title: MDAMB231 cells with knockout of MYSM1 at 96h replicate 3 [sample_414]

value: knockout

value: GATTAA


title: Mgcn2_RNA-seq

status: Public on Nov 03 2021

type: SRA

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: tars-/- embryos with knockdown of gcn2 by morpholino

library_source: transcriptomic

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)

molecule: total RNA

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: tars-/- embryos

tag: morpholino injection

value: knockdown of gcn2 by morpholino


title: MDAMB231 cells with knockout of MYSM1 at 96h replicate 2 [sample_404]

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

country: USA

institute: Harvard Medical School

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

organism: Homo sapiens

source_name: triple negative metastatic mammary adenocarcinoma

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).

tag: treatment

tag: concentration

tag: time

tag: replicate

tag: library

tag: well

tag: barcode

value: GATATA


title: MDAMB231 cells with knockout of FBXO8 at 96h replicate 3 [sample_411]

value: triple negative metastatic mammary adenocarcinoma

value: CTAAAA


title: MDAMB231 cells with knockout of NTC at 96h replicate 6 [sample_410]

value: NTC

value: CATAAA


title: MDAMB231 cells with knockout of MYSM1 at 96h replicate 1 [sample_403]

value: GATAAT


title: MDAMB231 cells with knockout of JOSD1 at 96h replicate 2 [sample_402]

value: GAAATT


title: Cs_1_4606.A

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: Cs+At
Cs_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: Chaetomium sp. MPI-CAGE-AT-0009

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: Dusa plants at 25% of SWC (Soil water content) vs full irrigated control, replicate 2

type: RNA

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

description: Raw data file in Genepix format

hyb_protocol: Hybridization was carried out according to the two-colour microarray-based gene expression analysis protocol (Agilent)

scan_protocol: Microarray slides were scanned using the Axon GenePix 4000B scanner (Molecular Devices)

data_processing: Axon GenePix 6.0 software was used for image analysis. Normalization and statistical analysis was carried out in the R environment using limma

organism: Persea americana

source_name: Root samples of Dusa plants, 25% SWC

label_protocol: 4-6ug of RNA was transcribed into single stranded cDNA priming with random nonamer and oligo(dT) primers, using the Superscript III Reverse transcriptase. Samples and controls labelled with Cy3 and Cy5 (CyDye Post-Labelling Reactive Dye Pack, GE Healthcare Life Sciences)

growth_protocol: ‘Dusa’ (Westfalia Estate, South Africa) plants were vegetatively propagated by Brokaw nursery (Brokaw España S.L.) using a modified Frohlich method (Frolich and Platt 1972). Plants were kept in a greenhouse under day light illumination and semi-controlled conditions of air temperature (T) and relative humidity (RH). Photosynthetic photon flux density (PPFD), T and RH conditions inside the greenhouse were continuously registered by a quantum sensor. Daily T was allowed to fluctuate according to external weather conditions, but its variation range inside the greenhouse was maintained between 20±10 °C by an automatic cooling system and heating when necessary. The RH values inside the greenhouse were always over 40%. Soil moisture was monitored in all plants with a wet sensor (HH2 Moisture meter, Delta-T Devices. Cambridge, England).

extract_protocol: Total RNA extracted using the CTAB extraction method

treatment_protocol: To investigate the physiological response of ‘Dusa’ rootstock to water stress, plants were subjected to water deprivation until soil water content (SWC) reached 50% (i.e. mild-WS) and 25% (i.e. severe-WS) of Field capacity (Fc). Once these levels were reached, plants were rewatered to assess the recovery process.

value: Dusa

value: Root

source_name: Root samples of uninfected susceptible plants


title: MDAMB231 cells with knockout of BRCC3 at 96h replicate 3 [sample_407]

value: knockout

value: ATTATC


title: Dusa plants at 50% of SWC (Soil water content) vs full irrigated control, replicate 2

description: Raw data file in Genepix format

source_name: Root samples of Dusa plants, 50% SWC

source_name: Root samples of well-watered plants


title: Dusa plants at 25% of SWC (Soil water content) vs full irrigated control, replicate 1

description: Raw data file in Genepix format

source_name: Root samples of susceptible plants infected with Rosellinia necatrix, 22hr post-infection


title: Dusa plants at 50% of SWC (Soil water content) vs full irrigated control, replicate 3

description: Raw data file in Genepix format


title: MDAMB231 cells with knockout of NTC at 96h replicate 5 [sample_405]

value: ATCTAT


title: Ps_1_4606.G

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

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


title: Hv_2_4606.T

description:
Pair of genomes mapped: Hv+At
Hv_fungalTranscriptome.csv

organism: Halenospora varia


title: MDAMB231 cells with knockout of MPND at 96h replicate 2 [sample_400]

value: MPND

value: CTATTA


title: Hv_3_4606.U


title: MDAMB231 cells with knockout of MPND at 96h replicate 1 [sample_399]

value: CTATAT


title: MDAMB231 cells with knockout of NTC at 96h replicate 4 [sample_396]

value: triple negative metastatic mammary adenocarcinoma

value: CAATAA


title: At-Mp_2_4426.M

description:
Pair of genomes mapped: Mp+At
Mp_fungalTranscriptome.csv
Mp_plantTranscriptome.csv

organism:
Arabidopsis thaliana
Macrophomina phaseolina

source_name: roots,mycelium

value: Mycelium-inoculated seeds


title: At-Mp_1_4426.E


title: Cs_2_4606.B


title: MDAMB231 cells with knockout of JOSD1 at 96h replicate 1 [sample_401]

value: CTTTAA


title: Dusa plants at 50% of SWC (Soil water content) vs full irrigated control, replicate 1

description: Raw data file in Genepix format


title: Cs_3_4606.C


title: At-Ta_3_4426.T

description:
Pair of genomes mapped: Ta+At
Ta_fungalTranscriptome.csv
Ta_plantTranscriptome.csv

organism:
Arabidopsis thaliana
Truncatella angustata


title: MDAMB231 cells with knockout of FBXO8 at 96h replicate 2 [sample_398]

value: CATTTA


title: MDAMB231 cells with knockout of FBXO8 at 96h replicate 1 [sample_397]

value: CATTAT


title: Hv_1_4606.S

value: 28 days post seed inoculation


title: Mp_3_4606.O

description:
Pair of genomes mapped: Mp+At
Mp_fungalTranscriptome.csv

organism: Macrophomina phaseolina

value: 100µM Pi MS-Agar


title: At-Mp_3_4426.U


title: MDAMB231 cells with knockout of USP17L2 at 96h replicate 2 [sample_394]

value: ATTTGT


title: MDAMB231 cells with knockout of NTC at 96h replicate 3 [sample_395]

value: NTC

value: CAAATA


title: Mp_2_4606.N

value: Mycelium inoculum deposited on medium


title: MDAMB231 cells with knockout of BRCC3 at 96h replicate 2 [sample_390]

value: knockout

value: ATTAGA


title: MDAMB231 cells with knockout of CYLD at 96h replicate 1 [sample_391]

value: CYLD

value: ATTCTA


title: MDAMB231 cells with knockout of USP17L2 at 96h replicate 1 [sample_393]

value: ATTTCA


title: MDAMB231 cells with knockout of COPS5 at 96h replicate 2 [sample_388]

value: triple negative metastatic mammary adenocarcinoma

value: ATGATA


title: MDAMB231 cells with knockout of BRCC3 at 96h replicate 1 [sample_389]

value: ATTACT


title: Ta_2_4606.K

description:
Pair of genomes mapped: Ta+At
Ta_fungalTranscriptome.csv

organism: Truncatella angustata


title: Ta_1_4606.J


title: At-Ta_2_4426.L

value: Mycelium-inoculated seeds


title: MDAMB231 cells with knockout of NTC at 96h replicate 2 [sample_386]

value: ATCATT


title: MDAMB231 cells with knockout of NTC at 96h replicate 1 [sample_385]

value: ATCAAA


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 6h replicate 3 [sample_381]

value: compound

value: TGCGCG


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 6h replicate 3 [sample_383]

value: TGGGCC


title: Mp_1_4606.M

value: 28 days post seed inoculation

value: 100µM Pi MS-Agar


title: MCF7 cells treated with 10 uM SB1-F-78 at 6h replicate 3 [sample_380]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: TCGGCG


title: At-Ta_1_4426.D


title: MCF7 cells treated with 4.96 uM AV-12 at 6h replicate 3 [sample_377]

value: GTGGGG


title: MDAMB231 cells treated with DMSO control at 6h replicate 7 [sample_382]

value: DMSO

value: TGCGGC


title: MDAMB231 cells treated with DMSO control at 6h replicate 8 [sample_384]

value: TGGGGG


title: MCF7 cells treated with 0.96 uM CGM097 at 6h replicate 3 [sample_379]

value: TCGCGG


title: MCF7 cells treated with 0.96 uM nutlin3a at 6h replicate 3 [sample_373]

value: GGTCCC


title: MCF7 cells treated with 4.96 uM ML323 at 6h replicate 3 [sample_378]

value: TCCCCG


title: Ta_3_4606.L

value: Mycelium inoculum deposited on medium


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 6h replicate 2 [sample_372]

value: GGGGTG


title: MDAMB231 cells with knockout of COPS5 at 96h replicate 1 [sample_387]

value: triple negative metastatic mammary adenocarcinoma

value: knockout

value: ATGAAT


title: MCF7 cells treated with 10 uM P5091 at 6h replicate 3 [sample_375]

value: compound

value: GTCGCG


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 6h replicate 3 [sample_374]

value: GGTGCG


title: MCF7 cells treated with DMSO control at 6h replicate 10 [sample_371]

value: breast ductal carcinoma cell line

value: ATGTTT


title: HPV+OPC pts285

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

source_name: HPV+OPC pts285

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: gender

value: Female

value: Stage IV

value: Stage III

tag: subset (n=235)

value: no


title: HPV+OPC pts284

source_name: HPV+OPC pts284

value: Stage II


title: HPV+OPC pts286

source_name: HPV+OPC pts286

value: Male

value: yes


title: HPV+OPC pts283

source_name: HPV+OPC pts283

value: Stage I


title: SMC-IL1b

city: charlottesville

first: Xiujie

last: Xie

state: VA

address: 409 Lane Rd MR4

institute: university of virginia

description: Gene expression data from human aorta smooth muscle cells treated with IL1b.

hyb_protocol: The fragmented target and probe array controls were hybridized for 16 hours.

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is scanned. Each complete probe array image is stored in a separate data file identified by the experiment name.

data_processing: The data were analyzed with Transcriptome Analysis Console (TCA4.0) using default analysis setting and normalization method.

source_name: aorta smooth muscle cell

label_protocol: Double-stranded cDNA is synthesized from total RNA. An in vitro transcription (IVT) reaction is then done to produce biotin-labeled cRNA from the cDNA.

growth_protocol: Human aortic smooth muscle cells (Lonza, cat #: CC-2571) were cultured in smooth muscle cell growth medium (SmGM, Lonza #CC-3182) with supplements.

extract_protocol: Total RNA was extracted from cells using the TRIzol reagent (15596026) following the manufacturer's instructions.

treatment_protocol: Cells were starved for 24 hours before adding cytokines (PDGFBB 40ug/ml; TGFb 20ug/ml; IL1b 10 ug/ml; TNFa 20ug/ml), stimulated for 24 hours before harvest.

tag: cell type

value: Aorta smooth muscle cells


title: SMC-TNFa

description: Gene expression data from human aorta smooth muscle cells treated with TNFa.

value: TNFa


title: SMC-PDGF-BB

description: Gene expression data from human aorta smooth muscle cells treated with PDGFBB.

value: PDGF-BB


title: MCF7 cells treated with 0.1 uM CGM097 at 6h replicate 3 [sample_368]

value: GGGAGG


title: HPV+OPC pts282

source_name: HPV+OPC pts282

tag: age


title: HPV+OPC pts280

source_name: HPV+OPC pts280


title: SMC-Mock

description: Gene expression data from human aorta smooth muscle cells.

value: Mock


title: HPV+OPC pts281

source_name: HPV+OPC pts281


title: HPV+OPC pts276

source_name: HPV+OPC pts276


title: HPV+OPC pts277

source_name: HPV+OPC pts277


title: HPV+OPC pts275

source_name: HPV+OPC pts275


title: HPV+OPC pts278

source_name: HPV+OPC pts278


title: MCF7 cells treated with 10 uM HBX19818 at 6h replicate 3 [sample_376]

value: compound

value: GTCGGC


title: SMC-TGFb

description: Gene expression data from human aorta smooth muscle cells treated with TGFb.

value: TGFb


title: MCF7 cells treated with 0.96 uM VLX1570 at 6h replicate 3 [sample_370]

value: breast ductal carcinoma cell line

value: GGGCTC


title: MCF7 cells treated with 0.96 uM VLX1570 at 6h replicate 2 [sample_364]

value: GGCAGC


title: MCF7 cells treated with 10 uM AZ1 at 6h replicate 3 [sample_363]

value: GGCACG


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 6h replicate 3 [sample_369]

value: GGGCGA


title: MCF7 cells treated with 0.1 uM HY50737 at 6h replicate 3 [sample_361]

value: GCTGGG


title: MCF7 cells treated with 10 uM SB1-F-57 at 6h replicate 3 [sample_367]

value: GGGACC


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 6h replicate 3 [sample_366]

value: GGCGGA


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 6h replicate 3 [sample_365]

value: GGCGCT


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 6h replicate 2 [sample_359]

source_name: triple negative metastatic mammary adenocarcinoma

value: TGGCCG


title: MCF7 cells treated with 0.96 uM nutlin3a at 6h replicate 2 [sample_362]

value: GGACGC


title: MDAMB231 cells with knockout of CYLD at 96h replicate 2 [sample_392]

value: triple negative metastatic mammary adenocarcinoma

value: knockout

value: CYLD

value: ATTGAA


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 6h replicate 3 [sample_358]

value: compound

value: TGCCCC


title: MDAMB231 cells treated with DMSO control at 6h replicate 6 [sample_360]

value: DMSO

value: TGGCGC


title: MCF7 cells treated with 0.96 uM HBX41108 at 6h replicate 3 [sample_356]

value: breast ductal carcinoma cell line

value: TCCGGG


title: MDAMB231 cells treated with DMSO control at 6h replicate 5 [sample_357]

value: TCGGGC


title: HPV+OPC pts272

source_name: HPV+OPC pts272

value: Male

value: Stage IV

value: Stage II

value: yes


title: HPV+OPC pts273

source_name: HPV+OPC pts273

value: Stage III


title: HPV+OPC pts279

source_name: HPV+OPC pts279


title: HPV+OPC pts269

source_name: HPV+OPC pts269

value: Stage I


title: HPV+OPC pts271

source_name: HPV+OPC pts271


title: HPV+OPC pts270

source_name: HPV+OPC pts270


title: HPV+OPC pts268

source_name: HPV+OPC pts268


title: HPV+OPC pts274

source_name: HPV+OPC pts274


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 6h replicate 3 [sample_354]

source_name: breast ductal carcinoma cell line

value: GTGGCC


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 6h replicate 3 [sample_352]

value: GTCCCC


title: MCF7 cells treated with 0.1 uM HY50737 at 6h replicate 2 [sample_353]

value: GTGCGC


title: MCF7 cells treated with 0.1 uM HY80020 at 6h replicate 3 [sample_355]

value: TCCCGC


title: MCF7 cells treated with 0.96 uM HY50737 at 6h replicate 3 [sample_351]

value: compound

value: GGTGGC


title: HPV+OPC pts267

source_name: HPV+OPC pts267

value: Female


title: MCF7 cells treated with 10 uM HBX19818 at 6h replicate 2 [sample_350]

value: GGGTGC


title: HPV+OPC pts265

source_name: HPV+OPC pts265


title: MCF7 cells treated with 0.1 uM CGM097 at 6h replicate 2 [sample_349]

value: breast ductal carcinoma cell line

value: GGGTCG


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 6h replicate 2 [sample_348]

value: GGGGCA


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 6h replicate 2 [sample_347]

value: GGGGAC


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 6h replicate 2 [sample_346]

value: GGGCCT


title: MCF7 cells treated with 0.96 uM HY80020 at 6h replicate 3 [sample_343]

value: GGCGTC


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 6h replicate 3 [sample_344]

value: GGCTCC


title: HPV+OPC pts264

source_name: HPV+OPC pts264

value: Male

value: Stage IV

value: yes


title: MCF7 cells treated with 10 uM nutlin3a at 6h replicate 3 [sample_345]

value: GGGCAG


title: HPV+OPC pts263

source_name: HPV+OPC pts263

value: Stage I

value: no


title: MCF7 cells treated with 0.1 uM HY80020 at 6h replicate 2 [sample_342]

value: compound

value: GGCGAG


title: HPV+OPC pts262

source_name: HPV+OPC pts262

value: Stage III


title: HPV+OPC pts266

source_name: HPV+OPC pts266

value: Female


title: MCF7 cells treated with 10 uM XL-9678-203C at 6h replicate 3 [sample_341]

value: breast ductal carcinoma cell line

value: GGCCAC


title: HPV+OPC pts259

source_name: HPV+OPC pts259

value: Stage II


title: HPV+OPC pts258

source_name: HPV+OPC pts258


title: HPV+OPC pts260

source_name: HPV+OPC pts260


title: HPV+OPC pts256

source_name: HPV+OPC pts256


title: HPV+OPC pts261

source_name: HPV+OPC pts261


title: HPV+OPC pts257

source_name: HPV+OPC pts257


title: HPV+OPC pts255

source_name: HPV+OPC pts255


title: HPV+OPC pts251

source_name: HPV+OPC pts251


title: HPV+OPC pts254

source_name: HPV+OPC pts254


title: HPV+OPC pts250

source_name: HPV+OPC pts250


title: HPV+OPC pts252

source_name: HPV+OPC pts252


title: MCF7 cells treated with 10 uM SB1-F-78 at 6h replicate 2 [sample_337]

source_name: breast ductal carcinoma cell line

value: GCTCGC


title: HPV+OPC pts247

source_name: HPV+OPC pts247


title: HPV+OPC pts248

source_name: HPV+OPC pts248


title: MCF7 cells treated with 0.96 uM AV-12 at 6h replicate 3 [sample_339]

value: GGAGCC


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 6h replicate 2 [sample_335]

source_name: triple negative metastatic mammary adenocarcinoma

value: GCGTGG


title: MCF7 cells treated with 0.96 uM CGM097 at 6h replicate 2 [sample_338]

value: GCTGCC


title: HPV+OPC pts253

source_name: HPV+OPC pts253

value: Male


title: HPV+OPC pts246

source_name: HPV+OPC pts246

value: Stage IV


title: MCF7 cells treated with 10 uM SB1-F-70 at 6h replicate 3 [sample_340]

value: GGAGGG


title: MDAMB231 cells treated with DMSO control at 6h replicate 4 [sample_336]

value: triple negative metastatic mammary adenocarcinoma

value: DMSO

value: GCTCCG


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 6h replicate 3 [sample_334]

value: compound

value: GCGGGA


title: MCF7 cells treated with 0.1 uM bortezomib at 6h replicate 3 [sample_332]

value: bortezomib

value: GCGCGT


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 6h replicate 2 [sample_331]

value: breast ductal carcinoma cell line

value: GCGCCA


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 6h replicate 3 [sample_330]

value: GCGACG


title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 6h replicate 3 [sample_333]

value: GCGGCT


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 6h replicate 3 [sample_329]

value: GCCTGC


title: MCF7 cells treated with 0.96 uM P5091 at 6h replicate 3 [sample_328]

value: GCCGGT


title: HPV+OPC pts242

source_name: HPV+OPC pts242

value: Stage II

value: yes


title: HPV+OPC pts243

source_name: HPV+OPC pts243

value: Male

value: Stage IV

value: Stage I


title: HPV+OPC pts241

source_name: HPV+OPC pts241

value: Female

value: no


title: HPV+OPC pts240

source_name: HPV+OPC pts240

value: Stage III


title: HPV+OPC pts238

source_name: HPV+OPC pts238


title: HPV+OPC pts244

source_name: HPV+OPC pts244


title: HPV+OPC pts245

source_name: HPV+OPC pts245


title: MCF7 cells treated with 10 uM SB1-F-70 at 6h replicate 2 [sample_326]

value: compound

value: GCCCGA


title: HPV+OPC pts239

source_name: HPV+OPC pts239


title: MCF7 cells treated with 0.96 uM CS5405 at 6h replicate 3 [sample_325]

value: GCCCCT


title: HPV+OPC pts237

source_name: HPV+OPC pts237


title: HPV+OPC pts235

source_name: HPV+OPC pts235


title: HPV+OPC pts233

source_name: HPV+OPC pts233


title: HPV+OPC pts236

source_name: HPV+OPC pts236


title: HPV+OPC pts234

source_name: HPV+OPC pts234


title: MCF7 cells treated with 0.96 uM P5091 at 6h replicate 2 [sample_324]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: GCCACC


title: HPV+OPC pts232

source_name: HPV+OPC pts232


title: HPV+OPC pts249

source_name: HPV+OPC pts249


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 6h replicate 3 [sample_322]

value: GCACCC


title: MCF7 cells treated with 0.96 uM CS5405 at 6h replicate 2 [sample_321]

value: GAGGGC


title: HPV+OPC pts230

source_name: HPV+OPC pts230


title: MCF7 cells treated with 0.96 uM AZ1 at 6h replicate 3 [sample_320]

value: GAGCCC


title: MCF7 cells treated with 0.96 uM CS5405 at 6h replicate 1 [sample_318]

value: GACCCG


title: HPV+OPC pts229

source_name: HPV+OPC pts229


title: MCF7 cells treated with 3 uM abemaciclib at 6h replicate 3 [sample_323]

value: abemaciclib

value: GCAGGC


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 6h replicate 3 [sample_317]

value: CTGGGC


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 6h replicate 1 [sample_327]

value: GCCGCA


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 6h replicate 1 [sample_316]

value: CTCGGG


title: HPV+OPC pts226

source_name: HPV+OPC pts226

value: Male

value: Stage IV

value: Stage I

value: yes


title: HPV+OPC pts228

source_name: HPV+OPC pts228

value: Stage III

value: Stage II


title: HPV+OPC pts227

source_name: HPV+OPC pts227


title: HPV+OPC pts225

source_name: HPV+OPC pts225


title: HPV+OPC pts224

source_name: HPV+OPC pts224


title: HPV+OPC pts222

source_name: HPV+OPC pts222


title: MCF7 cells treated with 0.96 uM HBX41108 at 6h replicate 2 [sample_319]

value: breast ductal carcinoma cell line

value: compound

value: GACGGG


title: HPV+OPC pts221

source_name: HPV+OPC pts221

value: no


title: MCF7 cells treated with DMSO control at 6h replicate 9 [sample_315]

value: DMSO

value: CTCCGC


title: MCF7 cells treated with 0.96 uM HY80020 at 6h replicate 2 [sample_314]

value: CGTGCC


title: HPV+OPC pts218

source_name: HPV+OPC pts218


title: HPV+OPC pts217

source_name: HPV+OPC pts217


title: HPV+OPC pts214

source_name: HPV+OPC pts214


title: HPV+OPC pts223

source_name: HPV+OPC pts223


title: HPV+OPC pts215

source_name: HPV+OPC pts215


title: HPV+OPC pts216

source_name: HPV+OPC pts216


title: HPV+OPC pts220

source_name: HPV+OPC pts220

value: Female


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 6h replicate 1 [sample_313]

source_name: breast ductal carcinoma cell line

value: CGTCGC


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 6h replicate 2 [sample_312]

source_name: triple negative metastatic mammary adenocarcinoma

value: GCGTCC


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 6h replicate 1 [sample_304]

value: GCCGAC


title: MCF7 cells treated with 10 uM SB1-F-70 at 6h replicate 1 [sample_306]

value: GCCTCG


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 6h replicate 3 [sample_310]

value: triple negative metastatic mammary adenocarcinoma

value: GCGGAG


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 6h replicate 3 [sample_308]

value: GCGCAC


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 6h replicate 2 [sample_302]

value: GCCCAG


title: MCF7 cells treated with DMSO control at 6h replicate 8 [sample_303]

value: GCCCTC


title: MCF7 cells treated with 0.96 uM CGM097 at 6h replicate 1 [sample_307]

value: breast ductal carcinoma cell line

value: GCGAGC


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 6h replicate 2 [sample_311]

value: compound

value: GCGGTC


title: MCF7 cells treated with 0.96 uM AZ1 at 6h replicate 2 [sample_299]

value: GCACGG


title: MCF7 cells treated with 10 uM XL-9678-203C at 6h replicate 2 [sample_298]

value: GAGGCG


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 6h replicate 3 [sample_309]

value: GCGCTG


title: MCF7 cells treated with 10 uM AZ1 at 6h replicate 2 [sample_305]

value: GCCGTG


title: HPV+OPC pts211

source_name: HPV+OPC pts211

value: Male

value: Stage IV

value: Stage II

value: yes


title: HPV+OPC pts212

source_name: HPV+OPC pts212

value: Female

value: Stage III


title: HPV+OPC pts219

source_name: HPV+OPC pts219

value: Stage I


title: HPV+OPC pts210

source_name: HPV+OPC pts210


title: HPV+OPC pts213

source_name: HPV+OPC pts213


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 6h replicate 3 [sample_294]

value: CTGGCG


title: HPV+OPC pts207

source_name: HPV+OPC pts207

value: no


title: HPV+OPC pts208

source_name: HPV+OPC pts208


title: HPV+OPC pts231

source_name: HPV+OPC pts231


title: HPV+OPC pts209

source_name: HPV+OPC pts209


title: MCF7 cells treated with 10 uM SB1-F-57 at 6h replicate 2 [sample_300]

value: breast ductal carcinoma cell line

value: GCAGCG


title: MCF7 cells treated with 0.96 uM HY50737 at 6h replicate 2 [sample_301]

value: compound

value: GCCAGG


title: HPV+OPC pts203

source_name: HPV+OPC pts203


title: MCF7 cells treated with 10 uM HBX19818 at 6h replicate 1 [sample_290]

value: CGTCCG


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 6h replicate 2 [sample_296]

value: GACGCC


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 6h replicate 2 [sample_297]

value: GAGCGG


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 6h replicate 2 [sample_293]

value: CTGCGG


title: MCF7 cells treated with 0.96 uM bortezomib at 6h replicate 3 [sample_292]

value: bortezomib

value: CTCCCG


title: HPV+OPC pts204

source_name: HPV+OPC pts204

value: Male

value: Stage IV


title: HPV+OPC pts206

source_name: HPV+OPC pts206

value: yes


title: MCF7 cells treated with 4.96 uM ML323 at 6h replicate 2 [sample_291]

value: CGTGGG


title: MCF7 cells treated with DMSO control at 6h replicate 7 [sample_295]

value: DMSO

value: GACCGC


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 6h replicate 2 [sample_289]

value: CGGTGG


title: HPV+OPC pts205

source_name: HPV+OPC pts205

value: Stage I

value: no


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 6h replicate 1 [sample_288]

value: triple negative metastatic mammary adenocarcinoma

value: compound

value: CGGTCC


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 6h replicate 3 [sample_285]

value: CGGCTG


title: HPV+OPC pts198

source_name: HPV+OPC pts198

value: Stage II


title: HPV+OPC pts196

source_name: HPV+OPC pts196


title: HPV+OPC pts195

source_name: HPV+OPC pts195

value: Stage III


title: HPV+OPC pts197

source_name: HPV+OPC pts197


title: HPV+OPC pts194

source_name: HPV+OPC pts194


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 6h replicate 1 [sample_286]

source_name: triple negative metastatic mammary adenocarcinoma

value: CGGGAG


title: MCF7 cells treated with 0.96 uM P5091 at 6h replicate 1 [sample_278]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: CGCCAG


title: MCF7 cells treated with 10 uM P5091 at 6h replicate 2 [sample_283]

value: CGGAGC


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 6h replicate 2 [sample_280]

value: CGCGAC


title: HPV+OPC pts202

source_name: HPV+OPC pts202

value: Female

value: Stage IV


title: HPV+OPC pts199

source_name: HPV+OPC pts199

value: Male

value: yes


title: MCF7 cells treated with DMSO control at 6h replicate 6 [sample_282]

value: DMSO

value: CGCTCG


title: MCF7 cells treated with 4.96 uM AV-12 at 6h replicate 2 [sample_281]

value: CGCGTG


title: HPV+OPC pts191

source_name: HPV+OPC pts191


title: HPV+OPC pts200

source_name: HPV+OPC pts200

value: Stage I


title: HPV+OPC pts190

source_name: HPV+OPC pts190


title: MCF7 cells treated with 0.3 uM abemaciclib at 6h replicate 3 [sample_279]

value: compound

value: abemaciclib

value: CGCCTC


title: MCF7 cells treated with 0.96 uM nutlin3a at 6h replicate 1 [sample_284]

value: CGGCAC


title: HPV+OPC pts192

source_name: HPV+OPC pts192

value: no


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 6h replicate 2 [sample_277]

value: breast ductal carcinoma cell line

value: CGCAGG


title: MCF7 cells treated with 10 uM SB1-F-22 at 6h replicate 3 [sample_276]

value: CGAGCG


title: HPV+OPC pts193

source_name: HPV+OPC pts193

value: Stage II


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 6h replicate 3 [sample_274]

value: CCTGCG


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 6h replicate 1 [sample_275]

value: CGACGG


title: MCF7 cells treated with 3 uM abemaciclib at 6h replicate 2 [sample_273]

value: CCTCGG


title: MCF7 cells treated with 0.1 uM bortezomib at 6h replicate 2 [sample_272]

value: bortezomib

value: CCGGTG


title: MCF7 cells treated with 0.96 uM HY50737 at 6h replicate 1 [sample_271]

value: CCGGGT


title: HPV+OPC pts187

source_name: HPV+OPC pts187

value: Male

value: Stage IV

value: Stage III

value: yes


title: HPV+OPC pts189

source_name: HPV+OPC pts189


title: HPV+OPC pts186

source_name: HPV+OPC pts186

value: Female

value: Stage I


title: HPV+OPC pts188

source_name: HPV+OPC pts188


title: HPV+OPC pts185

source_name: HPV+OPC pts185


title: HPV+OPC pts184

source_name: HPV+OPC pts184


title: HPV+OPC pts183

source_name: HPV+OPC pts183


title: MCF7 cells treated with 0.1 uM CGM097 at 6h replicate 1 [sample_269]

value: compound

value: CCGCAG


title: HPV+OPC pts201

source_name: HPV+OPC pts201


title: HPV+OPC pts182

source_name: HPV+OPC pts182


title: HPV+OPC pts176

source_name: HPV+OPC pts176


title: MCF7 cells treated with 0.96 uM AV-12 at 6h replicate 2 [sample_266]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: CCCCCA


title: MCF7 cells treated with 0.96 uM AZ1 at 6h replicate 1 [sample_267]

value: CCCGAG


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 6h replicate 1 [sample_268]

value: CCCGGA


title: MCF7 cells treated with 0.1 uM HY50737 at 6h replicate 1 [sample_265]

value: CCCCAC


title: MDAMB231 cells treated with DMSO control at 6h replicate 3 [sample_264]

source_name: triple negative metastatic mammary adenocarcinoma

value: DMSO

value: CGGGGA


title: MCF7 cells treated with 10 uM SB1-F-78 at 6h replicate 1 [sample_270]

value: CCGCGA


title: HPV+OPC pts175

source_name: HPV+OPC pts175

value: no


title: HPV+OPC pts179

source_name: HPV+OPC pts179

value: Male

value: Stage II


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 6h replicate 2 [sample_263]

value: triple negative metastatic mammary adenocarcinoma

value: CGGGCT


title: HPV+OPC pts178

source_name: HPV+OPC pts178

value: Stage IV

value: yes


title: HPV+OPC pts174

source_name: HPV+OPC pts174

value: Stage I


title: HPV+OPC pts177

source_name: HPV+OPC pts177


title: HPV+OPC pts181

source_name: HPV+OPC pts181

value: Female

value: Stage III


title: MDAMB231 cells treated with DMSO control at 6h replicate 2 [sample_262]

value: compound

value: CGGCGT


title: HPV+OPC pts180

source_name: HPV+OPC pts180


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 6h replicate 1 [sample_261]

value: CGGCCA


title: HPV+OPC pts173

source_name: HPV+OPC pts173


title: HPV+OPC pts172

source_name: HPV+OPC pts172


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 6h replicate 2 [sample_257]

value: breast ductal carcinoma cell line

value: CGCGCA


title: MCF7 cells treated with 10 uM XL-9678-188 at 6h replicate 3 [sample_259]

value: CGCTGC


title: HPV+OPC pts169

source_name: HPV+OPC pts169


title: HPV+OPC pts170

source_name: HPV+OPC pts170


title: MCF7 cells treated with DMSO control at 6h replicate 5 [sample_258]

value: DMSO

value: CGCGGT


title: HPV+OPC pts171

source_name: HPV+OPC pts171

value: Male


title: MCF7 cells treated with 0.1 uM CS5405 at 6h replicate 3 [sample_256]

value: CGCCGA


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 6h replicate 2 [sample_260]

value: CGGACG


title: MCF7 cells treated with 10 uM HBX41108 at 6h replicate 3 [sample_255]

value: CGCCCT


title: MCF7 cells treated with 10 uM P5091 at 6h replicate 1 [sample_254]

value: CGCACC


title: MCF7 cells treated with 0.1 uM CS5405 at 6h replicate 2 [sample_253]

value: CGAGGC


title: MCF7 cells treated with 10 uM nutlin3a at 6h replicate 2 [sample_252]

value: CGACCC


title: MCF7 cells treated with 0.96 uM HBX19818 at 6h replicate 3 [sample_251]

value: CCTGGC


title: HPV+OPC pts166

source_name: HPV+OPC pts166

value: Stage III

value: Stage II

value: yes


title: HPV+OPC pts168

source_name: HPV+OPC pts168

value: Stage IV


title: HPV+OPC pts167

source_name: HPV+OPC pts167

value: no


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 6h replicate 1 [sample_287]

value: triple negative metastatic mammary adenocarcinoma

value: compound

value: CGGGTC


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 6h replicate 3 [sample_249]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: CCGTCG


title: MCF7 cells treated with 0.96 uM HY80020 at 6h replicate 1 [sample_248]

value: CCGGCA


title: MCF7 cells treated with DMSO control at 6h replicate 4 [sample_247]

value: DMSO

value: CCGGAC


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 6h replicate 1 [sample_246]

value: CCGAGG


title: HPV+OPC pts163

source_name: HPV+OPC pts163

value: Female


title: HPV+OPC pts162

source_name: HPV+OPC pts162

value: Male


title: HPV+OPC pts161

source_name: HPV+OPC pts161

value: Stage I


title: MCF7 cells treated with 0.1 uM VLX1570 at 6h replicate 3 [sample_244]

value: CCCCTG


title: HPV+OPC pts160

source_name: HPV+OPC pts160


title: HPV+OPC pts157

source_name: HPV+OPC pts157


title: HPV+OPC pts159

source_name: HPV+OPC pts159


title: MCF7 cells treated with 10 uM XL-9678-188 at 6h replicate 2 [sample_245]

value: CCCTGG


title: HPV+OPC pts165

source_name: HPV+OPC pts165

value: Stage III

value: yes


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 6h replicate 1 [sample_243]

value: CCCCGT


title: HPV+OPC pts158

source_name: HPV+OPC pts158

value: Stage IV


title: HPV+OPC pts164

source_name: HPV+OPC pts164


title: MCF7 cells treated with 10 uM SB1-F-64 at 6h replicate 3 [sample_250]

value: compound

value: CCGTGC


title: MCF7 cells treated with 10 uM SB1-F-22 at 6h replicate 2 [sample_242]

value: breast ductal carcinoma cell line

value: CCCAGC


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 6h replicate 2 [sample_240]

source_name: triple negative metastatic mammary adenocarcinoma

value: CCAGGG


title: HPV+OPC pts154

source_name: HPV+OPC pts154


title: HPV+OPC pts155

source_name: HPV+OPC pts155

value: Stage II


title: HPV+OPC pts153

source_name: HPV+OPC pts153


title: HPV+OPC pts150

source_name: HPV+OPC pts150


title: HPV+OPC pts156

source_name: HPV+OPC pts156

value: no


title: HPV+OPC pts149

source_name: HPV+OPC pts149


title: HPV+OPC pts147

source_name: HPV+OPC pts147


title: MCF7 cells treated with 24.96 uM ML323 at 6h replicate 3 [sample_241]

source_name: breast ductal carcinoma cell line

value: CCCACG


title: MCF7 cells treated with 0.96 uM HBX19818 at 6h replicate 2 [sample_236]

value: CACGCG


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 6h replicate 1 [sample_234]

value: AGGGCG


title: HPV+OPC pts148

source_name: HPV+OPC pts148

value: Male

value: Stage I


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 6h replicate 1 [sample_238]

value: triple negative metastatic mammary adenocarcinoma

value: CAGGCC


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 6h replicate 2 [sample_239]

value: CCACGC


title: HPV+OPC pts145

source_name: HPV+OPC pts145

value: Stage III

value: yes


title: HPV+OPC pts152

source_name: HPV+OPC pts152


title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 6h replicate 2 [sample_237]

value: compound

value: CAGCGC


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 6h replicate 1 [sample_233]

value: breast ductal carcinoma cell line

value: AGGCGG


title: HPV+OPC pts151

source_name: HPV+OPC pts151

value: Stage IV


title: HPV+OPC pts146

source_name: HPV+OPC pts146

value: Stage II


title: HPV+OPC pts144

source_name: HPV+OPC pts144


title: MCF7 cells treated with 4.96 uM ML323 at 6h replicate 1 [sample_235]

value: CACCGG


title: MCF7 cells treated with 10 uM XL-9678-203C at 6h replicate 1 [sample_232]

value: AGCGCC


title: MCF7 cells treated with 10 uM HBX41108 at 6h replicate 1 [sample_226]

value: GGACCA


title: MCF7 cells treated with 10 uM HBX41108 at 6h replicate 2 [sample_230]

value: ACGGCC


title: MCF7 cells treated with 10 uM SB1-F-22 at 6h replicate 1 [sample_231]

value: AGCCGC


title: MCF7 cells treated with DMSO control at 6h replicate 3 [sample_229]

value: DMSO

value: ACGCGC


title: MCF7 cells treated with 0.3 uM abemaciclib at 6h replicate 2 [sample_224]

value: abemaciclib

value: TTTGGC


title: MCF7 cells treated with 0.1 uM CS5405 at 6h replicate 1 [sample_228]

value: ACCGCG


title: HPV+OPC pts143

source_name: HPV+OPC pts143

value: Male

value: Stage I

value: yes


title: HPV+OPC pts140

source_name: HPV+OPC pts140

value: Stage III


title: HPV+OPC pts142

source_name: HPV+OPC pts142

value: Female


title: HPV+OPC pts141

source_name: HPV+OPC pts141


title: HPV+OPC pts139

source_name: HPV+OPC pts139


title: HPV+OPC pts138

source_name: HPV+OPC pts138


title: HPV+OPC pts133

source_name: HPV+OPC pts133

value: Stage IV


title: HPV+OPC pts135

source_name: HPV+OPC pts135


title: MCF7 cells treated with 0.96 uM HBX41108 at 6h replicate 1 [sample_227]

value: breast ductal carcinoma cell line

value: compound

value: ACCCGG


title: MCF7 cells treated with 10 uM XL-9678-188 at 6h replicate 1 [sample_225]

value: CTCTCC


title: HPV+OPC pts128

source_name: HPV+OPC pts128


title: HPV+OPC pts137

source_name: HPV+OPC pts137

value: Stage II


title: MCF7 cells treated with 3 uM abemaciclib at 6h replicate 1 [sample_223]

source_name: breast ductal carcinoma cell line

value: TTGTCC


title: HPV+OPC pts134

source_name: HPV+OPC pts134


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 6h replicate 1 [sample_216]

source_name: triple negative metastatic mammary adenocarcinoma

value: CCACCG


title: MCF7 cells treated with 10 uM AZ1 at 6h replicate 1 [sample_222]

value: TCGAAG


title: HPV+OPC pts136

source_name: HPV+OPC pts136


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 6h replicate 1 [sample_215]

value: triple negative metastatic mammary adenocarcinoma

value: CAGGGG


title: MDAMB231 cells treated with DMSO control at 6h replicate 1 [sample_214]

value: DMSO

value: CAGCCG


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 6h replicate 1 [sample_217]

value: GGACAT


title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 6h replicate 1 [sample_213]

value: CACGGC


title: HPV+OPC pts132

source_name: HPV+OPC pts132

value: Male

value: yes


title: HPV+OPC pts129

source_name: HPV+OPC pts129

value: Female

value: Stage IV

value: Stage I

value: no


title: HPV+OPC pts131

source_name: HPV+OPC pts131


title: HPV+OPC pts125

source_name: HPV+OPC pts125


title: HPV+OPC pts123

source_name: HPV+OPC pts123

value: Stage III


title: HPV+OPC pts124

source_name: HPV+OPC pts124


title: HPV+OPC pts130

source_name: HPV+OPC pts130


title: MCF7 cells treated with 0.96 uM HBX19818 at 6h replicate 1 [sample_221]

value: breast ductal carcinoma cell line

value: compound

value: TCCAAC


title: MCF7 cells treated with 0.1 uM VLX1570 at 6h replicate 2 [sample_209]

value: AGCGGG


title: MCF7 cells treated with DMSO control at 6h replicate 2 [sample_207]

value: ACGGGG


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 6h replicate 2 [sample_220]

value: GTGACT


title: HPV+OPC pts127

source_name: HPV+OPC pts127


title: MCF7 cells treated with 10 uM SB1-F-64 at 6h replicate 2 [sample_218]

value: GGCAAT


title: HPV+OPC pts121

source_name: HPV+OPC pts121


title: HPV+OPC pts126

source_name: HPV+OPC pts126


title: HPV+OPC pts120

source_name: HPV+OPC pts120


title: HPV+OPC pts118

source_name: HPV+OPC pts118

value: Stage II


title: HPV+OPC pts119

source_name: HPV+OPC pts119


title: MCF7 cells treated with 10 uM SB1-F-57 at 6h replicate 1 [sample_206]

source_name: breast ductal carcinoma cell line

value: ACGCCG


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 6h replicate 1 [sample_205]

value: ACCGGC


title: MCF7 cells treated with 10 uM SB1-F-64 at 6h replicate 1 [sample_203]

value: GTACCG


title: MCF7 cells treated with 24.96 uM ML323 at 6h replicate 2 [sample_219]

value: GTCAAG


title: HPV+OPC pts113

source_name: HPV+OPC pts113

value: Male

value: yes


title: HPV+OPC pts112

source_name: HPV+OPC pts112

value: Stage IV

value: Stage I


title: MCF7 cells treated with DMSO control at 6h replicate 1 [sample_201]

value: DMSO

value: CCAACC


title: MCF7 cells treated with 10 uM nutlin3a at 6h replicate 1 [sample_212]

value: breast ductal carcinoma cell line

value: compound

value: CACCCC


title: MCF7 cells treated with 0.3 uM abemaciclib at 6h replicate 1 [sample_199]

value: abemaciclib

value: TCTGCA


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 6h replicate 1 [sample_198]

value: TAGTGG


title: HPV+OPC pts122

source_name: HPV+OPC pts122

value: Stage III

value: Stage II


title: HPV+OPC pts110

source_name: HPV+OPC pts110

value: Female


title: HPV+OPC pts111

source_name: HPV+OPC pts111


title: HPV+OPC pts108

source_name: HPV+OPC pts108


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 6h replicate 1 [sample_210]

value: AGGCCC


title: HPV+OPC pts107

source_name: HPV+OPC pts107


title: HPV+OPC pts114

source_name: HPV+OPC pts114


title: MCF7 cells treated with 0.96 uM bortezomib at 6h replicate 2 [sample_197]

value: bortezomib

value: GTTCGA


title: HPV+OPC pts117

source_name: HPV+OPC pts117

value: Male

value: yes


title: HPV+OPC pts116

source_name: HPV+OPC pts116

value: Stage IV

value: Stage I


title: MCF7 cells treated with 0.1 uM HY80020 at 6h replicate 1 [sample_195]

value: GGGATT


title: HPV+OPC pts115

source_name: HPV+OPC pts115


title: MCF7 cells treated with 0.1 uM bortezomib at 6h replicate 1 [sample_211]

value: breast ductal carcinoma cell line

value: AGGGGC


title: MCF7 cells treated with 0.1 uM VLX1570 at 6h replicate 1 [sample_208]

value: compound

value: AGCCCG


title: MDAMB231 cells treated with DMSO control at 24h replicate 8 [sample_191]

source_name: triple negative metastatic mammary adenocarcinoma

value: DMSO

value: GAAGAC


title: MCF7 cells treated with 24.96 uM ML323 at 6h replicate 1 [sample_204]

value: ACCCCC


title: MCF7 cells treated with 4.96 uM AV-12 at 6h replicate 1 [sample_202]

value: CCTTCC


title: HPV+OPC pts102

source_name: HPV+OPC pts102


title: MCF7 cells treated with 0.96 uM VLX1570 at 6h replicate 1 [sample_200]

value: TTCCTC


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 24h replicate 3 [sample_189]

value: triple negative metastatic mammary adenocarcinoma

value: CGACTT


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 24h replicate 2 [sample_190]

value: CGATTG


title: MCF7 cells treated with 4.96 uM ML323 at 24h replicate 3 [sample_186]

value: CAAGCT


title: HPV+OPC pts100

source_name: HPV+OPC pts100

value: Male

value: yes


title: HPV+OPC pts97

source_name: HPV+OPC pts97

value: Stage IV

value: Stage I


title: HPV+OPC pts109

source_name: HPV+OPC pts109

value: Stage III


title: HPV+OPC pts98

source_name: HPV+OPC pts98

value: Female

value: Stage II


title: HPV+OPC pts96

source_name: HPV+OPC pts96


title: HPV+OPC pts106

source_name: HPV+OPC pts106


title: MCF7 cells treated with 0.96 uM nutlin3a at 24h replicate 3 [sample_185]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: compound

value: ATCGAG


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 24h replicate 3 [sample_183]

value: TTGGAT


title: HPV+OPC pts105

source_name: HPV+OPC pts105


title: MCF7 cells treated with 0.96 uM AV-12 at 6h replicate 1 [sample_196]

value: GTACAC


title: HPV+OPC pts104

source_name: HPV+OPC pts104


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 6h replicate 1 [sample_194]

value: GCTTAC


title: MCF7 cells treated with 0.96 uM VLX1570 at 24h replicate 3 [sample_181]

value: TTTTAG


title: HPV+OPC pts103

source_name: HPV+OPC pts103


title: HPV+OPC pts101

source_name: HPV+OPC pts101


title: MCF7 cells treated with 0.96 uM bortezomib at 6h replicate 1 [sample_193]

value: bortezomib

value: GCTAGA


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 24h replicate 3 [sample_192]

value: triple negative metastatic mammary adenocarcinoma

value: GATCGT


title: MCF7 cells treated with 0.1 uM bortezomib at 24h replicate 3 [sample_188]

value: CATGGT


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 24h replicate 3 [sample_187]

value: CATCAG


title: MCF7 cells treated with 10 uM HBX41108 at 24h replicate 3 [sample_173]

value: TTATCA


title: MCF7 cells treated with 24.96 uM ML323 at 24h replicate 2 [sample_176]

value: TTCTAA


title: MCF7 cells treated with 24.96 uM ML323 at 24h replicate 3 [sample_184]

value: ACCGTA


title: MCF7 cells treated with 10 uM nutlin3a at 24h replicate 3 [sample_172]

value: TTAGAA


title: HPV+OPC pts99

source_name: HPV+OPC pts99

value: Male

value: Stage III

value: Stage II

value: yes


title: HPV+OPC pts92

source_name: HPV+OPC pts92

value: Stage IV


title: HPV+OPC pts93

source_name: HPV+OPC pts93


title: HPV+OPC pts91

source_name: HPV+OPC pts91


title: HPV+OPC pts89

source_name: HPV+OPC pts89


title: HPV+OPC pts88

source_name: HPV+OPC pts88


title: HPV+OPC pts86

source_name: HPV+OPC pts86

value: Stage I


title: HPV+OPC pts81

source_name: HPV+OPC pts81

value: Female


title: HPV+OPC pts78

source_name: HPV+OPC pts78

value: no


title: HPV+OPC pts94

source_name: HPV+OPC pts94


title: MCF7 cells treated with 0.96 uM AZ1 at 24h replicate 3 [sample_170]

value: breast ductal carcinoma cell line

value: compound

value: TTAAGA


title: HPV+OPC pts95

source_name: HPV+OPC pts95


title: HPV+OPC pts83

source_name: HPV+OPC pts83


title: HPV+OPC pts79

source_name: HPV+OPC pts79


title: MCF7 cells treated with 10 uM XL-9678-188 at 24h replicate 3 [sample_182]

source_name: breast ductal carcinoma cell line

value: TTTTCT


title: MCF7 cells treated with 0.1 uM CS5405 at 24h replicate 3 [sample_178]

value: TTTAAC


title: MCF7 cells treated with 10 uM SB1-F-22 at 24h replicate 3 [sample_180]

value: TTTCAA


title: MCF7 cells treated with 0.1 uM VLX1570 at 24h replicate 3 [sample_179]

value: TTTATG


title: MCF7 cells treated with 10 uM SB1-F-64 at 24h replicate 3 [sample_177]

value: TTGTTA


title: MDAMB231 cells treated with DMSO control at 24h replicate 7 [sample_167]

source_name: triple negative metastatic mammary adenocarcinoma

value: DMSO

value: CTAGTG


title: MCF7 cells treated with 0.96 uM CS5405 at 24h replicate 3 [sample_175]

value: TTCATA


title: MDAMB231 cells treated with 0.96 uM Pin1-3 at 24h replicate 1 [sample_168]

value: triple negative metastatic mammary adenocarcinoma

value: CTTCTG


title: MDAMB231 cells treated with DMSO control at 24h replicate 6 [sample_166]

value: CCGATT


title: MDAMB231 cells treated with 0.96 uM Pin1-3-AcA at 24h replicate 2 [sample_165]

value: CCACAT


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 24h replicate 3 [sample_164]

value: CAGTCA


title: MCF7 cells treated with 0.96 uM CGM097 at 24h replicate 3 [sample_174]

value: TTATGT


title: MCF7 cells treated with 0.3 uM abemaciclib at 24h replicate 3 [sample_163]

value: breast ductal carcinoma cell line

value: abemaciclib

value: CACCAA


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 24h replicate 3 [sample_161]

value: compound

value: AGACCT


title: MCF7 cells treated with 0.96 uM HBX41108 at 24h replicate 3 [sample_162]

value: AGGGAT


title: HPV+OPC pts87

source_name: HPV+OPC pts87

value: Male

value: Stage IV

value: Stage III

value: yes


title: MCF7 cells treated with 0.96 uM VLX1570 at 24h replicate 2 [sample_159]

value: TTTTGA


title: HPV+OPC pts90

source_name: HPV+OPC pts90


title: HPV+OPC pts85

source_name: HPV+OPC pts85


title: MCF7 cells treated with 0.1 uM HY80020 at 24h replicate 3 [sample_158]

value: TTTGTA


title: HPV+OPC pts80

source_name: HPV+OPC pts80

value: Female

value: Stage I

value: no


title: MCF7 cells treated with DMSO control at 24h replicate 10 [sample_171]

value: DMSO

value: TTACTA


title: HPV+OPC pts84

source_name: HPV+OPC pts84


title: MCF7 cells treated with 10 uM SB1-F-70 at 24h replicate 3 [sample_157]

value: breast ductal carcinoma cell line

value: TTTCTT


title: HPV+OPC pts68

source_name: HPV+OPC pts68


title: MCF7 cells treated with 4.96 uM AV-12 at 24h replicate 3 [sample_169]

value: TTAACT


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 24h replicate 3 [sample_154]

value: compound

value: TTGATT


title: HPV+OPC pts75

source_name: HPV+OPC pts75

value: Stage II


title: HPV+OPC pts74

source_name: HPV+OPC pts74


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 24h replicate 3 [sample_152]

value: TTCAAT


title: HPV+OPC pts82

source_name: HPV+OPC pts82

value: Male


title: HPV+OPC pts77

source_name: HPV+OPC pts77

value: Stage IV


title: HPV+OPC pts72

source_name: HPV+OPC pts72

value: Stage III

value: yes


title: HPV+OPC pts66

source_name: HPV+OPC pts66


title: HPV+OPC pts62

source_name: HPV+OPC pts62


title: MCF7 cells treated with 0.96 uM AZ1 at 24h replicate 2 [sample_151]

value: TTATTG


title: HPV+OPC pts76

source_name: HPV+OPC pts76


title: HPV+OPC pts63

source_name: HPV+OPC pts63


title: HPV+OPC pts61

source_name: HPV+OPC pts61


title: HPV+OPC pts59

source_name: HPV+OPC pts59


title: MCF7 cells treated with 10 uM SB1-F-57 at 24h replicate 3 [sample_150]

source_name: breast ductal carcinoma cell line

value: TTATAC


title: MCF7 cells treated with 10 uM AZ1 at 24h replicate 3 [sample_160]

value: TCTTTC


title: MCF7 cells treated with 0.96 uM HY50737 at 24h replicate 3 [sample_156]

value: TTTAGT


title: MCF7 cells treated with 0.1 uM CGM097 at 24h replicate 3 [sample_153]

value: TTGAAA


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 24h replicate 3 [sample_149]

value: TTAGTT


title: MCF7 cells treated with 0.96 uM HY80020 at 24h replicate 3 [sample_155]

value: breast ductal carcinoma cell line

value: TTTACA


title: MCF7 cells treated with 10 uM SB1-F-57 at 24h replicate 2 [sample_146]

value: TTAAAG


title: HPV+OPC pts67

source_name: HPV+OPC pts67

value: Stage I

value: no


title: HPV+OPC pts65

source_name: HPV+OPC pts65


title: HPV+OPC pts69

source_name: HPV+OPC pts69


title: HPV+OPC pts71

source_name: HPV+OPC pts71

value: Stage II


title: HPV+OPC pts70

source_name: HPV+OPC pts70


title: HPV+OPC pts57

source_name: HPV+OPC pts57

value: Female


title: HPV+OPC pts73

source_name: HPV+OPC pts73

value: Male


title: HPV+OPC pts55

source_name: HPV+OPC pts55


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 24h replicate 3 [sample_144]

source_name: triple negative metastatic mammary adenocarcinoma

value: compound

value: TGTTAT


title: HPV+OPC pts49

source_name: HPV+OPC pts49

value: Stage III


title: MCF7 cells treated with DMSO control at 24h replicate 9 [sample_145]

value: DMSO

value: TGTTTA


title: HPV+OPC pts51

source_name: HPV+OPC pts51

value: yes


title: HPV+OPC pts52

source_name: HPV+OPC pts52

value: Stage IV


title: HPV+OPC pts56

source_name: HPV+OPC pts56


title: HPV+OPC pts60

source_name: HPV+OPC pts60


title: HPV+OPC pts58

source_name: HPV+OPC pts58


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 24h replicate 2 [sample_148]

value: TTACAT


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 24h replicate 2 [sample_147]

value: TTAATC


title: MCF7 cells treated with 10 uM SB1-F-78 at 24h replicate 3 [sample_136]

value: breast ductal carcinoma cell line

value: TATTCA


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 24h replicate 3 [sample_143]

value: triple negative metastatic mammary adenocarcinoma

value: TGTATT


title: MDAMB231 cells treated with DMSO control at 24h replicate 5 [sample_142]

value: TGATAA


title: MCF7 cells treated with 0.96 uM SB1-F-70 at 24h replicate 1 [sample_139]

value: TCTAAT


title: MCF7 cells treated with 0.1 uM CS5405 at 24h replicate 2 [sample_134]

value: TATCTA


title: MCF7 cells treated with 0.1 uM HY80020 at 24h replicate 2 [sample_133]

value: TATCAT


title: HPV+OPC pts54

source_name: HPV+OPC pts54

value: Male


title: HPV+OPC pts53

source_name: HPV+OPC pts53

value: Female

value: no


title: HPV+OPC pts43

source_name: HPV+OPC pts43

value: Stage III


title: HPV+OPC pts42

source_name: HPV+OPC pts42


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 24h replicate 3 [sample_131]

source_name: breast ductal carcinoma cell line

value: compound

value: TATAAG


title: HPV+OPC pts48

source_name: HPV+OPC pts48

value: Stage IV


title: HPV+OPC pts45

source_name: HPV+OPC pts45

value: Stage I

value: yes


title: HPV+OPC pts41

source_name: HPV+OPC pts41


title: HPV+OPC pts40

source_name: HPV+OPC pts40


title: HPV+OPC pts39

source_name: HPV+OPC pts39


title: HPV+OPC pts38

source_name: HPV+OPC pts38

value: Stage II


title: MCF7 cells treated with DMSO control at 24h replicate 6 [sample_130]

value: breast ductal carcinoma cell line

value: DMSO

value: TAGATA


title: HPV+OPC pts64

source_name: HPV+OPC pts64


title: HPV+OPC pts50

source_name: HPV+OPC pts50


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 24h replicate 2 [sample_141]

source_name: triple negative metastatic mammary adenocarcinoma

value: TGAATA


title: HPV+OPC pts46

source_name: HPV+OPC pts46


title: HPV+OPC pts47

source_name: HPV+OPC pts47


title: HPV+OPC pts36

source_name: HPV+OPC pts36


title: MCF7 cells treated with DMSO control at 24h replicate 8 [sample_140]

value: TCTATA


title: HPV+OPC pts33

source_name: HPV+OPC pts33


title: MCF7 cells treated with 0.96 uM XL-9678-177A at 24h replicate 3 [sample_138]

value: TCAATT


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 24h replicate 3 [sample_122]

value: TAAACA


title: MCF7 cells treated with 0.96 uM HY50737 at 24h replicate 2 [sample_132]

value: TATACT


title: MCF7 cells treated with 0.96 uM CGM097 at 24h replicate 2 [sample_137]

value: TCAAAA


title: MCF7 cells treated with DMSO control at 24h replicate 7 [sample_135]

value: TATTAC


title: MCF7 cells treated with 0.1 uM HY50737 at 24h replicate 3 [sample_128]

value: TACATT


title: HPV+OPC pts44

source_name: HPV+OPC pts44

value: Male

value: Stage III


title: HPV+OPC pts29

source_name: HPV+OPC pts29

value: Female

value: Stage IV


title: MDAMB231 cells treated with 4.96 uM Pin1-3-AcA at 24h replicate 1 [sample_119]

value: triple negative metastatic mammary adenocarcinoma

value: compound

value: TGATTT


title: HPV+OPC pts27

source_name: HPV+OPC pts27

value: Stage I

value: yes


title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 24h replicate 2 [sample_118]

value: TGAAAT


title: HPV+OPC pts35

source_name: HPV+OPC pts35

value: Stage II


title: HPV+OPC pts37

source_name: HPV+OPC pts37


title: HPV+OPC pts34

source_name: HPV+OPC pts34

value: no


title: MCF7 cells treated with 0.96 uM P5091 at 24h replicate 3 [sample_127]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: TACAAA


title: MCF7 cells treated with 0.1 uM bortezomib at 24h replicate 2 [sample_115]

value: bortezomib

value: TCATAT


title: MCF7 cells treated with 0.96 uM HY80020 at 24h replicate 2 [sample_125]

value: TAATAG


title: HPV+OPC pts32

source_name: HPV+OPC pts32


title: HPV+OPC pts31

source_name: HPV+OPC pts31

value: Male


title: MCF7 cells treated with 24.96 uM WH-9943-091 at 24h replicate 2 [sample_124]

value: TAACTT


title: HPV+OPC pts23

source_name: HPV+OPC pts23


title: HPV+OPC pts22

source_name: HPV+OPC pts22

value: Stage III


title: MCF7 cells treated with 0.1 uM VLX1570 at 24h replicate 2 [sample_123]

value: TAACAA


title: MCF7 cells treated with 10 uM XL-9678-203C at 24h replicate 3 [sample_126]

value: TAATCT


title: HPV+OPC pts20

source_name: HPV+OPC pts20

value: Stage IV


title: HPV+OPC pts19

source_name: HPV+OPC pts19


title: HPV+OPC pts30

source_name: HPV+OPC pts30


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 24h replicate 2 [sample_121]

value: compound

value: TAAAAC


title: MDAMB231 cells treated with 10 uM BJP-6-5-3 at 24h replicate 3 [sample_120]

source_name: triple negative metastatic mammary adenocarcinoma

value: TGTAAA


title: HPV+OPC pts18

source_name: HPV+OPC pts18

value: Female

value: Stage I

value: yes


title: HPV+OPC pts17

source_name: HPV+OPC pts17

value: Stage II


title: HPV+OPC pts28

source_name: HPV+OPC pts28


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 24h replicate 3 [sample_117]

value: triple negative metastatic mammary adenocarcinoma

value: TCTTAA


title: HPV+OPC pts16

source_name: HPV+OPC pts16


title: MCF7 cells treated with 10 uM P5091 at 24h replicate 3 [sample_116]

value: breast ductal carcinoma cell line

value: TCATTA


title: MCF7 cells treated with 0.1 uM HY50737 at 24h replicate 2 [sample_114]

value: TATTTG


title: HPV+OPC pts24

source_name: HPV+OPC pts24

value: Male


title: MCF7 cells treated with 0.96 uM HBX19818 at 24h replicate 3 [sample_113]

value: TATTGT


title: HPV+OPC pts25

source_name: HPV+OPC pts25

value: Stage III


title: MCF7 cells treated with 4.96 uM AV-12 at 24h replicate 2 [sample_111]

value: TATGAA


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 24h replicate 3 [sample_112]

value: TATGTT


title: HPV+OPC pts21

source_name: HPV+OPC pts21

value: Stage IV


title: MCF7 cells treated with 0.1 uM CGM097 at 24h replicate 2 [sample_110]

value: compound

value: TATATC


title: MCF7 cells treated with 0.96 uM CS5405 at 24h replicate 2 [sample_109]

value: TATAGA


title: MCF7 cells treated with 10 uM SB1-F-57 at 24h replicate 1 [sample_102]

value: TAAGTA


title: MCF7 cells treated with 0.96 uM nutlin3a at 24h replicate 2 [sample_100]

value: TAAATG


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 24h replicate 3 [sample_108]

value: TAGTTT


title: HPV+OPC pts14

source_name: HPV+OPC pts14

value: yes


title: MCF7 cells treated with DMSO control at 24h replicate 5 [sample_107]

source_name: breast ductal carcinoma cell line

value: DMSO

value: TAGTAA


title: HPV+OPC pts10

source_name: HPV+OPC pts10


title: HPV+OPC pts15

source_name: HPV+OPC pts15

value: Female

value: Stage II


title: MCF7 cells treated with 0.96 uM AZ1 at 24h replicate 1 [sample_105]

value: breast ductal carcinoma cell line

value: TACTAT


title: HPV+OPC pts7

source_name: HPV+OPC pts7

value: Male

value: Stage I


title: HPV+OPC pts5

source_name: HPV+OPC pts5


title: MCF7 cells treated with 10 uM nutlin3a at 24h replicate 2 [sample_101]

value: TAAGAT


title: HPV+OPC pts4

source_name: HPV+OPC pts4

value: Stage IV


title: MCF7 cells treated with 10 uM HBX19818 at 24h replicate 3 [sample_104]

value: compound

value: TAATTC


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 24h replicate 3 [sample_106]

value: TACTTA


title: MCF7 cells treated with 10 uM SB1-F-64 at 24h replicate 2 [sample_129]

value: TAGAAT


title: HPV+OPC pts9

source_name: HPV+OPC pts9


title: HPV+OPC pts26

source_name: HPV+OPC pts26

value: Stage III

value: no


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 24h replicate 2 [sample_94]

source_name: triple negative metastatic mammary adenocarcinoma

value: GTAAAT


title: 3

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description:
A pool of 5 embryos at the 4-cell stage were subjected to cDNA synthesis
NTvsAm_oryx.csv

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism:
Mus musculus
Oryx dammah

source_name: Mouse 4-cell stage embryos

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until the 4-cell stage. At 40 hours post insemination (hpi), embryos were moved to KSOM medium containing 0.1 µg/ml demecolcine to arrest their cell cycle at G2/M phase. The demecolcine-treated embryos were subjected to nuclear transfer during 46-49 hpi, and the reconstructed NT embryos were further cultured in KSOM medium containing 0.1 µg/ml demecolcine with or without ?-amanitin till 70 hpi. To examine the effect of DNA replication on transcriptional reprogramming, nuclear transfer to 4-cell embryos was performed during 40-43 hpi, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 64 hpi. To examine the reprogramming ability of 2-cell embryos, nuclear transfer to 2-cell embryos was performed during 21-24 hpi for early 2-cell NT and 30-33 hpi for late 2-cell NT, and subsequently cultured in KSOM medium containing 0.1 µg/ml demecolcine till 45 hpi and 54 hpi, respectively.

extract_protocol:
After the removal of zona pellucida, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
The produced cDNA was amplified by PCR with 13 -14 cycles. The amplified cDNA was purified using AMPure XP beads (BECKMAN COULTER, A63882). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit (Thermo Scientific).

treatment_protocol: As described in the growth protocol, embryos were treated with 0.1 µg/ml demecolcine to arrest their cell cycle. To identify newly transcribed genes, NT embryos were cultured with or without α-amanitin, and transcriptomes were compared.

tag: strains

value: C57BL/6 and DBA/2 strains, and primary Oryx dammah cells

tag: alpha-amanitin

value: Minus

value: 4-cell stage embryos


title: MCF7 cells treated with DMSO control at 24h replicate 4 [sample_103]

tag: treatment

value: DMSO

value: TAATGA


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 24h replicate 3 [sample_95]

value: triple negative metastatic mammary adenocarcinoma

tag: concentration

value: GTTAAA


title: MCF7 cells treated with 0.96 uM P5091 at 24h replicate 2 [sample_92]

value: breast ductal carcinoma cell line

tag: time

value: GAATTA


title: MCF7 cells treated with 0.96 uM HBX41108 at 24h replicate 2 [sample_97]

tag: replicate

value: GTTTAT


title: MCF7 cells treated with 3 uM abemaciclib at 24h replicate 3 [sample_98]

value: compound

value: abemaciclib

tag: library

value: GTTTTA


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 24h replicate 3 [sample_96]

tag: well

value: GTTATT


title: MCF7 cells treated with 0.96 uM bortezomib at 24h replicate 3 [sample_99]

value: bortezomib

tag: barcode

value: TAAAGT


title: HPV+OPC pts3

source_name: HPV+OPC pts3

value: Male

value: Stage IV

value: Stage III

value: yes


title: HPV+OPC pts13

source_name: HPV+OPC pts13


title: HPV+OPC pts12

source_name: HPV+OPC pts12

value: Female

value: Stage I


title: HPV+OPC pts11

source_name: HPV+OPC pts11


title: HPV+OPC pts8

source_name: HPV+OPC pts8


title: HPV+OPC pts6

source_name: HPV+OPC pts6

value: Stage II


title: HPV+OPC pts2

source_name: HPV+OPC pts2


title: 2

value: C57BL/6 and DBA/2 strains, and primary Oryx dammah cells

value: Minus

tag: developmental stage

value: 4-cell stage embryos


title: aAm1

value: Plus


title: MDAMB231 cells treated with DMSO control at 24h replicate 4 [sample_93]

value: triple negative metastatic mammary adenocarcinoma

value: compound

value: DMSO

value: GATTAA


title: MCF7 cells treated with 3 uM abemaciclib at 24h replicate 2 [sample_90]

source_name: breast ductal carcinoma cell line

value: breast ductal carcinoma cell line

value: abemaciclib

value: CTTATA


title: HASMC Scramble siRNA, 2

first: Tao

last: Zhuang

address: 131 Dong’an Road

institute: Fudan University

description: Scramble siRNA 2

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .  After that, Ericscript (v0.5.5)  and rMATS(V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5)  was applied to align the clean reads to thegene set, a database for this organism built by BGI(Beijing  Genomic  Institute  in  ShenZhen),  which  known  and  novel,  coding transcripts  were  included, then expression level of gene was calculated by RSEM (v1.2.12).  The  heatmap  was  drawn by pheatmap(v1.0.8) according  to  the gene expression indifferent  samples.  Essentially,  differential  expression  analysis  was performed  using  the  DESeq2(v1.4.5) with Q  value ≤ 0.05. To  take  insight  to  the change     of     phenotype, GO     (http://www.geneontology.org/)     and     KEGG (https://www.kegg.jp/) enrichment  analysis  of  annotated  different  expression  gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based  on  Hypergeometric  test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)by bonferroni.
Supplementary_files_format_and_content: FPKM

source_name: Human aortic smooth muscle cells

growth_protocol: Human aortic VSMCs were purchased from ATCC company (PCS-100-012, USA) and cultured in Vascular Smooth Muscle Cell Growth Kit (PCS-100-042, USA ) supplemented with 10% FBS (Hyclone, USA).

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60mg of tissues were ground into powder by liquid nitrogenina 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3mL chloroform/isoamyl alcohol (24:1). The mix was shackedvigorously for 15s, and then centrifugedat 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phasewhere RNA remained was transferredinto a new tube withequal volume of supernatant of isopropyl alcohol,then centrifugedat 13,600rpm for 20 minutes at 4°C.After deserting the supernatant,the RNA pellet was washed twice with 1 mL75% ethanol,then the mix was centrifuged at 13,600rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: The siRNA were purchased from Genepharma company and transfected into cells using Lipofectamine 2000 (Invitrogen, Carlsbad, CA) for knockdown of MIA3.The sequence of the MIA3 oligos were 5’-CCAGGUAGUUCAUGAAUAU-3’.

value: Human aortic smooth muscle cells

tag: transfected with

value: Scramble siRNA


title: HASMC MIA3 siRNA, 2

description: MIA3 siRNA 2

value: MIA3 siRNA


title: 1


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 24h replicate 2 [sample_91]

value: GAATAT


title: aAm2


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 24h replicate 2 [sample_88]

value: CTAATT


title: HASMC MIA3 siRNA, 1

description: MIA3 siRNA 1


title: aAm3


title: MCF7 cells treated with 0.96 uM SB1-F-64 at 24h replicate 2 [sample_84]

value: CAAAAT


title: MCF7 cells treated with DMSO control at 24h replicate 3 [sample_86]

value: CATATT


title: MCF7 cells treated with 0.1 uM CS5405 at 24h replicate 1 [sample_87]

value: CTAAAA


title: M2-like macrophage co-culture

city: Hangzhou

first: Mengwen

last: Zhang

state: Zhejiang

address: 88 Jiefang Road

institute: Zhejiang University

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata.
We filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
We map those clean reads onto reference genome(hg19_UCSC_20180115), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection.
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.

source_name: human PBMC derived macrophages

growth_protocol: Human PBMCs were isolated from buffy coats from healthy donors according to standard procedures. Monocytes were purified from PBMCs using CD14+ magnetic microbeads (Miltenyi Biotec, GL, GER). Thereafter, the monocytes were cultured in macrophage complete medium with 100 ng/ml human recombinant M-CSF (Biolegend) for 6 days.

extract_protocol:
Tumor-educated macrophages were purified by CD11b+ magnetic microbeads (Miltenyi Biotec, GL, GER) according to the Direct Technique isolation instructions. Mono-cultured macrophages also underwent the same isolation process as a control. RNA was harvested using Trizol reagent.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and  subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq  platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: On Day 6, macrophages were treated with either 100 ng/ml human recombinant GM-CSF (Biolegend), 400 ng/ml LPS (Sigma) and 50 ng/ml IFN-γ (Biolegend) for M1 polarization or 100 ng/ml human recombinant M-CSF (Biolegend), 50 ng/ml IL-4 (Biolegend), 50 ng/ml IL-10 (Biolegend) and 50 ng/ml IL-13 (Biolegend) for M2 polarization for 24 hours.

value: macrophages

value: Co-culture with PDA cells for 24 hours


title: M2-like macrophage single culture

value: untreated


title: MCF7 cells treated with 0.96 uM HBX19818 at 24h replicate 2 [sample_85]

value: compound

value: CATAAA


title: HASMC Scramble siRNA, 1

description: Scramble siRNA 1


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 24h replicate 3 [sample_83]

value: ATTTTG


title: MCF7 cells treated with 0.1 uM XL-9678-177B at 24h replicate 2 [sample_89]

value: breast ductal carcinoma cell line

value: CTTAAT


title: HPV+OPC pts1

source_name: HPV+OPC pts1

value: Male

value: Stage IV

value: Stage III

value: no


title: MCF7 cells treated with 10 uM SB1-F-64 at 24h replicate 1 [sample_82]

value: ATTTAC


title: M1-like macrophage single culture


title: M0 macrophage co-culture


title: M1-like macrophage co-culture


title: M0 macrophage single culture


title: MCF7 cells treated with 10 uM HBX19818 at 24h replicate 2 [sample_77]

value: ATGTAA


title: HC03_dt_1

city: Hong Kong

first: KIM

last: Jin Young

address: Tat Chee Avenue, Kowloon, Hong Kong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
RNA-seq raw reads were mapped to the UCSC human reference genome (GRCh38) and calculation of gene counts using STAR (version 2.5.3a) with default parameters.
The multi-mapped reads were filtered out and only the uniquely mapped reads were retained.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: whole blood

extract_protocol:
5 milliliters of whole blood was collected in the PAXgene Blood RNA tubes (QIAGEN). Next day, RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN)
Libraries were prepared according to the library construction procedures of BGISEQ-500 and then sequenced on the BGIseq500 (Illumina) platforms (Beijing Genomics Institute, China)

tag: tissue

value: whole blood

tag: ms subtype

tag: sampling time

value: daytime

tag: disease state

value: Healthy


title: MCF7 cells treated with 0.96 uM AV-12 at 24h replicate 2 [sample_80]

value: ATTCAT


title: HC01_nt_1

value: nighttime


title: MCF7 cells treated with 0.96 uM AV-12 at 24h replicate 1 [sample_74]

value: ATATTC


title: MCF7 cells treated with 10 uM SB1-F-70 at 24h replicate 2 [sample_78]

value: compound

value: ATTAAG


title: MCF7 cells treated with 10 uM SB1-F-22 at 24h replicate 2 [sample_76]

value: ATCTTA


title: HC02_dt_1


title: HC03_nt_1


title: MCF7 cells treated with 0.96 uM HY50737 at 24h replicate 1 [sample_79]

value: breast ductal carcinoma cell line

value: ATTATC


title: HC02_nt_1


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 24h replicate 2 [sample_71]

value: triple negative metastatic mammary adenocarcinoma

value: GTAATA


title: MCF7 cells treated with 10 uM SB1-F-22 at 24h replicate 1 [sample_75]

value: ATCTAT


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 24h replicate 2 [sample_69]

value: GATAAT


title: MCF7 cells treated with 10 uM SB1-F-78 at 24h replicate 2 [sample_73]

value: ATATGA


title: MCF7 cells treated with 4.96 uM ML323 at 24h replicate 2 [sample_68]

value: GAAATT


title: MDAMB231 cells treated with 4.96 uM Pin1-3 at 24h replicate 2 [sample_72]

value: GTATAA


title: MS09_21_00

value: whole blood

value: Acute relapse

tag: disease-modifying treatment

value: Fingolimod

value: relapsing-remitting multiple sclerosis (RRMS)


title: MS09_15_30

value: daytime


title: MS08_21_00

value: nighttime

value: Interferon Beta-1a


title: MS05_21_00

value: Remission


title: MCF7 cells treated with 24.96 uM ML323 at 24h replicate 1 [sample_66]

value: breast ductal carcinoma cell line

value: compound

value: CTATTA


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 24h replicate 2 [sample_65]

value: CTATAT


title: MS05_14_00


title: MCF7 cells treated with 10 uM XL-9678-188 at 24h replicate 2 [sample_64]

value: CATTTA


title: MCF7 cells treated with 10 uM AZ1 at 24h replicate 2 [sample_63]

value: CATTAT


title: MS02_15_00


title: MS02_21_00


title: MDAMB231 cells treated with 4.96 uM BJP-6-115-3 at 24h replicate 1 [sample_70]

value: triple negative metastatic mammary adenocarcinoma

value: GATATA


title: MS08_14_00


title: MCF7 cells treated with 0.96 uM AV-12 at 24h replicate 3 [sample_81]

value: ATTGTT


title: MS06_21_00

value: whole blood

value: Remission with a recent relapse

value: Treatment naïve


title: MS01_15_00

value: relapsing-remitting multiple sclerosis (RRMS)


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 24h replicate 2 [sample_67]

value: CTTTAA


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 24h replicate 2 [sample_58]

value: ATTGAA


title: MS06_14_30

value: daytime


title: NEMEP promoter-KO-EB-Day3-1

city: Beijing

first: Haipeng

last: Fu

address: Shuangqing Road

institute: Tsinghua University

data_processing:
Illumina HiSeq PE150 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 version 2.1.0 with parameters --dta-cufflinks
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffquant following by cuffnorm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: mESCs were cultured on gelatin coated plates with 15% serum ESC culture medium . Day 3 EBs were cultured on bacteria plates without gelatin with 15% serum ESC culture medium withdrawl LIF. NEMEP WT or NEMEP promoter-KO  day 3 EBs were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted by commerical RNA extraction Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NEMEP WT or NEMEP promoter-KO ESCs were set up to EBs formation.Day 3 EBs were cultured on bacteria plates without gelatin with 15% serum ESC culture medium withdrawal LIF. And there is no other treatment for the sample used for RNA-seq.

tag: cell type

value: ES-derived mesendoderm cells

tag: strain

tag: genotype

value: NEMEP promoter-KO

value: ESCs were set up to EBs formation; day 3 EBs were harvested for RNA extraction


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 24h replicate 2 [sample_57]

value: breast ductal carcinoma cell line

value: compound

tag: treatment

value: ATTCTA


title: MCF7 cells treated with 0.1 uM CGM097 at 24h replicate 1 [sample_56]

tag: concentration

value: ATTAGA


title: WT-EB-Day3-1

value: WT


title: HC01_dt_1

value: Healthy


title: MCF7 cells treated with 0.96 uM SB1-F-74 at 24h replicate 2 [sample_55]

tag: time

value: ATTACT


title: MS03_14_00

value: whole blood

value: Remission

value: Fingolimod


title: MS03_21_00

value: nighttime

value: relapsing-remitting multiple sclerosis (RRMS)


title: MCF7 cells treated with 0.96 uM bortezomib at 24h replicate 2 [sample_62]

value: bortezomib

tag: replicate

value: CAATAA


title: MCF7 cells treated with 0.96 uM VLX1570 at 24h replicate 1 [sample_54]

tag: library

value: ATGATA


title: OAD(old mice, anagen, dWAT)

city: GuangZhou

first: Qian

last: Qu

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

description: dermal white adipose tissue of aged mice at anagen

data_processing:
Illumina bcl2fastq  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped GRCm38 whole genome using tophat2 with parameters -read-mismatches 2 -read-edit-dist 2 -max-intron-length 5000000 -library-type fr-unstranded -num-threads 8 -mate-inner-dist 40.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: C57BL/6 mouse

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s recommendations. RNA quality and quantity of all samples were evaluated by using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.5.
RNA libraries were pprepared for sequencing using standard Illumina protocals

treatment_protocol: Through microdissection, we separated dWAT from skin of aged mice (18 months) and young mice (2 months) in telogen and depilation-induced anagen for transcriptome comparing

value: dermal white adipose tissue

tag: age

value: 2 months

tag: hair cycle

value: anagen


title: MCF7 cells treated with 0.96 uM HBX41108 at 24h replicate 1 [sample_61]

value: breast ductal carcinoma cell line

value: compound

tag: well

tag: barcode

value: CAAATA


title: YAD(young mice, anagen, dWAT)

description: dermal white adipose tissue of young mice at anagen

tag: tissue


title: MS01_21_00

tag: ms subtype

value: Interferon Beta-1a


title: MCF7 cells treated with 4.96 uM WH-9943-091 at 24h replicate 1 [sample_60]

value: ATTTGT


title: MCF7 cells treated with 3 uM abemaciclib at 24h replicate 1 [sample_53]

value: abemaciclib

value: ATGAAT


title: NEMEP promoter-KO-EB-Day3-2

value: ES-derived mesendoderm cells

value: NEMEP promoter-KO

value: ESCs were set up to EBs formation; day 3 EBs were harvested for RNA extraction


title: MCF7 cells treated with 4.96 uM AV-12 at 24h replicate 1 [sample_59]

value: ATTTCA


title: MCF7 cells treated with 10 uM HBX41108 at 24h replicate 2 [sample_50]

value: ATATCT


title: HUCCT1-shControl#2

city: Jinan

first: Jianping

last: Song

state: Shandong

address: 107 Wenhua Xi Road, Jinan, Shandong Province, China.

institute: Qilu hospital of Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were filtered to obtain clean reads after removal of reads containing adapter and at low quality
High-quality reads were mapped to the human reference genome hg19 using HISAT2 software
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using StringTie software

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cholangiocarcinoma

tag: transfection

value: shControl

value: lenti-virus


title: YTD(young mice, telogen, dWAT)

description: dermal white adipose tissue of young mice at telogen

value: dermal white adipose tissue

value: 18 months

value: telogen


title: WT-EB-Day3-2

value: WT


title: OTD(old mice, telogen, dWAT)

description: dermal white adipose tissue of aged mice at telogen


title: MCF7 cells treated with 0.1 uM XL-9678-177A at 24h replicate 1 [sample_52]

value: breast ductal carcinoma cell line

value: compound

value: ATCATT


title: HUCCT1-shControl#3


title: MCF7 cells treated with 0.1 uM VLX1570 at 24h replicate 1 [sample_51]

value: ATCAAA


title: MCF7 cells treated with 10 uM XL-9678-188 at 24h replicate 1 [sample_49]

value: ATATAG


title: HUCCT1-shControl#1


title: MDAMB231 cells treated with DMSO control at 24h replicate 3 [sample_48]

value: triple negative metastatic mammary adenocarcinoma

value: DMSO

value: ATAGTA


title: MDAMB231 cells treated with 10 uM BJP-6-115-3 at 24h replicate 1 [sample_47]

value: ATAGAT


title: HUCCT1-shHMGA1#2


title: HUCCT1-shHMGA1#3


title: HUCCT1-shHMGA1#1


title: MCF7 cells treated with 0.96 uM SB1-F-78 at 24h replicate 1 [sample_44]

value: AGTTAA


title: MDAMB231 cells treated with DMSO control at 24h replicate 2 [sample_45]

value: ATAAGT


title: h1hESC_TB-EQ-75pcnt_51

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_51

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads trimmed to have length 51 bp using seqtk 1.0
Sequencing reads were mapped to GRCh38 Ensembl using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts csv

source_name: differentiated human embryonic stem cells

growth_protocol: Cells were grown as in GSE75748. EC: H1 were seeded in E8 with BMP4 (5ng/ml) and Activin A (25ng/ml) for the first 2 days, then switched to supplement with VEGF and WNT for 3 days. TB: H1 were seeded in E7 (E8 minus FGF2) with 50ng/ml BMP4 and SB431542.

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system. For EQ, EQ-Vary and EQ-75%, we retrieved the harvested cDNA, which are amplified full-length single-cell cDNAs identical to those in GSE75748.
For the EQ and EQ-75% experiments, 2.0 µL of the amplified/tagmented cDNA were used for pooling. In the EQ-Vary experiment, a single scaling factor was applied to generate variable amounts of the pooling volume. These pooled single-cell libraries were used in an AMpure XP Bead-based Dual Bead Cleanup and Size Selection reaction (Agencourt AMPure XP PCR Purification modified Instructions for Use, Beckman Coulter). In both bead cleanup reactions, 90% of AMPure XP beads were added to the amplified single-cell libraries to select for an approximate size range of 150-700 bp and incubated for 15 minutes at room temperature. Libraries bound to beads were then placed on a magnet for 5 minutes, washed twice with 70% Ethanol, eluted with Suspension Buffer (Nextera XT DNA Sample Preparation Index Kit, Illumina), and transferred to a new tube.  Final amplified and pooled single-cell libraries were quantified with the Qubit dsDNA HS Assay Kit (Q32854, Thermofisher) and Bioanalyzer High Sensitivity DNA Analysis Kit (5067-4626, Agilent).Libraries were multiplexed with 96 samples per lane and sequenced on an Illumina HiSeq3000 with paired-end 65 or 78 bp reads.
Single-cell RNA-Seq

tag: cell line

value: H1 hESC cell line

tag: sample type

value: TB

tag: equilization amt


title: h1hESC_TB-EQ-75pcnt_50

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_50


title: h1hESC_TB-EQ-75pcnt_49

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_49


title: h1hESC_TB-EQ-75pcnt_48

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_48


title: MCF7 cells treated with 0.96 uM XL-9678-188 at 24h replicate 1 [sample_42]

value: AGATAT


title: h1hESC_TB-EQ-75pcnt_47

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_47


title: MCF7 cells treated with 0.1 uM HY50737 at 24h replicate 1 [sample_40]

value: ACTATT


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 24h replicate 3 [sample_41]

value: AGAATT


title: h1hESC_TB-EQ-75pcnt_46

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_46


title: MCF7 cells treated with 0.96 uM HY80020 at 24h replicate 1 [sample_43]

value: AGTATA


title: MCF7 cells treated with 0.96 uM XL-9678-177B at 24h replicate 1 [sample_39]

value: breast ductal carcinoma cell line

value: ACTAAA


title: h1hESC_TB-EQ-75pcnt_45

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_45


title: MCF7 cells treated with 0.96 uM XL-9678-203C at 24h replicate 1 [sample_38]

value: compound

value: ACAAAT


title: MCF7 cells treated with 0.96 uM SB1-F-57 at 24h replicate 1 [sample_36]

value: AATTAG


title: MDAMB231 cells treated with 4.96 uM BJP-6-5-3 at 24h replicate 1 [sample_46]

source_name: triple negative metastatic mammary adenocarcinoma

value: ATAATG


title: h1hESC_TB-EQ-75pcnt_44

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_44


title: h1hESC_TB-EQ-75pcnt_41

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_41


title: MCF7 cells treated with 10 uM HBX19818 at 24h replicate 1 [sample_33]

value: AATATG


title: MCF7 cells treated with DMSO control at 24h replicate 2 [sample_35]

value: DMSO

value: AATGTA


title: MCF7 cells treated with 10 uM P5091 at 24h replicate 2 [sample_32]

value: AATAAC


title: MCF7 cells treated with 0.3 uM abemaciclib at 24h replicate 2 [sample_34]

value: abemaciclib

value: AATCAA


title: h1hESC_TB-EQ-75pcnt_38

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_38

value: H1 hESC cell line

value: TB


title: MCF7 cells treated with 0.3 uM abemaciclib at 24h replicate 1 [sample_31]

value: AAGTTA


title: h1hESC_TB-EQ-75pcnt_36

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_36


title: MCF7 cells treated with 0.1 uM bortezomib at 24h replicate 1 [sample_30]

value: bortezomib

value: AACTAA


title: MCF7 cells treated with 0.1 uM HY80020 at 24h replicate 1 [sample_29]

value: breast ductal carcinoma cell line

value: AACATA


title: MCF7 cells treated with 10 uM HBX41108 at 24h replicate 1 [sample_28]

value: compound

value: AAATGT


title: h1hESC_TB-EQ-75pcnt_33

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_33


title: h1hESC_TB-EQ-75pcnt_43

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_43


title: h1hESC_TB-EQ-75pcnt_35

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_35


title: MCF7 cells treated with 0.96 uM SB1-F-22 at 24h replicate 2 [sample_25]

value: AAACAT


title: MCF7 cells treated with 0.1 uM SB1-F-74 at 24h replicate 1 [sample_27]

value: AAATCA


title: h1hESC_TB-EQ-75pcnt_32

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_32


title: MCF7 cells treated with 0.96 uM P5091 at 24h replicate 1 [sample_26]

value: AAACTA


title: h1hESC_TB-EQ-75pcnt_31

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_31


title: h1hESC_TB-EQ-75pcnt_30

description:
EQ-75pcnt_ExpectedCounts.csv
TB-EQ-75pcnt_30