title: T-5470

description: ftATAC-seq data of mouse thymoctyes


title: T-5471

status: Public on Apr 28 2020

type: SRA

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

country: China

institute: University of Science and Technology of China

description: ftATAC-seq data of mouse thymoctyes

library_source: genomic

data_processing:
We used BOWTIE2 to map the trimmed sequencing data to the corresponding genome index and used PICARD for the sorting, duplicate removal, and fragment length counting of the aligned data.
We calls peaks from the merged single-cell profiles of all cells using MACS2 to ensure that the entire analysis is unsupervised. We then ranked and filtered out the low quality peaks based on the false discovery rate (Q-value).
Genomic locations of the peaks were annotated by HOMER, and motifs searched by FIMO.
We calculates the number of fragments and the percent of reads mapped to the TSS region (±2000 BP) for each cell, and filters out high quality cells for downstream analysis.
We integrate all processing steps as a pre-process script of APEC.
Genome_build: mm9
Supplementary_files_format_and_content: The cell.csv file is a CSV format file containing the information of filtered cells; the features.bed file is a BED format file containing the information of filtered peaks; the matrix.mtx file is the fragment count matrix stored in MTX format.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse thymoctyes

extract_protocol:
Thymus tissues isolated from 6- to 8-week-old male mice were gently ground in 1 mL of RPMI-1640. Thymocytes in a single-cell suspension were counted after passing through a 40 μm nylon mesh. A total of 1 × 106 thymocytes were stained with PerCP-Cy5.5-anti-CD45, PE-anti-CD8a and APC-Cy7-anti-CD4 antibodies (Biolegend) and then fixed in 1× PBS containing 1% methanal at room temperature for 5 min. After washing twice with 1× PBS, the cells were counted again. A total of 1 × 105 fixed cells were resuspended in 40 μL of 1× TD buffer (5 mM Tris-HCl, pH 8.0, 5 mM MgCl2 , and 10% DMF) containing 0.1% NP-40. Then, 10 μL of fluorescent transposomes were added and mixed gently. Fluorescent tagmentation was conducted at 55 °C for 30 min and stopped by adding 200 µL of 100 mM EDTA directly to the reaction mixture. The cells were loaded on a Sony SH800S sorter, and single cells of the CD45+/AF488-Tn5hi population were index-sorted into each well of 384-well plates. The 384-well plates used to acquire sorted cells were loaded with 2 µL of release buffer (50 mM EDTA, 0.02% SDS) before use. After sorting, the cells in the wells were incubated for 1 min. Plates that were not processed immediately were preserved at -80 °C.
To prepare a single-cell ATAC-seq library, plates containing fluorescently tagmented cells were incubated at 55 °C for 30 min. Then, 4.2 μL of PCR round 1 buffer (1 μL of 100 μM MgCl2, 3 μL of 2× I-5 PCR mix [MCLAB], and 0.1 μL each of 10 μM R1 and R2 primers) were added to each well, followed by PCR: 72 °C for 10 min; 98 °C for 3 min; 10 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Thereafter, each well received 4 µL of PCR round 2 buffer (2 μL of I-5 PCR Mix, 0.5 μL each of Ad1 and barcoded Ad2 primers, and 1 μL of ddH2O), and final PCR amplification was carried out: 98 °C for 3 min; 12 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Wells containing different Ad2 barcodes were collected together and purified with a QIAquick PCR purification kit (Qiagen).

tag: strain

tag: tissue

value: thymocytes

tag: age

value: 6-8 weeks


title: zebrafish_989s_P21

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the zebrafish reference genome (danRer11) using TapHat2, Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the three sample-plates (plate_123, plate_989, plate_990) were combined into one expression matrix file
counts data was processed and analyzed using velocyto, SingleCellExperiment and pagoda2 packages in R-software
Genome_build: GRCz11 (danRer11)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Danio rerio

source_name: zebrafish

extract_protocol:
FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin-EDTA and 10U Dnase I for 30min at 30°C
RNA libraries were prepared using standard SmartSeq2 protocol

value: embryo trunk

tag: starin

value: vegfc:Gal4FF;UASGFP; kdrl:mCherry

value: 48 hpf


title: zebrafish_989s_P2


title: zebrafish_989s_P7


title: T-5473

description: ftATAC-seq data of mouse thymoctyes


title: T-5469

description: ftATAC-seq data of mouse thymoctyes


title: T-5467

description: ftATAC-seq data of mouse thymoctyes


title: T-5468

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P19


title: zebrafish_989s_P17


title: zebrafish_989s_P18


title: zebrafish_989s_P5


title: T-5465

description: ftATAC-seq data of mouse thymoctyes


title: T-5466

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P16


title: T-5464

description: ftATAC-seq data of mouse thymoctyes


title: T-5472

description: ftATAC-seq data of mouse thymoctyes


title: T-5463

description: ftATAC-seq data of mouse thymoctyes


title: T-5462

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P13


title: zebrafish_989s_P15


title: T-5460

description: ftATAC-seq data of mouse thymoctyes


title: T-5461

description: ftATAC-seq data of mouse thymoctyes


title: T-5459

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P20


title: zebrafish_989s_P11


title: zebrafish_989s_O9


title: T-5455

description: ftATAC-seq data of mouse thymoctyes


title: T-5457

description: ftATAC-seq data of mouse thymoctyes


title: T-5456

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O8


title: zebrafish_989s_O7


title: T-5454

description: ftATAC-seq data of mouse thymoctyes


title: T-5453

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O6


title: zebrafish_989s_O5


title: T-5452

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O4


title: T-5450

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O3


title: T-5451

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P14


title: T-5449

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_P12


title: T-5458

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O23


title: T-5446

description: ftATAC-seq data of mouse thymoctyes


title: T-5447

description: ftATAC-seq data of mouse thymoctyes


title: T-5448

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O24


title: zebrafish_989s_O20


title: zebrafish_989s_O21


title: zebrafish_989s_P1


title: zebrafish_989s_P10


title: zebrafish_989s_O2


title: T-5445

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O18


title: T-5444

description: ftATAC-seq data of mouse thymoctyes


title: T-5442

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O19


title: T-5443

description: ftATAC-seq data of mouse thymoctyes


title: T-5441

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O17


title: zebrafish_989s_O16


title: zebrafish_989s_O15


title: T-5439

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O14


title: T-5438

description: ftATAC-seq data of mouse thymoctyes


title: T-5437

description: ftATAC-seq data of mouse thymoctyes


title: T-5436

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O12


title: T-5440

description: ftATAC-seq data of mouse thymoctyes


title: T-5435

description: ftATAC-seq data of mouse thymoctyes


title: T-5434

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O10


title: zebrafish_989s_O1


title: T-5433

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N9


title: zebrafish_989s_N8


title: zebrafish_989s_N7


title: T-5432

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_O11


title: zebrafish_989s_N5


title: zebrafish_989s_N4


title: T-5428

description: ftATAC-seq data of mouse thymoctyes


title: T-5427

description: ftATAC-seq data of mouse thymoctyes


title: T-5430

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N6


title: T-5426

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N3


title: zebrafish_989s_N24


title: zebrafish_989s_O13


title: T-5431

description: ftATAC-seq data of mouse thymoctyes


title: T-5425

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N22


title: T-5424

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N23


title: T-5423

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N21


title: T-5422

description: ftATAC-seq data of mouse thymoctyes


title: T-5421

description: ftATAC-seq data of mouse thymoctyes


title: T-5420

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N19


title: T-5419

description: ftATAC-seq data of mouse thymoctyes


title: T-5429

description: ftATAC-seq data of mouse thymoctyes


title: T-5418

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N17


title: zebrafish_989s_N18


title: T-5417

description: ftATAC-seq data of mouse thymoctyes


title: T-5416

description: ftATAC-seq data of mouse thymoctyes


title: T-5414

description: ftATAC-seq data of mouse thymoctyes


title: T-5413

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N15


title: zebrafish_989s_N16


title: T-5415

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N11


title: zebrafish_989s_N12


title: T-5412

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N2


title: zebrafish_989s_N10


title: zebrafish_989s_N1


title: T-5411

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M8


title: zebrafish_989s_M7


title: T-5409

description: ftATAC-seq data of mouse thymoctyes


title: T-5408

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_N20


title: zebrafish_989s_M9


title: T-5410

description: ftATAC-seq data of mouse thymoctyes


title: T-5407

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M6


title: zebrafish_989s_M5


title: T-5406

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M4


title: T-5405

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M2


title: zebrafish_989s_M3


title: T-5404

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M19


title: zebrafish_989s_M20


title: T-5256

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M23


title: zebrafish_989s_M24


title: zebrafish_989s_M17


title: zebrafish_989s_M22


title: T-5251

description: ftATAC-seq data of mouse thymoctyes


title: T-5248

description: ftATAC-seq data of mouse thymoctyes


title: T-5249

description: ftATAC-seq data of mouse thymoctyes


title: T-5255

description: ftATAC-seq data of mouse thymoctyes


title: T-5401

description: ftATAC-seq data of mouse thymoctyes


title: T-5403

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M15


title: T-5250

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M11


title: T-5402

description: ftATAC-seq data of mouse thymoctyes


title: T-5247

description: ftATAC-seq data of mouse thymoctyes


title: T-5254

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M18


title: T-5252

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M12


title: zebrafish_989s_M13


title: zebrafish_989s_M21


title: T-5245

description: ftATAC-seq data of mouse thymoctyes


title: T-5246

description: ftATAC-seq data of mouse thymoctyes


title: T-5244

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M10


title: T-5243

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_M1


title: zebrafish_989s_L9


title: zebrafish_989s_M16


title: T-5253

description: ftATAC-seq data of mouse thymoctyes


title: T-5241

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L4


title: zebrafish_989s_L3


title: zebrafish_989s_L7


title: T-5240

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L6


title: zebrafish_989s_L5


title: T-5236

description: ftATAC-seq data of mouse thymoctyes


title: T-5235

description: ftATAC-seq data of mouse thymoctyes


title: T-5234

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L24


title: T-5237

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L22


title: T-5242

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L20


title: zebrafish_989s_L2


title: T-5239

description: ftATAC-seq data of mouse thymoctyes


title: T-5230

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L18


title: T-5231

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L19


title: zebrafish_989s_L23


title: zebrafish_989s_L8


title: zebrafish_989s_L17


title: T-5228

description: ftATAC-seq data of mouse thymoctyes


title: T-5226

description: ftATAC-seq data of mouse thymoctyes


title: T-5238

description: ftATAC-seq data of mouse thymoctyes


title: T-5227

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L15


title: zebrafish_989s_L21


title: T-5222

description: ftATAC-seq data of mouse thymoctyes


title: T-5223

description: ftATAC-seq data of mouse thymoctyes


title: T-5224

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L12


title: zebrafish_989s_L13


title: T-5229

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L14


title: zebrafish_989s_L10


title: T-5232

description: ftATAC-seq data of mouse thymoctyes


title: T-5221

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L1


title: T-5220

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K9


title: zebrafish_989s_K7


title: zebrafish_989s_L16


title: zebrafish_989s_K8


title: T-5219

description: ftATAC-seq data of mouse thymoctyes


title: T-5218

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_L11


title: zebrafish_989s_K5


title: T-5215

description: ftATAC-seq data of mouse thymoctyes


title: T-5216

description: ftATAC-seq data of mouse thymoctyes


title: T-5212

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K23


title: T-5214

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K4


title: T-5213

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K21


title: zebrafish_989s_K3


title: zebrafish_989s_K24


title: zebrafish_989s_K22


title: T-5210

description: ftATAC-seq data of mouse thymoctyes


title: T-5209

description: ftATAC-seq data of mouse thymoctyes


title: T-5208

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K20


title: zebrafish_989s_K2


title: zebrafish_989s_K6


title: zebrafish_989s_K19


title: T-5233

description: ftATAC-seq data of mouse thymoctyes


title: T-5207

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K18


title: T-5205

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K17


title: T-5204

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K16


title: T-5211

description: ftATAC-seq data of mouse thymoctyes


title: T-5203

description: ftATAC-seq data of mouse thymoctyes


title: T-5202

description: ftATAC-seq data of mouse thymoctyes


title: T-5201

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K12


title: T-5198

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K11


title: zebrafish_989s_K10


title: T-5197

description: ftATAC-seq data of mouse thymoctyes


title: T-5217

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K1


title: zebrafish_989s_J9


title: T-5206

description: ftATAC-seq data of mouse thymoctyes


title: T-5195

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K15


title: T-5193

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J8


title: T-5194

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J7


title: zebrafish_989s_J6


title: T-5192

description: ftATAC-seq data of mouse thymoctyes


title: T-5190

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_K14


title: T-5200

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J4


title: zebrafish_989s_J3


title: zebrafish_989s_K13


title: T-5189

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J23


title: T-5188

description: ftATAC-seq data of mouse thymoctyes


title: T-5187

description: ftATAC-seq data of mouse thymoctyes


title: T-5186

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J21


title: T-5196

description: ftATAC-seq data of mouse thymoctyes


title: T-5185

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J20


title: zebrafish_989s_J2


title: zebrafish_989s_J5


title: T-5184

description: ftATAC-seq data of mouse thymoctyes


title: T-5183

description: ftATAC-seq data of mouse thymoctyes


title: T-5191

description: ftATAC-seq data of mouse thymoctyes


title: T-5181

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J19


title: T-5182

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J24


title: T-5179

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J18


title: zebrafish_989s_J16


title: zebrafish_989s_J15


title: zebrafish_989s_J22


title: T-5177

description: ftATAC-seq data of mouse thymoctyes


title: T-5178

description: ftATAC-seq data of mouse thymoctyes


title: T-5180

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J13


title: T-5176

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J14


title: zebrafish_989s_J11


title: zebrafish_989s_J17


title: zebrafish_989s_J12


title: T-5174

description: ftATAC-seq data of mouse thymoctyes


title: T-5173

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_J10


title: zebrafish_989s_J1


title: T-5172

description: ftATAC-seq data of mouse thymoctyes


title: T-5171

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I9


title: T-5170

description: ftATAC-seq data of mouse thymoctyes


title: T-5225

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I8


title: zebrafish_989s_I7


title: zebrafish_989s_I6


title: T-5169

description: ftATAC-seq data of mouse thymoctyes


title: T-5168

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I5


title: T-5167

description: ftATAC-seq data of mouse thymoctyes


title: T-5166

description: ftATAC-seq data of mouse thymoctyes


title: T-5165

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I4


title: zebrafish_989s_I24


title: T-5175

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I3


title: T-5164

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I21


title: zebrafish_989s_I20


title: T-5199

description: ftATAC-seq data of mouse thymoctyes


title: T-5163

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I2


title: zebrafish_989s_I19


title: T-5161

description: ftATAC-seq data of mouse thymoctyes


title: T-5160

description: ftATAC-seq data of mouse thymoctyes


title: T-5159

description: ftATAC-seq data of mouse thymoctyes


title: T-5158

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I18


title: zebrafish_989s_I17


title: T-5157

description: ftATAC-seq data of mouse thymoctyes


title: T-5155

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I15


title: T-5156

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I14


title: T-5154

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I22


title: zebrafish_989s_I12


title: T-5153

description: ftATAC-seq data of mouse thymoctyes


title: T-5152

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I11


title: zebrafish_989s_I13


title: zebrafish_989s_I10


title: T-5162

description: ftATAC-seq data of mouse thymoctyes


title: T-5151

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H9


title: T-5150

description: ftATAC-seq data of mouse thymoctyes


title: T-5149

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H8


title: T-5147

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H7


title: T-5148

description: ftATAC-seq data of mouse thymoctyes


title: T-5146

description: ftATAC-seq data of mouse thymoctyes


title: T-5145

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I16


title: zebrafish_989s_H5


title: T-5143

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H4


title: zebrafish_989s_H3


title: zebrafish_989s_H24


title: T-5141

description: ftATAC-seq data of mouse thymoctyes


title: T-5142

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_I1


title: T-5140

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H22


title: T-5139

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H23


title: zebrafish_989s_H20


title: zebrafish_989s_H21


title: zebrafish_989s_H2


title: T-5137

description: ftATAC-seq data of mouse thymoctyes


title: T-5138

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H19


title: T-5136

description: ftATAC-seq data of mouse thymoctyes


title: T-5135

description: ftATAC-seq data of mouse thymoctyes


title: T-5134

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H6


title: zebrafish_989s_H17


title: zebrafish_989s_H16


title: zebrafish_989s_H18


title: T-5133

description: ftATAC-seq data of mouse thymoctyes


title: T-5132

description: ftATAC-seq data of mouse thymoctyes


title: T-5144

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H15


title: T-5131

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H14


title: zebrafish_989s_H13


title: T-5130

description: ftATAC-seq data of mouse thymoctyes


title: T-5129

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H12


title: T-5127

description: ftATAC-seq data of mouse thymoctyes


title: T-5126

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H1


title: T-5125

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G9


title: T-5124

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G8


title: T-5123

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H10


title: T-5121

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G6


title: T-5122

description: ftATAC-seq data of mouse thymoctyes


title: T-5120

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G4


title: zebrafish_989s_G7


title: T-5118

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G24


title: T-5117

description: ftATAC-seq data of mouse thymoctyes


title: T-5116

description: ftATAC-seq data of mouse thymoctyes


title: T-5128

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_H11


title: zebrafish_989s_G22


title: T-5114

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G23


title: T-5115

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G20


title: zebrafish_989s_G21


title: T-5113

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G2


title: zebrafish_989s_G19


title: T-5111

description: ftATAC-seq data of mouse thymoctyes


title: T-5112

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G17


title: zebrafish_989s_G5


title: zebrafish_989s_G18


title: T-5109

description: ftATAC-seq data of mouse thymoctyes


title: T-5110

description: ftATAC-seq data of mouse thymoctyes


title: T-5119

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G3


title: T-5108

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G16


title: T-5107

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_G15


title: zebrafish_989s_G14


title: zebrafish_989s_G11


title: zebrafish_989s_G10


title: zebrafish_989s_G13


title: zebrafish_989s_G1


title: T-5106

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F9


title: zebrafish_989s_F8


title: T-5103

description: ftATAC-seq data of mouse thymoctyes


title: T-5104

description: ftATAC-seq data of mouse thymoctyes


title: T-5102

description: ftATAC-seq data of mouse thymoctyes


title: T-5105

description: ftATAC-seq data of mouse thymoctyes


title: T-5099

description: ftATAC-seq data of mouse thymoctyes


title: T-5100

description: ftATAC-seq data of mouse thymoctyes


title: T-5101

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F7


title: zebrafish_989s_F6


title: zebrafish_989s_F5


title: T-5098

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F4


title: zebrafish_989s_F3


title: T-5097

description: ftATAC-seq data of mouse thymoctyes


title: T-5095

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F24


title: T-5096

description: ftATAC-seq data of mouse thymoctyes


title: T-5094

description: ftATAC-seq data of mouse thymoctyes


title: T-5093

description: ftATAC-seq data of mouse thymoctyes


title: T-5092

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F21


title: zebrafish_989s_F23


title: zebrafish_989s_F22


title: T-5091

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F20


title: T-5090

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F2


title: zebrafish_989s_F19


title: T-5089

description: ftATAC-seq data of mouse thymoctyes


title: T-5088

description: ftATAC-seq data of mouse thymoctyes


title: T-5087

description: ftATAC-seq data of mouse thymoctyes


title: T-5086

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F16


title: zebrafish_989s_F15


title: zebrafish_989s_F18


title: T-5084

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F17


title: zebrafish_989s_F14


title: zebrafish_989s_F12


title: zebrafish_989s_F13


title: T-5085

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F11


title: T-5082

description: ftATAC-seq data of mouse thymoctyes


title: T-5080

description: ftATAC-seq data of mouse thymoctyes


title: T-5081

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_F10


title: zebrafish_989s_F1


title: T-5078

description: ftATAC-seq data of mouse thymoctyes


title: T-5079

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E9


title: zebrafish_989s_E8


title: T-5077

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E7


title: T-5076

description: ftATAC-seq data of mouse thymoctyes


title: T-5075

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E6


title: zebrafish_989s_E5


title: T-5083

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E4


title: zebrafish_989s_E3


title: zebrafish_989s_E24


title: T-5071

description: ftATAC-seq data of mouse thymoctyes


title: T-5073

description: ftATAC-seq data of mouse thymoctyes


title: T-5070

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E22


title: zebrafish_989s_E21


title: T-5069

description: ftATAC-seq data of mouse thymoctyes


title: T-5068

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E20


title: RNASeq_Ly49H_WT_D0_03

city: New York

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Mixed bone marrow chimera (WT - CD45.1 / KO - CD45.2)

data_processing:
BCL files were converted to fastq using bcl2fastq (v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.36).
Transcript quantification was performed by Salmon (v0.13.1) using arguments '-l IU --gcBias' and tximport (v1.10.1) using the UCSC mm10 known gene transcript assembly (v9).
DESeq2 (v1.22.2) was used to calculate differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts (1 count = 1 read pair) are provided in the rawCounts_byEntrezID.txt file as quantified by Salmon (v.13.1). Row names are Entrez IDs of the gene.

source_name: NK cells

extract_protocol:
Spleens were removed 2 days post MCMV infection, and Ly49H+ NK cells (TCRb- CD3e- NK1.1+ DX5+ Ly49H+) were sorted. Each sample represents an individual mouse. RNA was isolated using PicoPure RNA Isolation Kit (Cat# KIT0204 - Thermo Fisher) according to manufacturer's protocol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2ng total RNA with RNA integrity numbers ranging from 9.4 to 10 underwent amplification using SMART-seq V4 Ultra Low Input RNA kit (Clonetech Cat# 63488), with 12 cycles of PCR. Subsequently, 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries using KAPA Hyper Prep DNA library preparation kit (KAPA Biosystems KK8504) using 8 cycles of PCR.

treatment_protocol: In vivo MCMV infection

tag: mouse strain

value: Spleen

tag: days post infection

value: Day 2

tag: genotype/variation

value: wild-type or LDHA-deficient

tag: cell type

value: Natural Killer (NK) cells


title: RNASeq_Ly49H_WT_D2_01


title: RNASeq_Ly49H_WT_D0_02


title: RNASeq_Ly49H_KO_D2_03

value: LDHA-deficient


title: RNASeq_Ly49H_KO_D2_02


title: RNASeq_Ly49H_WT_D2_02


title: RNASeq_Ly49H_WT_D2_03


title: RNASeq_Ly49H_KO_D2_01


title: T-5074

description: ftATAC-seq data of mouse thymoctyes


title: RNASeq_Ly49H_KO_D0_03


title: zebrafish_989s_E19


title: T-5065

description: ftATAC-seq data of mouse thymoctyes


title: RNASeq_Ly49H_KO_D0_01


title: T-5072

description: ftATAC-seq data of mouse thymoctyes


title: T-5063

description: ftATAC-seq data of mouse thymoctyes


title: T-5064

description: ftATAC-seq data of mouse thymoctyes


title: T-5067

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E16


title: RNASeq_Ly49H_KO_D0_02


title: T-5062

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E2


title: T-5066

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E18


title: T-5061

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E13


title: zebrafish_989s_E17


title: zebrafish_989s_E14


title: zebrafish_989s_E12


title: T-5059

description: ftATAC-seq data of mouse thymoctyes


title: T-5058

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_E10


title: zebrafish_989s_E1


title: T-5057

description: ftATAC-seq data of mouse thymoctyes


title: T-5060

description: ftATAC-seq data of mouse thymoctyes


title: Liver Abhd15 KO, replicate 5

type: RNA

city: Graz

first: Juliane

last: Bogner-Strauss

address: Petersgasse 10-12/II

country: Austria

institute: Institute of Biochemistry, Graz University of Technology

description:
LIV_KO_5
Liver Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.1 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray Average) quantile normalization and signal extraction using R package oligo

label: Biotin

source_name: Liver Abhd15 KO

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Nr. 4211511, Affymetrix, Santa Clara, CA)  and GeneChip® WT Terminal Labeling  (Nr. 4214400, Affymetrix, Santa Clara, CA)

growth_protocol: WT and Abhd KO mice were placed for up to 14 weeks NC diet.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Described above (growth protocol)

tag: strain background

value: Abhd15 KO

tag: gender

value: male

tag: diet

value: Normal chow (NC)

value: Liver


title: Liver Abhd15 KO, replicate 3

description:
LIV_KO_3
Liver Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: Liver WT, replicate 3

description:
LIV_WT_3
Liver Gene expression data from a WT mouse placed for up to 14 weeks on NC

source_name: Liver WT

value: Wild Type (WT)


title: Liver Abhd15 KO, replicate 1

description:
LIV_KO_1
Liver Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: Liver Abhd15 KO, replicate 2

description:
LIV_KO_2
Liver Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: HC PBS rep3

city: Beijing

first: Ting

last: Xin

address: No.2 Yuanmingyuan West Road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description: gene_exp_HC PPD-B vs. HC PBS

data_processing:
For the sake of obtaining high-quality clean reads, the adapter sequence and low-quality sequences were trimmed in accordance with the following filtration criteria:(1) filter out the adapter sequence;(2) filter out the reads with more than 3% unknown bases;(3) filter out the reads with more than 50% low quality (Q< 3) bases.
All clean reads were mapped to the Bos taurus reference genome (UMD3.1.73) using TopHat2 software from Kim et al., . Genome Biol., 2013.
Genome_build: UMD3.1.73

organism: Bos taurus

source_name: peripheral blood mononuclear cell

extract_protocol:
About 50 ml of whole blood with anticoagulant (heparin) was collected aseptically from each animal. PBMCs were isolated using bovine lymphocyte-separation medium (Solarbio, China) by density-gradient centrifugation, per the manufacturer’s instructions. Red blood cells (RBC) were removed by RBC lysis, the cells were washed by PBS for three times. And then cells from each animal were counted and seeded into 12-well tissue culture plates at 5×106 cells/ml OpTmizer™ T-Cell Expansion SFM (Gibico) containing 1% L-Glutamine (Gibco) and 1% penicillin-streptomycin (Sigma-Aldrich, Ltd.). Subsequently, the PBMCs were stimulated with 300 IU PPD-B (3000 IU/mL, Prionics AG, Schlieren, Switzerland); unstimulated PBMCs (PBS-treated) from the same cattle were run as a negative control. Subsequently, PBMCs were incubated at 37℃ with 5% CO2, harvested for treatment 6 h post-stimulation. Total RNA was extracted using the TRIzol reagent.  TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peripheral blood mononuclear cell

tag: stimulus

value: PBS

tag: stages of btb progression

value: Healthy control


title: HC PBS rep2

description: gene_exp_bTB PCR-P PBS vs. HC PBS


title: Liver WT, replicate 1

description:
LIV_WT_1
Liver Gene expression data from a WT mouse placed for up to 14 weeks on NC


title: zebrafish_989s_E11


title: BAT Abhd15 KO, replicate 4

description:
BAT_KO_4
BAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC

source_name: BAT Abhd15 KO

value: Brown adipose tissue (BAT)


title: T-5056

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes

value: 6-8 weeks


title: BAT Abhd15 KO, replicate 3

description:
BAT_KO_3
BAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: HC PBS rep1


title: Liver Abhd15 KO, replicate 4

description:
LIV_KO_4
Liver Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: BAT Abhd15 KO, replicate 1

description:
BAT_KO_1
BAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: Liver WT, replicate 2

description:
LIV_WT_2
Liver Gene expression data from a WT mouse placed for up to 14 weeks on NC


title: BAT Abhd15 KO, replicate 5

description:
BAT_KO_5
BAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: BAT WT, replicate 1

description:
BAT_WT_1
BAT Gene expression data from a WT mouse placed for up to 14 weeks on NC

source_name: BAT WT


title: T-5055

description: ftATAC-seq data of mouse thymoctyes


title: HC PPD-B rep3

value: PPD-B


title: BAT WT, replicate 2

description:
BAT_WT_2
BAT Gene expression data from a WT mouse placed for up to 14 weeks on NC


title: zebrafish_989s_D9

value: embryo trunk

value: vegfc:Gal4FF;UASGFP; kdrl:mCherry

value: 48 hpf


title: zebrafish_989s_D8


title: BAT Abhd15 KO, replicate 2

description:
BAT_KO_2
BAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: T-5054

description: ftATAC-seq data of mouse thymoctyes


title: HC PPD-B rep2


title: HC PPD-B rep1


title: BAT WT, replicate 3

description:
BAT_WT_3
BAT Gene expression data from a WT mouse placed for up to 14 weeks on NC


title: bTB PCR-N PBS rep3

description: gene_exp_bTB PCR-N PBS vs. HC PBS

value: bTB PCR-N


title: T-5053

description: ftATAC-seq data of mouse thymoctyes


title: bTB PCR-N PPD-B rep3


title: zebrafish_989s_D5


title: zebrafish_989s_D4


title: bTB PCR-P PBS rep2

value: bTB PCR-P M. bovis shedding


title: bTB PCR-P PBS rep3


title: bTB PCR-N PPD-B rep2

description: gene_exp_bTB PCR-N PPD-B vs. bTB PCR-N PBS


title: T-5052

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D3


title: bTB PCR-N PPD-B rep1

description: gene_exp_bTB PCR-N PPD-B vs. HC PPD-B


title: T-5049

description: ftATAC-seq data of mouse thymoctyes


title: bTB PCR-P PBS rep1


title: zebrafish_989s_D24


title: bTB PCR-P PPD-B rep3

description: gene_exp_bTB PCR-P PPD-B vs. bTB PCR-P PBS


title: zebrafish_989s_D23


title: bTB PCR-P PPD-B rep2

description: gene_exp_bTB PCR-P PPD-B vs bTB PCR-N PPD-B


title: T-5048

description: ftATAC-seq data of mouse thymoctyes


title: Sample 96_NADcaptureSeq_Large_Fragmented_npy1Δ_N_rep3

city: Heidelberg

first: Yaqing

last: Zhang

state: baden württemberg

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nN_LF_rep3
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nN_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt

data_processing:
Illumina NextSeq basecalling.
NAD captureSeq Analysis: Standard Unfragmented NADcaptureSeq Analysis: Original reads were demultiplexed by the barcode without mismatch and quality controlled. Further 5’ end leading (G/N)n and 3’ end adapter (C NNNNNN AGATCG) were trimmed (minimum length 12 nt). Reads mapped to spiked-in internal standard (IS) RNAI sequence (bowtie -v 2, version 1.1.2) were counted. IS unmapped reads were classified as small RNA reads (12-17 nt) or normal RNA reads (>18nt). Normal RNA reads were mapped to the reference genome S. cerevisae BY4742 strain (BY4742_Toronto_2012, SGD) (bowtie -v 2). Reads mapped to either rRNAs or tRNAs were separated and counted individually. Remaining reads that cannot map to rRNAs were remapped to the reference genome (bowtie –best --strata -M 1 -m 20 -v 2). Sam files were converted to bam files then sorted (samtools, version 0.1.13). Bam files were used to generate wig file which normalized by RPM for single nucleotide polymorphism analysis. Sorted sam files were further filtered by strand-specific selection. the filter-passed reads also be counted (htseq-count -m intersection-nonempty, version 0.6.0) based on annotation gff3 file (BY4742_Toronto_2012, SGD, mRNA regions were annotated by their 5’ UTR region (-120 to +65, translation starting site (TLS) referred as ‘0’). Raw hits were analyzed by DESeq2 (version 1.4.5, relevant package from Bioconductor version 2.14) for NAD-RNA enrichment statistics.
Transcriptome Analysis: Raw reads were demultiplexed and quality controlled with same parameter as previous analysis. Reads with 5’-/3’- end adapters were properly trimmed then the raw sequences were reverse complemented. Mapped reads to the reference genome (bowtie, -v 2). For rRNAs and tRNAs independent mapping and counting as well as rRNAs-free reads counting (same annotation region on 5’ UTR of mRNA) was same as performing NAD captureSeq analysis. Same procedure to generate wig file and to differential expression statistics.
Genome_build: BY4742 Saccharomyces cerevisiae
Supplementary_files_format_and_content: tab-delimited text files include 1) the raw counts of RNA species("rawHits" label) and DESeq2 statistics for their normalized enrichment ("Stat" label)for both NAD captureSeq (UF, SF, LF) and Transcriptome (SC). WIG files were generated without rRNA reads and in standard format.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured with the standard condition, YPD medium, 30 degree, shaking. Cell pellets were harvest when OD590 was ~0.8.

extract_protocol:
Total RNAs from yeast BY4742 strains were isolated by hot phenol method (Collart and Oliviero, 2001) with minor change. Harvested cells (OD590 0.8) from 0.5 L YPD. Fast frozen by liquid nitrogen, stored at -80 °C until all samples ready. Cell pellets were defreezed on ice and washed with dH2O. Resuspend cell pellets in 8 mL TES solution (10mM Tris-HCl (pH 7.5), 10 mM EDTA, 0.5% SDS) and added 8 mL phenol (Carl ROTH). Vortexed thoroughly 1 min and incubated 60 min at 65 °C with occasional shaking (50 seconds/10 min, 550 rpm). Place on ice 15-20 min. Centrifugation with 14,000 g at 4 °C. Followed by phenol extraction, P/C/I purification, and chloroform purification. RNA was precipitated with 0.1 volume 3 M NaOAc (pH 5.5) and 2.5 volume ethanol at -20 °C overnight. Precipitated RNA was solved in 2 mL dH2O. Measured its concentration and determined the integrity by 1.2% formaldehyde denature agarose gel electrophoresis. Treated 1 mg RNA with 100U DNase I (Roche) in 1X DNase I buffer (Roche) at 37 °C, 40 min. Twice P/C/I purification. RNA was precipitated by ethanol at -20 °C overnight. Solve in 100 µL dH2O. Measured the RNA concentration and check its integrity as well as genome DNA (gDNA) residue by 1.2% formaldehyde denature agarose gel electrophoresis.
Standard unfragmented NAD captureSeq (UF): gDNA-free total RNA applied NAD-RNA capture protocol (Winz et al., 2017) with minor modification as followed. Biological triplicates of total RNA. 100 µg total RNA was treated with adenosine diphosphate-ribosylcyclase (ADPRC, self-prepared, 22.5 U), 10 µL 4-pentyn-1-ol (Sigma-Aldrich), 5 ng NAD-RNAI (self-prepared, spiked-in control, optional) in 100 µL reaction including 50 mM Na-HEPES (pH 7.0), 5 mM MgCl2 at 37 °C, 60 min. The reaction minus ADPRC was utilized as background (negative control). The reaction stopped by adding 100 µL dH2O and 200 µL P/C/I reagent. Performed twice P/C/I extraction with additional three times ether (Honeywell) extraction afterwards. Followed by copper-click reaction, streptavidin beads binding, preadenylated-3’-adaptor ligation, reverse transcription, CTP tailing, anchored-5’-adapotr ligation, cDNA PCR amplification with barcode are same as standard capture protocol. Quality control of libraries by sanger sequencing of spike-in RNAI amplicon as well as other cDNA amplicons which were amplified by adaptor-ligated sequence on cDNA library then cloned into plasmid(s). Size-selected PCR products within the range of 150-300 bp were purified by 10% native polyacrylamide gel eletrophoresis. Cleanness of primer-dimer was examined by Bioanalyzer 2100 (Agilent) using Agilent High Sensitivity DNA Kit. Concentration was measured by Qubit. Multiplexed primer-dimer-free library at final concentration ~20 nM accordingly. Based on to the size distribution of cDNA, either adding of 20% v3 Phix Control (Illumina) or using customer Illumina sequencing primer which has 3Gs at the end of standard Illumina sequencing primer to mitigate unbalance library before NextSeq 500/550 75bp SE sequencing. Fragmented NAD captureSeq: Biological triplicates of total RNA (gDNA-free). 100 µg total RNA with 5 ng NAD-RNAI (spiked-in control, optional) randomly sheared in 65 µL reaction containing 0.5 volume of alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH 9.3) at 94 °C (5 min for wild type strain, 20 min for npy1Δ strain). Checked the sheared fragments on 1.2% formaldehyde denature agarose gel. Additional add 200 µL dH2O and precipitate properly sheared RNA with 2.5 volume ethanol, 0.1 volume 3 M NaOAc (pH 5.5), 1 µL glycogen at -20 °C overnight. Precipitated RNA washed by 75% ethanol and solve in dH2O. Followed by treating each 100 µg RNA with 100 U T4 PNK (Thermo Scientific), along with 0.1 mM ATP, 100 mM imidazole-HCl (pH 6.0), 10 mM MgCl2, 10 mM β-mercaptoethanol, 10 µg BSA (Thermo Scientific) in a total volume 200 µL, 37 °C, 5.5 h. Twice P/C/I purification and triple ether extraction followed by ethanol precipitation. Precipitated RNA washed by 75% ethanol and solve in dH2O as library input for performing standard NAD captureSeq. Size-selected PCR products with the range of 150-300 bp (small fragmented NAD captureSeq library, SF) and 300-500 bp (large fragmented NAD captureSeq library, LF) were purified from 10% native polyacrylamide gel. Bioanalyzer quality control, library multiplex and sequence strategy are same as unfragmented NAD captureSeq. Sequenced by NextSeq 500/550 75bp SE.Transcriptome libraries: Biological triplicates of total RNA (gRNA-free). 1 µg total RNA was performed ribosome RNA deletion by Ribo-Zero rRNA Removal Kit (yeast, Illumina). rRNA-depleted RNAs were randomly sheared at 94 °C 10 min. Fragmented RNAs were processed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Barcoded PCR-amplified cDNA by NEBNext Multiplex Oligo for Illumina (NEB). Further cDNA size-selection in the range of 300-500 bp was performed by Agencourt RNAClean XP (Beckman Coulter). Samples were checked by Bioanalyzer and measured by Qubit. Multiplexed library was sequenced by NextSeq 500/550 75bp SE.

treatment_protocol: "S" for ADPRC full-treated while "N" for ADPRC minus control. "UF" represents unfragmented total RNA for library input, while "SF" and "LF" for small fragmented RNA library and large fragmented RNA library, respectivily. Details could be find in library construction protocol.

value: BY4742 npy1::kanMX4

tag: growth phase

value: Log phase


title: T-5047

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D7


title: zebrafish_989s_D6


title: bTB PCR-N PBS rep2

description: gene_exp_bTB PCR-N PBS vs. bTB PCR-P PBS


title: Sample 95_NADcaptureSeq_Large_Fragmented_npy1Δ_N_rep2

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nN_LF_rep2
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nN_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt


title: zebrafish_989s_D22


title: bTB PCR-N PBS rep1


title: Sample 94_NADcaptureSeq_Large_Fragmented_npy1Δ_N_rep1

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nN_LF_rep1
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nN_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt


title: T-5046

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D21


title: zebrafish_989s_D20


title: Sample 89_NADcaptureSeq_Large_Fragmented_WT_N_rep2

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtN_LF_rep2
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtN_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt

value: Mat{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0


title: Sample 91_NADcaptureSeq_Large_Fragmented_npy1Δ_S_rep1

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nS_LF_rep1
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nS_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt


title: T-5045

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D18


title: T-5050

description: ftATAC-seq data of mouse thymoctyes


title: Sample 93_NADcaptureSeq_Large_Fragmented_npy1Δ_S_rep3

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nS_LF_rep3
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nS_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt


title: Sample 88_NADcaptureSeq_Large_Fragmented_WT_N_rep1

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtN_LF_rep1
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtN_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt


title: T-5042

description: ftATAC-seq data of mouse thymoctyes


title: Sample 86_NADcaptureSeq_Large_Fragmented_WT_S_rep2

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtS_LF_rep2
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtS_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt


title: zebrafish_989s_D19


title: Sample 87_NADcaptureSeq_Large_Fragmented_WT_S_rep3

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtS_LF_rep3
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtS_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt


title: Sample 85_NADcaptureSeq_Large_Fragmented_WT_S_rep1

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtS_LF_rep1
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtS_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt


title: zebrafish_989s_D17


title: T-5051

description: ftATAC-seq data of mouse thymoctyes


title: T-5041

description: ftATAC-seq data of mouse thymoctyes


title: Sample 83_NADcaptureSeq_Small_Fragmented_npy1Δ_N_rep2

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nN_SF_rep2
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nN_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: zebrafish_989s_D16


title: Sample 92_NADcaptureSeq_Large_Fragmented_npy1Δ_S_rep2

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_nS_LF_rep2
File 'rawHits_n_LF.txt' generated based on the multiple samples #91-96
File 'Stat_n_LF_5UTRv.txt' generated based on the multiple samples #91-96
File 'nS_LF_merge_genome.wig' generated based on the multiple samples #91-96
processed data file:
rawHits_n_LF.txt
Stat_n_LF_5UTRv.txt


title: T-5040

description: ftATAC-seq data of mouse thymoctyes


title: T-5044

description: ftATAC-seq data of mouse thymoctyes


title: Sample 82_NADcaptureSeq_Small_Fragmented_npy1Δ_N_rep1

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nN_SF_rep1
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nN_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: zebrafish_989s_D15


title: T-5039

description: ftATAC-seq data of mouse thymoctyes


title: Sample 79_NADcaptureSeq_Small_Fragmented_npy1Δ_S_rep1

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nS_SF_rep1
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nS_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: Sample 80_NADcaptureSeq_Small_Fragmented_npy1Δ_S_rep2

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nS_SF_rep2
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nS_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: bTB PCR-P PPD-B rep1

description: gene_exp_bTB PCR-P PPD-B vs. HC PPD-B


title: Sample 84_NADcaptureSeq_Small_Fragmented_npy1Δ_N_rep3

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nN_SF_rep3
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nN_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: Sample 90_NADcaptureSeq_Large_Fragmented_WT_N_rep3

description:
HHT5LBGXY_YZ_Jul07_16s005393-1-1_wtN_LF_rep3
File 'rawHits_wt_LF.txt' generated based on the multiple samples #85-90
File 'Stat_wt_LF_5UTRv.txt' generated based on the multiple samples #85-90
File 'wtN_LF_merge_genome.wig' generated based on the multiple samples #85-90
processed data file:
rawHits_wt_LF.txt
Stat_wt_LF_5UTRv.txt


title: Sample 81_NADcaptureSeq_Small_Fragmented_npy1Δ_S_rep3

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_nS_SF_rep3
File 'rawHits_n_SF.txt' generated based on the multiple samples #79-84
File 'Stat_n_SF_5UTRv.txt' generated based on the multiple samples #79-84
File 'nS_SF_merge_genome.wig' generated based on the multiple samples #79-84
processed data file:
rawHits_n_SF.txt
Stat_n_SF_5UTRv.txt


title: T-5043

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D14


title: Sample 78_NADcaptureSeq_Small_Fragmented_WT_N_rep3

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtN_SF_rep3
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtN_SF_merge_genome.wig' generated based on the multiple samples #73-78
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: T-5038

description: ftATAC-seq data of mouse thymoctyes


title: T-5037

description: ftATAC-seq data of mouse thymoctyes


title: Sample 77_NADcaptureSeq_Small_Fragmented_WT_N_rep2

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtN_SF_rep2
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtN_SF_merge_genome.wig' generated based on the multiple samples #73-78
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: zebrafish_989s_D13


title: zebrafish_989s_D12


title: Sample 74_NADcaptureSeq_Small_Fragmented_WT_S_rep2

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtS_SF_rep2
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtS_SF_merge_genome.wig' generated based on the multiple samples #73-78
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: Sample 76_NADcaptureSeq_Small_Fragmented_WT_N_rep1

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtN_SF_rep1
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtN_SF_merge_genome.wig' generated based on the multiple samples #73-78
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: Sample 75_NADcaptureSeq_Small_Fragmented_WT_S_rep3

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtS_SF_rep3
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtS_SF_merge_genome.wig' generated based on the multiple samples #73-78
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: T-5036

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_D11


title: T-5035

description: ftATAC-seq data of mouse thymoctyes


title: Sample 72_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_N_rep3

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnN_UF_rep3
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnN_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt

value: BY4742 dxo1::natNT2 npy1::kanMX4 rai1::hphNT1


title: Sample 70_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_N_rep1

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnN_UF_rep1
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnN_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt


title: zebrafish_989s_D10


title: T-5034

description: ftATAC-seq data of mouse thymoctyes


title: Sample 71_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_N_rep2

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnN_UF_rep2
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnN_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt


title: T-5033

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C9


title: Sample 68_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_S_rep2

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnS_UF_rep2
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnS_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt


title: Sample 69_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_S_rep3

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnS_UF_rep3
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnS_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt


title: zebrafish_989s_C8


title: T-5031

description: ftATAC-seq data of mouse thymoctyes


title: T-5032

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C7


title: Sample 66_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_N_rep3

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnN_UF_rep3
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnN_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt

value: BY4742 npy1::kanMX4 rai1::hphNT1


title: Sample 64_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_N_rep1

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnN_UF_rep1
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnN_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt


title: Sample 63_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_S_rep3

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnS_UF_rep3
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnS_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt


title: Sample 67_NADcaptureSeq_Unfragmented_dxo1Δrai1Δnpy1Δ_S_rep1

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drnS_UF_rep1
File 'rawHits_drn_UF.txt' generated based on the multiple samples #67-72
File 'Stat_drn_UF_5UTRv.txt' generated based on the multiple samples #67-72
File 'drnS_UF_merge_genome.wig' generated based on the multiple samples #67-72
processed data file:
rawHits_drn_UF.txt
Stat_drn_UF_5UTRv.txt


title: Sample 65_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_N_rep2

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnN_UF_rep2
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnN_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt


title: T-5030

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C5


title: T-5029

description: ftATAC-seq data of mouse thymoctyes


title: Sample 73_NADcaptureSeq_Small_Fragmented_WT_S_rep1

description:
HW7GJBGXX_YZ_Mar16_16s001945-1-1_wtS_SF_rep1
File 'rawHits_wt_SF.txt' generated based on the multiple samples #73-78
File 'Stat_wt_SF_5UTRv.txt' generated based on the multiple samples #73-78
File 'wtS_SF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_SF.txt
Stat_wt_SF_5UTRv.txt


title: Sample 59_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_N_rep2

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drN_UF_rep2
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drN_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt

value: BY4742 dxo1::natNT2 rai1::hphNT1


title: Sample 61_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_S_rep1

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnS_UF_rep1
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnS_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt


title: Sample 60_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_N_rep3

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drN_UF_rep3
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drN_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt


title: Sample 58_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_N_rep1

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drN_UF_rep1
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drN_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt


title: T-5028

description: ftATAC-seq data of mouse thymoctyes


title: Sample 57_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_S_rep3

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drS_UF_rep3
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drS_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt


title: zebrafish_989s_C3


title: zebrafish_989s_D1


title: Sample 56_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_S_rep2

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drS_UF_rep2
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drS_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt


title: Sample 55_NADcaptureSeq_Unfragmented_dxo1Δrai1Δ_S_rep1

description:
H37WHBGX9_YZ_Oct15_18s005481-1_drS_UF_rep1
File 'rawHits_dr_UF.txt' generated based on the multiple samples #55-60
File 'Stat_dr_UF_5UTRv.txt' generated based on the multiple samples #55-60
File 'drS_UF_merge_genome.wig' generated based on the multiple samples #55-60
processed data file:
rawHits_dr_UF.txt
Stat_dr_UF_5UTRv.txt


title: T-5027

description: ftATAC-seq data of mouse thymoctyes


title: Sample 54_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_N_rep3

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnN_UF_rep3
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnN_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt

value: BY4742 dxo1::natNT2 npy1::kanMX4


title: T-5026

description: ftATAC-seq data of mouse thymoctyes


title: Sample 62_NADcaptureSeq_Unfragmented_rai1Δnpy1Δ_S_rep2

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rnS_UF_rep2
File 'rawHits_rn_UF.txt' generated based on the multiple samples #61-66
File 'Stat_rn_UF_5UTRv.txt' generated based on the multiple samples #61-66
File 'rnS_UF_merge_genome.wig' generated based on the multiple samples #61-66
processed data file:
rawHits_rn_UF.txt
Stat_rn_UF_5UTRv.txt


title: zebrafish_989s_C23


title: zebrafish_989s_C24


title: T-5025

description: ftATAC-seq data of mouse thymoctyes


title: Sample 53_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_N_rep2

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnN_UF_rep2
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnN_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt


title: zebrafish_989s_C22


title: T-5024

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C21


title: Sample 52_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_N_rep1

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnN_UF_rep1
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnN_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt


title: zebrafish_989s_C6


title: Sample 51_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_S_rep3

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnS_UF_rep3
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnS_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt


title: T-5023

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C20


title: T-5022

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C2


title: Sample 50_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_S_rep2

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnS_UF_rep2
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnS_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt


title: Sample 46_NADcaptureSeq_Unfragmented_rai1Δ_N_rep1

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rN_UF_rep1
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rN_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt

value: BY4742 rai1::hphNT1


title: Sample 49_NADcaptureSeq_Unfragmented_dxo1Δnpy1Δ_S_rep1

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dnS_UF_rep1
File 'rawHits_dn_UF.txt' generated based on the multiple samples #49-54
File 'Stat_dn_UF_5UTRv.txt' generated based on the multiple samples #49-54
File 'dnS_UF_merge_genome.wig' generated based on the multiple samples #49-54
processed data file:
rawHits_dn_UF.txt
Stat_dn_UF_5UTRv.txt


title: Sample 48_NADcaptureSeq_Unfragmented_rai1Δ_N_rep3

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rN_UF_rep3
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rN_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt


title: Sample 44_NADcaptureSeq_Unfragmented_rai1Δ_S_rep2

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rS_UF_rep2
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rS_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt


title: Sample 43_NADcaptureSeq_Unfragmented_rai1Δ_S_rep1

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rS_UF_rep1
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rS_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt


title: T-5020

description: ftATAC-seq data of mouse thymoctyes


title: Sample 42_NADcaptureSeq_Unfragmented_dxo1Δ_N_rep3

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dN_UF_rep3
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dN_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt

value: BY4742 dxo1::natNT2


title: zebrafish_989s_C19


title: Sample 41_NADcaptureSeq_Unfragmented_dxo1Δ_N_rep2

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dN_UF_rep2
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dN_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt


title: T-5021

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: zebrafish_989s_C18


title: Sample 40_NADcaptureSeq_Unfragmented_dxo1Δ_N_rep1

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dN_UF_rep1
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dN_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt


title: T-5019

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: T-5018

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C17


title: Sample 39_NADcaptureSeq_Unfragmented_dxo1Δ_S_rep3

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dS_UF_rep3
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dS_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt


title: Sample 38_NADcaptureSeq_Unfragmented_dxo1Δ_S_rep2

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dS_UF_rep2
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dS_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt


title: zebrafish_989s_C16


title: Sample 47_NADcaptureSeq_Unfragmented_rai1Δ_N_rep2

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rN_UF_rep2
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rN_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt


title: Sample 37_NADcaptureSeq_Unfragmented_dxo1Δ_S_rep1

description:
HWVVVBGX7_YZ_Oct15_18s005859-1-1_dS_UF_rep1
File 'rawHits_d_UF.txt' generated based on the multiple samples #37-42
File 'Stat_d_UF_5UTRv.txt' generated based on the multiple samples #37-42
File 'dS_UF_merge_genome.wig' generated based on the multiple samples #37-42
processed data file:
rawHits_d_UF.txt
Stat_d_UF_5UTRv.txt


title: T-5017

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C14


title: Sample 35_NADcaptureSeq_Unfragmented_npy1Δ_N_rep2

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nN_UF_rep2
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nN_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: Sample 36_NADcaptureSeq_Unfragmented_npy1Δ_N_rep3

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nN_UF_rep3
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nN_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: Sample 45_NADcaptureSeq_Unfragmented_rai1Δ_S_rep3

description:
H2YT2BGX9_YZ_Oct15_18s005479-1-1_rS_UF_rep3
File 'rawHits_r_UF.txt' generated based on the multiple samples #43-48
File 'Stat_r_UF_5UTRv.txt' generated based on the multiple samples #43-48
File 'rS_UF_merge_genome.wig' generated based on the multiple samples #43-48
processed data file:
rawHits_r_UF.txt
Stat_r_UF_5UTRv.txt


title: T-5016

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C13


title: Sample 33_NADcaptureSeq_Unfragmented_npy1Δ_S_rep3

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nS_UF_rep3
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nS_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: T-5015

description: ftATAC-seq data of mouse thymoctyes


title: Sample 32_NADcaptureSeq_Unfragmented_npy1Δ_S_rep2

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nS_UF_rep2
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nS_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: T-5014

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_C11


title: Sample 28_NADcaptureSeq_Unfragmented_WT_N_rep1

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtN_UF_rep1
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtN_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: T-5013

description: ftATAC-seq data of mouse thymoctyes


title: Sample 27_NADcaptureSeq_Unfragmented_WT_S_rep3

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtS_UF_rep3
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtS_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: zebrafish_989s_C10


title: Sample 29_NADcaptureSeq_Unfragmented_WT_N_rep2

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtN_UF_rep2
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtN_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: Sample 26_NADcaptureSeq_Unfragmented_WT_S_rep2

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtS_UF_rep2
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtS_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: Sample 30_NADcaptureSeq_Unfragmented_WT_N_rep3

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtN_UF_rep3
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtN_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: T-5012

description: ftATAC-seq data of mouse thymoctyes


title: Sample 25_NADcaptureSeq_Unfragmented_WT_S_rep1

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_wtS_UF_rep1
File 'rawHits_wt_UF.txt' generated based on the multiple samples #25-30
File 'Stat_wt_UF_5UTRv.txt' generated based on the multiple samples #25-30
File 'wtS_UF_merge_genome.wig' generated based on the multiple samples #25-30
processed data file:
rawHits_wt_UF.txt
Stat_wt_UF_5UTRv.txt


title: zebrafish_989s_C1


title: T-5011

description: ftATAC-seq data of mouse thymoctyes


title: Sample 34_NADcaptureSeq_Unfragmented_npy1Δ_N_rep1

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nN_UF_rep1
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nN_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: zebrafish_989s_C12


title: T-5010

description: ftATAC-seq data of mouse thymoctyes


title: Sample 24_Transcriptome_dxo1Δrai1Δnpy1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_drn_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drnVSdn_5UTRv.txt' generated based on the multiple samples #13-15 and samples #22-24
File 'Stat_Transcriptome_drnVSdr_5UTRv.txt' generated based on the multiple samples #16-18 and samples #22-24
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_drn_merge_genome.wig' generated based on the multiple samples #22-24
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drnVSdn_5UTRv.txt
Stat_Transcriptome_drnVSdr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: T-5009

description: ftATAC-seq data of mouse thymoctyes


title: Sample 22_Transcriptome_dxo1Δrai1Δnpy1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_drn_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drnVSdn_5UTRv.txt' generated based on the multiple samples #13-15 and samples #22-24
File 'Stat_Transcriptome_drnVSdr_5UTRv.txt' generated based on the multiple samples #16-18 and samples #22-24
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_drn_merge_genome.wig' generated based on the multiple samples #22-24
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drnVSdn_5UTRv.txt
Stat_Transcriptome_drnVSdr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: Sample 21_Transcriptome_rai1Δnpy1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_rn_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_rn_merge_genome.wig' generated based on the multiple samples #19-21
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rnVSn_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: zebrafish_989s_B9


title: Sample 20_Transcriptome_rai1Δnpy1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_rn_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_rn_merge_genome.wig' generated based on the multiple samples #19-21
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rnVSn_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: zebrafish_989s_B7


title: T-5008

description: ftATAC-seq data of mouse thymoctyes


title: Sample 19_Transcriptome_rai1Δnpy1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_rn_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_rn_merge_genome.wig' generated based on the multiple samples #19-21
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rnVSn_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: Sample 18_Transcriptome_dxo1Δrai1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dr_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-20
File 'SC_dr_merge_genome.wig' generated based on the multiple samples #16-18
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drVSd_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt


title: Sample 17_Transcriptome_dxo1Δrai1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dr_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-19
File 'SC_dr_merge_genome.wig' generated based on the multiple samples #16-18
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drVSd_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt


title: zebrafish_989s_B6


title: Sample 31_NADcaptureSeq_Unfragmented_npy1Δ_S_rep1

description:
H37WLBGXY_YZ_Jul21_16s005391-1-1_nS_UF_rep1
File 'rawHits_n_UF.txt' generated based on the multiple samples #31-36
File 'Stat_n_UF_5UTRv.txt' generated based on the multiple samples #31-36
File 'nS_UF_merge_genome.wig' generated based on the multiple samples #31-36
processed data file:
rawHits_n_UF.txt
Stat_n_UF_5UTRv.txt


title: zebrafish_989s_B8


title: Sample 16_Transcriptome_dxo1Δrai1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dr_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-18
File 'SC_dr_merge_genome.wig' generated based on the multiple samples #16-18
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drVSd_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt


title: T-5007

description: ftATAC-seq data of mouse thymoctyes


title: Sample 15_Transcriptome_dxo1Δnpy1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dn_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'SC_dn_merge_genome.wig' generated based on the multiple samples #13-15
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt


title: zebrafish_989s_B5


title: Sample 14_Transcriptome_dxo1Δnpy1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dn_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'SC_dn_merge_genome.wig' generated based on the multiple samples #13-15
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt


title: T-5006

description: ftATAC-seq data of mouse thymoctyes


title: Sample 23_Transcriptome_dxo1Δrai1Δnpy1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_drn_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_drnVSdn_5UTRv.txt' generated based on the multiple samples #13-15 and samples #22-24
File 'Stat_Transcriptome_drnVSdr_5UTRv.txt' generated based on the multiple samples #16-18 and samples #22-24
File 'Stat_Transcriptome_drnVSrn_5UTRv.txt' generated based on the multiple samples #19-21 and samples #22-24
File 'SC_drn_merge_genome.wig' generated based on the multiple samples #22-24
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_drnVSdn_5UTRv.txt
Stat_Transcriptome_drnVSdr_5UTRv.txt
Stat_Transcriptome_drnVSrn_5UTRv.txt


title: zebrafish_989s_B4


title: Sample 13_Transcriptome_dxo1Δnpy1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_dn_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'SC_dn_merge_genome.wig' generated based on the multiple samples #13-15
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt


title: Sample 11_Transcriptome_rai1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_r_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-19
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'SC_r_merge_genome.wig' generated based on the multiple samples #10-12
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rVSwt_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt


title: Sample 12_Transcriptome_rai1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_r_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-20
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'SC_r_merge_genome.wig' generated based on the multiple samples #10-12
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rVSwt_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt


title: T-5005

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_B3


title: Sample 10_Transcriptome_rai1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_r_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'Stat_Transcriptome_drVSr_5UTRv.txt' generated based on the multiple samples #10-12 and samples #16-18
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #7-9 and samples #19-21
File 'SC_r_merge_genome.wig' generated based on the multiple samples #10-12
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_rVSwt_5UTRv.txt
Stat_Transcriptome_drVSr_5UTRv.txt
Stat_Transcriptome_rnVSr_5UTRv.txt


title: zebrafish_989s_B24


title: zebrafish_989s_B23


title: Sample 9_Transcriptome_dxo1Δ_rep3

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_d_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'SC_d_merge_genome.wig' generated based on the multiple samples #7-9
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_drVSd_5UTRv.txt


title: Sample 8_Transcriptome_dxo1Δ_rep2

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_d_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'SC_d_merge_genome.wig' generated based on the multiple samples #7-9
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_drVSd_5UTRv.txt


title: T-5002

description: ftATAC-seq data of mouse thymoctyes


title: T-5004

description: ftATAC-seq data of mouse thymoctyes


title: Sample 7_Transcriptome_dxo1Δ_rep1

description:
H5F72BGX9_YZ_Sep26_18s005836-1-1_SC_d_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_dnVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #13-15
File 'Stat_Transcriptome_drVSd_5UTRv.txt' generated based on the multiple samples #7-9 and samples #16-18
File 'SC_d_merge_genome.wig' generated based on the multiple samples #7-9
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_dnVSd_5UTRv.txt
Stat_Transcriptome_drVSd_5UTRv.txt


title: T-5001

description: ftATAC-seq data of mouse thymoctyes


title: DP-4288

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_B20


title: zebrafish_989s_B2


title: zebrafish_989s_B22


title: Sample 4_Transcriptome_npy1Δ_rep1

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_n_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'SC_n_merge_genome.wig' generated based on the multiple samples #4-6
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt
Stat_Transcriptome_rnVSn_5UTRv.txt