title: Triple-negative breast cancer primary cell line BCSC3 infected with IRAK2 knockdown vector, biological replicate 2

value: Isolated from triple-negative breast cancer tumor


title: Triple-negative breast cancer primary cell line BCSC3 infected with control vector, biological replicate 3

status: Public on Sep 15 2022

type: SRA

city: Aachen

first: Jochen

last: Maurer

state: NRW

address: Pauwelsstraße 30

country: Germany

institute: RWTH Uniklinik Aachen

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (Illumina). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.4 implemented in Nextflow 21.04.0 using Docker 20.10.8 with the minimal command.
Lane-level reads were trimmed using Trim Galore 0.6.7  and aligned to the human genome (GRCh38.p13) using STAR 2.7.9a. The gene-level assignment was performed using Salmon v1.5.2.
Analysis was performed using custom scripts in R version 4.1.1 using the DESeq2 v.1.32.0 framework. Differential expression analysis was done with DESEQ2 package in R and following the instruction for Salmon quantification.
Processed data files are in bigWig format which were generated by bedGraphToBigWig in nfcore/rnaseq pipeline.
Assembly: GRCh38.p13
Supplementary files format and content: bigWig
Supplementary files format and content: salmon.merged.gene_counts.xlsx

molecule: total RNA

organism: Homo sapiens

source_name: Isolated from triple-negative breast cancer tumor

extract_protocol:
RNA was extracted from cells pellet using miRNeasy® mini kit (Qiagen, 1038703).
The library preparation method used was Invitrogen™ Collibri™ 3’ mRNA Library Prep Kit.

tag: tissue

tag: cell line

tag: cell type

value: Breast cancer stem cell

tag: genotype

value: Control

tag: treatment

value: Lentivirally transduced with inducible control vector


title: Triple-negative breast cancer primary cell line BCSC3 infected with IRAK2 knockdown vector, biological replicate 1

value: IRAK2 knockdown

value: Lentivirally transduced with IRAK2 inducible knockdown vector


title: Triple-negative breast cancer primary cell line BCSC1 infected with IRAK2 knockdown vector, biological replicate 2


title: Triple-negative breast cancer primary cell line BCSC3 infected with control vector, biological replicate 2


title: Triple-negative breast cancer primary cell line BCSC1 infected with IRAK2 knockdown vector, biological replicate 1


title: Triple-negative breast cancer primary cell line BCSC1 infected with control vector, biological replicate 3


title: Triple-negative breast cancer primary cell line BCSC3 infected with control vector, biological replicate 1


title: Triple-negative breast cancer primary cell line BCSC1 infected with control vector, biological replicate 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell379

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

country: USA

institute: Dana-Farber Cancer Institute

description:
SMART-seq2
SM4C1r5-P4-H07

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned by bowtie, and gene counts were quantified using RSEM as transcript-per-million, or TPM.
Expression levels were calculated as Ei,j = log2(TPMi,j/10 + 1) for gene i in sample j. TPM values were divided by 10 for better approximation of the estimated complexity of single-cell libraries.
We filtered out low quality cells with less than 2,500 detected genes or an average housekeeping expression level below 2.5 and removed low expressed genes with TPM greater than 16 in less than 5 cells.
We defined relative expression as centered expression levels, Eri,j = Ei,j − average[Ei,1...n] for the remaining cells and genes.
Assembly: hg19
Supplementary files format and content: TPM values for each gene in each cell and in every condition. Control AAVS1 (CTRL) and SMARCA4 knockout (SM4KO) TPM data are gathered in one csv file per replicate.

growth_protocol: BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2

value: SMARCA4 knockout

value: nucleofection

tag: time

value: 4 days


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell380

description:
SMART-seq2
SM4C1r5-P4-H08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell383

description:
SMART-seq2
SM4C1r5-P4-H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell381

description:
SMART-seq2
SM4C1r5-P4-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell382

description:
SMART-seq2
SM4C1r5-P4-H10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell377

description:
SMART-seq2
SM4C1r5-P4-H05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell378

description:
SMART-seq2
SM4C1r5-P4-H06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell375

description:
SMART-seq2
SM4C1r5-P4-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell374

description:
SMART-seq2
SM4C1r5-P4-H02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell373

description:
SMART-seq2
SM4C1r5-P4-H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell376

description:
SMART-seq2
SM4C1r5-P4-H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell372

description:
SMART-seq2
SM4C1r5-P4-G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell370

description:
SMART-seq2
SM4C1r5-P4-G10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell368

description:
SMART-seq2
SM4C1r5-P4-G08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell369

description:
SMART-seq2
SM4C1r5-P4-G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell371

description:
SMART-seq2
SM4C1r5-P4-G11


title: Triple-negative breast cancer primary cell line BCSC1 infected with IRAK2 knockdown vector, biological replicate 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell367

description:
SMART-seq2
SM4C1r5-P4-G07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell384

description:
SMART-seq2
SM4C1r5-P4-H12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell364

description:
SMART-seq2
SM4C1r5-P4-G04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell363

description:
SMART-seq2
SM4C1r5-P4-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell362

description:
SMART-seq2
SM4C1r5-P4-G02


title: Triple-negative breast cancer primary cell line BCSC1 infected with control vector, biological replicate 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell360

description:
SMART-seq2
SM4C1r5-P4-F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell365

description:
SMART-seq2
SM4C1r5-P4-G05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell359

description:
SMART-seq2
SM4C1r5-P4-F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell357

description:
SMART-seq2
SM4C1r5-P4-F09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell356

description:
SMART-seq2
SM4C1r5-P4-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell358

description:
SMART-seq2
SM4C1r5-P4-F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell355

description:
SMART-seq2
SM4C1r5-P4-F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell351

description:
SMART-seq2
SM4C1r5-P4-F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell349

description:
SMART-seq2
SM4C1r5-P4-F01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell348

description:
SMART-seq2
SM4C1r5-P4-E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell354

description:
SMART-seq2
SM4C1r5-P4-F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell347

description:
SMART-seq2
SM4C1r5-P4-E11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell352

description:
SMART-seq2
SM4C1r5-P4-F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell353

description:
SMART-seq2
SM4C1r5-P4-F05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell350

description:
SMART-seq2
SM4C1r5-P4-F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell342

description:
SMART-seq2
SM4C1r5-P4-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell343

description:
SMART-seq2
SM4C1r5-P4-E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell341

description:
SMART-seq2
SM4C1r5-P4-E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell361

description:
SMART-seq2
SM4C1r5-P4-G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell339

description:
SMART-seq2
SM4C1r5-P4-E03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell345

description:
SMART-seq2
SM4C1r5-P4-E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell346

description:
SMART-seq2
SM4C1r5-P4-E10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell337

description:
SMART-seq2
SM4C1r5-P4-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell340

description:
SMART-seq2
SM4C1r5-P4-E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell332

description:
SMART-seq2
SM4C1r5-P4-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell338

description:
SMART-seq2
SM4C1r5-P4-E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell336

description:
SMART-seq2
SM4C1r5-P4-D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell334

description:
SMART-seq2
SM4C1r5-P4-D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell366

description:
SMART-seq2
SM4C1r5-P4-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell335

description:
SMART-seq2
SM4C1r5-P4-D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell333

description:
SMART-seq2
SM4C1r5-P4-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell344

description:
SMART-seq2
SM4C1r5-P4-E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell328

description:
SMART-seq2
SM4C1r5-P4-D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell329

description:
SMART-seq2
SM4C1r5-P4-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell321

description:
SMART-seq2
SM4C1r5-P4-C09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell326

description:
SMART-seq2
SM4C1r5-P4-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell327

description:
SMART-seq2
SM4C1r5-P4-D03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell325

description:
SMART-seq2
SM4C1r5-P4-D01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell330

description:
SMART-seq2
SM4C1r5-P4-D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell322

description:
SMART-seq2
SM4C1r5-P4-C10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell324

description:
SMART-seq2
SM4C1r5-P4-C12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell323

description:
SMART-seq2
SM4C1r5-P4-C11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell320

description:
SMART-seq2
SM4C1r5-P4-C08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell319

description:
SMART-seq2
SM4C1r5-P4-C07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell317

description:
SMART-seq2
SM4C1r5-P4-C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell318

description:
SMART-seq2
SM4C1r5-P4-C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell316

description:
SMART-seq2
SM4C1r5-P4-C04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell315

description:
SMART-seq2
SM4C1r5-P4-C03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell331

description:
SMART-seq2
SM4C1r5-P4-D07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell311

description:
SMART-seq2
SM4C1r5-P4-B11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell313

description:
SMART-seq2
SM4C1r5-P4-C01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell312

description:
SMART-seq2
SM4C1r5-P4-B12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell310

description:
SMART-seq2
SM4C1r5-P4-B10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell309

description:
SMART-seq2
SM4C1r5-P4-B09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell308

description:
SMART-seq2
SM4C1r5-P4-B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell305

description:
SMART-seq2
SM4C1r5-P4-B05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell306

description:
SMART-seq2
SM4C1r5-P4-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell304

description:
SMART-seq2
SM4C1r5-P4-B04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell307

description:
SMART-seq2
SM4C1r5-P4-B07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell303

description:
SMART-seq2
SM4C1r5-P4-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell302

description:
SMART-seq2
SM4C1r5-P4-B02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell301

description:
SMART-seq2
SM4C1r5-P4-B01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell298

description:
SMART-seq2
SM4C1r5-P4-A10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell296

description:
SMART-seq2
SM4C1r5-P4-A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell295

description:
SMART-seq2
SM4C1r5-P4-A07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell294

description:
SMART-seq2
SM4C1r5-P4-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell293

description:
SMART-seq2
SM4C1r5-P4-A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell300

description:
SMART-seq2
SM4C1r5-P4-A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell299

description:
SMART-seq2
SM4C1r5-P4-A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell290

description:
SMART-seq2
SM4C1r5-P4-A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell291

description:
SMART-seq2
SM4C1r5-P4-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell314

description:
SMART-seq2
SM4C1r5-P4-C02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell287

description:
SMART-seq2
SM4C1r5-P3-H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell286

description:
SMART-seq2
SM4C1r5-P3-H10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell289

description:
SMART-seq2
SM4C1r5-P4-A01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell288

description:
SMART-seq2
SM4C1r5-P3-H12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell285

description:
SMART-seq2
SM4C1r5-P3-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell283

description:
SMART-seq2
SM4C1r5-P3-H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell282

description:
SMART-seq2
SM4C1r5-P3-H06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell281

description:
SMART-seq2
SM4C1r5-P3-H05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell280

description:
SMART-seq2
SM4C1r5-P3-H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell279

description:
SMART-seq2
SM4C1r5-P3-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell278

description:
SMART-seq2
SM4C1r5-P3-H02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell277

description:
SMART-seq2
SM4C1r5-P3-H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell297

description:
SMART-seq2
SM4C1r5-P4-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell276

description:
SMART-seq2
SM4C1r5-P3-G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell275

description:
SMART-seq2
SM4C1r5-P3-G11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell273

description:
SMART-seq2
SM4C1r5-P3-G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell292

description:
SMART-seq2
SM4C1r5-P4-A04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell271

description:
SMART-seq2
SM4C1r5-P3-G07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell270

description:
SMART-seq2
SM4C1r5-P3-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell269

description:
SMART-seq2
SM4C1r5-P3-G05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell268

description:
SMART-seq2
SM4C1r5-P3-G04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell267

description:
SMART-seq2
SM4C1r5-P3-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell263

description:
SMART-seq2
SM4C1r5-P3-F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell265

description:
SMART-seq2
SM4C1r5-P3-G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell284

description:
SMART-seq2
SM4C1r5-P3-H08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell261

description:
SMART-seq2
SM4C1r5-P3-F09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell260

description:
SMART-seq2
SM4C1r5-P3-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell254

description:
SMART-seq2
SM4C1r5-P3-F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell259

description:
SMART-seq2
SM4C1r5-P3-F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell257

description:
SMART-seq2
SM4C1r5-P3-F05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell255

description:
SMART-seq2
SM4C1r5-P3-F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell274

description:
SMART-seq2
SM4C1r5-P3-G10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell262

description:
SMART-seq2
SM4C1r5-P3-F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell252

description:
SMART-seq2
SM4C1r5-P3-E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell253

description:
SMART-seq2
SM4C1r5-P3-F01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell251

description:
SMART-seq2
SM4C1r5-P3-E11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell250

description:
SMART-seq2
SM4C1r5-P3-E10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell272

description:
SMART-seq2
SM4C1r5-P3-G08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell246

description:
SMART-seq2
SM4C1r5-P3-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell266

description:
SMART-seq2
SM4C1r5-P3-G02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell249

description:
SMART-seq2
SM4C1r5-P3-E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell245

description:
SMART-seq2
SM4C1r5-P3-E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell247

description:
SMART-seq2
SM4C1r5-P3-E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell256

description:
SMART-seq2
SM4C1r5-P3-F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell264

description:
SMART-seq2
SM4C1r5-P3-F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell243

description:
SMART-seq2
SM4C1r5-P3-E03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell258

description:
SMART-seq2
SM4C1r5-P3-F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell239

description:
SMART-seq2
SM4C1r5-P3-D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell240

description:
SMART-seq2
SM4C1r5-P3-D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell238

description:
SMART-seq2
SM4C1r5-P3-D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell237

description:
SMART-seq2
SM4C1r5-P3-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell235

description:
SMART-seq2
SM4C1r5-P3-D07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell248

description:
SMART-seq2
SM4C1r5-P3-E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell233

description:
SMART-seq2
SM4C1r5-P3-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell234

description:
SMART-seq2
SM4C1r5-P3-D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell232

description:
SMART-seq2
SM4C1r5-P3-D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell230

description:
SMART-seq2
SM4C1r5-P3-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell244

description:
SMART-seq2
SM4C1r5-P3-E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell229

description:
SMART-seq2
SM4C1r5-P3-D01


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell226

description:
SMART-seq2
SM4C1r5-P3-C10


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell225

description:
SMART-seq2
SM4C1r5-P3-C09


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell227

description:
SMART-seq2
SM4C1r5-P3-C11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell242

description:
SMART-seq2
SM4C1r5-P3-E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell223

description:
SMART-seq2
SM4C1r5-P3-C07


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell228

description:
SMART-seq2
SM4C1r5-P3-C12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell222

description:
SMART-seq2
SM4C1r5-P3-C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell241

description:
SMART-seq2
SM4C1r5-P3-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell306

description:
SMART-seq2
SM4KOB1-P1-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell305

description:
SMART-seq2
SM4KOB1-P1-B05


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell224

description:
SMART-seq2
SM4C1r5-P3-C08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell303

description:
SMART-seq2
SM4KOB1-P1-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell221

description:
SMART-seq2
SM4C1r5-P3-C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell302

description:
SMART-seq2
SM4KOB1-P1-B02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell300

description:
SMART-seq2
SM4KOB1-P1-A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell236

description:
SMART-seq2
SM4C1r5-P3-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell301

description:
SMART-seq2
SM4KOB1-P1-B01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell298

description:
SMART-seq2
SM4KOB1-P1-A10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell297

description:
SMART-seq2
SM4KOB1-P1-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell299

description:
SMART-seq2
SM4KOB1-P1-A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep3_cell231

description:
SMART-seq2
SM4C1r5-P3-D03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell296

description:
SMART-seq2
SM4KOB1-P1-A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell295

description:
SMART-seq2
SM4KOB1-P1-A07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell292

description:
SMART-seq2
SM4KOB1-P1-A04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell291

description:
SMART-seq2
SM4KOB1-P1-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell293

description:
SMART-seq2
SM4KOB1-P1-A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell290

description:
SMART-seq2
SM4KOB1-P1-A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell304

description:
SMART-seq2
SM4KOB1-P1-B04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell289

description:
SMART-seq2
SM4KOB1-P1-A01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell285

description:
SMART-seq2
BT869SM4KOC2-P2-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell287

description:
SMART-seq2
BT869SM4KOC2-P2-H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell288

description:
SMART-seq2
BT869SM4KOC2-P2-H12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell281

description:
SMART-seq2
BT869SM4KOC2-P2-H05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell283

description:
SMART-seq2
BT869SM4KOC2-P2-H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell280

description:
SMART-seq2
BT869SM4KOC2-P2-H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell282

description:
SMART-seq2
BT869SM4KOC2-P2-H06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell276

description:
SMART-seq2
BT869SM4KOC2-P2-G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell277

description:
SMART-seq2
BT869SM4KOC2-P2-H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell279

description:
SMART-seq2
BT869SM4KOC2-P2-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell278

description:
SMART-seq2
BT869SM4KOC2-P2-H02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell273

description:
SMART-seq2
BT869SM4KOC2-P2-G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell272

description:
SMART-seq2
BT869SM4KOC2-P2-G08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell294

description:
SMART-seq2
SM4KOB1-P1-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell270

description:
SMART-seq2
BT869SM4KOC2-P2-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell269

description:
SMART-seq2
BT869SM4KOC2-P2-G05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell267

description:
SMART-seq2
BT869SM4KOC2-P2-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell271

description:
SMART-seq2
BT869SM4KOC2-P2-G07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell268

description:
SMART-seq2
BT869SM4KOC2-P2-G04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell275

description:
SMART-seq2
BT869SM4KOC2-P2-G11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell274

description:
SMART-seq2
BT869SM4KOC2-P2-G10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell265

description:
SMART-seq2
BT869SM4KOC2-P2-G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell266

description:
SMART-seq2
BT869SM4KOC2-P2-G02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell286

description:
SMART-seq2
BT869SM4KOC2-P2-H10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell264

description:
SMART-seq2
BT869SM4KOC2-P2-F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell284

description:
SMART-seq2
BT869SM4KOC2-P2-H08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell262

description:
SMART-seq2
BT869SM4KOC2-P2-F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell263

description:
SMART-seq2
BT869SM4KOC2-P2-F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell259

description:
SMART-seq2
BT869SM4KOC2-P2-F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell260

description:
SMART-seq2
BT869SM4KOC2-P2-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell261

description:
SMART-seq2
BT869SM4KOC2-P2-F09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell257

description:
SMART-seq2
BT869SM4KOC2-P2-F05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell256

description:
SMART-seq2
BT869SM4KOC2-P2-F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell254

description:
SMART-seq2
BT869SM4KOC2-P2-F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell258

description:
SMART-seq2
BT869SM4KOC2-P2-F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell255

description:
SMART-seq2
BT869SM4KOC2-P2-F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell251

description:
SMART-seq2
BT869SM4KOC2-P2-E11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell249

description:
SMART-seq2
BT869SM4KOC2-P2-E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell250

description:
SMART-seq2
BT869SM4KOC2-P2-E10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell244

description:
SMART-seq2
BT869SM4KOC2-P2-E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell246

description:
SMART-seq2
BT869SM4KOC2-P2-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell242

description:
SMART-seq2
BT869SM4KOC2-P2-E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell245

description:
SMART-seq2
BT869SM4KOC2-P2-E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell243

description:
SMART-seq2
BT869SM4KOC2-P2-E03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell241

description:
SMART-seq2
BT869SM4KOC2-P2-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell247

description:
SMART-seq2
BT869SM4KOC2-P2-E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell252

description:
SMART-seq2
BT869SM4KOC2-P2-E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell248

description:
SMART-seq2
BT869SM4KOC2-P2-E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell253

description:
SMART-seq2
BT869SM4KOC2-P2-F01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell237

description:
SMART-seq2
BT869SM4KOC2-P2-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell233

description:
SMART-seq2
BT869SM4KOC2-P2-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell234

description:
SMART-seq2
BT869SM4KOC2-P2-D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell238

description:
SMART-seq2
BT869SM4KOC2-P2-D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell232

description:
SMART-seq2
BT869SM4KOC2-P2-D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell231

description:
SMART-seq2
BT869SM4KOC2-P2-D03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell229

description:
SMART-seq2
BT869SM4KOC2-P2-D01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell235

description:
SMART-seq2
BT869SM4KOC2-P2-D07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell230

description:
SMART-seq2
BT869SM4KOC2-P2-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell236

description:
SMART-seq2
BT869SM4KOC2-P2-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell226

description:
SMART-seq2
BT869SM4KOC2-P2-C10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell225

description:
SMART-seq2
BT869SM4KOC2-P2-C09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell228

description:
SMART-seq2
BT869SM4KOC2-P2-C12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell227

description:
SMART-seq2
BT869SM4KOC2-P2-C11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell240

description:
SMART-seq2
BT869SM4KOC2-P2-D12


title: ChIP-Seq_input

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

country: China

institute: National Key Laboratory of Crop Genetic Improvement

library_source: genomic

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with bwa mem
The reads with mapping quality lower 30 and duplication were filtered by samtools
MACS2 were used to call the peak
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: bogWig file by deepTools bamCoverage

molecule: genomic DNA

organism: Oryza sativa Indica Group

source_name: mature leaf

extract_protocol:
Rice tissues were crosslinked with 1% formaldehyde and quenched with 0.2 M glycine.
0.5 to 1g of the sample was ground into a fine powder in liquid nitrogen, the chromatin was fragmented into 200-600 bp by ultrasound processing using Bioruptor (Diagenode). The lysates were incubated at 4 °C for 1 to 6 h and rotated to form antibody-bead complexes. After reverse cross-linking of DNA and protein, ChIP-DNA was extracted using phenol: chloroform: isoamyl alcohol (P3803; Sigma-Aldrich). ChIP-DNA libraries were prepared by Illumina® (New England BioLabs, E7645) using the NEBNext® Ultra™ II DNA Library Preparation Kit. AMPure XP beads (Beckman, A63881) were used to select 250-650 bp library fragments.

tag: cultivar

value: Minghui 63

value: mature leaf


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell239

description:
SMART-seq2
BT869SM4KOC2-P2-D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell224

description:
SMART-seq2
BT869SM4KOC2-P2-C08


title: ChIP-Seq_DD-ZT20-rep2

value: constant dark (DD)

tag: time-point

tag: chip antibody

value: H3K9ac (Abcam, AB10812)


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell222

description:
SMART-seq2
BT869SM4KOC2-P2-C06


title: ChIP-Seq_DD-ZT12-rep2


title: ChIP-Seq_DD-ZT20-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell220

description:
SMART-seq2
BT869SM4KOC2-P2-C04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell221

description:
SMART-seq2
BT869SM4KOC2-P2-C05


title: ChIP-Seq_DD-ZT16-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell218

description:
SMART-seq2
BT869SM4KOC2-P2-C02


title: ChIP-Seq_DD-ZT16-rep2


title: ChIP-Seq_DD-ZT12-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell219

description:
SMART-seq2
BT869SM4KOC2-P2-C03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell217

description:
SMART-seq2
BT869SM4KOC2-P2-C01


title: ChIP-Seq_DD-ZT4-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell215

description:
SMART-seq2
BT869SM4KOC2-P2-B11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell214

description:
SMART-seq2
BT869SM4KOC2-P2-B10


title: ChIP-Seq_DD-ZT4-rep1


title: ChIP-Seq_DD-ZT8-rep2


title: ChIP-Seq_DD-ZT0-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell213

description:
SMART-seq2
BT869SM4KOC2-P2-B09


title: ChIP-Seq_DD-ZT8-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell212

description:
SMART-seq2
BT869SM4KOC2-P2-B08


title: ChIP-Seq_LD-ZT20-rep2

value: 12 h light/12 h dark (LD)


title: ChIP-Seq_DD-ZT0-rep1


title: ChIP-Seq_LD-ZT20-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell210

description:
SMART-seq2
BT869SM4KOC2-P2-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell211

description:
SMART-seq2
BT869SM4KOC2-P2-B07


title: ChIP-Seq_LD-ZT16-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell223

description:
SMART-seq2
BT869SM4KOC2-P2-C07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell216

description:
SMART-seq2
BT869SM4KOC2-P2-B12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell209

description:
SMART-seq2
BT869SM4KOC2-P2-B05


title: ChIP-Seq_LD-ZT16-rep1


title: ChIP-Seq_LD-ZT12-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell206

description:
SMART-seq2
BT869SM4KOC2-P2-B02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell208

description:
SMART-seq2
BT869SM4KOC2-P2-B04


title: ChIP-Seq_LD-ZT8-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell204

description:
SMART-seq2
BT869SM4KOC2-P2-A12


title: ChIP-Seq_LD-ZT4-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell202

description:
SMART-seq2
BT869SM4KOC2-P2-A10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell201

description:
SMART-seq2
BT869SM4KOC2-P2-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell205

description:
SMART-seq2
BT869SM4KOC2-P2-B01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell200

description:
SMART-seq2
BT869SM4KOC2-P2-A08


title: ChIP-Seq_LD-ZT4-rep1


title: ChIP-Seq_LD-ZT12-rep1


title: ChIP-Seq_LD-ZT0-rep2


title: ChIP-Seq_LD-ZT0-rep1


title: ChIP-Seq_LL-ZT20-rep1

value: constant light (LL)


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell203

description:
SMART-seq2
BT869SM4KOC2-P2-A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell199

description:
SMART-seq2
BT869SM4KOC2-P2-A07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell197

description:
SMART-seq2
BT869SM4KOC2-P2-A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell198

description:
SMART-seq2
BT869SM4KOC2-P2-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell196

description:
SMART-seq2
BT869SM4KOC2-P2-A04


title: ChIP-Seq_LL-ZT16-rep1


title: ChIP-Seq_LL-ZT20-rep2


title: ChIP-Seq_LL-ZT16-rep2


title: ChIP-Seq_LL-ZT12-rep2


title: ChIP-Seq_LL-ZT12-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell195

description:
SMART-seq2
BT869SM4KOC2-P2-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell194

description:
SMART-seq2
BT869SM4KOC2-P2-A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell207

description:
SMART-seq2
BT869SM4KOC2-P2-B03


title: ChIP-Seq_LL-ZT8-rep2


title: ChIP-Seq_LD-ZT8-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell193

description:
SMART-seq2
BT869SM4KOC2-P2-A01


title: ChIP-Seq_LL-ZT8-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell191

description:
SMART-seq2
BT869SM4KOC1-P2-H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell192

description:
SMART-seq2
BT869SM4KOC1-P2-H12


title: ChIP-Seq_LL-ZT4-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell190

description:
SMART-seq2
BT869SM4KOC1-P2-H10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell189

description:
SMART-seq2
BT869SM4KOC1-P2-H09


title: ChIP-Seq_LL-ZT4-rep2


title: ChIP-Seq_LL-ZT0-rep1


title: ChIP-Seq_LL-ZT0-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell187

description:
SMART-seq2
BT869SM4KOC1-P2-H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell184

description:
SMART-seq2
BT869SM4KOC1-P2-H04


title: RNA-Seq_DD-ZT16-rep2

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with HISAT2
The FPKM was calculated by Cufflinks v2.1.1
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The expression of each gene was quantified using HTSeq

extract_protocol:
RNA was harvested using RNeasy Plant Mini Kit (Qiagen). 0.5-1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant for RNA-seq according to the manufacturer’s recommendations.


title: RNA-Seq_DD-ZT20-rep2


title: RNA-Seq_DD-ZT20-rep1


title: RNA-Seq_DD-ZT16-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell185

description:
SMART-seq2
BT869SM4KOC1-P2-H05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell182

description:
SMART-seq2
BT869SM4KOC1-P2-H02


title: RNA-Seq_DD-ZT8-rep2


title: RNA-Seq_DD-ZT12-rep1


title: RNA-Seq_DD-ZT8-rep1


title: RNA-Seq_DD-ZT12-rep2


title: RNA-Seq_DD-ZT4-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell179

description:
SMART-seq2
BT869SM4KOC1-P2-G11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell181

description:
SMART-seq2
BT869SM4KOC1-P2-H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell180

description:
SMART-seq2
BT869SM4KOC1-P2-G12


title: RNA-Seq_DD-ZT4-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell178

description:
SMART-seq2
BT869SM4KOC1-P2-G10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell177

description:
SMART-seq2
BT869SM4KOC1-P2-G09


title: RNA-Seq_DD-ZT0-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell188

description:
SMART-seq2
BT869SM4KOC1-P2-H08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell186

description:
SMART-seq2
BT869SM4KOC1-P2-H06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell176

description:
SMART-seq2
BT869SM4KOC1-P2-G08


title: RNA-Seq_DD-ZT0-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell175

description:
SMART-seq2
BT869SM4KOC1-P2-G07


title: RNA-Seq_LD-ZT20-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell174

description:
SMART-seq2
BT869SM4KOC1-P2-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell173

description:
SMART-seq2
BT869SM4KOC1-P2-G05


title: RNA-Seq_LD-ZT16-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell183

description:
SMART-seq2
BT869SM4KOC1-P2-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell171

description:
SMART-seq2
BT869SM4KOC1-P2-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell172

description:
SMART-seq2
BT869SM4KOC1-P2-G04


title: RNA-Seq_LD-ZT12-rep1


title: RNA-Seq_LD-ZT8-rep2


title: RNA-Seq_LD-ZT12-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell169

description:
SMART-seq2
BT869SM4KOC1-P2-G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell170

description:
SMART-seq2
BT869SM4KOC1-P2-G02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell168

description:
SMART-seq2
BT869SM4KOC1-P2-F12


title: RNA-Seq_LD-ZT8-rep1


title: RNA-Seq_LD-ZT4-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell166

description:
SMART-seq2
BT869SM4KOC1-P2-F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell167

description:
SMART-seq2
BT869SM4KOC1-P2-F11


title: RNA-Seq_LD-ZT4-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell165

description:
SMART-seq2
BT869SM4KOC1-P2-F09


title: RNA-Seq_LD-ZT0-rep2


title: RNA-Seq_LD-ZT0-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell164

description:
SMART-seq2
BT869SM4KOC1-P2-F08


title: RNA-Seq_LD-ZT20-rep1


title: RNA-Seq_LL-ZT20-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell163

description:
SMART-seq2
BT869SM4KOC1-P2-F07


title: RNA-Seq_LL-ZT16-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell162

description:
SMART-seq2
BT869SM4KOC1-P2-F06


title: RNA-Seq_LL-ZT20-rep1


title: RNA-Seq_LL-ZT16-rep1


title: RNA-Seq_LD-ZT16-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell161

description:
SMART-seq2
BT869SM4KOC1-P2-F05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell159

description:
SMART-seq2
BT869SM4KOC1-P2-F03


title: RNA-Seq_LL-ZT12-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell160

description:
SMART-seq2
BT869SM4KOC1-P2-F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell158

description:
SMART-seq2
BT869SM4KOC1-P2-F02


title: RNA-Seq_LL-ZT12-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell157

description:
SMART-seq2
BT869SM4KOC1-P2-F01


title: RNA-Seq_LL-ZT8-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell155

description:
SMART-seq2
BT869SM4KOC1-P2-E11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell156

description:
SMART-seq2
BT869SM4KOC1-P2-E12


title: RNA-Seq_LL-ZT8-rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell154

description:
SMART-seq2
BT869SM4KOC1-P2-E10


title: RNA-Seq_LL-ZT0-rep2


title: RNA-Seq_LL-ZT4-rep2


title: RNA-Seq_LL-ZT4-rep1


title: RNA-Seq_LL-ZT0-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell152

description:
SMART-seq2
BT869SM4KOC1-P2-E08


title: BL-Hi-C_LL-ZT20-rep1

data_processing:
Raw BL-Hi-C data were analyzed using the ChIA-PET pipeline
MH63 rice reference genome using BWA with up to two mismatches allowed
PETs were  used for further classification as self-ligation,inter-ligation, and other PETs
interactions with an FDR < 0.05 and Paired-End Tag count (PETcount) ≥ 3 were selected for further analysis
Assembly: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The hic format file was converted by juicer_tools

extract_protocol:
Mature rice leaves were dual cross-linked with 1% formaldehyde (SIGMA, F8775) for 10 min and 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min at 25 ℃, after which glycine was added to a final concentration of 0.2 M to stop the cross-linking reaction.
Isolated rice nuclei were digested into fragments with the MboI restriction enzyme (NEB, R0147). DNA fragments were used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no.M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of DNA fragments was performed using a biotinylated bridge linker (forward strand:5′-[5Phos] CGCGATATC/iBIOdT/TATCTGACT-3′, reverse strand:5′-[5Phos] GTCAGATAAGATATCGCGT-3′) in situ. The protein-DNA complex was reverse cross-linked, and BL Hi-C libraries were prepared using Tn5 transposase (VAHTS; cat. no.TD501).
BL-Hi-C


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell151

description:
SMART-seq2
BT869SM4KOC1-P2-E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell149

description:
SMART-seq2
BT869SM4KOC1-P2-E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell148

description:
SMART-seq2
BT869SM4KOC1-P2-E04


title: BL-Hi-C_LL-ZT8-rep2


title: BL-Hi-C_LL-ZT8-rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell147

description:
SMART-seq2
BT869SM4KOC1-P2-E03


title: Stromal cell line MS5 coculture-rep 3

city: BIRMINGHAM

first: Paloma

last: GARCIA

address: INSTITUTE OF BIOMEDICAL RESEARCH, THE MEDICAL SCHOOL,, UNIVERSITY OF BIRMINGHAM

country: United Kingdom

institute: University of Birmingham

data_processing:
Libraries were prepared with HiSeq2500 Illumina platform
Quality control metrics were obtained with FastQC 0.11.7 software.
Sequenced reads were alingled and quantitated using Kallisto v0.43.0 with parameters -b 100. For the alignment a Kallisto index file was generated from Mus musculus Ensembl version 38 cDNA fasta file. Estimated counts and TPM values for each transcript were calculated by Kallisto in abundance.tsv files.
TPM values at gene level were obtained from transcripts counts with Sleuth v0.30.0 R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files for each sample from Kallisto with the following fields for each transcript: target_id, length, effective length, estimated counts and TPM.

organism: Mus musculus

source_name: Stromal cell line MS5 coculture

growth_protocol: RPMI 1640 media supplemented with 15% (v/v) FBS, 2 mmol/L L-glutamine and 100 U/ml Penicillin/Streptomycin (all from Thermo Fisher Scientific).

extract_protocol:
Cells were separated and washed with PBS prior to RNA extraction with TRIzol (Gibco) according to the manufacturer’s protocol. RNA was purified with RNeasy Plus Micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Co-cultures were plated in a 4:1 AML (SKM1)-stromal ratio, and 750.000 cells/ml density of SKM1 cells over confluent stromal cells for 24h.

value: Stromal cell line MS5

tag: protocol

value: co-cultured with leukemic cells (SKM1)


title: BL-Hi-C_LL-ZT20-rep2


title: Stromal cell line MS5 coculture-rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell145

description:
SMART-seq2
BT869SM4KOC1-P2-E01


title: Stromal cell line MS5 coculture-rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell150

description:
SMART-seq2
BT869SM4KOC1-P2-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell146

description:
SMART-seq2
BT869SM4KOC1-P2-E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell143

description:
SMART-seq2
BT869SM4KOC1-P2-D11


title: Stromal cell line MS5 only-rep 3

source_name: Stromal cell line MS5 only

value: cultured alone


title: Stromal cell line MS5 only-rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell153

description:
SMART-seq2
BT869SM4KOC1-P2-E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell141

description:
SMART-seq2
BT869SM4KOC1-P2-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell140

description:
SMART-seq2
BT869SM4KOC1-P2-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell139

description:
SMART-seq2
BT869SM4KOC1-P2-D07


title: Stromal cell line MS5 only-rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell138

description:
SMART-seq2
BT869SM4KOC1-P2-D06


title: Pt28

city: Dunedin

first: Peter

middle: Averill

last: Stockwell

state: Otago

address: Hanover Street

department: Pathology

country: New Zealand

institute: University of Otag

data_processing:
adaptor trimmed using the cutadapt tool
mapped to the human genome (assembly GRCh37) using HISAT2
discarding results with a Phred score lower than Q20 (accuracy of 99%)
The read counts for each sample were retrieved, first by exon, and then summarized by gene using featureCount
To avoid spurious alignment, a mapping quality of 10 was used.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file include raw count values for each Sample

source_name: FFPE Tumour tissue

extract_protocol:
RNA was extracted from macrodissected FFPE tissue samples using an Qiagen RNeasy mini prep kit
RNA-Seq libraries were prepared using 500 ng of RNA for each sample following TrueSeq mRNA stranded library prep kit (RS-122-2101; Illumina, CA, USA)

value: FFPE Tumour tissue

value: melanoma

value: pre-anti-PD-1 therapy


title: Pt29


title: Pt27


title: Pt26


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell137

description:
SMART-seq2
BT869SM4KOC1-P2-D05


title: Pt25


title: Pt24


title: Pt23


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell134

description:
SMART-seq2
BT869SM4KOC1-P2-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell144

description:
SMART-seq2
BT869SM4KOC1-P2-D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell133

description:
SMART-seq2
BT869SM4KOC1-P2-D01


title: Pt20


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell142

description:
SMART-seq2
BT869SM4KOC1-P2-D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell135

description:
SMART-seq2
BT869SM4KOC1-P2-D03


title: ACRJ-PC28 cells (passage 5)

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

data_processing:
Raw sequence data processing Illumina’s RTA and CASAVA pipeline
Quality Assessment Sequencing datasets were quality assessed using fastqc (v. 0.11.9).
Sequencing reads trimming for adoptor sequence/low quality reads Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.38
Trimmed sequence reads were mapping Trimmed sequence reads were mapped to Homo_sapiens.GRCh38.cdna.all.fa Ensembl v.101
Quantification of gene isoforms Salmon v.1.2.0
Assembly: Homo_sapiens.GRCh38.cdna.all.fa Ensembl v.101
Supplementary files format and content: .txt, raw read counts, normalized read counts (TPM)

growth_protocol: ACRJ-PC28 cells were maintained in Keratinocyte serum-free medium (KSFM, Thermofisher Scientific;#131-500A) supplemented with 5 ng/ml epidermal growth factor (Millipore Sigma; Burlington, Massachusetts, USA, #E9644), 50 μg/ml bovine pituitary extract (Millipore Sigma; #P1167), 100 ng/ml Hydrocortisone (Millipore Sigma #H0888), 5μg/ml Insulin (Millipore Sigma; #I9278), 5μg/ml Apo-Transferin (Millipore Sigma; #T1147), 0.5 ng/ml Recombinant Tumor Growth Factor- Alpha (Millipore Sigma; # GF313) and 1μM Epinephrine (Millipore Sigma; # E4642).

extract_protocol:
RNA was extracted with High Pure RNA Isolation Kit (Roche, Basel, Switzerland; # 11 828 665 001). The RNA concentration was 1837.6 ng/ul and 260/280 ratio was 2.11. Total RNA of 1.0 ug was used for the construction of sequencing library.
Paired-end library of the prostate cancer cell line was constructed using NEBNext Ultra Directional RNA kit.

value: prostate cancer cell line

value: 97% African ancestry, male by birth

value: 69-year-old Jamaican male with a PSA of 441.2 ng/ml, diagnosed with prostate cancer adenocarcinoma (Gleason Score; 4+4) with perineural involvement


title: Pt21


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell132

description:
SMART-seq2
BT869SM4KOC1-P2-C12

value: SMARCA4 knockout

value: nucleofection


title: Pt10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell130

description:
SMART-seq2
BT869SM4KOC1-P2-C10

value: 4 days


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell128

description:
SMART-seq2
BT869SM4KOC1-P2-C08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell131

description:
SMART-seq2
BT869SM4KOC1-P2-C11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell129

description:
SMART-seq2
BT869SM4KOC1-P2-C09


title: Pt8


title: Pt7


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell127

description:
SMART-seq2
BT869SM4KOC1-P2-C07


title: Pt6


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell125

description:
SMART-seq2
BT869SM4KOC1-P2-C05


title: Pt4


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell126

description:
SMART-seq2
BT869SM4KOC1-P2-C06


title: Pt5


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell136

description:
SMART-seq2
BT869SM4KOC1-P2-D04


title: Pt22


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell121

description:
SMART-seq2
BT869SM4KOC1-P2-C01


title: Pt1


title: Pt2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell122

description:
SMART-seq2
BT869SM4KOC1-P2-C02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell119

description:
SMART-seq2
BT869SM4KOC1-P2-B11


title: Pt9


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell117

description:
SMART-seq2
BT869SM4KOC1-P2-B09


title: CYB561A3-TG, 1

city: Philadelphia

first: Yuanqing

last: Feng

state: Pennsylvania

address: 430 Clinical Research Building, 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Checked fastq reads quality using FastQC v0.11.8 (fastqc --noextract --format fastq -t 10 )
Trim adapter and remove low quality reads using fastp v0.20.0 with default setting
Trimmed sequence reads were mapped to transcriptome(hg38) and performed transcript quantification  using kallisto (V0.46.2) quant with default settings.
Gene-level expression matrix  based on transcript-level data were generated using Tximport v1.24.0
Read count data was imported to DEseq2 (v1.36.0) to perform diffrential expression analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: MNT-1 cells

growth_protocol: MNT-1 cells (ATCC, #CRL- 3450), a gift from Dr. Michael S. Marks at Children’s Hospital of Philadelphia Research Institute, were grown in DMEM (Gibco, #11965084) supplemented with 20% Fetal Bovine Serum (FBS), 1% GlutaMAX (Gibco, #35050061), 1% NEAA (Gibco, #10370021),1% penicillin/streptomycin (Gibco, #15140122), and 10% AIM-V (Gibco, # 12055-091).

extract_protocol:
RNA was harvested using Zymo Direct-zol RNA miniPrep, 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were contructed at using Genewiz Standard RNA-Seq service (PolyA selected)

value: MNT-1 cells

value: melanoma cell


title: CYB561A3-TG, 3


title: GFP-TG-control,3

value: GFP-TG-control


title: CYB561A3-TG, 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell116

description:
SMART-seq2
BT869SM4KOC1-P2-B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell114

description:
SMART-seq2
BT869SM4KOC1-P2-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell124

description:
SMART-seq2
BT869SM4KOC1-P2-C04


title: Pt3


title: GFP-TG-control,1


title: CYB561A3-E1-CRISPRi, 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell112

description:
SMART-seq2
BT869SM4KOC1-P2-B04


title: GFP-TG-control,2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell123

description:
SMART-seq2
BT869SM4KOC1-P2-C03


title: OCA2-E2-CRISPRi, 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell113

description:
SMART-seq2
BT869SM4KOC1-P2-B05


title: CYB561A3-E1-CRISPRi, 2


title: OCA2-E2-CRISPRi, 2


title: OCA2-E2-CRISPRi, 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell108

description:
SMART-seq2
BT869SM4KOC1-P2-A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell110

description:
SMART-seq2
BT869SM4KOC1-P2-B02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell109

description:
SMART-seq2
BT869SM4KOC1-P2-B01


title: CRISPRi-Control, 3

value: CRISPRi-Control


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell120

description:
SMART-seq2
BT869SM4KOC1-P2-B12


title: CRISPRi-Control, 2


title: CYB561A3-CDS-KO, 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell118

description:
SMART-seq2
BT869SM4KOC1-P2-B10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell107

description:
SMART-seq2
BT869SM4KOC1-P2-A11


title: CYB561A3-CDS-KO, 2


title: CRISPRi-Control, 1


title: CYB561A3-E1-CRISPRi, 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell111

description:
SMART-seq2
BT869SM4KOC1-P2-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell101

description:
SMART-seq2
BT869SM4KOC1-P2-A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell106

description:
SMART-seq2
BT869SM4KOC1-P2-A10


title: MITF-E1-CRISPR-KO, 1


title: MITF-E1-CRISPR-KO, 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell99

description:
SMART-seq2
BT869SM4KOC1-P2-A03


title: CYB561A3-CDS-KO, 1


title: MITF-E1-CRISPR-KO, 3


title: CYB561A3-E1-CRISPR-KO, 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell103

description:
SMART-seq2
BT869SM4KOC1-P2-A07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell100

description:
SMART-seq2
BT869SM4KOC1-P2-A04


title: CYB561A3-E1-CRISPR-KO, 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell98

description:
SMART-seq2
BT869SM4KOC1-P2-A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell97

description:
SMART-seq2
BT869SM4KOC1-P2-A01


title: KO-Control, 3

value: CRISPRKO-Control


title: CYB561A3-E1-CRISPR-KO, 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell105

description:
SMART-seq2
BT869SM4KOC1-P2-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell96

description:
SMART-seq2
BT869SM4KOB1-P2-H12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell95

description:
SMART-seq2
BT869SM4KOB1-P2-H11


title: KO-Control, 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell104

description:
SMART-seq2
BT869SM4KOC1-P2-A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell94

description:
SMART-seq2
BT869SM4KOB1-P2-H10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell93

description:
SMART-seq2
BT869SM4KOB1-P2-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell102

description:
SMART-seq2
BT869SM4KOC1-P2-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell92

description:
SMART-seq2
BT869SM4KOB1-P2-H08


title: CC plasma exosomes rep8

city: Shanghai

first: Liang

last: Li

state: Shanghai

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

description: Identification of plasma exosomal microRNAs signature

data_processing:
The 50nt raw reads set obtained by Illumina HiseqTM 2500 sequencing were filtered through removing the joints at both ends of reads, removing low-quality reads, decontaminating and other processes to obtain clean reads.
The sequence length distribution and the common sequences among the samples were statistically analyzed.
Clean reads were classified and annotated to obtain the composition and expression level information of all kinds of small RNA in the samples.
After all small RNA fragments were annotated, the remaining small RNA fragments were used to predict new small RNA.
Genome_build: hg18

source_name: Exosomes isolated from plasma

extract_protocol:
Exosomal total RNAs were isolated from plasma-derived exosomes using exoEasy Maxi Kit (76064, Qiagen) following the manufacturer’s instructions.
From total RNA extraction to final cDNA library preparation mainly includes the following steps: total RNA is attached to 5 'and 3' connectors respectively;The first strand cDNA is synthesized;PCR amplification;The cDNA libraries with inserts of about 18-40nt were obtained by gel electrophoresis, and then sequenced by sequencing machine

treatment_protocol: For plasma-derived exosomes purification, venous blood samples of GBC and CC patients were collected using anticoagulation tube (containing EDTA) (GD050EK2, Gongdong). Exosomes were purified using exoEasy Maxi Kit (76064, Qiagen) according to the manufacturer’s instructions.

tag: age

tag: gender

value: Male

tag: disease state

value: chronic cholecystitis


title: CC plasma exosomes rep7

value: Female


title: CC plasma exosomes rep6


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell91

description:
SMART-seq2
BT869SM4KOB1-P2-H07


title: CC plasma exosomes rep5


title: CC plasma exosomes rep4


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell89

description:
SMART-seq2
BT869SM4KOB1-P2-H05


title: CC plasma exosomes rep3


title: CC plasma exosomes rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell90

description:
SMART-seq2
BT869SM4KOB1-P2-H06


title: CC plasma exosomes rep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell86

description:
SMART-seq2
BT869SM4KOB1-P2-H02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell87

description:
SMART-seq2
BT869SM4KOB1-P2-H03


title: GBC plasma exosomes rep8

value: Gallbladder carcinoma


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell85

description:
SMART-seq2
BT869SM4KOB1-P2-H01


title: KO-Control, 2


title: GBC plasma exosomes rep7


title: GBC plasma exosomes rep6


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell84

description:
SMART-seq2
BT869SM4KOB1-P2-G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell83

description:
SMART-seq2
BT869SM4KOB1-P2-G11


title: GBC plasma exosomes rep5


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell81

description:
SMART-seq2
BT869SM4KOB1-P2-G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell82

description:
SMART-seq2
BT869SM4KOB1-P2-G10


title: GBC plasma exosomes rep3


title: GBC plasma exosomes rep4


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell80

description:
SMART-seq2
BT869SM4KOB1-P2-G08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell79

description:
SMART-seq2
BT869SM4KOB1-P2-G07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell78

description:
SMART-seq2
BT869SM4KOB1-P2-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell88

description:
SMART-seq2
BT869SM4KOB1-P2-H04


title: GBC plasma exosomes rep2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell77

description:
SMART-seq2
BT869SM4KOB1-P2-G05


title: GBC plasma exosomes rep1


title: exercised 1

first: Yifang

last: Liu

address: 77 Avenue Louis Pasteur, NRB 336

institute: Harvard Medical School

description: polyA-selected mRNA

data_processing:
The quality of the sequencing reads was checked using the FASTQC package and reads were mapped onto the Drosophila genome (release 6) using the STAR aligner package.
The read counts were calculated using featureCounts.
The subsequent read counts matrix was further processed in R software using the Deseq2 package for normalization and differential gene expression analysis.
Genome_build: Drosophila genome (release 6)
Supplementary_files_format_and_content: Excel files include the expression values for each sample

organism: Drosophila melanogaster

source_name: body wall muscles

growth_protocol: All stocks were maintained at 25oC and experiments were performed at room temperature unless specified otherwise. Egg laying cages were set up by crossing ~150 virgin females and ~120 males in 100 ml volume cages. Crosses were maintained on grape juice plates supplemented with yeast paste and were kept at 25oC under 60% humidity. Egg collections were started from day 4 onwards post mating. Collections were done for a 3-hour time period every day with a small dab of yeast paste on the grape juice plates. The dab of yeast paste was removed after egg collection and the plates were incubated upside down at 25oC until larvae started hatching. First instar larvae were collected 24 hours after the end of egg collection and 60 animals were transferred to standard food vials for acute exercise training.

extract_protocol:
Total RNA was extracted from larval cuticle preparations using a Qiagen RNAeasy mini prep kit as per the manufacturer’s instructions.
The total RNA was shipped on dry ice to the Columbia Genome Center (CGC; Columbia University, New York, NY) for standard sample processing and raw data analysis.
RNAseq on mRNA-selected samples were performed by the Sulzberger Columbia Genome Center, Columbia University, using an Illumina HISEQ 2500 instrument. We obtained approximately 30 million single-end reads per biological replicate. The quality of the sequencing reads was checked using the FASTQC package and reads were mapped onto the Drosophila genome (release 6) using the STAR aligner package.

treatment_protocol: We induced an acute exercise program with a series of repetitive muscle contractions over a period of 2 hours. The acute exercise paradigm consisted of 8 rapid contractions consisting of 1 sec each of light stimulation interspersed by 2 seconds of no light stimulus followed by a 30 second break (rest). This cycle was repeated 3 times before giving the animals a 5 min of rest period. The entire exercise cycle was repeated in a loop for 2 hours. At the end of the acute exercise paradigm the larvae remained inactive and devoid of any contractile action for a short period of time.

tag: developmental stage

value: third larval instar (L3)

value: acute exercise


title: exercised 2

description: polyA-selected mRNA


title: exercised 3

description: polyA-selected mRNA


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell73

description:
SMART-seq2
BT869SM4KOB1-P2-G01


title: control 2

description: polyA-selected mRNA

value: control


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell72

description:
SMART-seq2
BT869SM4KOB1-P2-F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell76

description:
SMART-seq2
BT869SM4KOB1-P2-G04


title: control 3

description: polyA-selected mRNA


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell71

description:
SMART-seq2
BT869SM4KOB1-P2-F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell70

description:
SMART-seq2
BT869SM4KOB1-P2-F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell69

description:
SMART-seq2
BT869SM4KOB1-P2-F09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell68

description:
SMART-seq2
BT869SM4KOB1-P2-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell67

description:
SMART-seq2
BT869SM4KOB1-P2-F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell66

description:
SMART-seq2
BT869SM4KOB1-P2-F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell75

description:
SMART-seq2
BT869SM4KOB1-P2-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell74

description:
SMART-seq2
BT869SM4KOB1-P2-G02


title: RNAseq_BT869_DMSO_24h_biolrep2

data_processing:
Raw fastq reads were aligned using bowtie (v.0.12.7) and gene counts were quantified using RSEM (v1.2.19).
Differential expressed genes between SMARCA4 knockout and untreated cells, as well as between inhibitor and DMSO treated cells were determined using DESeq2 and default parameters (v1.30.1).
Gene counts of each sample were normalized by DESeq2’s median of ratios method and fitted with a negative binomial regression model. Differentially expressed genes were assessed using Wald’s test.
Assembly: hg19
Supplementary files format and content: Raw counts csv file for knockout experiments in BT869 cells.
Supplementary files format and content: Raw counts csv file for drug treatments using the BRG1/BRM inhibitors compound 11 (C11) and compound 14 (C14) with DMSO serving as negative control in BT869 cells.

growth_protocol: BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks, humidified atmosphere, 5% CO2, and at 37C.

extract_protocol:
Total RNA was extracted from frozen cell pellets using the Qiagen RNeasy mini plus kit (Cat# 74134), and RNA concentrations were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Library preparation and sequencing was performed by Novogene. In brief, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The original raw data from Illumina platform were transformed to Sequenced Reads, known as Raw Data or RAW Reads, by base calling. Raw data were recorded in a FASTQ file, which contained sequencing reads and corresponding sequencing quality.

treatment_protocol:
CRISPR/Cas9 mediated knockout of SMARCA4 or AAVS1 was performed on BT869 neurosphere cells. Four days post-nucleofection, neurospheres were collected and frozen at -80°C for future RNA isolation.
BT869 cells were treated with either DMSO (control samples) or 1 μM of BRG1/BRM inhibitors (Compounds 11 and 14), and cells were collected 24 hours post treatment and frozen at -80°C for future RNA isolation.

value: wildtype

value: DMSO


title: RNAseq_BT869_Compound14_24h_biolrep2

value: 1uM BRG1/BRM inhibitor Compound 14


title: RNAseq_BT869_DMSO_24h_biolrep1


title: RNAseq_BT869_AAVS1ko_d4

value: AAVS1 control knockout

value: nucleofection


title: RNAseq_BT869_Compound11_24h_biolrep2

value: 1uM BRG1/BRM inhibitor Compound 11


title: RNAseq_BT869_Compound11_24h_biolrep1


title: RNAseq_BT869_Compound14_24h_biolrep1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell64

description:
SMART-seq2
BT869SM4KOB1-P2-F04

value: SMARCA4 knockout

value: 4 days


title: exosomes from blood, A4

city: shandong

first: zhaogang

last: dong

address: No.107 wenhua west road ,jinan ,shandong province

institute: qilu hospital of shandong university

description: Full transcriptional group

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: counts, FPKMs

source_name: exosomes from blood

growth_protocol: from human blood

extract_protocol:
RNA Sample Kit
 total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

treatment_protocol: Ultra-high speed centrifugation

value: healthy control

value: Venous blood

tag: sample type

value: exosomes

value: Extract from plasma around 24 h


title: RNAseq_BT869_SMARCA4ko_d4


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell63

description:
SMART-seq2
BT869SM4KOB1-P2-F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell65

description:
SMART-seq2
BT869SM4KOB1-P2-F05


title: exosomes from blood, A2

description: Full transcriptional group


title: control 1

description: polyA-selected mRNA


title: exosomes from blood, A1

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell61

description:
SMART-seq2
BT869SM4KOB1-P2-F01


title: exosomes from blood, 81

description: Full transcriptional group

value: gastric cancer


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell60

description:
SMART-seq2
BT869SM4KOB1-P2-E12


title: exosomes from blood, A3

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell59

description:
SMART-seq2
BT869SM4KOB1-P2-E11


title: exosomes from blood, 57

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell58

description:
SMART-seq2
BT869SM4KOB1-P2-E10


title: exosomes from blood, 419

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell57

description:
SMART-seq2
BT869SM4KOB1-P2-E09


title: exosomes from blood, 401

description: Full transcriptional group


title: exosomes from blood, 380

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell53

description:
SMART-seq2
BT869SM4KOB1-P2-E05


title: exosomes from blood, 221

description: Full transcriptional group


title: exosomes from blood, 228

description: Full transcriptional group


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell55

description:
SMART-seq2
BT869SM4KOB1-P2-E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell54

description:
SMART-seq2
BT869SM4KOB1-P2-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell50

description:
SMART-seq2
BT869SM4KOB1-P2-E02


title: exosomes from blood, 369

description: Full transcriptional group


title: LiverC_Cattle_input

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
We used Trim Galore v0.4.0 and FastQC v0.11.2 software to trim the raw reads and obtain sequence quality reports.
The clean reads were mapping to the corresponding reference genome of each species using BWA-MEM software v0.7.17  with the default parameters,uplicated alignment reads were removed using the Picard Tools v2.25.0 with the parameter “REMOVE_DUPLICATES = true”.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
narrow peaks using MACS2 v2.1.1 with options “-q 0.01”.
bigWig files were generated using deepTools v3.1.1 with the follow parameters “--normalizeUsing CPM”.
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Bos taurus

source_name: liver

extract_protocol: none provided by the submitter

value: liver


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell52

description:
SMART-seq2
BT869SM4KOB1-P2-E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell56

description:
SMART-seq2
BT869SM4KOB1-P2-E08


title: LiverC_Cattle_H3K27ac

value: H3K27ac (Abcam ab4729)


title: LiverA_Cattle_input


title: LiverB_Cattle_input


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell62

description:
SMART-seq2
BT869SM4KOB1-P2-F02


title: LiverC_Cattle_H3K4me3

value: H3K4me3 (Abcam ab85850)


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell49

description:
SMART-seq2
BT869SM4KOB1-P2-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell48

description:
SMART-seq2
BT869SM4KOB1-P2-D12


title: LiverB_Cattle_H3K4me3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell47

description:
SMART-seq2
BT869SM4KOB1-P2-D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell44

description:
SMART-seq2
BT869SM4KOB1-P2-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell45

description:
SMART-seq2
BT869SM4KOB1-P2-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell51

description:
SMART-seq2
BT869SM4KOB1-P2-E03


title: LiverA_Cattle_H3K4me3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell43

description:
SMART-seq2
BT869SM4KOB1-P2-D07


title: rat, 2VO_rep3

first: Kaiyue

last: Zhao

address: 1 Tiantan Xili, Dongcheng District, Beijing

department: Institute of medicinal biotechnology

institute: Peking union medical college

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Cutadapt V1.14 was used to remove adaptors (cutoff value Q lower than 20). The clean reads were obtained by using Trimmomatic V0.36 after removing low-quality bases at both ends. Reads were compared with the reference genome via miRBase database.
DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if q-value <0.001 and |FoldChange| >2.
Assembly: the rats reference genome (http://asia.ensembl.org/ index.html)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: cerebral cortex

growth_protocol: All the animals were housed under a 12-h light-dark cycle (lights on 8 a.m.) at 25°C and 60 ± 10% humidity and given ad libitum access to food and water.

extract_protocol:
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Next, miRNA sequencing libraries were constructed using TruSeq Small RNA Sample Prep Kits (RS-200-0024, Illumina, USA) following manufacturer’s recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system. mRNA sequencing libraries were constructed from six total RNA samples using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601-02, Vazyme, China)

treatment_protocol: Rats were anesthetized with 2% sodium pentobarbital administered intraperitoneally (30mg/kg). The surgery gently separated the bilateral common carotid arteries permanently ligated with 5-0 silk thread. Rats in the sham group underwent the same procedure with the exception of arterial ligation. Each group contained three rats. The cerebral cortex was collected after the Morris water maze test and quickly preserved in liquid nitrogen.

value: cerebral cortex

tag: strain

value: Sprague-Dawley

value: bilateral common carotid artery occlusion


title: LiverB_Cattle_H3K27ac


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell42

description:
SMART-seq2
BT869SM4KOB1-P2-D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell41

description:
SMART-seq2
BT869SM4KOB1-P2-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell46

description:
SMART-seq2
BT869SM4KOB1-P2-D10


title: rat, 2VO_rep1


title: rat, sham operated_rep3

value: sham surgery


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell40

description:
SMART-seq2
BT869SM4KOB1-P2-D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell38

description:
SMART-seq2
BT869SM4KOB1-P2-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell39

description:
SMART-seq2
BT869SM4KOB1-P2-D03


title: small RNA-Seq Col-0, Fe resupply, biol rep 3

city: Amherst

first: Elsbeth

last: Walker

address: 611 N Pleasant St Morrill Science Center IV South

department: Biology

institute: University of Massachusetts Amherst

description: Col-0, Fe resupply, biol rep 3

data_processing:
Cutadapt was used to remove adapter sequences
Shortstack was used to align, annotate, and quantify small RNAs.
The search size parameter for discovering sRNA loci with Shortstack was between 17 and 29 nt long
After processing the raw reads, raw read counts were used as input for differential expression analysis with DESeq2
Assembly: TAIR10
Supplementary files format and content: matrix table of normalized abundance measurements, output of DESeq2

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Wild type Arabidopsis thaliana accession Columbia-0 (Col-0) was used for all experiments. Seeds were planted directly onto Pro-mix potting soil pre-treated with Gnatrol (Valent Bioscience Corporation) and stratified for three days at 4°C. Growth chamber conditions for soil-grown plants were 16 hours light (110 μmol∙m–2∙s–1), 8 hours dark at 22°C.

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Kit (Zymo Research) with DNase I treatment according to the manufacturer's instructions.
Libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina using manufacturer's instructions

treatment_protocol: +Fe samples: plants were grown on 1/2XMS+ Fe for 14 days, then were transferred to fresh MS+Fe for 3 days, and finally were transferred to 1/2XMS+Fe for 24 hours; -Fe samples: plants were grown on 1/2XMS+ Fe for 14 days, then were transferred to MS-Fe for 3 days, and finally were transferred to fresh 1/2XMS-Fe for 24 hours; resupply samples: plants were grown on 1/2XMS+ Fe for 14 days, then were transferred to MS-Fe for 3 days, and finally were transferred to 1/2XMS+Fe for 24 hours.

value: shoot

value: WT

tag: ecotype

value: Fe resupply


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell37

description:
SMART-seq2
BT869SM4KOB1-P2-D01

value: SMARCA4 knockout

value: nucleofection


title: rat, sham operated_rep1

tag: tissue


title: small RNA-Seq Col-0, Fe resupply, biol rep 1

description: Col-0, Fe resupply, biol rep 1


title: small RNA-Seq Col-0, Fe resupply, biol rep 2

description: Col-0, Fe resupply, biol rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell32

description:
SMART-seq2
BT869SM4KOB1-P2-C08

tag: cell line

value: 4 days


title: rat, sham operated_rep2


title: small RNA-Seq Col-0, -Fe, biol rep 3

description: Col-0, -Fe, biol rep 3

value: Fe deficiency


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell34

description:
SMART-seq2
BT869SM4KOB1-P2-C10

tag: cell type


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell35

description:
SMART-seq2
BT869SM4KOB1-P2-C11

tag: genotype


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell36

description:
SMART-seq2
BT869SM4KOB1-P2-C12

tag: treatment


title: rat, 2VO_rep2


title: small RNA-Seq Col-0, +Fe, biol rep 3

description: Col-0, +Fe, biol rep 3

value: control


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell33

description:
SMART-seq2
BT869SM4KOB1-P2-C09

tag: time


title: small RNA-Seq Col-0, -Fe, biol rep 1

description: Col-0, -Fe, biol rep 1


title: small RNA-Seq Col-0, -Fe, biol rep 2

description: Col-0, -Fe, biol rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell30

description:
SMART-seq2
BT869SM4KOB1-P2-C06


title: small RNA-Seq Col-0, +Fe, biol rep 2

description: Col-0, +Fe, biol rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell31

description:
SMART-seq2
BT869SM4KOB1-P2-C07


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell29

description:
SMART-seq2
BT869SM4KOB1-P2-C05


title: small RNA-Seq Col-0, +Fe, biol rep 1

description: Col-0, +Fe, biol rep 1


title: RNA-Seq Col-0, Fe resupply, biol rep 3

description: Col-0, Fe resupply, biol rep 3

data_processing:
Adapter sequences and low-quality reads were removed from raw reads with Trimmomatic v0.36.5
Mapping of reads to the Arabidopsis TAIR10 genome was carried out using HISAT2 v2.1.0
Reads were assembled into transcripts using StringTie v1.3.3.2
Differential gene expression analysis was performed using edgeR v3.20.7.2
Assembly: TAIR10
Supplementary files format and content: table of differentially expressed genes for each contrast of interest

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Kit (Zymo Research) with DNase I treatment according to the manufacturer's instructions.
Libraries were prepared using NEBNext Ultra II RNA Library Prep kit for Illumina following manufacturer's protocols.


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell27

description:
SMART-seq2
BT869SM4KOB1-P2-C03


title: RNA-Seq Col-0, Fe resupply, biol rep 2

description: Col-0, Fe resupply, biol rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell26

description:
SMART-seq2
BT869SM4KOB1-P2-C02


title: RNA-Seq Col-0, Fe resupply, biol rep 1

description: Col-0, Fe resupply, biol rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell25

description:
SMART-seq2
BT869SM4KOB1-P2-C01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell24

description:
SMART-seq2
BT869SM4KOB1-P2-B12


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell23

description:
SMART-seq2
BT869SM4KOB1-P2-B11


title: RNA-Seq Col-0, -Fe, biol rep 1

description: Col-0, -Fe, biol rep 1


title: RNA-Seq Col-0, +Fe, biol rep 3

description: Col-0, +Fe, biol rep 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell21

description:
SMART-seq2
BT869SM4KOB1-P2-B09


title: RNA-Seq Col-0, +Fe, biol rep 1

description: Col-0, +Fe, biol rep 1


title: RNA-Seq Col-0, +Fe, biol rep 2

description: Col-0, +Fe, biol rep 2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell28

description:
SMART-seq2
BT869SM4KOB1-P2-C04


title: PC rep 1

city: Guangzhou

first: jinfeng

last: fu

state: Guangdong

address: Wushan Street

department: School of Food Science and Engineering

institute: South China University of Technology

data_processing:
Illumina Casava 1.7 software used for baswcalling
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or loe-quality sequence, the mapped to mm8 whole genome using bowtie V0.12.2 with parameters
reads per kilobase of exon per megabase of library size (RPKM) wrer calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, Exons from all isoforms
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

extract_protocol:
liver was removed, flash-frozen in liquid nitrogen, and stored at -80 ° C,A total amount of 1 μg RNA per sample was used as input material for the RNA  sample preparations.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® following the manufacturer’s recommendations

tag: Sex

value: male

value: 18 weeks old

value: obesity

value: the positive control, fed with orlistat


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell19

description:
SMART-seq2
BT869SM4KOB1-P2-B07

data_processing:
Raw sequencing reads were aligned by bowtie, and gene counts were quantified using RSEM as transcript-per-million, or TPM.
Expression levels were calculated as Ei,j = log2(TPMi,j/10 + 1) for gene i in sample j. TPM values were divided by 10 for better approximation of the estimated complexity of single-cell libraries.
We filtered out low quality cells with less than 2,500 detected genes or an average housekeeping expression level below 2.5 and removed low expressed genes with TPM greater than 16 in less than 5 cells.
We defined relative expression as centered expression levels, Eri,j = Ei,j − average[Ei,1...n] for the remaining cells and genes.
Assembly: hg19
Supplementary files format and content: TPM values for each gene in each cell and in every condition. Control AAVS1 (CTRL) and SMARCA4 knockout (SM4KO) TPM data are gathered in one csv file per replicate.

extract_protocol:
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell17

description:
SMART-seq2
BT869SM4KOB1-P2-B05


title: PC rep 2

value: liver


title: PC rep 3


title: OC rep 2

value: the obesity control, fed with water


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell20

description:
SMART-seq2
BT869SM4KOB1-P2-B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell22

description:
SMART-seq2
BT869SM4KOB1-P2-B10


title: OC rep 3


title: OC rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell18

description:
SMART-seq2
BT869SM4KOB1-P2-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell16

description:
SMART-seq2
BT869SM4KOB1-P2-B04


title: RNA-Seq Col-0, -Fe, biol rep 3

description: Col-0, -Fe, biol rep 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell13

description:
SMART-seq2
BT869SM4KOB1-P2-B01


title: NC rep 2

value: health

value: the normal control, fed with water


title: RNA-Seq Col-0, -Fe, biol rep 2

description: Col-0, -Fe, biol rep 2


title: MD rep 3

value: the treatment group, fed with the medium doses of plantain


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell11

description:
SMART-seq2
BT869SM4KOB1-P2-A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell9

description:
SMART-seq2
BT869SM4KOB1-P2-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell15

description:
SMART-seq2
BT869SM4KOB1-P2-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell14

description:
SMART-seq2
BT869SM4KOB1-P2-B02


title: MD rep 2


title: LD rep 2

value: the treatment group, fed with the low doses of plantain


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell7

description:
SMART-seq2
BT869SM4KOB1-P2-A07


title: MD rep 1


title: NC rep 1


title: HD rep 3

value: the treatment group, fed with the high doses of plantain


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell6

description:
SMART-seq2
BT869SM4KOB1-P2-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell8

description:
SMART-seq2
BT869SM4KOB1-P2-A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell10

description:
SMART-seq2
BT869SM4KOB1-P2-A10


title: LD rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell4

description:
SMART-seq2
BT869SM4KOB1-P2-A04


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell5

description:
SMART-seq2
BT869SM4KOB1-P2-A05


title: LD rep 3


title: HD rep 2


title: NC rep 3


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell12

description:
SMART-seq2
BT869SM4KOB1-P2-A12


title: HD rep 1


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell3

description:
SMART-seq2
BT869SM4KOB1-P2-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell1

description:
SMART-seq2
BT869SM4KOB1-P2-A01


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell2

description:
SMART-seq2
BT869SM4KOB1-P2-A02


title: Plate9-319-Liver

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Plate 9_LIVER_B12

data_processing: Data were processed using the Tempo-SeqR software package

source_name: Liver

growth_protocol: Male and female SD rats were placed on NTP-2000 diet and housed up to 5 animals per cage. After a 10-14 day quarantine, 8-10 week old animals were randomly assigned to treatment and control groups.

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

treatment_protocol: Each of six chemicals was given at nine doses (5 mL/kg dosing volume) to the treatment groups. A vehicle control group was also included for each treatment group. Rats received the test formulations via gavage for five consecutive days.

value: Sprague Dawley (SD)

value: Female

value: Liver

tag: chemical

value: 10:2 FTOH

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: Plate9-318-Liver

description: Plate 9_LIVER_E05


title: Plate9-316-Liver

description: Plate 9_LIVER_G04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell192

description:
SMART-seq2
BT869AAVSID4R4-P1-H12

value: AAVS1 control knockout

value: nucleofection

value: 4 days


title: Plate9-315-Liver

description: Plate 9_LIVER_D04

value: Male


title: Plate9-311-Liver

description: Plate 9_LIVER_A05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell191

description:
SMART-seq2
BT869AAVSID4R4-P1-H11


title: Plate9-312-Liver

description: Plate 9_LIVER_C10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell190

description:
SMART-seq2
BT869AAVSID4R4-P1-H10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell188

description:
SMART-seq2
BT869AAVSID4R4-P1-H08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell189

description:
SMART-seq2
BT869AAVSID4R4-P1-H09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell187

description:
SMART-seq2
BT869AAVSID4R4-P1-H07


title: Plate9-310-Liver

description: Plate 9_LIVER_A02


title: Plate9-309-Liver

description: Plate 9_LIVER_E11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell184

description:
SMART-seq2
BT869AAVSID4R4-P1-H04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell186

description:
SMART-seq2
BT869AAVSID4R4-P1-H06


title: Plate9-308-Liver

description: Plate 9_LIVER_C07


title: Plate9-307-Liver

description: Plate 9_LIVER_A08


title: Plate9-304-Liver

description: Plate 9_LIVER_G11


title: Plate9-306-Liver

description: Plate 9_LIVER_E02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell181

description:
SMART-seq2
BT869AAVSID4R4-P1-H01


title: Plate9-305-Liver

description: Plate 9_LIVER_D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep2_cell115

description:
SMART-seq2
BT869SM4KOC1-P2-B07

value: SMARCA4 knockout


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell185

description:
SMART-seq2
BT869AAVSID4R4-P1-H05


title: Plate9-302-Liver

description: Plate 9_LIVER_A11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell180

description:
SMART-seq2
BT869AAVSID4R4-P1-G12


title: Plate9-300-Liver

description: Plate 9_LIVER_G07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell179

description:
SMART-seq2
BT869AAVSID4R4-P1-G11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell178

description:
SMART-seq2
BT869AAVSID4R4-P1-G10


title: Plate9-298-Liver

description: Plate 9_LIVER_H06


title: Plate9-299-Liver

description: Plate 9_LIVER_C05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell177

description:
SMART-seq2
BT869AAVSID4R4-P1-G09


title: Plate9-297-Liver

description: Plate 9_LIVER_G05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell183

description:
SMART-seq2
BT869AAVSID4R4-P1-H03


title: Plate9-295-Liver

description: Plate 9_LIVER_D08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell176

description:
SMART-seq2
BT869AAVSID4R4-P1-G08


title: Plate9-294-Liver

description: Plate 9_LIVER_G10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell182

description:
SMART-seq2
BT869AAVSID4R4-P1-H02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell174

description:
SMART-seq2
BT869AAVSID4R4-P1-G06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell175

description:
SMART-seq2
BT869AAVSID4R4-P1-G07


title: Plate9-292-Liver

description: Plate 9_LIVER_F08


title: Plate9-291-Liver

description: Plate 9_LIVER_E08


title: Plate9-288-Liver

description: Plate 9_LIVER_H03


title: Plate9-290-Liver

description: Plate 9_LIVER_H01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell172

description:
SMART-seq2
BT869AAVSID4R4-P1-G04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell168

description:
SMART-seq2
BT869AAVSID4R4-P1-F12


title: Plate9-289-Liver

description: Plate 9_LIVER_F07


title: Plate9-284-Liver

description: Plate 9_LIVER_D02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell169

description:
SMART-seq2
BT869AAVSID4R4-P1-G01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell171

description:
SMART-seq2
BT869AAVSID4R4-P1-G03


title: Plate9-287-Liver

description: Plate 9_LIVER_C06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell167

description:
SMART-seq2
BT869AAVSID4R4-P1-F11


title: Plate9-286-Liver

description: Plate 9_LIVER_B09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell170

description:
SMART-seq2
BT869AAVSID4R4-P1-G02


title: Plate9-283-Liver

description: Plate 9_LIVER_D10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell166

description:
SMART-seq2
BT869AAVSID4R4-P1-F10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell165

description:
SMART-seq2
BT869AAVSID4R4-P1-F09


title: Plate9-282-Liver

description: Plate 9_LIVER_G03


title: Plate9-281-Liver

description: Plate 9_LIVER_C02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell163

description:
SMART-seq2
BT869AAVSID4R4-P1-F07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell173

description:
SMART-seq2
BT869AAVSID4R4-P1-G05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell164

description:
SMART-seq2
BT869AAVSID4R4-P1-F08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell162

description:
SMART-seq2
BT869AAVSID4R4-P1-F06


title: Plate9-278-Liver

description: Plate 9_LIVER_B02


title: Plate9-279-Liver

description: Plate 9_LIVER_H11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell161

description:
SMART-seq2
BT869AAVSID4R4-P1-F05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell160

description:
SMART-seq2
BT869AAVSID4R4-P1-F04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell159

description:
SMART-seq2
BT869AAVSID4R4-P1-F03


title: Plate9-273-Liver

description: Plate 9_LIVER_F04


title: Plate9-275-Liver

description: Plate 9_LIVER_A07


title: Plate9-277-Liver

description: Plate 9_LIVER_H08


title: Plate9-276-Liver

description: Plate 9_LIVER_B04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell155

description:
SMART-seq2
BT869AAVSID4R4-P1-E11


title: Plate9-270-Liver

description: Plate 9_LIVER_C04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell154

description:
SMART-seq2
BT869AAVSID4R4-P1-E10


title: Plate9-272-Liver

description: Plate 9_LIVER_C11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell152

description:
SMART-seq2
BT869AAVSID4R4-P1-E08


title: Plate9-269-Liver

description: Plate 9_LIVER_H07


title: Plate9-271-Liver

description: Plate 9_LIVER_G06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell151

description:
SMART-seq2
BT869AAVSID4R4-P1-E07


title: Plate9-267-Liver

description: Plate 9_LIVER_D03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell150

description:
SMART-seq2
BT869AAVSID4R4-P1-E06


title: Plate9-280-Liver

description: Plate 9_LIVER_A12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell149

description:
SMART-seq2
BT869AAVSID4R4-P1-E05


title: Plate9-265-Liver

description: Plate 9_LIVER_H05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell158

description:
SMART-seq2
BT869AAVSID4R4-P1-F02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell148

description:
SMART-seq2
BT869AAVSID4R4-P1-E04


title: Plate9-263-Liver

description: Plate 9_LIVER_E12


title: Plate9-260-Liver

description: Plate 9_LIVER_C09


title: Plate9-258-Liver

description: Plate 9_LIVER_A03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell153

description:
SMART-seq2
BT869AAVSID4R4-P1-E09


title: Plate9-259-Liver

description: Plate 9_LIVER_B10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell143

description:
SMART-seq2
BT869AAVSID4R4-P1-D11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell156

description:
SMART-seq2
BT869AAVSID4R4-P1-E12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell157

description:
SMART-seq2
BT869AAVSID4R4-P1-F01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell144

description:
SMART-seq2
BT869AAVSID4R4-P1-D12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell145

description:
SMART-seq2
BT869AAVSID4R4-P1-E01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell142

description:
SMART-seq2
BT869AAVSID4R4-P1-D10


title: Plate9-256-Liver

description: Plate 9_LIVER_D12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell141

description:
SMART-seq2
BT869AAVSID4R4-P1-D09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell140

description:
SMART-seq2
BT869AAVSID4R4-P1-D08


title: Plate9-254-Liver

description: Plate 9_LIVER_A09


title: Plate9-252-Liver

description: Plate 9_LIVER_F09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell138

description:
SMART-seq2
BT869AAVSID4R4-P1-D06


title: Plate9-251-Liver

description: Plate 9_LIVER_F10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell137

description:
SMART-seq2
BT869AAVSID4R4-P1-D05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell146

description:
SMART-seq2
BT869AAVSID4R4-P1-E02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell147

description:
SMART-seq2
BT869AAVSID4R4-P1-E03


title: Plate9-262-Liver

description: Plate 9_LIVER_E04


title: Plate9-266-Liver

description: Plate 9_LIVER_H02


title: Plate9-249-Liver

description: Plate 9_LIVER_B08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell136

description:
SMART-seq2
BT869AAVSID4R4-P1-D04


title: Plate9-250-Liver

description: Plate 9_LIVER_G02


title: Plate9-257-Liver

description: Plate 9_LIVER_A04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell135

description:
SMART-seq2
BT869AAVSID4R4-P1-D03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell134

description:
SMART-seq2
BT869AAVSID4R4-P1-D02


title: Plate9-247-Liver

description: Plate 9_LIVER_E07


title: Plate9-245-Liver

description: Plate 9_LIVER_E10


title: Plate9-248-Liver

description: Plate 9_LIVER_E09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell132

description:
SMART-seq2
BT869AAVSID4R4-P1-C12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell133

description:
SMART-seq2
BT869AAVSID4R4-P1-D01


title: Plate9-246-Liver

description: Plate 9_LIVER_G09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell131

description:
SMART-seq2
BT869AAVSID4R4-P1-C11


title: Plate9-244-Liver

description: Plate 9_LIVER_B11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell130

description:
SMART-seq2
BT869AAVSID4R4-P1-C10


title: Plate9-255-Liver

description: Plate 9_LIVER_G08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell129

description:
SMART-seq2
BT869AAVSID4R4-P1-C09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell139

description:
SMART-seq2
BT869AAVSID4R4-P1-D07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell128

description:
SMART-seq2
BT869AAVSID4R4-P1-C08


title: Plate9-241-Liver

description: Plate 9_LIVER_E03


title: Plate9-239-Liver

description: Plate 9_LIVER_G12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell126

description:
SMART-seq2
BT869AAVSID4R4-P1-C06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell127

description:
SMART-seq2
BT869AAVSID4R4-P1-C07


title: Plate9-240-Liver

description: Plate 9_LIVER_F03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell125

description:
SMART-seq2
BT869AAVSID4R4-P1-C05


title: Plate9-237-Liver

description: Plate 9_LIVER_B06


title: Plate9-236-Liver

description: Plate 9_LIVER_H09


title: Plate9-234-Liver

description: Plate 9_LIVER_C03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell123

description:
SMART-seq2
BT869AAVSID4R4-P1-C03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell124

description:
SMART-seq2
BT869AAVSID4R4-P1-C04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell122

description:
SMART-seq2
BT869AAVSID4R4-P1-C02


title: Plate9-232-Liver

description: Plate 9_LIVER_F02


title: Plate9-230-Liver

description: Plate 9_LIVER_B05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell120

description:
SMART-seq2
BT869AAVSID4R4-P1-B12


title: Plate9-231-Liver

description: Plate 9_LIVER_F06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell117

description:
SMART-seq2
BT869AAVSID4R4-P1-B09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell121

description:
SMART-seq2
BT869AAVSID4R4-P1-C01


title: Plate9-227-Liver

description: Plate 9_LIVER_C08


title: Plate9-228-Liver

description: Plate 9_LIVER_G01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell119

description:
SMART-seq2
BT869AAVSID4R4-P1-B11


title: Plate9-243-Liver

description: Plate 9_LIVER_H12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell118

description:
SMART-seq2
BT869AAVSID4R4-P1-B10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell116

description:
SMART-seq2
BT869AAVSID4R4-P1-B08


title: Plate9-225-Liver

description: Plate 9_LIVER_E06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell115

description:
SMART-seq2
BT869AAVSID4R4-P1-B07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell114

description:
SMART-seq2
BT869AAVSID4R4-P1-B06


title: Plate9-223-Liver

description: Plate 9_LIVER_D11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell111

description:
SMART-seq2
BT869AAVSID4R4-P1-B03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell112

description:
SMART-seq2
BT869AAVSID4R4-P1-B04


title: Plate9-221-Liver

description: Plate 9_LIVER_D09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell110

description:
SMART-seq2
BT869AAVSID4R4-P1-B02


title: Plate9-226-Liver

description: Plate 9_LIVER_B03


title: Plate9-229-Liver

description: Plate 9_LIVER_B07


title: Plate9-222-Liver

description: Plate 9_LIVER_A06


title: Plate9-233-Liver

description: Plate 9_LIVER_C12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell109

description:
SMART-seq2
BT869AAVSID4R4-P1-B01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell108

description:
SMART-seq2
BT869AAVSID4R4-P1-A12


title: Plate9-219-Liver

description: Plate 9_LIVER_D06


title: Plate9-224-Liver

description: Plate 9_LIVER_F12


title: Plate9-218-Liver

description: Plate 9_LIVER_A10


title: Plate9-220-Liver

description: Plate 9_LIVER_H04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell106

description:
SMART-seq2
BT869AAVSID4R4-P1-A10


title: Plate9-216-Liver

description: Plate 9_LIVER_D07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell107

description:
SMART-seq2
BT869AAVSID4R4-P1-A11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell105

description:
SMART-seq2
BT869AAVSID4R4-P1-A09


title: Plate8-537-Kidney

description: Plate 8_KIDNEY_D04

source_name: Kidney

value: Kidney

value: corn oil