6 antibody (Active motif; Cat#65683) in 1x DRIP binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4°C, followed by incubation with protein A/G magnetic beads (Invitrogen) for an additional 2 hours. Bound beads were collected using a magnetic rack, washed 3 times with 1x DRIP binding buffer, and eluted with DRIP elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 minutes at 55°C. DNA was purified using phenol/chloroform extraction coupled with ethanol precipitation. Quantitative PCR was performed to confirm the R-loop enrichment at the FOS and EGR1 genebodies.
Immunoprecipitated DNA from DRIP experiment, together with input DNA were all subjected to end repair, dA-tailing and ligation of Illumina sequencing adapters according to the instructions from KAPA Hyper Prep Kits (Kapa Biosystems). After ligation, the final PCR amplification was performed with KAPA Hifi Hotstart Readymix (2x, Kapa Biosystems), Illumina universal primer and Illumina index primer. Barcoded libraries were pooled and sequenced on Illumina HiSeq X platform with 150 bp paired-end reads.

treatment_protocol: Both M231 and MCF10A cells were routinely maintained in serum containing media described above. For serum deprivation in M231 cells, serum-containing medium was removed and cells were washed three times in PBS and cultured in serum-free medium for 24 hours. After 24 hours of serum starvation, serum-containing medium was added back to the cells and cells were harvested for DRIP-seq at 30 minutes, 1 hour, 3 hours and 6 hours.

value: breast cell line

tag: genotype/variation

value: wildtype

tag: antibody


title: RNaseH_M231_serumwithdraw_24h

description: Culture under serum starving condition (24h).

source_name: breast cancer cell line MDA-MB-231

value: breast cancer cell line


title: RNaseH_M231_serumrefeeding_6h

description: Culture under serum refeeding condition (6h).

value: female

value: Serum refeeding (6h)


title: RNaseH_M231_serumrefeeding_3h

description: Culture under serum refeeding condition (3h).

value: Serum refeeding (3h)


title: RNaseH_M231_serumrefeeding_30min

description: Culture under serum refeeding condition (30min).

value: Serum refeeding (30min)


title: RNaseH_M231_NR4A1WT_2

description: Culture under serum condition.

value: NR4A1 wildtype


title: RNaseH_M231_NR4A1WT_1

description: Culture under serum condition.

value: Serum


title: S96_MCF10A_in_serum

description: Culture under serum condition.


title: RNaseH_M231_NR4A1KO

description: Culture under serum condition.

value: NR4A1 knockout


title: S96_M231_serumwithdraw_24h

value: Serum starvation (24h)


title: S96_M231_serumrefeeding_6h


title: S96_M231_serumrefeeding_30min


title: S96_M231_NR4A1WT_1

description: Culture under serum condition.


title: PRO-seq_MCF10A_serumrefeeding_3h

library_source: transcriptomic

data_processing:
Library strategy: PRO-seq
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using BWA (v0.7.15).
Quality control on reads was done using package ATACseqQC.
PCR duplicates were removed using sambamba13 and potential mouse reads were further removed using a custom Java script with the criteria of (1) more than 2 mismatches; (2) human genome alignment score ratio less than 0.67 and mapping quality less than 30.
BigWig files for visualization were created using deeptools with CPM function.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

molecule: total RNA

extract_protocol:
MCF10A or M231 cells were first washed with cold PBS to remove dead cells and harvested by scraping and centrifugation at 4°C. Cell pellets were resuspended in ice-cold permeabilization buffer (10 mM Tris-HCl, pH 7.4 (Sigma), 300 mM sucrose (Sigma), 10 mM KCl (Sigma), 5 mM MgCl2 (Ambion), 1 mM EGTA (Sigma), 0.05% Tween-20 (Sigma), 0.1% NP40 substitute (Roche), 0.5 mM DTT (Promega), one tablet of protease inhibitors cocktail (Roche) per 50 ml and 4 units/ml RNase inhibitor (Ambion)) on ice for 5 minutes. After centrifugation, cells were washed twice with ice-cold permeabilization buffer, resuspended in storage buffer (10 mM Tris-HCl, pH 8.0 (Sigma), 25% (vol/vol) glycerol (Sigma), 5 mM MgCl2 (Ambion), 0.1 mM EDTA (Sigma) and 5 mM DTT (Promega)) and immediately frozen in liquid nitrogen.
Nuclear run on reactions were carried out on permeabilized cells by adding the same volume of pre-warmed 2x nuclear run on mix (10 mM Tris-HCl pH 8.0 (Sigma), 300 mM KCl (Sigma), 1% Sarkosyl (Sigma), 5 mM MgCl2 (Ambion), 1 mM DTT (Promega), 200 mM biotin-11-A/C/G/UTP (Perkin-Elmer), 0.8 units/mL RNase inhibitor (Ambion)) and incubating at 37°C for 3 minutes. Total RNA was extracted using Trizol LS reagent (Invitrogen) and further fragmented by base hydrolysis in NaOH solution (Sigma) on ice for 10 minutes. Fragmented RNA was bound with prewashed streptavidin-coated magnetic beads (M280, Invitrogen) in binding buffer (10 mM Tris-HCl, pH 7.4 (Sigma), 300 mM NaCl (Sigma) and 0.1% (vol/vol) Triton X-100 (Sigma) in nuclease-free H2O). After washing with ice-cold high-salt wash buffer and low-salt wash buffer, bound RNA was extracted from beads with Trizol reagent (Invitrogen). RNA was then subjected to 3’RNA adapter ligation (IDT, 5’-GAUCGUCGGACUGUAGAACUCUGAAC-/inverted dT/- 3’) in the presence of T4 RNA ligase I (New England Biolabs). Ligated RNA was further enriched by another round of streptavidin-coated magnetic beads incubation, followed by washing and extraction using Trizol reagent (Invitrogen). RNA was then treated with RNA 5’Pyrophosphohydrolase (RppH, New England Biolabs) at 37°C for 1 hour, followed by treatment with Polynucleotide Kinase (PNK, New England Biolabs) at 37°C for 1 hour. After another round of streptavidin beads incubation, and washing and extraction with Trizol reagent (Invitrogen), 5’RNA adapter (IDT, 5’-CCUUGGCACCCGAGAAUUCCA-3’) was ligated to the RNA molecules using T4 RNA ligase I (New England Biolabs), and the ligated RNA was enriched using incubation with streptavidin beads, washed and again extracted using Trizol reagent (Invitrogen). Reverse transcription was performed with RP1 primer (IDT , 5’- AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3’) in the presence of Superscript III RT enzyme (Invitrogen). PCR amplification was carried out with Phusion DNA polymerase (Invitrogen) together with RP1 primer and RPI-n primer (IDT, 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCA CCCGAGAATTCCA-3’, where the six N’s indicate barcodes for Illumina TruSeq multiplexing) for 16 cycles. qPCR was performed against IEG and non IEG genebody regions after PCR amplification (same primers for NR4A1 ChIP) and nuclear run on signal enrichment was calculated based on qPCR results. Only the qPCR confirmed samples were subjected to size selection by running an 8% native PAGE gel (Thermofisher), and 140-350 bp DNA fragments were excised and recovered. Final libraries were sequenced in Illumina HiSeq X platform with 150 bp paired-end reads.

treatment_protocol: Both M231 and MCF10A cells were routinely maintained in serum containing media described above. For serum deprivation in MCF10A cells, serum-containing medium was removed and cells were washed three times in PBS and cultured in serum-free medium for 24 hours. After 24 hours of serum starvation, serum-containing medium was added back to the cells and cells were harvested for PRO-seq at 1 hour and 3 hours.


title: S96_M231_serumrefeeding_1h

description: Culture under serum refeeding condition (1h).

value: Serum refeeding (1h)


title: S96_M231_NR4A1KO_1

description: Culture under serum condition.


title: PRO-seq_MCF10A_serumrefeeding_1h


title: S96_M231_NR4A1WT_2

description: Culture under serum condition.


title: S96_M231_NR4A1KO_3

description: Culture under serum condition.


title: PRO-seq_MCF10A_serumwithdraw_24h


title: RNaseH_M231_serumrefeeding_1h


title: S96_M231_NR4A1KO_2

description: Culture under serum condition.


title: PRO-seq_M231_NR4A1KO_1

description: Culture under serum condition.


title: PRO-seq_M231_NR4A1KO_2

description: Culture under serum condition.


title: PRO-seq_M231_NR4A1WT_1

description: Culture under serum condition.


title: M231_regular_in_serum_rep2

description: polyA RNA

data_processing:
Reads trimmed for adapter pollutions and low quality using Trimgalore (v0.4.3).
Aligned to the human genome (hg19 assembly) using Tophat2 (v2.1.1) with parameter of no-novel-juncs18.
Gene expression was determined using Htseq (v2.1.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: htseq count format.

growth_protocol: MDA-MB-231 (M231) cells were purchased from ATCC. M231 were grown under adherent condition with 10% FBS (Gibco) in DMEM high glucose medium (Gibco).

extract_protocol:
Bulk RNA was extracted from cultured cells using RNeasy Micro kit (QIAGEN) with on-column DNA digestion.
RNA-seq library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7530L).

treatment_protocol: Guide RNAs (gRNAs) were designed using CRISPR design online tool (http://crispr.mit.edu/), and then cloned into CRISPR/Cas9 plasmids: pX458 (Addgene#48138) or pX459 (Addgene#62988). Sequences of the gRNA were further confirmed using Sanger sequencing. For each gene, at least two gRNAs were designed to target the 5’ exonic region and introduce a frame shift mutation. Cas9 and gRNA plasmids were delivered into cell lines through Lipofectamine 3000 (Invitrogen, for pX458/pX459 plasmids). Genomic DNA was isolated followed by PCR and Sanger sequencing to verify the genome editing efficiency.


title: M231_regular_in_serum_rep1

description: polyA RNA


title: S96_M231_serumrefeeding_3h


title: PRO-seq_M231_NR4A1WT_2

description: Culture under serum condition.


title: M231_NR4A1KO_14C8

description: polyA RNA


title: M231_NR4A1KO_14E10

description: polyA RNA


title: PRO-seq_MCF10A_in_serum

description: Culture under serum condition.


title: MCF7_TP53KD cells treated with 4.995004995 uM nutlin3a at 24h replicate 3 [sample_1036]

first: Clemens

last: Hug

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

data_processing:
The data was separated by well barcode and the reads were converted to counts using the bcbio-nextgen single cell RNA-seq analysis pipeline (https://bcbio- nextgen.readthedocs.io/en/latest/). The pipeline removes any barcodes that differ by more than one base from an expected barcode and uses unique molecular identifiers (UMIs) to identify unique reads and remove PCR duplicates.
RapMap was used to align reads to the transcriptome (GRCh38). The R package DESeq2 (version 1.30.0) was used for differential expression analysis, and the R package gseaMultilevel was used for gene set enrichment analysis of all genes sorted by the log2 fold change (adjusted p-value < 0.05) using Molecular Signatures Database (MSigDB) gene sets.
Genome_build: GRCh38.98

molecule: polyA RNA

source_name: breast ductal carcinoma cell line with TP53 knockout

growth_protocol: MDAMB231 (ATCC cat no.) was maintained in DMEM media (Corning 10-017-CV) with 10% FBS (Life Technologies 26140-079) and 1% penicillin/streptomycin (Corning 30-002-Cl). MCF7 (ATCC cat no) was maintained in EMEM media with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Cells were lysed 96 hours post crRNA transfection or 24 hours post inhibitor treatment; the plates were washed one time with PBS on a plate washer (BioTek). The PBS was removed (leaving ~15 uL/well residual volume), and 30 uL/well 1 X lysis buffer (1x Qiagen TCL, 1% beta-mercaptoethanol) was added. The plates were incubated for 5 minutes at room temperature to aid cell lysis, and then frozen at -80˚C until RNA extraction. The DGE RNA-seq was performed as previously published (Semrau et al., 2017; Soumillon et al., 2014) with modifications described previously (Schauer et al., 2020) (full protocol at https://www.protocols.io/view/3-39-dge-high-throughput-rna-library-preparation-bumynu7w).
The Nextera DNA kit was used to prepare the sequencing library following the manufacturer’s instructions. 55 ng of cDNA was tagmented for 5 minutes at 55 ̊C and purified using a Zymo DNA Clean & Concetrator-5 column. The cDNA was amplified (7 cycles) then purified using a 0.9x ratio of AMPure XP magnetic beads. The Agilent BioAnalyzer HS DNA Kit was used to assess the library size distribution before qPCR quantification and sequencing at the Harvard Medical School Biopolymers Facility (paired end sequencing was performed on an Illumina NextSeq).
high-throughput, low-cost RNA-sequencing method (3’ Digital Gene Expression or 3’DGE-seq)

treatment_protocol: MDAMB231 Cas9-Flag and MCF7 Cas9-Flag expressing cells were seeded in 96 well plates (4000 cells/well) and allowed to adhere for 24 hours. crRNAs were resuspended in 10 mM Tris-HCl Buffer pH 7.4 (Dharmacon B-006000-100) and four crRNA guides per DUB were pooled to increase knockout efficiency. Guide transfection was performed according to the recommended manufacturer protocol with optimized conditions as follows. Cells were transfected with 25 nM crRNA and 25 nM tracr RNA using 0.2 uL/well Dharmafect 4, triplicate transfections were performed per condition. The media was replaced 16-18 hours post transfection.    In parallel, MDAMB231 (12,000 cells/well), MCF7 parental (10,000 cells/well), and MCF7 TP53 shRNA (10,000 cells/well) were seeded in 96 well plate format and allowed to adhere for 24 hours. DUB inhibitors and DMSO were dispensed into the 96 well plate using a d300 digital dispenser (Hewlett-Packard).

value: compound

tag: treatment

tag: concentration

tag: time

tag: replicate

tag: library

tag: well

tag: barcode

value: TCGGCG


title: MDAMB231 cells treated with 19.99992 uM bin-01-108 at 24h replicate 3 [sample_1035]

source_name: triple negative metastatic mammary adenocarcinoma

value: TCCCCG


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177B at 24h replicate 3 [sample_1037]

value: breast ductal carcinoma cell line with TP53 knockout

value: TGCGGC


title: MDAMB231 cells treated with 19.99992 uM bin-01-108 at 24h replicate 2 [sample_1034]

value: triple negative metastatic mammary adenocarcinoma

value: GTCGGC


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 9 [sample_1038]

value: DMSO

value: TGGGGG


title: MDAMB231 cells treated with 19.99992 uM AV-11324-34 at 24h replicate 3 [sample_1032]

value: GGGGTG


title: MDAMB231 cells treated with 19.99992 uM AV-11324-34 at 24h replicate 2 [sample_1031]

value: GGGCTC


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 8 [sample_1025]

value: GCGGGA


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177A at 24h replicate 3 [sample_1026]

value: GCTCCG


title: MDAMB231 cells treated with DMSO control at 24h replicate 19 [sample_1027]

value: GGACGC


title: MDAMB231 cells treated with 19.99992 uM AV-11324-5 at 24h replicate 3 [sample_1028]

value: GGCAGC


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 7 [sample_1024]

value: GCGCGT


title: M231_NR4A1KO_14H5

description: polyA RNA

tag: cell line

value: breast cancer cell line

value: female

value: NR4A1 knockout


title: MDAMB231 cells treated with 4.98999505 uM F-76 at 24h replicate 3 [sample_1022]

value: compound

value: GCCGGT


title: MDAMB231 cells treated with 19.99992 uM bin-01-113 at 24h replicate 3 [sample_1023]

value: GCGACG


title: HealthyDonor_Tcell_unstim_rep3

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped using STAR_2.6.1d aligner.
FeatureCounts v2.0.0 was used to generate the raw counts.
Genome_build: human genome GRCh37.p13 (Genome Reference Consortium 622 Human Reference 37), INSDC Assembly GCA_000001405.14, Feb 2009
Supplementary_files_format_and_content: raw read count .txt file

source_name: Primary T cells

growth_protocol: Primary T cells that were expanded by activation with antibodies to CD3 and CD28 for 3 days then cultured and maintained in cRPMI plus IL-2 (100 U/mL) supplementation

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen)
Reverse transcription and cDNA pre-amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech/Takara). Libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera Index Kit (Illumina).
mRNA libraries were pooled and paired-end 150-bp sequencing was performed on the Illumina HiSeqX platform.

treatment_protocol: Expanded primary T cells from healthy controls and patients were stimulated with 20 ng/mL PMA and 450 ug/mL ionomycin in cRPMI. Cells were harvested at 3 hours and 6 hours post-stimulation and immediately frozen at -80°C. After the 6-hour time point, the remaining cells were washed twice to remove residual PMA/ionomycin. Culturing was then continued, and cells were harvested at 12 hours and 21 hours post-stimulation and immediately frozen.

tag: disease state

value: Healthy donor 3

tag: cell type

value: Primary T cells

tag: pma stimulation

value: Unstimulated


title: MDAMB231 cells treated with 19.99992 uM SB1-B-70 at 24h replicate 2 [sample_1018]

value: triple negative metastatic mammary adenocarcinoma

value: GAGCCC


title: MDAMB231 cells treated with 19.99992 uM SB1-B-70 at 24h replicate 3 [sample_1021]

value: GCCCGA


title: MCF7_TP53KD cells treated with 4.995004995 uM nutlin3a at 24h replicate 2 [sample_1012]

value: breast ductal carcinoma cell line with TP53 knockout

value: CGGCAC


title: MDAMB231 cells treated with 19.99992 uM SB1-B-57 at 24h replicate 3 [sample_1016]

value: CTCGGG


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177A at 24h replicate 2 [sample_1014]

value: CGGTCC


title: MDAMB231 cells treated with DMSO control at 24h replicate 17 [sample_1017]

value: DMSO

value: GACCCG


title: MDAMB231 cells treated with 19.99992 uM SB1-B-56-P2 at 24h replicate 3 [sample_1020]

value: GCCACC


title: MDAMB231 cells treated with DMSO control at 24h replicate 18 [sample_1019]

value: GCACCC


title: MDAMB231 cells treated with 4.98999505 uM CSN5i-3 at 24h replicate 2 [sample_1015]

value: compound

value: CGTGCC


title: MDAMB231 cells treated with 4.98999505 uM CSN5i-3 at 24h replicate 3 [sample_1033]

value: GGTGCG


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 6 [sample_1013]

value: CGGGAG


title: MDAMB231 cells treated with DMSO control at 24h replicate 20 [sample_1030]

value: GGGAGG


title: MDAMB231 cells treated with 4.98999505 uM F-76 at 24h replicate 2 [sample_1011]

value: CGCTCG


title: MDAMB231 cells treated with DMSO control at 24h replicate 16 [sample_1009]

value: triple negative metastatic mammary adenocarcinoma

value: CGCCAG


title: MDAMB231 cells treated with 19.99992 uM SB1-B-58 at 24h replicate 3 [sample_1029]

value: GGCGGA


title: MDAMB231 cells treated with 19.99992 uM XL-9872-40 at 24h replicate 3 [sample_1008]

value: CGAGCG


title: MDAMB231 cells treated with 19.99992 uM bin-01-113 at 24h replicate 2 [sample_1007]

value: CCTGCG


title: MDAMB231 cells treated with 19.99992 uM SB1-B-56-P2 at 24h replicate 2 [sample_1010]

value: CGCGAC


title: MDAMB231 cells treated with 19.99992 uM AV-11324-5 at 24h replicate 2 [sample_1006]

value: CCGGTG


title: MDAMB231 cells treated with 4.98999505 uM CSN5i-3 at 24h replicate 1 [sample_1005]

value: CCGCGA


title: MDAMB231 cells treated with 19.99992 uM AV-11324-34 at 24h replicate 1 [sample_1004]

value: CCCGGA


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 5 [sample_1002]

value: breast ductal carcinoma cell line with TP53 knockout

value: DMSO

value: CCAGGG


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177A at 24h replicate 1 [sample_1001]

value: compound

value: CAGGCC


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 4 [sample_1000]

value: CACGCG


title: MDAMB231 cells treated with 19.99992 uM SB1-B-56-P2 at 24h replicate 1 [sample_998]

value: AGCGCC


title: MDAMB231 cells treated with DMSO control at 24h replicate 14 [sample_997]

value: ACGGCC


title: MDAMB231 cells treated with DMSO control at 24h replicate 15 [sample_999]

value: triple negative metastatic mammary adenocarcinoma

value: AGGGCG


title: MDAMB231 cells treated with DMSO control at 24h replicate 13 [sample_996]

value: ACCGCG


title: MDAMB231 cells treated with 19.99992 uM SB1-B-58 at 24h replicate 2 [sample_995]

value: GGACCA


title: MDAMB231 cells treated with 4.98999505 uM F-76 at 24h replicate 1 [sample_993]

value: TCGAAG


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177B at 24h replicate 2 [sample_989]

value: CGATTG


title: MDAMB231 cells treated with 19.99992 uM XL-9872-40 at 24h replicate 1 [sample_991]

value: GGCAAT


title: MDAMB231 cells treated with 19.99992 uM SB1-B-58 at 24h replicate 1 [sample_992]

value: GTGACT


title: MDAMB231 cells treated with 19.99992 uM SB1-B-57 at 24h replicate 1 [sample_986]

value: ACCGTA


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 3 [sample_990]

value: breast ductal carcinoma cell line with TP53 knockout

value: GATCGT


title: MDAMB231 cells treated with 19.99992 uM SB1-B-70 at 24h replicate 1 [sample_985]

value: TTTTCT


title: MDAMB231 cells treated with 19.99992 uM bin-01-113 at 24h replicate 1 [sample_984]

value: compound

value: TTTCAA


title: MDAMB231 cells treated with 19.99992 uM SB1-B-57 at 24h replicate 2 [sample_987]

value: CAAGCT


title: MDAMB231 cells treated with DMSO control at 24h replicate 9 [sample_980]

value: DMSO

value: TTAGAA


title: MCF7_TP53KD cells treated with 0.999000999 uM XL177B at 24h replicate 1 [sample_978]

value: TGTTAT


title: MCF7_parental cells treated with DMSO control at 24h replicate 9 [sample_977]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: TGATAA


title: MDAMB231 cells treated with DMSO control at 24h replicate 12 [sample_983]

value: triple negative metastatic mammary adenocarcinoma

value: TTTAAC


title: MDAMB231 cells treated with DMSO control at 24h replicate 10 [sample_981]

value: TTATGT


title: MDAMB231 cells treated with 19.99992 uM bin-01-108 at 24h replicate 1 [sample_1003]

value: CCCCCA


title: MCF7_parental cells treated with 1.001992 uM XL177A at 24h replicate 3 [sample_976]

value: TCTATA


title: MDAMB231 cells treated with DMSO control at 24h replicate 11 [sample_982]

value: TTCTAA


title: MCF7_parental cells treated with 4.98999505 uM F-76 at 24h replicate 3 [sample_975]

value: TCAATT


title: MCF7_parental cells treated with 4.98999505 uM XL-10320-62A at 24h replicate 3 [sample_974]

value: TATTCA


title: MCF7_parental cells treated with 19.99992 uM E218-1700 at 24h replicate 3 [sample_972]

value: TATACT


title: MCF7_parental cells treated with DMSO control at 24h replicate 8 [sample_973]

value: compound

value: TATCTA


title: MDAMB231 cells treated with 19.99992 uM XL-9872-40 at 24h replicate 2 [sample_994]

value: TTTGGC


title: MCF7_parental cells treated with DMSO control at 24h replicate 7 [sample_971]

value: DMSO

value: TAGATA


title: MCF7_parental cells treated with 19.99992 uM AV-9606-95 at 24h replicate 3 [sample_969]

value: TAATCT


title: MCF7_parental cells treated with 19.99992 uM E218-1700 at 24h replicate 2 [sample_970]

value: breast ductal carcinoma cell line

value: TACATT


title: MCF7_parental cells treated with 4.98999505 uM nutlin3a at 24h replicate 3 [sample_968]

value: TAACTT


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 2 [sample_988]

value: breast ductal carcinoma cell line with TP53 knockout

value: CATGGT


title: MCF7_TP53KD cells treated with 4.995004995 uM nutlin3a at 24h replicate 1 [sample_966]

value: GTTATT


title: MDAMB231 cells treated with 19.99992 uM AV-11324-5 at 24h replicate 1 [sample_979]

value: triple negative metastatic mammary adenocarcinoma

value: TTAAGA


title: MCF7_parental cells treated with 10.01992 uM WH-9943-103C at 24h replicate 3 [sample_964]

value: GAATTA


title: MCF7_parental cells treated with 4.98999505 uM F-76 at 24h replicate 2 [sample_967]

value: TAAACA


title: MCF7_parental cells treated with 19.99992 uM AV-9606-95 at 24h replicate 2 [sample_965]

value: GTAAAT


title: MCF7_parental cells treated with 1.001992 uM XL177B at 24h replicate 3 [sample_963]

value: compound

value: CTTATA


title: MCF7_parental cells treated with 1.001992 uM XL177B at 24h replicate 2 [sample_961]

value: CATATT


title: MCF7_parental cells treated with DMSO control at 24h replicate 4 [sample_958]

value: DMSO

value: ATTCAT


title: MCF7_parental cells treated with 10.01992 uM WH-9943-103C at 24h replicate 2 [sample_959]

value: ATTTAC


title: MCF7_parental cells treated with DMSO control at 24h replicate 6 [sample_962]

value: breast ductal carcinoma cell line

value: CTAATT


title: MCF7_parental cells treated with DMSO control at 24h replicate 5 [sample_960]

value: CAAAAT


title: MCF7_parental cells treated with 4.98999505 uM XL-10320-62A at 24h replicate 2 [sample_955]

value: ATATTC


title: MCF7_parental cells treated with DMSO control at 24h replicate 3 [sample_957]

value: ATTAAG


title: MCF7_parental cells treated with 1.001992 uM XL177A at 24h replicate 2 [sample_956]

value: ATCTTA


title: MCF7_parental cells treated with 19.99992 uM AV-9606-95 at 24h replicate 1 [sample_953]

value: ATAATG


title: MCF7_parental cells treated with DMSO control at 24h replicate 2 [sample_952]

value: AGTTAA


title: MCF7_parental cells treated with 4.98999505 uM nutlin3a at 24h replicate 2 [sample_950]

value: ACTATT


title: MCF7_parental cells treated with 1.001992 uM XL177B at 24h replicate 1 [sample_951]

value: AGATAT


title: MCF7_parental cells treated with 4.98999505 uM F-76 at 24h replicate 1 [sample_947]

value: AATCAA


title: MCF7_parental cells treated with 4.98999505 uM XL-10320-62A at 24h replicate 1 [sample_946]

value: compound

value: AATAAC


title: MCF7_parental cells treated with 10.01992 uM WH-9943-103C at 24h replicate 1 [sample_949]

value: ACAAAT


title: MCF7_parental cells treated with DMSO control at 24h replicate 1 [sample_945]

value: DMSO

value: AACTAA


title: MCF7_parental cells treated with 1.001992 uM XL177A at 24h replicate 1 [sample_944]

value: AAATGT


title: MCF7_parental cells treated with 19.99992 uM E218-1700 at 24h replicate 1 [sample_948]

value: breast ductal carcinoma cell line

value: AATTAG


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 9 [sample_942]

value: triple negative metastatic mammary adenocarcinoma

value: knockout

value: GCGTGG


title: MCF7_parental cells treated with 4.98999505 uM nutlin3a at 24h replicate 1 [sample_943]

value: AAACTA


title: MDAMB231 cells with knockout of NTC at 96h replicate 69 [sample_941]

value: NTC

value: GCGGCT


title: MDAMB231 cells with knockout of NTC at 96h replicate 68 [sample_940]

value: GCGCCA


title: MDAMB231 cells with knockout of NTC at 96h replicate 67 [sample_939]

value: GCCTGC


title: MDAMB231 cells with knockout of UBAP1 at 96h replicate 3 [sample_937]

value: GCCCCT


title: MDAMB231 cells with knockout of NTC_2x at 96h replicate 3 [sample_938]

value: GCCGCA


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 8 [sample_934]

value: GACGGG


title: MCF7_TP53KD cells treated with DMSO control at 24h replicate 1 [sample_954]

value: breast ductal carcinoma cell line with TP53 knockout

value: compound

value: ATAGTA


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 6 [sample_935]

value: GAGGGC


title: MDAMB231 cells with knockout of USP5 at 96h replicate 6 [sample_930]

value: CGGCTG


title: MDAMB231 cells with knockout of USP8 at 96h replicate 6 [sample_933]

value: CTGGGC


title: MDAMB231 cells with knockout of USP10 at 96h replicate 6 [sample_931]

value: triple negative metastatic mammary adenocarcinoma

value: CGGGTC


title: MDAMB231 cells with knockout of USP14_UCHL5 at 96h replicate 3 [sample_926]

value: knockout

value: CGCAGG


title: MDAMB231 cells with knockout of USP5_USP14 at 96h replicate 3 [sample_932]

value: CTCCGC


title: BRx82_day0_ovary

description: Ovary metastasis.

value: xenograft ovary metastasis

value: day 0

value: breast cancer circulating tumor cells

tag: gender

value: female

tag: rnase


title: MDAMB231 cells with knockout of USP25 at 96h replicate 6 [sample_927]

value: CGCCTC


title: MDAMB231 cells with knockout of USP14 at 96h replicate 6 [sample_925]

value: CGACGG


title: MDAMB231 cells with knockout of untreated at 96h replicate 21 [sample_924]

value: untreated

value: CCTCGG


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 6 [sample_923]

value: CCGGGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 66 [sample_936]

value: NTC

value: GCAGGC


title: MDAMB231 cells with knockout of STAMBP_USP8 at 96h replicate 3 [sample_921]

value: CCCGAG


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 6 [sample_919]

value: triple negative metastatic mammary adenocarcinoma

value: STAMBP

value: CAGCGC


title: MDAMB231 cells with knockout of PTPN23 at 96h replicate 3 [sample_918]

value: knockout

value: CACCGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 63 [sample_917]

value: AGGCGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 64 [sample_920]

value: CCACGC


title: MDAMB231 cells with knockout of MINDY2 at 96h replicate 3 [sample_916]

value: AGCCGC


title: MDAMB231 cells with knockout of ICE1 at 96h replicate 3 [sample_914]

value: ACCCGG


title: MDAMB231 cells with knockout of ICE2 at 96h replicate 3 [sample_915]

value: ACGCGC


title: MDAMB231 cells with knockout of USP25_USP28 at 96h replicate 3 [sample_928]

value: CGCGTG


title: MDAMB231 cells with knockout of HECTD1 at 96h replicate 3 [sample_912]

value: TTGTCC


title: MCF7 cells with knockout of USP7 at 96h replicate 6 [sample_909]

value: breast ductal carcinoma cell line

value: GAAGAC


title: MDAMB231 cells with knockout of ELL at 96h replicate 3 [sample_911]

value: ELL

value: TCCAAC


title: MDAMB231 cells with knockout of HGS at 96h replicate 3 [sample_913]

value: HGS

value: CTCTCC


title: MDAMB231 cells with knockout of USP28 at 96h replicate 6 [sample_929]

value: triple negative metastatic mammary adenocarcinoma

value: CGGAGC


title: MCF7 cells with knockout of PTPN23 at 96h replicate 3 [sample_907]

value: knockout

value: CATCAG


title: MCF7 cells with knockout of NTC at 96h replicate 14 [sample_903]

value: NTC

value: TTTATG


title: MCF7 cells with knockout of VCPIP1 at 96h replicate 3 [sample_904]

value: TTTTAG


title: MDAMB231 cells with knockout of EAF1 at 96h replicate 3 [sample_910]

value: GTCAAG


title: MCF7 cells with knockout of USP9x at 96h replicate 3 [sample_902]

value: TTGTTA


title: MCF7 cells with knockout of UBAP1 at 96h replicate 3 [sample_908]

value: CGACTT


title: MCF7 cells with knockout of NTC at 96h replicate 15 [sample_906]

value: ATCGAG


title: MCF7 cells with knockout of ZRANB1 at 96h replicate 3 [sample_905]

value: breast ductal carcinoma cell line

value: TTGGAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 65 [sample_922]

value: CCGCAG


title: MCF7 cells with knockout of USP38 at 96h replicate 3 [sample_897]

value: TGAATA


title: MCF7 cells with knockout of USP14_UCHL5 at 96h replicate 3 [sample_896]

value: TCTAAT


title: MCF7 cells with knockout of USP14 at 96h replicate 3 [sample_895]

value: TCAAAA


title: MCF7 cells with knockout of USP10 at 96h replicate 3 [sample_898]

value: TGTATT


title: MCF7 cells with knockout of USP7 at 96h replicate 5 [sample_900]

value: TTATCA


title: MCF7 cells with knockout of UCHL5 at 96h replicate 3 [sample_893]

value: knockout

value: TATCAT


title: MCF7 cells with knockout of UCHL3 at 96h replicate 3 [sample_892]

value: TATAAG


title: MCF7 cells with knockout of untreated at 96h replicate 3 [sample_894]

value: untreated

value: TATTAC


title: MCF7 cells with knockout of UBR5 at 96h replicate 3 [sample_891]

value: TAGAAT


title: MCF7 cells with knockout of USP8 at 96h replicate 3 [sample_901]

value: TTCATA


title: MCF7 cells with knockout of OTUD5 at 96h replicate 3 [sample_888]

value: TAACAA


title: MCF7 cells with knockout of NTC at 96h replicate 13 [sample_890]

value: NTC

value: TACAAA


title: MCF7 cells with knockout of NTC at 96h replicate 11 [sample_886]

value: breast ductal carcinoma cell line

value: GATTAA


title: MCF7 cells with knockout of USPL1 at 96h replicate 3 [sample_889]

value: TAATAG


title: MCF7 cells with knockout of NTC at 96h replicate 12 [sample_887]

value: GTTAAA


title: MCF7 cells with knockout of USP42 at 96h replicate 3 [sample_899]

value: TTACTA


title: MCF7 cells with knockout of ICE1 at 96h replicate 3 [sample_884]

value: CTTAAT


title: MCF7 cells with knockout of ICE2 at 96h replicate 3 [sample_885]

value: GAATAT


title: MCF7 cells with knockout of HUWE1 at 96h replicate 3 [sample_883]

value: knockout

value: CTAAAA


title: MCF7 cells with knockout of ELL at 96h replicate 3 [sample_880]

value: ELL

value: ATTGTT


title: MCF7 cells with knockout of HECTD1 at 96h replicate 3 [sample_881]

value: ATTTTG


title: MDAMB231 cells with knockout of NTC at 96h replicate 60 [sample_873]

value: triple negative metastatic mammary adenocarcinoma

value: GCCTCG


title: MDAMB231 cells with knockout of NTC at 96h replicate 62 [sample_875]

value: GCGGAG


title: MDAMB231 cells with knockout of NTC at 96h replicate 61 [sample_874]

value: NTC

value: GCGCAC


title: MDAMB231 cells with knockout of NTC_2x at 96h replicate 2 [sample_872]

value: GCCGAC


title: MCF7 cells with knockout of C16orf72 at 96h replicate 3 [sample_878]

value: breast ductal carcinoma cell line

value: ATGTAA


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 7 [sample_876]

value: GCGTCC


title: MCF7 cells with knockout of EAF1 at 96h replicate 3 [sample_879]

value: ATTATC


title: MDAMB231 cells with knockout of NTC at 96h replicate 59 [sample_870]

value: GCAGCG


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 5 [sample_869]

value: GAGGCG


title: MDAMB231 cells with knockout of USP5_USP14 at 96h replicate 2 [sample_866]

value: knockout

value: CTCCCG


title: MDAMB231 cells with knockout of USP8 at 96h replicate 5 [sample_867]

value: CTGGCG


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 6 [sample_868]

value: GACGCC


title: MDAMB231 cells with knockout of USP25_USP28 at 96h replicate 2 [sample_862]

value: CGCGGT


title: MDAMB231 cells with knockout of USP10 at 96h replicate 5 [sample_865]

value: triple negative metastatic mammary adenocarcinoma

value: CGGGGA


title: MDAMB231 cells with knockout of USP5 at 96h replicate 5 [sample_864]

value: CGGCGT


title: MDAMB231 cells with knockout of USP25 at 96h replicate 5 [sample_861]

value: CGCCGA


title: MCF7 cells with knockout of HGS at 96h replicate 3 [sample_882]

value: HGS

value: CATAAA


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 5 [sample_857]

value: CCGGCA


title: MDAMB231 cells with knockout of untreated at 96h replicate 20 [sample_858]

value: untreated

value: CCGTGC


title: MDAMB231 cells with knockout of USP14_UCHL5 at 96h replicate 2 [sample_860]

value: CGCACC


title: MDAMB231 cells with knockout of NTC at 96h replicate 58 [sample_856]

value: NTC

value: CCGAGG


title: MDAMB231 cells with knockout of STAMBP_USP8 at 96h replicate 2 [sample_855]

value: knockout

value: CCCCTG


title: MCF7 cells with knockout of BAP1 at 96h replicate 3 [sample_877]

value: breast ductal carcinoma cell line

value: ATCTAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 57 [sample_854]

value: CCACCG


title: MDAMB231 cells with knockout of UBAP1 at 96h replicate 2 [sample_871]

value: triple negative metastatic mammary adenocarcinoma

value: GCCCAG


title: MDAMB231 cells with knockout of USP28 at 96h replicate 5 [sample_863]

value: CGGACG


title: MDAMB231 cells with knockout of NTC at 96h replicate 56 [sample_851]

value: AGGCCC


title: MDAMB231 cells with knockout of PTPN23 at 96h replicate 2 [sample_852]

value: CACCCC


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 5 [sample_853]

value: STAMBP

value: CAGCCG


title: MDAMB231 cells with knockout of MINDY2 at 96h replicate 2 [sample_850]

value: AGCCCG


title: MDAMB231 cells with knockout of ICE2 at 96h replicate 2 [sample_849]

value: ACGCCG


title: MDAMB231 cells with knockout of ICE1 at 96h replicate 2 [sample_848]

value: ACCCCC


title: MDAMB231 cells with knockout of EAF1 at 96h replicate 2 [sample_844]

value: GTACAC


title: MCF7 cells with knockout of UBAP1 at 96h replicate 2 [sample_842]

value: CCGATT


title: MCF7 cells with knockout of NTC at 96h replicate 10 [sample_840]

value: knockout

value: NTC

value: AGGGAT


title: MDAMB231 cells with knockout of USP14 at 96h replicate 5 [sample_859]

value: CGACCC


title: MDAMB231 cells with knockout of ELL at 96h replicate 2 [sample_845]

value: ELL

value: TAGTGG


title: MCF7 cells with knockout of PTPN23 at 96h replicate 2 [sample_841]

value: breast ductal carcinoma cell line

value: CAGTCA


title: MCF7 cells with knockout of NTC at 96h replicate 9 [sample_837]

value: TTTAGT


title: MCF7 cells with knockout of ZRANB1 at 96h replicate 2 [sample_839]

value: TCTTTC


title: MCF7 cells with knockout of VCPIP1 at 96h replicate 2 [sample_838]

value: TTTGTA


title: MCF7 cells with knockout of USP7 at 96h replicate 3 [sample_834]

value: TTATAC


title: MCF7 cells with knockout of USP8 at 96h replicate 2 [sample_835]

value: TTCAAT


title: MCF7 cells with knockout of USP42 at 96h replicate 2 [sample_833]

value: TTACAT


title: MCF7 cells with knockout of USP10 at 96h replicate 2 [sample_832]

value: TGTAAA


title: MCF7 cells with knockout of USP38 at 96h replicate 2 [sample_831]

value: TGAAAT


title: MCF7 cells with knockout of USP14_UCHL5 at 96h replicate 2 [sample_830]

value: TCATTA


title: MCF7 cells with knockout of UCHL5 at 96h replicate 2 [sample_827]

value: knockout

value: TATATC


title: MCF7 cells with knockout of UCHL3 at 96h replicate 2 [sample_826]

value: TAGTTT


title: MCF7 cells with knockout of untreated at 96h replicate 2 [sample_828]

value: untreated

value: TATGTT


title: MCF7 cells with knockout of USP14 at 96h replicate 2 [sample_829]

value: TATTTG


title: MDAMB231 cells with knockout of HECTD1 at 96h replicate 2 [sample_846]

value: triple negative metastatic mammary adenocarcinoma

value: TTCCTC


title: MCF7 cells with knockout of OTUD5 at 96h replicate 2 [sample_822]

value: breast ductal carcinoma cell line

value: TAAATG


title: MCF7 cells with knockout of NTC at 96h replicate 7 [sample_821]

value: NTC

value: GTATAA


title: MCF7 cells with knockout of ICE2 at 96h replicate 2 [sample_819]

value: GAAATT


title: MCF7 cells with knockout of USPL1 at 96h replicate 2 [sample_823]

value: TAAGTA


title: MCF7 cells with knockout of NTC at 96h replicate 8 [sample_824]

value: TAATTC


title: MCF7 cells with knockout of NTC at 96h replicate 6 [sample_820]

value: GATATA


title: MCF7 cells with knockout of USP7 at 96h replicate 4 [sample_843]

value: CTTCTG


title: MCF7 cells with knockout of USP9x at 96h replicate 2 [sample_836]

value: knockout

value: TTGATT


title: MDAMB231 cells with knockout of HGS at 96h replicate 2 [sample_847]

value: HGS

value: CCTTCC


title: MCF7 cells with knockout of UBR5 at 96h replicate 2 [sample_825]

value: TACTTA


title: MCF7 cells with knockout of HGS at 96h replicate 2 [sample_816]

value: CAATAA


title: MCF7 cells with knockout of C16orf72 at 96h replicate 2 [sample_812]

value: ATGATA


title: MCF7 cells with knockout of BAP1 at 96h replicate 2 [sample_811]

value: ATCATT


title: MCF7 cells with knockout of HUWE1 at 96h replicate 2 [sample_817]

value: breast ductal carcinoma cell line

value: CATTTA


title: MDAMB231 cells with knockout of NTC at 96h replicate 55 [sample_809]

value: triple negative metastatic mammary adenocarcinoma

value: NTC

value: GCGCTG


title: MCF7 cells with knockout of HECTD1 at 96h replicate 2 [sample_815]

value: ATTTGT


title: MCF7 cells with knockout of ICE1 at 96h replicate 2 [sample_818]

value: CTATTA


title: MDAMB231 cells with knockout of NTC at 96h replicate 53 [sample_807]

value: GCCGTG


title: MDAMB231 cells with knockout of NTC at 96h replicate 52 [sample_804]

value: GCACGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 54 [sample_808]

value: knockout

value: GCGAGC


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 4 [sample_802]

value: GACCGC


title: MDAMB231 cells with knockout of USP8 at 96h replicate 4 [sample_801]

value: CTGCGG


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 4 [sample_803]

value: GAGCGG


title: MDAMB231 cells with knockout of USP28 at 96h replicate 4 [sample_797]

value: CGCTGC


title: MDAMB231 cells with knockout of USP5_USP14 at 96h replicate 1 [sample_800]

value: CGTGGG


title: MDAMB231 cells with knockout of USP5 at 96h replicate 4 [sample_798]

value: CGGCCA


title: MDAMB231 cells with knockout of USP10 at 96h replicate 4 [sample_799]

value: CGGGCT


title: MDAMB231 cells with knockout of USP25 at 96h replicate 4 [sample_795]

value: CGCCCT


title: MCF7 cells with knockout of EAF1 at 96h replicate 2 [sample_813]

value: breast ductal carcinoma cell line

value: ATTAGA


title: MCF7 cells with knockout of ELL at 96h replicate 2 [sample_814]

value: ELL

value: ATTGAA


title: MDAMB231 cells with knockout of USP14 at 96h replicate 4 [sample_793]

value: triple negative metastatic mammary adenocarcinoma

value: CCTGGC


title: MDAMB231 cells with knockout of untreated at 96h replicate 19 [sample_792]

value: untreated

value: CCGTCG


title: MDAMB231 cells with knockout of USP14_UCHL5 at 96h replicate 1 [sample_794]

value: knockout

value: CGAGGC


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 4 [sample_791]

value: CCGGAC


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 5 [sample_810]

value: GCGGTC


title: MDAMB231 cells with knockout of NTC at 96h replicate 51 [sample_790]

value: NTC

value: CCCTGG


title: MDAMB231 cells with knockout of UBAP1 at 96h replicate 1 [sample_805]

value: GCCAGG


title: MDAMB231 cells with knockout of NTC_2x at 96h replicate 1 [sample_806]

value: GCCCTC


title: MDAMB231 cells with knockout of PTPN23 at 96h replicate 1 [sample_786]

value: AGGGGC


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 4 [sample_787]

value: STAMBP

value: CACGGC


title: MDAMB231 cells with knockout of NTC at 96h replicate 50 [sample_788]

value: CAGGGG


title: MDAMB231 cells with knockout of MINDY2 at 96h replicate 1 [sample_784]

value: ACGGGG


title: MDAMB231 cells with knockout of ICE2 at 96h replicate 1 [sample_783]

value: triple negative metastatic mammary adenocarcinoma

value: ACCGGC


title: MDAMB231 cells with knockout of ICE1 at 96h replicate 1 [sample_782]

value: GTACCG


title: MDAMB231 cells with knockout of HECTD1 at 96h replicate 1 [sample_780]

value: TCTGCA


title: MDAMB231 cells with knockout of USP25_USP28 at 96h replicate 1 [sample_796]

value: knockout

value: CGCGCA


title: MDAMB231 cells with knockout of ELL at 96h replicate 1 [sample_779]

value: ELL

value: GTTCGA


title: MDAMB231 cells with knockout of EAF1 at 96h replicate 1 [sample_778]

value: GGGATT


title: MCF7 cells with knockout of USP7 at 96h replicate 2 [sample_777]

value: breast ductal carcinoma cell line

value: CTAGTG


title: MDAMB231 cells with knockout of HGS at 96h replicate 1 [sample_781]

value: HGS

value: CCAACC


title: MCF7 cells with knockout of UBAP1 at 96h replicate 1 [sample_776]

value: CCACAT


title: MCF7 cells with knockout of NTC at 96h replicate 5 [sample_774]

value: NTC

value: AGACCT


title: MCF7 cells with knockout of PTPN23 at 96h replicate 1 [sample_775]

value: CACCAA


title: MCF7 cells with knockout of NTC at 96h replicate 4 [sample_771]

value: TTTACA


title: MCF7 cells with knockout of VCPIP1 at 96h replicate 1 [sample_772]

value: TTTCTT


title: MDAMB231 cells with knockout of STAMBP_USP8 at 96h replicate 1 [sample_789]

value: triple negative metastatic mammary adenocarcinoma

value: CCCCGT


title: MCF7 cells with knockout of USP9x at 96h replicate 1 [sample_770]

value: knockout

value: TTGAAA


title: MCF7 cells with knockout of USP42 at 96h replicate 1 [sample_767]

value: TTAATC


title: MCF7 cells with knockout of USP8 at 96h replicate 1 [sample_769]

value: TTATTG


title: MCF7 cells with knockout of USP7 at 96h replicate 1 [sample_768]

value: TTAGTT


title: MCF7 cells with knockout of USP10 at 96h replicate 1 [sample_766]

value: breast ductal carcinoma cell line

value: TGATTT


title: MCF7 cells with knockout of USP14_UCHL5 at 96h replicate 1 [sample_764]

value: TCATAT


title: MCF7 cells with knockout of USP38 at 96h replicate 1 [sample_765]

value: TCTTAA


title: MCF7 cells with knockout of USP14 at 96h replicate 1 [sample_763]

value: TATTGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 49 [sample_785]

value: NTC

value: AGCGGG


title: MCF7 cells with knockout of UCHL5 at 96h replicate 1 [sample_761]

value: TATAGA


title: MCF7 cells with knockout of untreated at 96h replicate 1 [sample_762]

value: untreated

value: TATGAA


title: MCF7 cells with knockout of UBR5 at 96h replicate 1 [sample_759]

value: TACTAT


title: MCF7 cells with knockout of UCHL3 at 96h replicate 1 [sample_760]

value: TAGTAA


title: MCF7 cells with knockout of NTC at 96h replicate 3 [sample_758]

value: knockout

value: TAATGA


title: MCF7 cells with knockout of USPL1 at 96h replicate 1 [sample_757]

value: TAAGAT


title: MCF7 cells with knockout of NTC at 96h replicate 2 [sample_755]

value: GTAATA


title: MCF7 cells with knockout of OTUD5 at 96h replicate 1 [sample_756]

value: TAAAGT


title: MCF7 cells with knockout of NTC at 96h replicate 1 [sample_754]

value: breast ductal carcinoma cell line

value: GATAAT


title: MCF7 cells with knockout of ZRANB1 at 96h replicate 1 [sample_773]

value: TTTTGA


title: MCF7 cells with knockout of ICE2 at 96h replicate 1 [sample_753]

value: CTTTAA


title: MCF7 cells with knockout of HUWE1 at 96h replicate 1 [sample_751]

value: CATTAT


title: MCF7 cells with knockout of ICE1 at 96h replicate 1 [sample_752]

value: CTATAT


title: MCF7 cells with knockout of HGS at 96h replicate 1 [sample_750]

value: HGS

value: CAAATA


title: MCF7 cells with knockout of ELL at 96h replicate 1 [sample_748]

value: ELL

value: ATTCTA


title: MDAMB231 cells with knockout of untreated at 96h replicate 18 [sample_744]

value: triple negative metastatic mammary adenocarcinoma

value: untreated

value: GCGGCT


title: MCF7 cells with knockout of BAP1 at 96h replicate 1 [sample_745]

value: knockout

value: ATCAAA


title: MCF7 cells with knockout of EAF1 at 96h replicate 1 [sample_747]

value: ATTACT


title: MDAMB231 cells with knockout of STAT3 at 96h replicate 3 [sample_743]

value: GCGCCA


title: MDAMB231 cells with knockout of USP6 at 96h replicate 3 [sample_742]

value: GCCTGC


title: MDAMB231 cells with knockout of NTC at 96h replicate 48 [sample_740]

value: NTC

value: GCCCCT


title: MDAMB231 cells with knockout of USP46 at 96h replicate 3 [sample_741]

value: GCCGCA


title: MDAMB231 cells with knockout of NTC at 96h replicate 47 [sample_735]

value: CTCCGC


title: MDAMB231 cells with knockout of UCK2 at 96h replicate 3 [sample_736]

value: CTGGGC


title: MDAMB231 cells with knockout of USP27X at 96h replicate 3 [sample_738]

value: GAGGGC


title: MCF7 cells with knockout of C16orf72 at 96h replicate 1 [sample_746]

value: breast ductal carcinoma cell line

value: ATGAAT


title: MDAMB231 cells with knockout of USP16 at 96h replicate 3 [sample_737]

value: GACGGG


title: MDAMB231 cells with knockout of STAT3 at 96h replicate 2 [sample_732]

value: triple negative metastatic mammary adenocarcinoma

value: GCGCAC


title: MDAMB231 cells with knockout of untreated at 96h replicate 17 [sample_734]

value: untreated

value: GCGGAG


title: MDAMB231 cells with knockout of USP6 at 96h replicate 2 [sample_730]

value: knockout

value: GCCTCG


title: MDAMB231 cells with knockout of STAT3 at 96h replicate 1 [sample_731]

value: GCGAGC


title: MDAMB231 cells with knockout of USP6 at 96h replicate 1 [sample_729]

value: GCCGTG


title: MDAMB231 cells with knockout of untreated at 96h replicate 16 [sample_733]

value: GCGCTG


title: MDAMB231 cells with knockout of USP46 at 96h replicate 2 [sample_728]

value: GCCGAC


title: MDAMB231 cells with knockout of NTC at 96h replicate 46 [sample_726]

value: NTC

value: GCCCAG


title: MCF7 cells with knockout of HECTD1 at 96h replicate 1 [sample_749]

value: ATTTCA


title: MDAMB231 cells with knockout of USP36 at 96h replicate 2 [sample_724]

value: GCAGCG


title: MDAMB231 cells with knockout of USP27X at 96h replicate 2 [sample_722]

value: GAGGCG


title: MDAMB231 cells with knockout of USP36 at 96h replicate 1 [sample_723]

value: GCACGG


title: MDAMB231 cells with knockout of USP36 at 96h replicate 3 [sample_739]

value: GCAGGC


title: MDAMB231 cells with knockout of USP16 at 96h replicate 2 [sample_720]

value: triple negative metastatic mammary adenocarcinoma

value: GACGCC


title: MDAMB231 cells with knockout of USP16 at 96h replicate 1 [sample_719]

value: GACCGC


title: MDAMB231 cells with knockout of UCK2 at 96h replicate 2 [sample_718]

value: CTGGCG


title: MDAMB231 cells with knockout of UCK2 at 96h replicate 1 [sample_717]

value: knockout

value: CTGCGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 44 [sample_716]

value: CTCCCG


title: MDAMB231 cells with knockout of NTC at 96h replicate 45 [sample_725]

value: GCCAGG


title: MDAMB231 cells with knockout of FBXO7 at 96h replicate 3 [sample_712]

value: CGCGTG


title: MDAMB231 cells with knockout of NTC at 96h replicate 43 [sample_715]

value: CGTGGG


title: MDAMB231 cells with knockout of OTUD6B at 96h replicate 3 [sample_713]

value: CGGAGC


title: MDAMB231 cells with knockout of TNFAIP3 at 96h replicate 3 [sample_714]

value: CGGCTG


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 3 [sample_711]

value: CGCCTC


title: MDAMB231 cells with knockout of untreated at 96h replicate 15 [sample_710]

value: untreated

value: CGCAGG


title: MDAMB231 cells with knockout of USP50 at 96h replicate 3 [sample_709]

value: CGACGG


title: MDAMB231 cells with knockout of USP31 at 96h replicate 3 [sample_707]

value: CCGGGT


title: MDAMB231 cells with knockout of USP21 at 96h replicate 3 [sample_706]

value: triple negative metastatic mammary adenocarcinoma

value: CCGCAG


title: MDAMB231 cells with knockout of USP27X at 96h replicate 1 [sample_721]

value: GAGCGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 42 [sample_705]

value: NTC

value: CCCGAG


title: MDAMB231 cells with knockout of OTUD6B at 96h replicate 2 [sample_702]

value: knockout

value: CGGACG


title: MDAMB231 cells with knockout of TNFAIP3 at 96h replicate 1 [sample_703]

value: CGGCCA


title: MDAMB231 cells with knockout of FBXO7 at 96h replicate 1 [sample_699]

value: CGCGCA


title: MDAMB231 cells with knockout of FBXO7 at 96h replicate 2 [sample_700]

value: CGCGGT


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 2 [sample_698]

value: CGCCGA


title: MDAMB231 cells with knockout of USPL1 at 96h replicate 1 [sample_697]

value: CGCCCT


title: MDAMB231 cells with knockout of OTUD6B at 96h replicate 1 [sample_701]

value: CGCTGC


title: MDAMB231 cells with knockout of untreated at 96h replicate 14 [sample_696]

value: untreated

value: CGCACC


title: MDAMB231 cells with knockout of untreated at 96h replicate 13 [sample_695]

value: CGAGGC


title: MDAMB231 cells with knockout of USP40 at 96h replicate 2 [sample_692]

value: CCGTGC


title: MDAMB231 cells with knockout of USP31 at 96h replicate 1 [sample_689]

value: triple negative metastatic mammary adenocarcinoma

value: CCGGAC


title: MDAMB231 cells with knockout of USP40 at 96h replicate 1 [sample_691]

value: CCGTCG


title: MDAMB231 cells with knockout of USP50 at 96h replicate 2 [sample_694]

value: CGACCC


title: MDAMB231 cells with knockout of USP21 at 96h replicate 2 [sample_688]

value: CCGAGG


title: MDAMB231 cells with knockout of USP21 at 96h replicate 1 [sample_687]

value: knockout

value: CCCTGG


title: MDAMB231 cells with knockout of USP50 at 96h replicate 1 [sample_693]

value: CCTGGC


title: MDAMB231 cells with knockout of USP31 at 96h replicate 2 [sample_690]

value: CCGGCA


title: MDAMB231 cells with knockout of NTC at 96h replicate 40 [sample_685]

value: NTC

value: CCCCGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 41 [sample_686]

value: CCCCTG


title: MDAMB231 cells with knockout of USP40 at 96h replicate 3 [sample_708]

value: CCTCGG


title: MDAMB231 cells with knockout of OTUB1 at 96h replicate 3 [sample_681]

value: AGCCGC


title: MDAMB231 cells with knockout of PSMD14 at 96h replicate 3 [sample_682]

value: AGGCGG


title: MDAMB231 cells with knockout of UBTD1 at 96h replicate 3 [sample_683]

value: CACCGG


title: MDAMB231 cells with knockout of Lipofectamine at 96h replicate 3 [sample_680]

value: Lipofectamine

value: ACGCGC


title: MDAMB231 cells with knockout of USP11 at 96h replicate 3 [sample_684]

value: triple negative metastatic mammary adenocarcinoma

value: CAGCGC


title: MDAMB231 cells with knockout of BAP1 at 96h replicate 3 [sample_679]

value: ACCCGG


title: MDAMB231 cells with knockout of TNFAIP3 at 96h replicate 2 [sample_704]

value: CGGCGT


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 3 [sample_678]

value: knockout

value: CTCTCC


title: MDAMB231 cells with knockout of VCPIP1 at 96h replicate 3 [sample_676]

value: TCCAAC


title: MDAMB231 cells with knockout of YOD1 at 96h replicate 3 [sample_677]

value: TTGTCC


title: MDAMB231 cells with knockout of PSMD14 at 96h replicate 2 [sample_670]

value: AGGCCC


title: MDAMB231 cells with knockout of UBTD1 at 96h replicate 1 [sample_671]

value: AGGGGC


title: MDAMB231 cells with knockout of USP11 at 96h replicate 1 [sample_673]

value: CACGGC


title: MDAMB231 cells with knockout of USP11 at 96h replicate 2 [sample_674]

value: CAGCCG


title: MDAMB231 cells with knockout of UBTD1 at 96h replicate 2 [sample_672]

value: CACCCC


title: MDAMB231 cells with knockout of OTUB1 at 96h replicate 2 [sample_668]

value: AGCCCG


title: MDAMB231 cells with knockout of USP46 at 96h replicate 1 [sample_727]

value: GCCCTC


title: MDAMB231 cells with knockout of YOD1 at 96h replicate 2 [sample_660]

value: TTCCTC


title: MDAMB231 cells with knockout of BAP1 at 96h replicate 2 [sample_664]

value: ACCCCC


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 2 [sample_662]

value: triple negative metastatic mammary adenocarcinoma

value: CCTTCC


title: MDAMB231 cells with knockout of Lipofectamine at 96h replicate 1 [sample_665]

value: Lipofectamine

value: ACCGGC


title: MDAMB231 cells with knockout of ZRANB1 at 96h replicate 1 [sample_661]

value: knockout

value: CCAACC


title: MDAMB231 cells with knockout of BAP1 at 96h replicate 1 [sample_663]

value: GTACCG


title: MDAMB231 cells with knockout of YOD1 at 96h replicate 1 [sample_659]

value: TCTGCA


title: MDAMB231 cells with knockout of VCPIP1 at 96h replicate 2 [sample_658]

value: TAGTGG


title: MDAMB231 cells with knockout of VCPIP1 at 96h replicate 1 [sample_657]

value: GTTCGA


title: MDAMB231 cells with knockout of untreated at 96h replicate 10 [sample_655]

value: untreated

value: GGGATT


title: MDAMB231 cells with knockout of USP9X at 96h replicate 3 [sample_653]

value: CATCAG


title: MDAMB231 cells with knockout of USP9Y at 96h replicate 3 [sample_654]

value: CGACTT


title: MDAMB231 cells with knockout of untreated at 96h replicate 11 [sample_656]

value: GTACAC


title: MDAMB231 cells with knockout of untreated at 96h replicate 12 [sample_675]

value: GTCAAG


title: MDAMB231 cells with knockout of USP8 at 96h replicate 3 [sample_652]

value: ATCGAG


title: MDAMB231 cells with knockout of USP7 at 96h replicate 3 [sample_651]

value: triple negative metastatic mammary adenocarcinoma

value: TTGGAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 39 [sample_650]

value: NTC

value: TTTTAG


title: MDAMB231 cells with knockout of PAN2 at 96h replicate 3 [sample_647]

value: knockout

value: TTCATA


title: MDAMB231 cells with knockout of PSMD14 at 96h replicate 1 [sample_669]

value: AGCGGG


title: MDAMB231 cells with knockout of USP54 at 96h replicate 3 [sample_649]

value: TTTATG


title: MDAMB231 cells with knockout of USP9Y at 96h replicate 2 [sample_644]

value: CCGATT


title: MDAMB231 cells with knockout of NTC at 96h replicate 38 [sample_645]

value: TTACTA


title: MDAMB231 cells with knockout of USP9X at 96h replicate 2 [sample_642]

value: CAGTCA


title: MDAMB231 cells with knockout of USP51 at 96h replicate 3 [sample_646]

value: TTATCA


title: MDAMB231 cells with knockout of USP9X at 96h replicate 1 [sample_641]

value: CACCAA


title: MDAMB231 cells with knockout of USP9Y at 96h replicate 1 [sample_643]

value: CCACAT


title: MDAMB231 cells with knockout of OTUB1 at 96h replicate 1 [sample_667]

value: ACGGGG


title: MDAMB231 cells with knockout of Lipofectamine at 96h replicate 2 [sample_666]

value: Lipofectamine

value: ACGCCG


title: MDAMB231 cells with knockout of NTC at 96h replicate 37 [sample_636]

value: triple negative metastatic mammary adenocarcinoma

value: TTTGTA


title: MDAMB231 cells with knockout of USP54 at 96h replicate 2 [sample_634]

value: TTTAGT


title: MDAMB231 cells with knockout of USP54 at 96h replicate 1 [sample_633]

value: TTTACA


title: MDAMB231 cells with knockout of USP53 at 96h replicate 1 [sample_631]

value: knockout

value: TTGAAA


title: MDAMB231 cells with knockout of PAN2 at 96h replicate 2 [sample_630]

value: TTCAAT


title: MDAMB231 cells with knockout of USP7 at 96h replicate 2 [sample_638]

value: TCTTTC


title: MDAMB231 cells with knockout of USP51 at 96h replicate 2 [sample_628]

value: TTATAC


title: MDAMB231 cells with knockout of USP7 at 96h replicate 1 [sample_637]

value: TTTTGA


title: MDAMB231 cells with knockout of NTC at 96h replicate 35 [sample_626]

value: NTC

value: TTACAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 36 [sample_635]

value: TTTCTT


title: MDAMB231 cells with knockout of USP49 at 96h replicate 3 [sample_623]

value: TCTAAT


title: MDAMB231 cells with knockout of PAN2 at 96h replicate 1 [sample_629]

value: TTATTG


title: MDAMB231 cells with knockout of USP53 at 96h replicate 2 [sample_632]

value: TTGATT


title: MDAMB231 cells with knockout of USP53 at 96h replicate 3 [sample_648]

value: TTGTTA


title: MDAMB231 cells with knockout of NTC at 96h replicate 34 [sample_625]

value: triple negative metastatic mammary adenocarcinoma

value: TTAATC


title: MDAMB231 cells with knockout of USP51 at 96h replicate 1 [sample_627]

value: TTAGTT


title: MDAMB231 cells with knockout of USP8 at 96h replicate 2 [sample_640]

value: AGGGAT


title: MDAMB231 cells with knockout of USP5 at 96h replicate 3 [sample_624]

value: knockout

value: TGAATA


title: MDAMB231 cells with knockout of USP45 at 96h replicate 3 [sample_619]

value: TATAAG


title: MDAMB231 cells with knockout of USP43 at 96h replicate 3 [sample_617]

value: TACAAA


title: MDAMB231 cells with knockout of untreated at 96h replicate 9 [sample_615]

value: untreated

value: TAACAA


title: MDAMB231 cells with knockout of USP48 at 96h replicate 2 [sample_610]

value: TATTTG


title: MDAMB231 cells with knockout of USP48 at 96h replicate 3 [sample_622]

value: TCAAAA


title: MDAMB231 cells with knockout of USP47 at 96h replicate 3 [sample_621]

value: TATTAC


title: MDAMB231 cells with knockout of USP48 at 96h replicate 1 [sample_609]

value: TATTGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 33 [sample_620]

value: NTC

value: TATCAT


title: MDAMB231 cells with knockout of USP44 at 96h replicate 3 [sample_618]

value: TAGAAT


title: MDAMB231 cells with knockout of USP42 at 96h replicate 3 [sample_616]

value: triple negative metastatic mammary adenocarcinoma

value: TAATAG


title: MDAMB231 cells with knockout of USP8 at 96h replicate 1 [sample_639]

value: AGACCT


title: MDAMB231 cells with knockout of USP5 at 96h replicate 2 [sample_614]

value: TGAAAT


title: MDAMB231 cells with knockout of USP44 at 96h replicate 2 [sample_602]

value: knockout

value: TACTTA


title: MDAMB231 cells with knockout of USP5 at 96h replicate 1 [sample_613]

value: TCTTAA


title: MDAMB231 cells with knockout of USP45 at 96h replicate 1 [sample_603]

value: TAGTAA


title: MDAMB231 cells with knockout of USP49 at 96h replicate 2 [sample_612]

value: TCATTA


title: MDAMB231 cells with knockout of USP42 at 96h replicate 2 [sample_598]

value: TAAGTA


title: MDAMB231 cells with knockout of USP49 at 96h replicate 1 [sample_611]

value: TCATAT


title: MDAMB231 cells with knockout of untreated at 96h replicate 7 [sample_595]

value: untreated

value: TAAAGT


title: MDAMB231 cells with knockout of USP47 at 96h replicate 2 [sample_608]

value: TATGTT


title: MDAMB231 cells with knockout of USP47 at 96h replicate 1 [sample_607]

value: TATGAA


title: MDAMB231 cells with knockout of NTC at 96h replicate 32 [sample_606]

value: NTC

value: TATATC


title: MDAMB231 cells with knockout of USP44 at 96h replicate 1 [sample_601]

value: triple negative metastatic mammary adenocarcinoma

value: TACTAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 31 [sample_605]

value: TATAGA


title: MDAMB231 cells with knockout of USP45 at 96h replicate 2 [sample_604]

value: TAGTTT


title: MDAMB231 cells with knockout of USP39 at 96h replicate 3 [sample_593]

value: knockout

value: GAATAT


title: MDAMB231 cells with knockout of USP43 at 96h replicate 2 [sample_600]

value: TAATTC


title: MDAMB231 cells with knockout of USP43 at 96h replicate 1 [sample_599]

value: TAATGA


title: MDAMB231 cells with knockout of USP42 at 96h replicate 1 [sample_597]

value: TAAGAT


title: MDAMB231 cells with knockout of USP39 at 96h replicate 2 [sample_582]

value: GAAATT


title: MDAMB231 cells with knockout of USP4 at 96h replicate 3 [sample_594]

value: GATTAA


title: MDAMB231 cells with knockout of USP39 at 96h replicate 1 [sample_581]

value: CTTTAA


title: MDAMB231 cells with knockout of USP38 at 96h replicate 2 [sample_580]

value: CTATTA


title: MDAMB231 cells with knockout of untreated at 96h replicate 8 [sample_596]

value: untreated

value: TAAATG


title: MDAMB231 cells with knockout of USP37 at 96h replicate 3 [sample_591]

value: CTAAAA


title: MDAMB231 cells with knockout of USP34 at 96h replicate 3 [sample_588]

value: ATTGTT


title: MDAMB231 cells with knockout of USP38 at 96h replicate 3 [sample_592]

value: triple negative metastatic mammary adenocarcinoma

value: CTTAAT


title: MDAMB231 cells with knockout of USP37 at 96h replicate 2 [sample_578]

value: CATTTA


title: MDAMB231 cells with knockout of USP38 at 96h replicate 1 [sample_579]

value: CTATAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 28 [sample_576]

value: knockout

value: NTC

value: CAATAA


title: MDAMB231 cells with knockout of USP32 at 96h replicate 3 [sample_586]

value: ATGTAA


title: MDAMB231 cells with knockout of NTC at 96h replicate 29 [sample_585]

value: ATCTAT


title: MDAMB231 cells with knockout of USP4 at 96h replicate 2 [sample_584]

value: GATATA


title: MDAMB231 cells with knockout of USP33 at 96h replicate 3 [sample_587]

value: ATTATC


title: MDAMB231 cells with knockout of USP33 at 96h replicate 1 [sample_569]

value: ATTACT


title: MDAMB231 cells with knockout of USP34 at 96h replicate 1 [sample_571]

value: ATTCTA


title: MDAMB231 cells with knockout of USP32 at 96h replicate 1 [sample_567]

value: ATGAAT


title: MDAMB231 cells with knockout of USP4 at 96h replicate 1 [sample_583]

value: GATAAT


title: MDAMB231 cells with knockout of USP37 at 96h replicate 1 [sample_577]

value: CATTAT


title: MDAMB231 cells with knockout of USP35 at 96h replicate 2 [sample_574]

value: ATTTGT


title: MDAMB231 cells with knockout of USP35 at 96h replicate 1 [sample_573]

value: triple negative metastatic mammary adenocarcinoma

value: ATTTCA


title: MDAMB231 cells with knockout of NTC at 96h replicate 27 [sample_575]

value: CAAATA


title: MDAMB231 cells with knockout of NTC at 96h replicate 30 [sample_590]

value: CATAAA


title: MDAMB231 cells with knockout of USP35 at 96h replicate 3 [sample_589]

value: knockout

value: ATTTTG


title: MDAMB231 cells with knockout of USP25 at 96h replicate 3 [sample_558]

value: GAGGGC


title: MDAMB231 cells with knockout of USP24 at 96h replicate 3 [sample_557]

value: GACGGG


title: MDAMB231 cells with knockout of KRAS at 96h replicate 3 [sample_555]

value: KRAS

value: CTCCGC


title: MDAMB231 cells with knockout of USP30 at 96h replicate 1 [sample_553]

value: GCGCTG


title: MDAMB231 cells with knockout of USP26 at 96h replicate 3 [sample_559]

value: GCAGGC


title: MDAMB231 cells with knockout of USP22 at 96h replicate 3 [sample_556]

value: CTGGGC


title: MDAMB231 cells with knockout of NTC at 96h replicate 26 [sample_566]

value: NTC

value: ATCATT


title: MDAMB231 cells with knockout of NTC at 96h replicate 25 [sample_565]

value: ATCAAA


title: MDAMB231 cells with knockout of USP32 at 96h replicate 2 [sample_568]

value: ATGATA


title: MDAMB231 cells with knockout of USP30 at 96h replicate 3 [sample_564]

value: triple negative metastatic mammary adenocarcinoma

value: GCGGCT


title: MDAMB231 cells with knockout of USP3 at 96h replicate 2 [sample_552]

value: GCGCAC


title: MDAMB231 cells with knockout of USP3 at 96h replicate 3 [sample_563]

value: GCGCCA


title: MDAMB231 cells with knockout of NTC at 96h replicate 24 [sample_560]

value: knockout

value: GCCCCT


title: MDAMB231 cells with knockout of USP30 at 96h replicate 2 [sample_554]

value: GCGGAG


title: MDAMB231 cells with knockout of USP33 at 96h replicate 2 [sample_570]

value: ATTAGA


title: MDAMB231 cells with knockout of USP29 at 96h replicate 2 [sample_550]

value: GCCTCG


title: MDAMB231 cells with knockout of USP28 at 96h replicate 3 [sample_561]

value: GCCGCA


title: MDAMB231 cells with knockout of USP28 at 96h replicate 1 [sample_547]

value: GCCCTC


title: MDAMB231 cells with knockout of USP3 at 96h replicate 1 [sample_551]

value: GCGAGC


title: MDAMB231 cells with knockout of USP26 at 96h replicate 1 [sample_543]

value: GCACGG


title: MDAMB231 cells with knockout of USP29 at 96h replicate 1 [sample_549]

value: GCCGTG


title: MDAMB231 cells with knockout of NTC at 96h replicate 23 [sample_546]

value: NTC

value: GCCCAG


title: MDAMB231 cells with knockout of USP28 at 96h replicate 2 [sample_548]

value: GCCGAC


title: MDAMB231 cells with knockout of USP25 at 96h replicate 1 [sample_541]

value: triple negative metastatic mammary adenocarcinoma

value: GAGCGG


title: MDAMB231 cells with knockout of USP34 at 96h replicate 2 [sample_572]

value: ATTGAA


title: MDAMB231 cells with knockout of NTC at 96h replicate 22 [sample_545]

value: GCCAGG


title: MDAMB231 cells with knockout of USP29 at 96h replicate 3 [sample_562]

value: knockout

value: GCCTGC


title: MDAMB231 cells with knockout of USP26 at 96h replicate 2 [sample_544]

value: GCAGCG


title: MDAMB231 cells with knockout of USP25 at 96h replicate 2 [sample_542]

value: GAGGCG


title: MDAMB231 cells with knockout of USP22 at 96h replicate 2 [sample_538]

value: CTGGCG


title: MDAMB231 cells with knockout of USP19 at 96h replicate 3 [sample_532]

value: CGCGTG


title: MDAMB231 cells with knockout of USP18 at 96h replicate 3 [sample_531]

value: CGCCTC


title: MDAMB231 cells with knockout of USP24 at 96h replicate 2 [sample_540]

value: GACGCC


title: MDAMB231 cells with knockout of USP24 at 96h replicate 1 [sample_539]

value: GACCGC


title: MDAMB231 cells with knockout of USP22 at 96h replicate 1 [sample_537]

value: CTGCGG


title: MDAMB231 cells with knockout of KRAS at 96h replicate 2 [sample_536]

value: KRAS

value: CTCCCG


title: MDAMB231 cells with knockout of USP20 at 96h replicate 3 [sample_534]

value: CGGCTG


title: MDAMB231 cells with knockout of KRAS at 96h replicate 1 [sample_535]

value: triple negative metastatic mammary adenocarcinoma

value: CGTGGG


title: MDAMB231 cells with knockout of USP2 at 96h replicate 3 [sample_533]

value: CGGAGC


title: MDAMB231 cells with knockout of USP20 at 96h replicate 1 [sample_523]

value: CGGCCA


title: MDAMB231 cells with knockout of USP20 at 96h replicate 2 [sample_524]

value: knockout

value: CGGCGT


title: MDAMB231 cells with knockout of USP15 at 96h replicate 3 [sample_529]

value: CGACGG


title: MDAMB231 cells with knockout of USP14 at 96h replicate 3 [sample_528]

value: CCTCGG


title: MDAMB231 cells with knockout of USP2 at 96h replicate 1 [sample_521]

value: CGCTGC


title: MDAMB231 cells with knockout of USP13 at 96h replicate 3 [sample_527]

value: CCGGGT


title: MDAMB231 cells with knockout of USP18 at 96h replicate 1 [sample_517]

value: CGCCCT


title: MDAMB231 cells with knockout of NTC at 96h replicate 21 [sample_525]

value: NTC

value: CCCGAG


title: MDAMB231 cells with knockout of USP14 at 96h replicate 2 [sample_512]

value: CCGTGC


title: MDAMB231 cells with knockout of USP15 at 96h replicate 2 [sample_514]

value: CGACCC


title: MDAMB231 cells with knockout of USP13 at 96h replicate 1 [sample_509]

value: CCGGAC


title: MDAMB231 cells with knockout of USP13 at 96h replicate 2 [sample_510]

value: CCGGCA


title: MDAMB231 cells with knockout of USP14 at 96h replicate 1 [sample_511]

value: triple negative metastatic mammary adenocarcinoma

value: CCGTCG


title: MDAMB231 cells with knockout of USP15 at 96h replicate 1 [sample_513]

value: CCTGGC


title: MDAMB231 cells with knockout of USP2 at 96h replicate 2 [sample_522]

value: CGGACG


title: MDAMB231 cells with knockout of USP12 at 96h replicate 1 [sample_507]

value: knockout

value: CCCTGG


title: MDAMB231 cells with knockout of USP1 at 96h replicate 3 [sample_503]

value: CACCGG


title: MDAMB231 cells with knockout of untreated at 96h replicate 4 [sample_515]

value: untreated

value: CGAGGC


title: MDAMB231 cells with knockout of UEVLD at 96h replicate 3 [sample_501]

value: UEVLD

value: AGCCGC


title: MDAMB231 cells with knockout of USP12 at 96h replicate 3 [sample_526]

value: CCGCAG


title: MDAMB231 cells with knockout of USP18 at 96h replicate 2 [sample_518]

value: CGCCGA


title: MDAMB231 cells with knockout of UFD1L at 96h replicate 3 [sample_502]

value: AGGCGG


title: MDAMB231 cells with knockout of NTC at 96h replicate 18 [sample_500]

value: NTC

value: ACGCGC


title: MDAMB231 cells with knockout of untreated at 96h replicate 5 [sample_516]

value: CGCACC


title: MDAMB231 cells with knockout of UCHL3 at 96h replicate 3 [sample_498]

value: triple negative metastatic mammary adenocarcinoma

value: CTCTCC


title: MDAMB231 cells with knockout of untreated at 96h replicate 6 [sample_530]

value: CGCAGG


title: MDAMB231 cells with knockout of USP12 at 96h replicate 2 [sample_508]

value: CCGAGG


title: MDAMB231 cells with knockout of USP19 at 96h replicate 1 [sample_519]

value: knockout

value: CGCGCA


title: MDAMB231 cells with knockout of UBTD2 at 96h replicate 3 [sample_496]

value: TCCAAC


title: MDAMB231 cells with knockout of UCHL1 at 96h replicate 3 [sample_497]

value: TTGTCC


title: MDAMB231 cells with knockout of USP10 at 96h replicate 1 [sample_493]

value: CACGGC


title: MDAMB231 cells with knockout of NTC at 96h replicate 19 [sample_505]

value: CCCCGT


title: MDAMB231 cells with knockout of USP10 at 96h replicate 3 [sample_504]

value: CAGCGC


title: MDAMB231 cells with knockout of NTC at 96h replicate 20 [sample_506]

value: CCCCTG


title: MDAMB231 cells with knockout of USP1 at 96h replicate 2 [sample_492]

value: CACCCC


title: MDAMB231 cells with knockout of USP1 at 96h replicate 1 [sample_491]

value: AGGGGC


title: MDAMB231 cells with knockout of UEVLD at 96h replicate 1 [sample_487]

value: UEVLD

value: ACGGGG


title: MDAMB231 cells with knockout of USP19 at 96h replicate 2 [sample_520]

value: CGCGGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 16 [sample_485]

value: triple negative metastatic mammary adenocarcinoma

value: NTC

value: ACCGGC


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 2 [sample_484]

value: ACCCCC


title: MDAMB231 cells with knockout of UCHL3 at 96h replicate 1 [sample_481]

value: knockout

value: CCAACC


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 1 [sample_483]

value: GTACCG


title: MDAMB231 cells with knockout of MYC at 96h replicate 3 [sample_495]

value: MYC

value: GTCAAG


title: MDAMB231 cells with knockout of USP10 at 96h replicate 2 [sample_494]

value: CAGCCG


title: MDAMB231 cells with knockout of UBTD2 at 96h replicate 1 [sample_477]

value: GTTCGA


title: MDAMB231 cells with knockout of UFD1L at 96h replicate 1 [sample_489]

value: AGCGGG


title: MDAMB231 cells with knockout of UEVLD at 96h replicate 2 [sample_488]

value: AGCCCG


title: MDAMB231 cells with knockout of MYC at 96h replicate 1 [sample_475]

value: GGGATT


title: MDAMB231 cells with knockout of NTC at 96h replicate 17 [sample_486]

value: ACGCCG


title: MDAMB231 cells with knockout of UCHL1 at 96h replicate 1 [sample_479]

value: TCTGCA


title: MDAMB231 cells with knockout of UBL3 at 96h replicate 3 [sample_471]

value: TTGGAT


title: MDAMB231 cells with knockout of UBL5 at 96h replicate 1 [sample_461]

value: triple negative metastatic mammary adenocarcinoma

value: CACCAA


title: MDAMB231 cells with knockout of NTC at 96h replicate 13 [sample_456]

value: NTC

value: TTTGTA


title: MDAMB231 cells with knockout of UBL3 at 96h replicate 2 [sample_458]

value: knockout

value: TCTTTC


title: MDAMB231 cells with knockout of UBL4A at 96h replicate 2 [sample_460]

value: AGGGAT


title: MDAMB231 cells with knockout of UCHL5 at 96h replicate 3 [sample_499]

value: ACCCGG


title: MDAMB231 cells with knockout of UCHL3 at 96h replicate 2 [sample_482]

value: CCTTCC


title: MDAMB231 cells with knockout of JOSD2 at 96h replicate 3 [sample_466]

value: TTATCA


title: MDAMB231 cells with knockout of UBL5 at 96h replicate 2 [sample_462]

value: CAGTCA


title: MDAMB231 cells with knockout of UCHL1 at 96h replicate 2 [sample_480]

value: TTCCTC


title: MDAMB231 cells with knockout of STAMBPL1 at 96h replicate 3 [sample_469]

value: TTTATG


title: MDAMB231 cells with knockout of UBTD2 at 96h replicate 2 [sample_478]

value: TAGTGG


title: MDAMB231 cells with knockout of MYC at 96h replicate 2 [sample_476]

value: MYC

value: GTACAC


title: MDAMB231 cells with knockout of UBR1 at 96h replicate 3 [sample_474]

value: CGACTT


title: MDAMB231 cells with knockout of UBL5 at 96h replicate 3 [sample_473]

value: triple negative metastatic mammary adenocarcinoma

value: CATCAG


title: MDAMB231 cells with knockout of UFD1L at 96h replicate 2 [sample_490]

value: AGGCCC


title: MDAMB231 cells with knockout of NTC at 96h replicate 15 [sample_470]

value: NTC

value: TTTTAG


title: MDAMB231 cells with knockout of SENP2 at 96h replicate 2 [sample_450]

value: knockout

value: TTCAAT


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 3 [sample_468]

value: STAMBP

value: TTGTTA


title: MDAMB231 cells with knockout of SENP2 at 96h replicate 3 [sample_467]

value: TTCATA


title: MDAMB231 cells with knockout of NTC at 96h replicate 14 [sample_465]

value: TTACTA


title: MDAMB231 cells with knockout of NTC at 96h replicate 11 [sample_446]

value: TTACAT


title: MDAMB231 cells with knockout of UBR1 at 96h replicate 2 [sample_464]

value: CCGATT


title: MDAMB231 cells with knockout of UBR1 at 96h replicate 1 [sample_463]

value: CCACAT


title: MDAMB231 cells with knockout of UBL4A at 96h replicate 1 [sample_459]

value: AGACCT


title: MDAMB231 cells with knockout of UBL4A at 96h replicate 3 [sample_472]

value: ATCGAG


title: MDAMB231 cells with knockout of UBL3 at 96h replicate 1 [sample_457]

value: TTTTGA


title: MDAMB231 cells with knockout of NTC at 96h replicate 12 [sample_455]

value: triple negative metastatic mammary adenocarcinoma

value: TTTCTT


title: MDAMB231 cells with knockout of STAMBPL1 at 96h replicate 2 [sample_454]

value: TTTAGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 9 [sample_440]

value: NTC

value: TATCAT


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 2 [sample_452]

value: knockout

value: TTGATT


title: MDAMB231 cells with knockout of OTUD5 at 96h replicate 3 [sample_439]

value: TATAAG


title: MDAMB231 cells with knockout of STAMBPL1 at 96h replicate 1 [sample_453]

value: TTTACA


title: MDAMB231 cells with knockout of STAMBP at 96h replicate 1 [sample_451]

value: STAMBP

value: TTGAAA


title: MDAMB231 cells with knockout of SENP2 at 96h replicate 1 [sample_449]

value: TTATTG


title: MDAMB231 cells with knockout of JOSD2 at 96h replicate 2 [sample_448]

value: TTATAC


title: MDAMB231 cells with knockout of JOSD2 at 96h replicate 1 [sample_447]

value: TTAGTT


title: MDAMB231 cells with knockout of OTUD7B at 96h replicate 2 [sample_430]

value: TATTTG


title: MDAMB231 cells with knockout of NTC at 96h replicate 10 [sample_445]

value: TTAATC


title: MDAMB231 cells with knockout of PARP11 at 96h replicate 3 [sample_443]

value: TCTAAT


title: MDAMB231 cells with knockout of OTUD7A at 96h replicate 3 [sample_441]

value: triple negative metastatic mammary adenocarcinoma

value: TATTAC


title: MDAMB231 cells with knockout of NTC at 96h replicate 7 [sample_425]

value: TATAGA


title: MDAMB231 cells with knockout of OTUD1 at 96h replicate 3 [sample_437]

value: TACAAA


title: MDAMB231 cells with knockout of OTUD7A at 96h replicate 1 [sample_427]

value: TATGAA


title: MDAMB231 cells with knockout of OTUB2 at 96h replicate 3 [sample_436]

value: knockout

value: TAATAG


title: MDAMB231 cells with knockout of untreated at 96h replicate 3 [sample_435]

value: untreated

value: TAACAA


title: MDAMB231 cells with knockout of PRPF8 at 96h replicate 1 [sample_433]

value: TCTTAA


title: MDAMB231 cells with knockout of PARP11 at 96h replicate 2 [sample_432]

value: TCATTA


title: MDAMB231 cells with knockout of PRPF8 at 96h replicate 2 [sample_434]

value: TGAAAT


title: MDAMB231 cells with knockout of OTUD4 at 96h replicate 2 [sample_422]

value: TACTTA


title: MDAMB231 cells with knockout of PRPF8 at 96h replicate 3 [sample_444]

value: TGAATA


title: MDAMB231 cells with knockout of OTUD7B at 96h replicate 3 [sample_442]

value: TCAAAA


title: MDAMB231 cells with knockout of PARP11 at 96h replicate 1 [sample_431]

value: TCATAT


title: MDAMB231 cells with knockout of OTUD7B at 96h replicate 1 [sample_429]

value: TATTGT


title: MDAMB231 cells with knockout of OTUD7A at 96h replicate 2 [sample_428]

value: triple negative metastatic mammary adenocarcinoma

value: TATGTT


title: MDAMB231 cells with knockout of OTUB2 at 96h replicate 2 [sample_418]

value: TAAGTA


title: Sperk_RNA-seq

city: Shanghai

first: Chun-hui

last: Xu

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

country: China

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

description: sibling embryos with knockdown of perk by morpholino

data_processing:
Clean sequenced reads were alignmented to GRCz10 by HISAT2 (2.0.5) with default parameters; alignmented SAM files were handled using samtools(1.7); aligned reads were extracted by Gfold(V1.1.4) with default parameters; FPKM were calculated by R script on its defination.(RNA-seq)
The homologous gene of human was extracted  from R packages biomaRt(2.383.0), then match to the FPKM data.
Genome_build: GRCz10 for RNA-seq
Supplementary_files_format_and_content: FPKM files were calculated by definition.(RNA-seq)

organism: Danio rerio

source_name: total embryos

growth_protocol: All embryos were incubated in egg water containing 0.045% 1-phenyl-2-thiourea (PTU Sigma) to prevent pigmentation at 28.5 ℃.

extract_protocol:
At 36 hpf, RNA was extracted with TRIzol Reagent (Ambion 15596018).
Libraries were generated using the NEBNext® UltraTM RNA library Prep Kit for Illumna® (NEB)  and sequenced on an Illumina Hiseq platform.

treatment_protocol: Morpholinos of gcn2 or perk were injected into one-cell stage embryos and the uninjected embryos were also subjected as control.

tag: tissue

value: total embryos

tag: age

value: 36 hours-post-fertilization

tag: genotype

value: WT (sibling embryos)

tag: morpholino injection

value: knockdown of perk by morpholino


title: MDAMB231 cells with knockout of OTUD4 at 96h replicate 3 [sample_438]

value: knockout

tag: treatment

value: TAGAAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 8 [sample_426]

value: NTC

tag: concentration

value: TATATC


title: Sctrl_RNA-seq

description: uninjected sibling embryos

value: uninjected


title: MDAMB231 cells with knockout of untreated at 96h replicate 1 [sample_415]

value: untreated

tag: time

value: TAAAGT


title: Mperk_RNA-seq

description: tars-/- embryos with knockdown of perk by morpholino

value: tars-/- embryos


title: MDAMB231 cells with knockout of OTUD5 at 96h replicate 2 [sample_424]

tag: replicate

value: TAGTTT


title: MDAMB231 cells with knockout of JOSD1 at 96h replicate 3 [sample_413]

tag: library

value: GAATAT


title: MDAMB231 cells with knockout of OTUD4 at 96h replicate 1 [sample_421]

value: triple negative metastatic mammary adenocarcinoma

tag: well

value: TACTAT


title: MDAMB231 cells with knockout of OTUD1 at 96h replicate 2 [sample_420]

tag: barcode

value: TAATTC


title: MDAMB231 cells with knockout of OTUD1 at 96h replicate 1 [sample_419]

value: TAATGA


title: Sgcn2_RNA-seq

description: sibling embryos with knockdown of gcn2 by morpholino

value: total embryos

value: 36 hours-post-fertilization

value: knockdown of gcn2 by morpholino


title: MDAMB231 cells with knockout of OTUB2 at 96h replicate 1 [sample_417]

value: knockout

value: TAAGAT


title: MDAMB231 cells with knockout of USP17L2 at 96h replicate 3 [sample_409]

value: ATTTTG


title: MDAMB231 cells with knockout of CYLD at 96h replicate 3 [sample_408]

value: CYLD

value: ATTGTT


title: MDAMB231 cells with knockout of untreated at 96h replicate 2 [sample_416]

value: untreated

value: TAAATG


title: MDAMB231 cells with knockout of COPS5 at 96h replicate 3 [sample_406]

value: ATGTAA


title: Ps_2_4606.H

city: Cologne

first: Fantin

last: Mesny

address: Carl-von-Linné-Weg 10

department: Plant-Microbes interaction

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description:
Pair of genomes mapped: Ps+At
Ps_fungalTranscriptome.csv

data_processing:
Raw-RNASeq reads were trimmed with Trimmomatic and parameters TRAILING:20 AVGQUAL:20 HEADCROP:10 MINLEN:100
Trimmed reads were mapped onto pairs of reference genomes using HiSat2
Per-gene read counts were retrieved from HiSat2 alignments using FeatureCounts
RPKM values were calculated from FeatureCounts data
Differential gene expression analyses were conducted with DESeq2, independently for plant and fungal transcriptomes
Genome_build: TAIR10.1
Genome_build: https://mycocosm.jgi.doe.gov/Chame1/Chame1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Parch1/Parch1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Phapo1/Phapo1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Truan1/Truan1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Macpha1/Macpha1.home.html
Genome_build: https://mycocosm.jgi.doe.gov/Zalva1/Zalva1.home.html
Supplementary_files_format_and_content: Files '_fungalTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of fungal genes in planta vs. on medium. This file also provide RPKM values in control (mycelium grown on medium) and test (fungus in planta) conditions
Supplementary_files_format_and_content: Files '_plantTranscriptome.csv’ correspond to the DESeq2 differential expression analysis of  A. thaliana genes mock-inoculated vs. inoculated with mycelium. This file also provide RPKM values in control (mock-treated plants) and test (plant inoculated with mycelium) conditions

organism: Phaeosphaeria sp. MPI-PUGE-AT-0046c

source_name: mycelium

growth_protocol: Seven A. thaliana seeds (or 16 drops of 10µL crushed mycelium solution) were grown in a sterile plate gnotobiotic system filled with an agar medium (described in Gruber et al. 201 - 100µM inorganic Phosphate). Culture was carried out in growth cabinets for 28 days at 21 °C for 10 hours with light (intensity 4), and at 19 °C and 14 hours in the dark.

extract_protocol:
Total RNA was extracted from plant roots or mycelium grown on medium using Qiagen RNEasy Plant Mini Kit
An RNAseq library was prepared with the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and then sequenced in single read mode on a HiSeq 3000 system

treatment_protocol: Prior to growth, plant seeds were inoculated with fungal mycelium or mock solution. For the control conditions, fungal inoculum were grown on the same agar-based culture medium.

tag: developmental stage

value: 28 days post seed inoculation

tag: strain

tag: culture medium

value: 100µM Pi MS-Agar

tag: inoculation

value: Mycelium inoculum deposited on medium


title: Ps_3_4606.I


title: MDAMB231 cells with knockout of OTUD5 at 96h replicate 1 [sample_423]

value: triple negative metastatic mammary adenocarcinoma

value: TAGTAA


title: MDAMB231 cells with knockout of MPND at 96h replicate 3 [sample_412]

value: MPND

value: CTTAAT


title: Mctrl_RNA-seq

description: uninjected tars-/- embryos

value: total embryos

value: 36 hours-post-fertilization

value: tars-/- embryos

value: uninjected